Fix to multinode code

This will also become useful on BG/Q, so will move out from SSE4 into a general area.
Lifted the Eigen half precision from web. Looks sensible, but not extensively regressed
against the intrinsics implementation yet.

.gitignore

@@ -9,6 +9,7 @@
 ################
 *~
 *#
+*.sublime-*
 
 # Precompiled Headers #
 #######################
@@ -104,3 +105,15 @@ lib/fftw/*
 ##################
 m4/lt*
 m4/libtool.m4
+
+# Buck files #
+##############
+.buck*
+buck-out
+BUCK
+make-bin-BUCK.sh
+
+# generated sources #
+#####################
+lib/qcd/spin/gamma-gen/*.h
+lib/qcd/spin/gamma-gen/*.cc

.travis.yml

@@ -7,7 +7,7 @@ cache:
 matrix:
   include:
     - os:        osx
-      osx_image: xcode7.2
+      osx_image: xcode8.3
       compiler: clang
     - compiler: gcc
       addons:
@@ -73,8 +73,6 @@ before_install:
     - if [[ "$TRAVIS_OS_NAME" == "linux" ]] && [[ "$CC" == "clang" ]]; then export LD_LIBRARY_PATH="${GRIDDIR}/clang/lib:${LD_LIBRARY_PATH}"; fi
     - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then brew update; fi
     - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then brew install libmpc; fi
-    - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then brew install openmpi; fi
-    - if [[ "$TRAVIS_OS_NAME" == "osx" ]] && [[ "$CC" == "gcc" ]]; then brew install gcc5; fi
     
 install:
     - export CC=$CC$VERSION
@@ -92,15 +90,14 @@ script:
     - cd build
     - ../configure --enable-precision=single --enable-simd=SSE4 --enable-comms=none
     - make -j4 
-    - ./benchmarks/Benchmark_dwf --threads 1
+    - ./benchmarks/Benchmark_dwf --threads 1 --debug-signals
     - echo make clean
     - ../configure --enable-precision=double --enable-simd=SSE4 --enable-comms=none
     - make -j4
-    - ./benchmarks/Benchmark_dwf --threads 1
+    - ./benchmarks/Benchmark_dwf --threads 1 --debug-signals
     - echo make clean
-    - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then export CXXFLAGS='-DMPI_UINT32_T=MPI_UNSIGNED -DMPI_UINT64_T=MPI_UNSIGNED_LONG'; fi
-    - ../configure --enable-precision=single --enable-simd=SSE4 --enable-comms=mpi-auto
-    - make -j4
+    - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then ../configure --enable-precision=single --enable-simd=SSE4 --enable-comms=mpi-auto CXXFLAGS='-DMPI_UINT32_T=MPI_UNSIGNED -DMPI_UINT64_T=MPI_UNSIGNED_LONG'; fi
+    - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then make -j4; fi
     - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then mpirun.openmpi -n 2 ./benchmarks/Benchmark_dwf --threads 1 --mpi 2.1.1.1; fi
-    - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then mpirun -n 2 ./benchmarks/Benchmark_dwf --threads 1 --mpi 2.1.1.1; fi
+
 

Makefile.am

@@ -1,5 +1,5 @@
 # additional include paths necessary to compile the C++ library
-SUBDIRS = lib benchmarks tests
+SUBDIRS = lib benchmarks tests extras
 
 include $(top_srcdir)/doxygen.inc
 

TODO

@@ -1,6 +1,26 @@
 TODO:
 ---------------
 
+Peter's work list:
+2)- Precision conversion and sort out localConvert      <-- 
+3)- Remove DenseVector, DenseMatrix; Use Eigen instead. <-- started 
+4)- Binary I/O speed up & x-strips
+-- Profile CG, BlockCG, etc... Flop count/rate -- PARTIAL, time but no flop/s yet
+-- Physical propagator interface
+-- Conserved currents
+-- GaugeFix into central location
+-- Multigrid Wilson and DWF, compare to other Multigrid implementations
+-- HDCR resume
+
+Recent DONE 
+-- Cut down the exterior overhead                      <-- DONE
+-- Interior legs from SHM comms                        <-- DONE
+-- Half-precision comms                                <-- DONE
+-- Merge high precision reduction into develop        
+-- multiRHS DWF; benchmark on Cori/BNL for comms elimination
+   -- slice* linalg routines for multiRHS, BlockCG    
+
+-----
 * Forces; the UdSdU  term in gauge force term is half of what I think it should
   be. This is a consequence of taking ONLY the first term in:
 
@@ -21,16 +41,8 @@ TODO:
   This means we must double the force in the Test_xxx_force routines, and is the origin of the factor of two.
   This 2x is applied by hand in the fermion routines and in the Test_rect_force routine.
 
-
-Policies:
-
-* Link smearing/boundary conds; Policy class based implementation ; framework more in place
-
 * Support different boundary conditions (finite temp, chem. potential ... )
 
-* Support different fermion representations? 
-  - contained entirely within the integrator presently
-
 - Sign of force term.
 
 - Reversibility test.
@@ -41,11 +53,6 @@ Policies:
 
 - Audit oIndex usage for cb behaviour
 
-- Rectangle gauge actions.
-  Iwasaki,
-  Symanzik,
-  ... etc...
-
 - Prepare multigrid for HMC. - Alternate setup schemes.
 
 - Support for ILDG --- ugly, not done
@@ -55,9 +62,11 @@ Policies:
 - FFTnD ?
 
 - Gparity; hand opt use template specialisation elegance to enable the optimised paths ?
+
 - Gparity force term; Gparity (R)HMC.
-- Random number state save restore
+
 - Mobius implementation clean up to rmove #if 0 stale code sequences
+
 - CG -- profile carefully, kernel fusion, whole CG performance measurements.
 
 ================================================================
@@ -90,6 +99,7 @@ Insert/Extract
 Not sure of status of this -- reverify. Things are working nicely now though.
 
 * Make the Tensor types and Complex etc... play more nicely.
+
   - TensorRemove is a hack, come up with a long term rationalised approach to Complex vs. Scalar<Scalar<Scalar<Complex > > >
     QDP forces use of "toDouble" to get back to non tensor scalar. This role is presently taken TensorRemove, but I
     want to introduce a syntax that does not require this.
@@ -112,6 +122,8 @@ Not sure of status of this -- reverify. Things are working nicely now though.
 RECENT
 ---------------
 
+  - Support different fermion representations? -- DONE
+  - contained entirely within the integrator presently
   - Clean up HMC                                                             -- DONE
   - LorentzScalar<GaugeField> gets Gauge link type (cleaner).                -- DONE
   - Simplified the integrators a bit.                                        -- DONE
@@ -123,6 +135,26 @@ RECENT
   - Parallel io improvements                                  -- DONE
   - Plaquette and link trace checks into nersc reader from the Grid_nersc_io.cc test. -- DONE
 
+
+DONE:
+- MultiArray -- MultiRHS done
+- ConjugateGradientMultiShift -- DONE
+- MCR                         -- DONE
+- Remez -- Mike or Boost?     -- DONE
+- Proto (ET)                  -- DONE
+- uBlas                       -- DONE ; Eigen
+- Potentially Useful Boost libraries -- DONE ; Eigen
+- Aligned allocator; memory pool -- DONE
+- Multiprecision              -- DONE
+- Serialization               -- DONE
+- Regex -- Not needed
+- Tokenize -- Why?
+
+- Random number state save restore -- DONE
+- Rectangle gauge actions. -- DONE
+  Iwasaki,
+  Symanzik,
+  ... etc...
 Done: Cayley, Partial , ContFrac force terms.
 
 DONE
@@ -207,6 +239,7 @@ Done
 FUNCTIONALITY: it pleases me to keep track of things I have done (keeps me arguably sane)
 ======================================================================================================
 
+* Link smearing/boundary conds; Policy class based implementation ; framework more in place -- DONE
 * Command line args for geometry, simd, etc. layout. Is it necessary to have -- DONE
   user pass these? Is this a QCD specific?
 

benchmarks/Benchmark_comms.cc

@@ -48,9 +48,9 @@ int main (int argc, char ** argv)
   std::cout<<GridLogMessage << "= Benchmarking concurrent halo exchange in "<<nmu<<" dimensions"<<std::endl;
   std::cout<<GridLogMessage << "===================================================================================================="<<std::endl;
   std::cout<<GridLogMessage << "  L  "<<"\t\t"<<" Ls  "<<"\t\t"<<"bytes"<<"\t\t"<<"MB/s uni"<<"\t\t"<<"MB/s bidi"<<std::endl;
-  int maxlat=16;
-  for(int lat=4;lat<=maxlat;lat+=2){
-    for(int Ls=1;Ls<=16;Ls*=2){
+  int maxlat=24;
+  for(int lat=4;lat<=maxlat;lat+=4){
+    for(int Ls=8;Ls<=32;Ls*=2){
 
       std::vector<int> latt_size  ({lat*mpi_layout[0],
       				    lat*mpi_layout[1],
@@ -124,8 +124,8 @@ int main (int argc, char ** argv)
   std::cout<<GridLogMessage << "  L  "<<"\t\t"<<" Ls  "<<"\t\t"<<"bytes"<<"\t\t"<<"MB/s uni"<<"\t\t"<<"MB/s bidi"<<std::endl;
 
 
-  for(int lat=4;lat<=maxlat;lat+=2){
-    for(int Ls=1;Ls<=16;Ls*=2){
+  for(int lat=4;lat<=maxlat;lat+=4){
+    for(int Ls=8;Ls<=32;Ls*=2){
 
       std::vector<int> latt_size  ({lat,lat,lat,lat});
 
@@ -194,14 +194,14 @@ int main (int argc, char ** argv)
   }  
 
 
-  Nloop=100;
+  Nloop=10;
   std::cout<<GridLogMessage << "===================================================================================================="<<std::endl;
   std::cout<<GridLogMessage << "= Benchmarking concurrent STENCIL halo exchange in "<<nmu<<" dimensions"<<std::endl;
   std::cout<<GridLogMessage << "===================================================================================================="<<std::endl;
   std::cout<<GridLogMessage << "  L  "<<"\t\t"<<" Ls  "<<"\t\t"<<"bytes"<<"\t\t"<<"MB/s uni"<<"\t\t"<<"MB/s bidi"<<std::endl;
 
-  for(int lat=4;lat<=maxlat;lat+=2){
-    for(int Ls=1;Ls<=16;Ls*=2){
+  for(int lat=4;lat<=maxlat;lat+=4){
+    for(int Ls=8;Ls<=32;Ls*=2){
 
       std::vector<int> latt_size  ({lat*mpi_layout[0],
       				    lat*mpi_layout[1],
@@ -281,8 +281,8 @@ int main (int argc, char ** argv)
   std::cout<<GridLogMessage << "===================================================================================================="<<std::endl;
   std::cout<<GridLogMessage << "  L  "<<"\t\t"<<" Ls  "<<"\t\t"<<"bytes"<<"\t\t"<<"MB/s uni"<<"\t\t"<<"MB/s bidi"<<std::endl;
 
-  for(int lat=4;lat<=maxlat;lat+=2){
-    for(int Ls=1;Ls<=16;Ls*=2){
+  for(int lat=4;lat<=maxlat;lat+=4){
+    for(int Ls=8;Ls<=32;Ls*=2){
 
       std::vector<int> latt_size  ({lat*mpi_layout[0],
       				    lat*mpi_layout[1],
@@ -324,8 +324,8 @@ int main (int argc, char ** argv)
 					    (void *)&rbuf[mu][0],
 					    recv_from_rank,
 					    bytes);
-	    //	    Grid.StencilSendToRecvFromComplete(requests);
-	    //	    requests.resize(0);
+	    Grid.StencilSendToRecvFromComplete(requests);
+	    requests.resize(0);
 
 	    comm_proc = mpi_layout[mu]-1;
 	  

benchmarks/Benchmark_dwf.cc

@@ -37,27 +37,27 @@ struct scal {
   d internal;
 };
 
-  Gamma::GammaMatrix Gmu [] = {
-    Gamma::GammaX,
-    Gamma::GammaY,
-    Gamma::GammaZ,
-    Gamma::GammaT
+  Gamma::Algebra Gmu [] = {
+    Gamma::Algebra::GammaX,
+    Gamma::Algebra::GammaY,
+    Gamma::Algebra::GammaZ,
+    Gamma::Algebra::GammaT
   };
 
 typedef WilsonFermion5D<DomainWallVec5dImplR> WilsonFermion5DR;
 typedef WilsonFermion5D<DomainWallVec5dImplF> WilsonFermion5DF;
 typedef WilsonFermion5D<DomainWallVec5dImplD> WilsonFermion5DD;
 
-
 int main (int argc, char ** argv)
 {
   Grid_init(&argc,&argv);
 
+
   int threads = GridThread::GetThreads();
   std::cout<<GridLogMessage << "Grid is setup to use "<<threads<<" threads"<<std::endl;
 
   std::vector<int> latt4 = GridDefaultLatt();
-  const int Ls=8;
+  const int Ls=16;
   GridCartesian         * UGrid   = SpaceTimeGrid::makeFourDimGrid(GridDefaultLatt(), GridDefaultSimd(Nd,vComplex::Nsimd()),GridDefaultMpi());
   GridRedBlackCartesian * UrbGrid = SpaceTimeGrid::makeFourDimRedBlackGrid(UGrid);
   GridCartesian         * FGrid   = SpaceTimeGrid::makeFiveDimGrid(Ls,UGrid);
@@ -72,34 +72,65 @@ int main (int argc, char ** argv)
   std::vector<int> seeds4({1,2,3,4});
   std::vector<int> seeds5({5,6,7,8});
   
+  std::cout << GridLogMessage << "Initialising 4d RNG" << std::endl;
   GridParallelRNG          RNG4(UGrid);  RNG4.SeedFixedIntegers(seeds4);
+  std::cout << GridLogMessage << "Initialising 5d RNG" << std::endl;
   GridParallelRNG          RNG5(FGrid);  RNG5.SeedFixedIntegers(seeds5);
+  std::cout << GridLogMessage << "Initialised RNGs" << std::endl;
 
   LatticeFermion src   (FGrid); random(RNG5,src);
+#if 0
+  src = zero;
+  {
+    std::vector<int> origin({0,0,0,latt4[2]-1,0});
+    SpinColourVectorF tmp;
+    tmp=zero;
+    tmp()(0)(0)=Complex(-2.0,0.0);
+    std::cout << " source site 0 " << tmp<<std::endl;
+    pokeSite(tmp,src,origin);
+  }
+#else
+  RealD N2 = 1.0/::sqrt(norm2(src));
+  src = src*N2;
+#endif
+
+
   LatticeFermion result(FGrid); result=zero;
   LatticeFermion    ref(FGrid);    ref=zero;
   LatticeFermion    tmp(FGrid);
   LatticeFermion    err(FGrid);
 
+  std::cout << GridLogMessage << "Drawing gauge field" << std::endl;
   LatticeGaugeField Umu(UGrid); 
-  random(RNG4,Umu);
-
-  LatticeGaugeField Umu5d(FGrid); 
+  SU3::HotConfiguration(RNG4,Umu); 
+  std::cout << GridLogMessage << "Random gauge initialised " << std::endl;
+#if 0
+  Umu=1.0;
+  for(int mu=0;mu<Nd;mu++){
+    LatticeColourMatrix ttmp(UGrid);
+    ttmp = PeekIndex<LorentzIndex>(Umu,mu);
+    //    if (mu !=2 ) ttmp = 0;
+    //    ttmp = ttmp* pow(10.0,mu);
+    PokeIndex<LorentzIndex>(Umu,ttmp,mu);
+  }
+  std::cout << GridLogMessage << "Forced to diagonal " << std::endl;
+#endif
 
+  ////////////////////////////////////
+  // Naive wilson implementation
+  ////////////////////////////////////
   // replicate across fifth dimension
+  LatticeGaugeField Umu5d(FGrid); 
+  std::vector<LatticeColourMatrix> U(4,FGrid);
   for(int ss=0;ss<Umu._grid->oSites();ss++){
     for(int s=0;s<Ls;s++){
       Umu5d._odata[Ls*ss+s] = Umu._odata[ss];
     }
   }
-
-  ////////////////////////////////////
-  // Naive wilson implementation
-  ////////////////////////////////////
-  std::vector<LatticeColourMatrix> U(4,FGrid);
   for(int mu=0;mu<Nd;mu++){
     U[mu] = PeekIndex<LorentzIndex>(Umu5d,mu);
   }
+  std::cout << GridLogMessage << "Setting up Cshift based reference " << std::endl;
 
   if (1)
   {
@@ -121,8 +152,6 @@ int main (int argc, char ** argv)
 
   RealD NP = UGrid->_Nprocessors;
 
-  DomainWallFermionR Dw(Umu,*FGrid,*FrbGrid,*UGrid,*UrbGrid,mass,M5);
-
   std::cout << GridLogMessage<< "*****************************************************************" <<std::endl;
   std::cout << GridLogMessage<< "* Kernel options --dslash-generic, --dslash-unroll, --dslash-asm" <<std::endl;
   std::cout << GridLogMessage<< "*****************************************************************" <<std::endl;
@@ -136,10 +165,13 @@ int main (int argc, char ** argv)
   if ( WilsonKernelsStatic::Opt == WilsonKernelsStatic::OptInlineAsm ) std::cout << GridLogMessage<< "* Using Asm Nc=3   WilsonKernels" <<std::endl;
   std::cout << GridLogMessage<< "*****************************************************************" <<std::endl;
 
-  int ncall =100;
+  DomainWallFermionR Dw(Umu,*FGrid,*FrbGrid,*UGrid,*UrbGrid,mass,M5);
+  int ncall =1000;
   if (1) {
     FGrid->Barrier();
     Dw.ZeroCounters();
+    Dw.Dhop(src,result,0);
+    std::cout<<GridLogMessage<<"Called warmup"<<std::endl;
     double t0=usecond();
     for(int i=0;i<ncall;i++){
       __SSC_START;
@@ -153,16 +185,53 @@ int main (int argc, char ** argv)
     double flops=1344*volume*ncall;
 
     std::cout<<GridLogMessage << "Called Dw "<<ncall<<" times in "<<t1-t0<<" us"<<std::endl;
-    std::cout<<GridLogMessage << "norm result "<< norm2(result)<<std::endl;
-    std::cout<<GridLogMessage << "norm ref    "<< norm2(ref)<<std::endl;
+    //    std::cout<<GridLogMessage << "norm result "<< norm2(result)<<std::endl;
+    //    std::cout<<GridLogMessage << "norm ref    "<< norm2(ref)<<std::endl;
     std::cout<<GridLogMessage << "mflop/s =   "<< flops/(t1-t0)<<std::endl;
     std::cout<<GridLogMessage << "mflop/s per rank =  "<< flops/(t1-t0)/NP<<std::endl;
     err = ref-result; 
     std::cout<<GridLogMessage << "norm diff   "<< norm2(err)<<std::endl;
+
+    /*
+    if(( norm2(err)>1.0e-4) ) { 
+      std::cout << "RESULT\n " << result<<std::endl;
+      std::cout << "REF   \n " << ref   <<std::endl;
+      std::cout << "ERR   \n " << err   <<std::endl;
+      FGrid->Barrier();
+      exit(-1);
+    }
+    */
     assert (norm2(err)< 1.0e-4 );
     Dw.Report();
   }
 
+  DomainWallFermionRL DwH(Umu,*FGrid,*FrbGrid,*UGrid,*UrbGrid,mass,M5);
+  if (1) {
+    FGrid->Barrier();
+    DwH.ZeroCounters();
+    DwH.Dhop(src,result,0);
+    double t0=usecond();
+    for(int i=0;i<ncall;i++){
+      __SSC_START;
+      DwH.Dhop(src,result,0);
+      __SSC_STOP;
+    }
+    double t1=usecond();
+    FGrid->Barrier();
+    
+    double volume=Ls;  for(int mu=0;mu<Nd;mu++) volume=volume*latt4[mu];
+    double flops=1344*volume*ncall;
+
+    std::cout<<GridLogMessage << "Called half prec comms Dw "<<ncall<<" times in "<<t1-t0<<" us"<<std::endl;
+    std::cout<<GridLogMessage << "mflop/s =   "<< flops/(t1-t0)<<std::endl;
+    std::cout<<GridLogMessage << "mflop/s per rank =  "<< flops/(t1-t0)/NP<<std::endl;
+    err = ref-result; 
+    std::cout<<GridLogMessage << "norm diff   "<< norm2(err)<<std::endl;
+
+    assert (norm2(err)< 1.0e-3 );
+    DwH.Report();
+  }
+
   if (1)
   {
 
@@ -183,20 +252,12 @@ int main (int argc, char ** argv)
 
     WilsonFermion5DR sDw(Umu,*sFGrid,*sFrbGrid,*sUGrid,*sUrbGrid,M5);
 
-    for(int x=0;x<latt4[0];x++){
-    for(int y=0;y<latt4[1];y++){
-    for(int z=0;z<latt4[2];z++){
-    for(int t=0;t<latt4[3];t++){
-    for(int s=0;s<Ls;s++){
-      std::vector<int> site({s,x,y,z,t});
-      SpinColourVector tmp;
-      peekSite(tmp,src,site);
-      pokeSite(tmp,ssrc,site);
-    }}}}}
+    localConvert(src,ssrc);
     std::cout<<GridLogMessage<< "src norms "<< norm2(src)<<" " <<norm2(ssrc)<<std::endl;
     FGrid->Barrier();
-    double t0=usecond();
+    sDw.Dhop(ssrc,sresult,0);
     sDw.ZeroCounters();
+    double t0=usecond();
     for(int i=0;i<ncall;i++){
       __SSC_START;
       sDw.Dhop(ssrc,sresult,0);
@@ -210,46 +271,47 @@ int main (int argc, char ** argv)
     std::cout<<GridLogMessage << "Called Dw s_inner "<<ncall<<" times in "<<t1-t0<<" us"<<std::endl;
     std::cout<<GridLogMessage << "mflop/s =   "<< flops/(t1-t0)<<std::endl;
     std::cout<<GridLogMessage << "mflop/s per rank =  "<< flops/(t1-t0)/NP<<std::endl;
+    //    std::cout<<GridLogMessage<< "res norms "<< norm2(result)<<" " <<norm2(sresult)<<std::endl;
     sDw.Report();
-  
-    if(0){
-      for(int i=0;i< PerformanceCounter::NumTypes(); i++ ){
-	sDw.Dhop(ssrc,sresult,0);
-	PerformanceCounter Counter(i);
-	Counter.Start();
-	sDw.Dhop(ssrc,sresult,0);
-	Counter.Stop();
-	Counter.Report();
-      }
-    }
-
-    std::cout<<GridLogMessage<< "res norms "<< norm2(result)<<" " <<norm2(sresult)<<std::endl;
-
     RealD sum=0;
-    for(int x=0;x<latt4[0];x++){
-    for(int y=0;y<latt4[1];y++){
-    for(int z=0;z<latt4[2];z++){
-    for(int t=0;t<latt4[3];t++){
-    for(int s=0;s<Ls;s++){
-      std::vector<int> site({s,x,y,z,t});
-      SpinColourVector normal, simd;
-      peekSite(normal,result,site);
-      peekSite(simd,sresult,site);
-      sum=sum+norm2(normal-simd);
-      if (norm2(normal-simd) > 1.0e-6 ) {
-	std::cout << "site "<<x<<","<<y<<","<<z<<","<<t<<","<<s<<" "<<norm2(normal-simd)<<std::endl;
-	std::cout << "site "<<x<<","<<y<<","<<z<<","<<t<<","<<s<<" normal "<<normal<<std::endl;
-	std::cout << "site "<<x<<","<<y<<","<<z<<","<<t<<","<<s<<" simd   "<<simd<<std::endl;
-      }
-    }}}}}
-    std::cout<<GridLogMessage<<" difference between normal and simd is "<<sum<<std::endl;
-    assert (sum< 1.0e-4 );
 
+    err=zero;
+    localConvert(sresult,err);
+    err = err - ref;
+    sum = norm2(err);
+    std::cout<<GridLogMessage<<" difference between normal ref and simd is "<<sum<<std::endl;
+    if(sum > 1.0e-4 ){
+      std::cout<< "sD REF\n " <<ref << std::endl;
+      std::cout<< "sD ERR   \n " <<err  <<std::endl;
+    }
+    //    assert(sum < 1.0e-4);
 
-    if (1) {
+    err=zero;
+    localConvert(sresult,err);
+    err = err - result;
+    sum = norm2(err);
+    std::cout<<GridLogMessage<<" difference between normal result and simd is "<<sum<<std::endl;
+    if(sum > 1.0e-4 ){
+      std::cout<< "sD REF\n " <<result << std::endl;
+      std::cout<< "sD ERR   \n " << err  <<std::endl;
+    }
+    assert(sum < 1.0e-4);
+    
+    if(1){
+      std::cout << GridLogMessage<< "*********************************************************" <<std::endl;
+      std::cout << GridLogMessage<< "* Benchmarking WilsonFermion5D<DomainWallVec5dImplR>::DhopEO "<<std::endl;
+      std::cout << GridLogMessage<< "* Vectorising fifth dimension by "<<vComplex::Nsimd()<<std::endl;
+      if ( sizeof(Real)==4 )   std::cout << GridLogMessage<< "* SINGLE precision "<<std::endl;
+      if ( sizeof(Real)==8 )   std::cout << GridLogMessage<< "* DOUBLE precision "<<std::endl;
+      if ( WilsonKernelsStatic::Opt == WilsonKernelsStatic::OptGeneric   ) 
+	std::cout << GridLogMessage<< "* Using GENERIC Nc WilsonKernels" <<std::endl;
+      if ( WilsonKernelsStatic::Opt == WilsonKernelsStatic::OptHandUnroll) 
+	std::cout << GridLogMessage<< "* Using Nc=3       WilsonKernels" <<std::endl;
+      if ( WilsonKernelsStatic::Opt == WilsonKernelsStatic::OptInlineAsm ) 
+	std::cout << GridLogMessage<< "* Using Asm Nc=3   WilsonKernels" <<std::endl;
+      std::cout << GridLogMessage<< "*********************************************************" <<std::endl;
 
       LatticeFermion sr_eo(sFGrid);
-
       LatticeFermion ssrc_e (sFrbGrid);
       LatticeFermion ssrc_o (sFrbGrid);
       LatticeFermion sr_e   (sFrbGrid);
@@ -257,33 +319,23 @@ int main (int argc, char ** argv)
 
       pickCheckerboard(Even,ssrc_e,ssrc);
       pickCheckerboard(Odd,ssrc_o,ssrc);
-
-      setCheckerboard(sr_eo,ssrc_o);
-      setCheckerboard(sr_eo,ssrc_e);
+      //      setCheckerboard(sr_eo,ssrc_o);
+      //      setCheckerboard(sr_eo,ssrc_e);
 
       sr_e = zero;
       sr_o = zero;
 
-      std::cout << GridLogMessage<< "*********************************************************" <<std::endl;
-      std::cout << GridLogMessage<< "* Benchmarking WilsonFermion5D<DomainWallVec5dImplR>::DhopEO "<<std::endl;
-      std::cout << GridLogMessage<< "* Vectorising fifth dimension by "<<vComplex::Nsimd()<<std::endl;
-      if ( sizeof(Real)==4 )   std::cout << GridLogMessage<< "* SINGLE precision "<<std::endl;
-      if ( sizeof(Real)==8 )   std::cout << GridLogMessage<< "* DOUBLE precision "<<std::endl;
-      if ( WilsonKernelsStatic::Opt == WilsonKernelsStatic::OptGeneric   ) std::cout << GridLogMessage<< "* Using GENERIC Nc WilsonKernels" <<std::endl;
-      if ( WilsonKernelsStatic::Opt == WilsonKernelsStatic::OptHandUnroll) std::cout << GridLogMessage<< "* Using Nc=3       WilsonKernels" <<std::endl;
-      if ( WilsonKernelsStatic::Opt == WilsonKernelsStatic::OptInlineAsm ) std::cout << GridLogMessage<< "* Using Asm Nc=3   WilsonKernels" <<std::endl;
-      std::cout << GridLogMessage<< "*********************************************************" <<std::endl;
-
       FGrid->Barrier();
+      sDw.DhopEO(ssrc_o, sr_e, DaggerNo);
       sDw.ZeroCounters();
-      sDw.stat.init("DhopEO");
+      //      sDw.stat.init("DhopEO");
       double t0=usecond();
       for (int i = 0; i < ncall; i++) {
         sDw.DhopEO(ssrc_o, sr_e, DaggerNo);
       }
       double t1=usecond();
       FGrid->Barrier();
-      sDw.stat.print();
+      //      sDw.stat.print();
 
       double volume=Ls;  for(int mu=0;mu<Nd;mu++) volume=volume*latt4[mu];
       double flops=(1344.0*volume*ncall)/2;
@@ -298,22 +350,26 @@ int main (int argc, char ** argv)
 
       pickCheckerboard(Even,ssrc_e,sresult);
       pickCheckerboard(Odd ,ssrc_o,sresult);
+
       ssrc_e = ssrc_e - sr_e;
       RealD error = norm2(ssrc_e);
-
       std::cout<<GridLogMessage << "sE norm diff   "<< norm2(ssrc_e)<< "  vec nrm"<<norm2(sr_e) <<std::endl;
-      ssrc_o = ssrc_o - sr_o;
 
+      ssrc_o = ssrc_o - sr_o;
       error+= norm2(ssrc_o);
       std::cout<<GridLogMessage << "sO norm diff   "<< norm2(ssrc_o)<< "  vec nrm"<<norm2(sr_o) <<std::endl;
-      if(error>1.0e-4) { 
+
+      if(( error>1.0e-4) ) { 
 	setCheckerboard(ssrc,ssrc_o);
 	setCheckerboard(ssrc,ssrc_e);
-	std::cout<< ssrc << std::endl;
+	std::cout<< "DIFF\n " <<ssrc << std::endl;
+	setCheckerboard(ssrc,sr_o);
+	setCheckerboard(ssrc,sr_e);
+	std::cout<< "CBRESULT\n " <<ssrc << std::endl;
+	std::cout<< "RESULT\n " <<sresult<< std::endl;
       }
+      assert(error<1.0e-4);
     }
-
-
   }
 
   if (1)
@@ -321,28 +377,33 @@ int main (int argc, char ** argv)
     ref = zero;
     for(int mu=0;mu<Nd;mu++){
 
-      //    ref =  src - Gamma(Gamma::GammaX)* src ; // 1+gamma_x
+      //    ref =  src - Gamma(Gamma::Algebra::GammaX)* src ; // 1+gamma_x
       tmp = U[mu]*Cshift(src,mu+1,1);
       for(int i=0;i<ref._odata.size();i++){
-  ref._odata[i]+= tmp._odata[i] + Gamma(Gmu[mu])*tmp._odata[i]; ;
+	ref._odata[i]+= tmp._odata[i] + Gamma(Gmu[mu])*tmp._odata[i]; ;
       }
 
       tmp =adj(U[mu])*src;
       tmp =Cshift(tmp,mu+1,-1);
       for(int i=0;i<ref._odata.size();i++){
-  ref._odata[i]+= tmp._odata[i] - Gamma(Gmu[mu])*tmp._odata[i]; ;
+	ref._odata[i]+= tmp._odata[i] - Gamma(Gmu[mu])*tmp._odata[i]; ;
       }
     }
     ref = -0.5*ref;
   }
+  //  dump=1;
   Dw.Dhop(src,result,1);
   std::cout << GridLogMessage << "Compare to naive wilson implementation Dag to verify correctness" << std::endl;
   std::cout<<GridLogMessage << "Called DwDag"<<std::endl;
-  std::cout<<GridLogMessage << "norm result "<< norm2(result)<<std::endl;
-  std::cout<<GridLogMessage << "norm ref    "<< norm2(ref)<<std::endl;
+  std::cout<<GridLogMessage << "norm dag result "<< norm2(result)<<std::endl;
+  std::cout<<GridLogMessage << "norm dag ref    "<< norm2(ref)<<std::endl;
   err = ref-result; 
-  std::cout<<GridLogMessage << "norm diff   "<< norm2(err)<<std::endl;
-  assert(norm2(err)<1.0e-4);
+  std::cout<<GridLogMessage << "norm dag diff   "<< norm2(err)<<std::endl;
+  if((norm2(err)>1.0e-4)){
+	std::cout<< "DAG RESULT\n "  <<ref     << std::endl;
+	std::cout<< "DAG sRESULT\n " <<result  << std::endl;
+	std::cout<< "DAG ERR   \n "  << err    <<std::endl;
+  }
   LatticeFermion src_e (FrbGrid);
   LatticeFermion src_o (FrbGrid);
   LatticeFermion r_e   (FrbGrid);
@@ -350,13 +411,18 @@ int main (int argc, char ** argv)
   LatticeFermion r_eo  (FGrid);
 
 
-  std::cout<<GridLogMessage << "Calling Deo and Doe and assert Deo+Doe == Dunprec"<<std::endl;
+  std::cout<<GridLogMessage << "Calling Deo and Doe and //assert Deo+Doe == Dunprec"<<std::endl;
   pickCheckerboard(Even,src_e,src);
   pickCheckerboard(Odd,src_o,src);
 
   std::cout<<GridLogMessage << "src_e"<<norm2(src_e)<<std::endl;
   std::cout<<GridLogMessage << "src_o"<<norm2(src_o)<<std::endl;
 
+
+  // S-direction is INNERMOST and takes no part in the parity.
+  static int Opt;  // these are a temporary hack
+  static int Comms;  // these are a temporary hack
+
   std::cout << GridLogMessage<< "*********************************************************" <<std::endl;
   std::cout << GridLogMessage<< "* Benchmarking DomainWallFermionR::DhopEO                "<<std::endl;
   std::cout << GridLogMessage<< "* Vectorising space-time by "<<vComplex::Nsimd()<<std::endl;
@@ -369,6 +435,7 @@ int main (int argc, char ** argv)
   {
     Dw.ZeroCounters();
     FGrid->Barrier();
+    Dw.DhopEO(src_o,r_e,DaggerNo);
     double t0=usecond();
     for(int i=0;i<ncall;i++){
       Dw.DhopEO(src_o,r_e,DaggerNo);
@@ -396,14 +463,19 @@ int main (int argc, char ** argv)
 
   err = r_eo-result; 
   std::cout<<GridLogMessage << "norm diff   "<< norm2(err)<<std::endl;
-  assert(norm2(err)<1.0e-4);
+  if((norm2(err)>1.0e-4)){
+	std::cout<< "Deo RESULT\n " <<r_eo << std::endl;
+	std::cout<< "Deo REF\n " <<result  << std::endl;
+	std::cout<< "Deo ERR   \n " << err <<std::endl;
+  }
 
   pickCheckerboard(Even,src_e,err);
   pickCheckerboard(Odd,src_o,err);
   std::cout<<GridLogMessage << "norm diff even  "<< norm2(src_e)<<std::endl;
   std::cout<<GridLogMessage << "norm diff odd   "<< norm2(src_o)<<std::endl;
-  assert(norm2(src_e)<1.0e-4);
-  assert(norm2(src_o)<1.0e-4);
+
+  //assert(norm2(src_e)<1.0e-4);
+  //assert(norm2(src_o)<1.0e-4);
 
   Grid_finalize();
 }

benchmarks/Benchmark_dwf_sweep.cc

@@ -37,11 +37,11 @@ struct scal {
   d internal;
 };
 
-  Gamma::GammaMatrix Gmu [] = {
-    Gamma::GammaX,
-    Gamma::GammaY,
-    Gamma::GammaZ,
-    Gamma::GammaT
+  Gamma::Algebra Gmu [] = {
+    Gamma::Algebra::GammaX,
+    Gamma::Algebra::GammaY,
+    Gamma::Algebra::GammaZ,
+    Gamma::Algebra::GammaT
   };
 
 void benchDw(std::vector<int> & L, int Ls, int threads, int report =0 );

benchmarks/Benchmark_memory_asynch.cc

@@ -66,7 +66,8 @@ int main (int argc, char ** argv)
 
     Vec tsum; tsum = zero;
 
-    GridParallelRNG          pRNG(&Grid);      pRNG.SeedRandomDevice();
+    GridParallelRNG          pRNG(&Grid);      
+    pRNG.SeedFixedIntegers(std::vector<int>({56,17,89,101}));
 
     std::vector<double> stop(threads);
     Vector<Vec> sum(threads);
@@ -77,8 +78,7 @@ int main (int argc, char ** argv)
     }
 
     double start=usecond();
-PARALLEL_FOR_LOOP
-    for(int t=0;t<threads;t++){
+    parallel_for(int t=0;t<threads;t++){
 
       sum[t] = x[t]._odata[0];
       for(int i=0;i<Nloop;i++){

benchmarks/Benchmark_memory_bandwidth.cc

@@ -65,7 +65,7 @@ int main (int argc, char ** argv)
 
       uint64_t Nloop=NLOOP;
 
-      //      GridParallelRNG          pRNG(&Grid);      pRNG.SeedRandomDevice();
+      //      GridParallelRNG          pRNG(&Grid);      pRNG.SeedFixedIntegers(std::vector<int>({45,12,81,9});
 
       LatticeVec z(&Grid); //random(pRNG,z);
       LatticeVec x(&Grid); //random(pRNG,x);
@@ -100,7 +100,7 @@ int main (int argc, char ** argv)
       int vol = latt_size[0]*latt_size[1]*latt_size[2]*latt_size[3];
       GridCartesian     Grid(latt_size,simd_layout,mpi_layout);
 
-      //      GridParallelRNG          pRNG(&Grid);      pRNG.SeedRandomDevice();
+      //      GridParallelRNG          pRNG(&Grid);      pRNG.SeedFixedIntegers(std::vector<int>({45,12,81,9});
 
       LatticeVec z(&Grid); //random(pRNG,z);
       LatticeVec x(&Grid); //random(pRNG,x);
@@ -138,7 +138,7 @@ int main (int argc, char ** argv)
 
       GridCartesian     Grid(latt_size,simd_layout,mpi_layout);
 
-      //      GridParallelRNG          pRNG(&Grid);      pRNG.SeedRandomDevice();
+      //      GridParallelRNG          pRNG(&Grid);      pRNG.SeedFixedIntegers(std::vector<int>({45,12,81,9});
 
       LatticeVec z(&Grid); //random(pRNG,z);
       LatticeVec x(&Grid); //random(pRNG,x);
@@ -173,7 +173,7 @@ int main (int argc, char ** argv)
       uint64_t Nloop=NLOOP;
       GridCartesian     Grid(latt_size,simd_layout,mpi_layout);
 
-      //      GridParallelRNG          pRNG(&Grid);      pRNG.SeedRandomDevice();
+      //      GridParallelRNG          pRNG(&Grid);      pRNG.SeedFixedIntegers(std::vector<int>({45,12,81,9});
       LatticeVec z(&Grid); //random(pRNG,z);
       LatticeVec x(&Grid); //random(pRNG,x);
       LatticeVec y(&Grid); //random(pRNG,y);

benchmarks/Benchmark_mooee.cc

@@ -113,6 +113,36 @@ int main (int argc, char ** argv)
     std::cout<<GridLogMessage << "Called " #A " "<< (t1-t0)/ncall<<" us"<<std::endl;\
     std::cout<<GridLogMessage << "******************"<<std::endl;
 
+#define BENCH_ZDW(A,in,out)			\
+    zDw.CayleyZeroCounters();			\
+    zDw. A (in,out);				\
+    FGrid->Barrier();				\
+    t0=usecond();				\
+    for(int i=0;i<ncall;i++){			\
+      zDw. A (in,out);				\
+    }						\
+    t1=usecond();				\
+    FGrid->Barrier();				\
+    zDw.CayleyReport();							\
+    std::cout<<GridLogMessage << "Called ZDw " #A " "<< (t1-t0)/ncall<<" us"<<std::endl;\
+    std::cout<<GridLogMessage << "******************"<<std::endl;
+
+#define BENCH_DW_SSC(A,in,out)			\
+    Dw.CayleyZeroCounters();			\
+    Dw. A (in,out);				\
+    FGrid->Barrier();				\
+    t0=usecond();				\
+    for(int i=0;i<ncall;i++){			\
+      __SSC_START ;				\
+      Dw. A (in,out);				\
+      __SSC_STOP ;				\
+    }						\
+    t1=usecond();				\
+    FGrid->Barrier();				\
+    Dw.CayleyReport();					\
+    std::cout<<GridLogMessage << "Called " #A " "<< (t1-t0)/ncall<<" us"<<std::endl;\
+    std::cout<<GridLogMessage << "******************"<<std::endl;
+
 #define BENCH_DW_MEO(A,in,out)			\
     Dw.CayleyZeroCounters();			\
     Dw. A (in,out,0);				\
@@ -148,9 +178,15 @@ int main (int argc, char ** argv)
     LatticeFermion sref(sFGrid);
     LatticeFermion result(sFGrid);
 
+
     std::cout<<GridLogMessage << "Constructing Vec5D Dw "<<std::endl;
     DomainWallFermionVec5dR Dw(Umu,*sFGrid,*sFrbGrid,*sUGrid,*sUrbGrid,mass,M5);
 
+    RealD b=1.5;// Scale factor b+c=2, b-c=1
+    RealD c=0.5;
+    std::vector<ComplexD> gamma(Ls,std::complex<double>(1.0,0.0));
+    ZMobiusFermionVec5dR zDw(Umu,*sFGrid,*sFrbGrid,*sUGrid,*sUrbGrid,mass,M5,gamma,b,c);
+
     std::cout<<GridLogMessage << "Calling Dhop "<<std::endl;
     FGrid->Barrier();
 
@@ -173,10 +209,13 @@ int main (int argc, char ** argv)
 
     BENCH_DW_MEO(Dhop    ,src,result);
     BENCH_DW_MEO(DhopEO  ,src_o,r_e);
-    BENCH_DW(Meooe   ,src_o,r_e);
+    BENCH_DW_SSC(Meooe   ,src_o,r_e);
     BENCH_DW(Mooee   ,src_o,r_o);
     BENCH_DW(MooeeInv,src_o,r_o);
 
+    BENCH_ZDW(Mooee   ,src_o,r_o);
+    BENCH_ZDW(MooeeInv,src_o,r_o);
+
   }
 
   Grid_finalize();

benchmarks/Benchmark_staggered.cc

@@ -0,0 +1,134 @@
+    /*************************************************************************************
+
+    Grid physics library, www.github.com/paboyle/Grid 
+
+    Source file: ./benchmarks/Benchmark_staggered.cc
+
+    Copyright (C) 2015
+
+Author: Peter Boyle <paboyle@ph.ed.ac.uk>
+Author: paboyle <paboyle@ph.ed.ac.uk>
+
+    This program is free software; you can redistribute it and/or modify
+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation; either version 2 of the License, or
+    (at your option) any later version.
+
+    This program is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+
+    You should have received a copy of the GNU General Public License along
+    with this program; if not, write to the Free Software Foundation, Inc.,
+    51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+
+    See the full license in the file "LICENSE" in the top level distribution directory
+    *************************************************************************************/
+    /*  END LEGAL */
+#include <Grid/Grid.h>
+
+using namespace std;
+using namespace Grid;
+using namespace Grid::QCD;
+
+int main (int argc, char ** argv)
+{
+  Grid_init(&argc,&argv);
+
+  std::vector<int> latt_size   = GridDefaultLatt();
+  std::vector<int> simd_layout = GridDefaultSimd(Nd,vComplex::Nsimd());
+  std::vector<int> mpi_layout  = GridDefaultMpi();
+  GridCartesian               Grid(latt_size,simd_layout,mpi_layout);
+  GridRedBlackCartesian     RBGrid(latt_size,simd_layout,mpi_layout);
+
+  int threads = GridThread::GetThreads();
+  std::cout<<GridLogMessage << "Grid is setup to use "<<threads<<" threads"<<std::endl;
+  std::cout<<GridLogMessage << "Grid floating point word size is REALF"<< sizeof(RealF)<<std::endl;
+  std::cout<<GridLogMessage << "Grid floating point word size is REALD"<< sizeof(RealD)<<std::endl;
+  std::cout<<GridLogMessage << "Grid floating point word size is REAL"<< sizeof(Real)<<std::endl;
+
+  std::vector<int> seeds({1,2,3,4});
+  GridParallelRNG          pRNG(&Grid);
+  pRNG.SeedFixedIntegers(seeds);
+  //  pRNG.SeedFixedIntegers(std::vector<int>({45,12,81,9});
+
+  typedef typename ImprovedStaggeredFermionR::FermionField FermionField; 
+  typename ImprovedStaggeredFermionR::ImplParams params; 
+
+  FermionField src   (&Grid); random(pRNG,src);
+  FermionField result(&Grid); result=zero;
+  FermionField    ref(&Grid);    ref=zero;
+  FermionField    tmp(&Grid);    tmp=zero;
+  FermionField    err(&Grid);    tmp=zero;
+  LatticeGaugeField Umu(&Grid); random(pRNG,Umu);
+  std::vector<LatticeColourMatrix> U(4,&Grid);
+
+  double volume=1;
+  for(int mu=0;mu<Nd;mu++){
+    volume=volume*latt_size[mu];
+  }  
+
+  // Only one non-zero (y)
+#if 0
+  Umu=zero;
+  Complex cone(1.0,0.0);
+  for(int nn=0;nn<Nd;nn++){
+    random(pRNG,U[nn]);
+    if(1) {
+      if (nn!=2) { U[nn]=zero; std::cout<<GridLogMessage << "zeroing gauge field in dir "<<nn<<std::endl; }
+      //      else       { U[nn]= cone;std::cout<<GridLogMessage << "unit gauge field in dir "<<nn<<std::endl; }
+      else       { std::cout<<GridLogMessage << "random gauge field in dir "<<nn<<std::endl; }
+    }
+    PokeIndex<LorentzIndex>(Umu,U[nn],nn);
+  }
+#endif
+
+  for(int mu=0;mu<Nd;mu++){
+    U[mu] = PeekIndex<LorentzIndex>(Umu,mu);
+  }
+  ref = zero;
+  /*  
+  { // Naive wilson implementation
+    ref = zero;
+    for(int mu=0;mu<Nd;mu++){
+      //    ref =  src + Gamma(Gamma::GammaX)* src ; // 1-gamma_x
+      tmp = U[mu]*Cshift(src,mu,1);
+      for(int i=0;i<ref._odata.size();i++){
+	ref._odata[i]+= tmp._odata[i] - Gamma(Gmu[mu])*tmp._odata[i]; ;
+      }
+
+      tmp =adj(U[mu])*src;
+      tmp =Cshift(tmp,mu,-1);
+      for(int i=0;i<ref._odata.size();i++){
+	ref._odata[i]+= tmp._odata[i] + Gamma(Gmu[mu])*tmp._odata[i]; ;
+      }
+    }
+  }
+  ref = -0.5*ref;
+  */
+
+  RealD mass=0.1;
+  RealD c1=9.0/8.0;
+  RealD c2=-1.0/24.0;
+  RealD u0=1.0;
+  ImprovedStaggeredFermionR Ds(Umu,Umu,Grid,RBGrid,mass,c1,c2,u0,params);
+  
+  std::cout<<GridLogMessage << "Calling Ds"<<std::endl;
+  int ncall=1000;
+  double t0=usecond();
+  for(int i=0;i<ncall;i++){
+    Ds.Dhop(src,result,0);
+  }
+  double t1=usecond();
+  double flops=(16*(3*(6+8+8)) + 15*3*2)*volume*ncall; // == 66*16 +  == 1146
+  
+  std::cout<<GridLogMessage << "Called Ds"<<std::endl;
+  std::cout<<GridLogMessage << "norm result "<< norm2(result)<<std::endl;
+  std::cout<<GridLogMessage << "norm ref    "<< norm2(ref)<<std::endl;
+  std::cout<<GridLogMessage << "mflop/s =   "<< flops/(t1-t0)<<std::endl;
+  err = ref-result; 
+  std::cout<<GridLogMessage << "norm diff   "<< norm2(err)<<std::endl;
+
+  Grid_finalize();
+}

benchmarks/Benchmark_su3.cc

@@ -55,7 +55,7 @@ int main (int argc, char ** argv)
       std::vector<int> latt_size  ({lat*mpi_layout[0],lat*mpi_layout[1],lat*mpi_layout[2],lat*mpi_layout[3]});
       int vol = latt_size[0]*latt_size[1]*latt_size[2]*latt_size[3];
       GridCartesian     Grid(latt_size,simd_layout,mpi_layout);
-      //      GridParallelRNG          pRNG(&Grid);      pRNG.SeedRandomDevice();
+      //      GridParallelRNG          pRNG(&Grid);      pRNG.SeedFixedIntegers(std::vector<int>({45,12,81,9});
 
       LatticeColourMatrix z(&Grid);// random(pRNG,z);
       LatticeColourMatrix x(&Grid);// random(pRNG,x);
@@ -88,7 +88,7 @@ int main (int argc, char ** argv)
       int vol = latt_size[0]*latt_size[1]*latt_size[2]*latt_size[3];
 
       GridCartesian     Grid(latt_size,simd_layout,mpi_layout);
-      //      GridParallelRNG          pRNG(&Grid);      pRNG.SeedRandomDevice();
+      //      GridParallelRNG          pRNG(&Grid);      pRNG.SeedFixedIntegers(std::vector<int>({45,12,81,9});
 
       LatticeColourMatrix z(&Grid); //random(pRNG,z);
       LatticeColourMatrix x(&Grid); //random(pRNG,x);
@@ -119,7 +119,7 @@ int main (int argc, char ** argv)
       int vol = latt_size[0]*latt_size[1]*latt_size[2]*latt_size[3];
 
       GridCartesian     Grid(latt_size,simd_layout,mpi_layout);
-      //      GridParallelRNG          pRNG(&Grid);      pRNG.SeedRandomDevice();
+      //      GridParallelRNG          pRNG(&Grid);      pRNG.SeedFixedIntegers(std::vector<int>({45,12,81,9});
 
       LatticeColourMatrix z(&Grid); //random(pRNG,z);
       LatticeColourMatrix x(&Grid); //random(pRNG,x);
@@ -150,7 +150,7 @@ int main (int argc, char ** argv)
       int vol = latt_size[0]*latt_size[1]*latt_size[2]*latt_size[3];
 
       GridCartesian     Grid(latt_size,simd_layout,mpi_layout);
-      //      GridParallelRNG          pRNG(&Grid);      pRNG.SeedRandomDevice();
+      //      GridParallelRNG          pRNG(&Grid);      pRNG.SeedFixedIntegers(std::vector<int>({45,12,81,9});
 
       LatticeColourMatrix z(&Grid); //random(pRNG,z);
       LatticeColourMatrix x(&Grid); //random(pRNG,x);

benchmarks/Benchmark_wilson.cc

@@ -37,11 +37,11 @@ struct scal {
   d internal;
 };
 
-  Gamma::GammaMatrix Gmu [] = {
-    Gamma::GammaX,
-    Gamma::GammaY,
-    Gamma::GammaZ,
-    Gamma::GammaT
+  Gamma::Algebra Gmu [] = {
+    Gamma::Algebra::GammaX,
+    Gamma::Algebra::GammaY,
+    Gamma::Algebra::GammaZ,
+    Gamma::Algebra::GammaT
   };
 
 bool overlapComms = false;
@@ -69,7 +69,7 @@ int main (int argc, char ** argv)
   std::vector<int> seeds({1,2,3,4});
   GridParallelRNG          pRNG(&Grid);
   pRNG.SeedFixedIntegers(seeds);
-  //  pRNG.SeedRandomDevice();
+  //  pRNG.SeedFixedIntegers(std::vector<int>({45,12,81,9});
 
   LatticeFermion src   (&Grid); random(pRNG,src);
   LatticeFermion result(&Grid); result=zero;
@@ -106,7 +106,7 @@ int main (int argc, char ** argv)
   { // Naive wilson implementation
     ref = zero;
     for(int mu=0;mu<Nd;mu++){
-      //    ref =  src + Gamma(Gamma::GammaX)* src ; // 1-gamma_x
+      //    ref =  src + Gamma(Gamma::Algebra::GammaX)* src ; // 1-gamma_x
       tmp = U[mu]*Cshift(src,mu,1);
       for(int i=0;i<ref._odata.size();i++){
 	ref._odata[i]+= tmp._odata[i] - Gamma(Gmu[mu])*tmp._odata[i]; ;
@@ -159,7 +159,7 @@ int main (int argc, char ** argv)
     ref = zero;
     for(int mu=0;mu<Nd;mu++){
 
-      //    ref =  src - Gamma(Gamma::GammaX)* src ; // 1+gamma_x
+      //    ref =  src - Gamma(Gamma::Algebra::GammaX)* src ; // 1+gamma_x
       tmp = U[mu]*Cshift(src,mu,1);
       for(int i=0;i<ref._odata.size();i++){
 	ref._odata[i]+= tmp._odata[i] + Gamma(Gmu[mu])*tmp._odata[i]; ;

benchmarks/Benchmark_wilson_sweep.cc

@@ -30,11 +30,11 @@ struct scal {
   d internal;
 };
 
-Gamma::GammaMatrix Gmu [] = {
-  Gamma::GammaX,
-  Gamma::GammaY,
-  Gamma::GammaZ,
-  Gamma::GammaT
+Gamma::Algebra Gmu [] = {
+    Gamma::Algebra::GammaX,
+    Gamma::Algebra::GammaY,
+    Gamma::Algebra::GammaZ,
+    Gamma::Algebra::GammaT
 };
 
 bool overlapComms = false;

configure.ac

@@ -6,7 +6,7 @@ AC_CANONICAL_TARGET
 AM_INIT_AUTOMAKE(subdir-objects)
 AC_CONFIG_MACRO_DIR([m4])
 AC_CONFIG_SRCDIR([lib/Grid.h])
-AC_CONFIG_HEADERS([lib/Config.h])
+AC_CONFIG_HEADERS([lib/Config.h],[sed -i 's|PACKAGE_|GRID_|' lib/Config.h])
 m4_ifdef([AM_SILENT_RULES], [AM_SILENT_RULES([yes])])
 
 ############### Checks for programs
@@ -83,6 +83,18 @@ case ${ac_LAPACK} in
         AC_DEFINE([USE_LAPACK],[1],[use LAPACK]);;
 esac
 
+############### FP16 conversions
+AC_ARG_ENABLE([sfw-fp16],
+    [AC_HELP_STRING([--enable-sfw-fp16=yes|no], [enable software fp16 comms])], 
+    [ac_SFW_FP16=${enable_sfw_fp16}], [ac_SFW_FP16=yes])
+case ${ac_SFW_FP16} in
+    yes)
+      AC_DEFINE([SFW_FP16],[1],[software conversion to fp16]);;
+    no);;
+    *)
+      AC_MSG_ERROR(["SFW FP16 option not supported ${ac_SFW_FP16}"]);;
+esac
+
 ############### MKL
 AC_ARG_ENABLE([mkl],
     [AC_HELP_STRING([--enable-mkl=yes|no|prefix], [enable Intel MKL for LAPACK & FFTW])],
@@ -99,6 +111,13 @@ case ${ac_MKL} in
         AC_DEFINE([USE_MKL], [1], [Define to 1 if you use the Intel MKL]);;
 esac
 
+############### HDF5
+AC_ARG_WITH([hdf5],
+    [AS_HELP_STRING([--with-hdf5=prefix],
+    [try this for a non-standard install prefix of the HDF5 library])],
+    [AM_CXXFLAGS="-I$with_hdf5/include $AM_CXXFLAGS"]
+    [AM_LDFLAGS="-L$with_hdf5/lib $AM_LDFLAGS"])
+
 ############### first-touch
 AC_ARG_ENABLE([numa],
     [AC_HELP_STRING([--enable-numa=yes|no|prefix], [enable first touch numa opt])], 
@@ -145,6 +164,12 @@ AC_SEARCH_LIBS([fftw_execute], [fftw3],
                [AC_DEFINE([HAVE_FFTW], [1], [Define to 1 if you have the `FFTW' library])]
                [have_fftw=true])
 
+AC_SEARCH_LIBS([H5Fopen], [hdf5_cpp],
+               [AC_DEFINE([HAVE_HDF5], [1], [Define to 1 if you have the `HDF5' library])]
+               [have_hdf5=true]
+               [LIBS="${LIBS} -lhdf5"], [], [-lhdf5])
+AM_CONDITIONAL(BUILD_HDF5, [ test "${have_hdf5}X" == "trueX" ])
+
 CXXFLAGS=$CXXFLAGS_CPY
 LDFLAGS=$LDFLAGS_CPY
 
@@ -163,19 +188,26 @@ case ${ax_cv_cxx_compiler_vendor} in
     case ${ac_SIMD} in
       SSE4)
         AC_DEFINE([SSE4],[1],[SSE4 intrinsics])
-        SIMD_FLAGS='-msse4.2';;
+	case ${ac_SFW_FP16} in
+	  yes)
+	  SIMD_FLAGS='-msse4.2';;
+	  no)
+	  SIMD_FLAGS='-msse4.2 -mf16c';;
+	  *)
+          AC_MSG_ERROR(["SFW_FP16 must be either yes or no value ${ac_SFW_FP16} "]);;
+	esac;;
       AVX)
         AC_DEFINE([AVX1],[1],[AVX intrinsics])
-        SIMD_FLAGS='-mavx';;
+        SIMD_FLAGS='-mavx -mf16c';;
       AVXFMA4)
         AC_DEFINE([AVXFMA4],[1],[AVX intrinsics with FMA4])
-        SIMD_FLAGS='-mavx -mfma4';;
+        SIMD_FLAGS='-mavx -mfma4 -mf16c';;
       AVXFMA)
         AC_DEFINE([AVXFMA],[1],[AVX intrinsics with FMA3])
-        SIMD_FLAGS='-mavx -mfma';;
+        SIMD_FLAGS='-mavx -mfma -mf16c';;
       AVX2)
         AC_DEFINE([AVX2],[1],[AVX2 intrinsics])
-        SIMD_FLAGS='-mavx2 -mfma';;
+        SIMD_FLAGS='-mavx2 -mfma -mf16c';;
       AVX512)
         AC_DEFINE([AVX512],[1],[AVX512 intrinsics])
         SIMD_FLAGS='-mavx512f -mavx512pf -mavx512er -mavx512cd';;
@@ -306,9 +338,9 @@ AM_CONDITIONAL(BUILD_COMMS_MPI3L, [ test "${comms_type}X" == "mpi3lX" ] )
 AM_CONDITIONAL(BUILD_COMMS_NONE,  [ test "${comms_type}X" == "noneX" ])
 
 ############### RNG selection
-AC_ARG_ENABLE([rng],[AC_HELP_STRING([--enable-rng=ranlux48|mt19937],\
+AC_ARG_ENABLE([rng],[AC_HELP_STRING([--enable-rng=ranlux48|mt19937|sitmo],\
 	            [Select Random Number Generator to be used])],\
-	            [ac_RNG=${enable_rng}],[ac_RNG=ranlux48])
+	            [ac_RNG=${enable_rng}],[ac_RNG=sitmo])
 
 case ${ac_RNG} in
      ranlux48)
@@ -317,6 +349,9 @@ case ${ac_RNG} in
      mt19937)
       AC_DEFINE([RNG_MT19937],[1],[RNG_MT19937] )
      ;;
+     sitmo)
+      AC_DEFINE([RNG_SITMO],[1],[RNG_SITMO] )
+     ;;
      *)
       AC_MSG_ERROR([${ac_RNG} unsupported --enable-rng option]); 
      ;;
@@ -381,16 +416,19 @@ AC_CONFIG_FILES(tests/IO/Makefile)
 AC_CONFIG_FILES(tests/core/Makefile)
 AC_CONFIG_FILES(tests/debug/Makefile)
 AC_CONFIG_FILES(tests/forces/Makefile)
+AC_CONFIG_FILES(tests/hadrons/Makefile)
 AC_CONFIG_FILES(tests/hmc/Makefile)
 AC_CONFIG_FILES(tests/solver/Makefile)
 AC_CONFIG_FILES(tests/qdpxx/Makefile)
+AC_CONFIG_FILES(tests/testu01/Makefile)
 AC_CONFIG_FILES(benchmarks/Makefile)
+AC_CONFIG_FILES(extras/Makefile)
+AC_CONFIG_FILES(extras/Hadrons/Makefile)
 AC_OUTPUT
 
 echo "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 Summary of configuration for $PACKAGE v$VERSION
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
 ----- PLATFORM ----------------------------------------
 architecture (build)        : $build_cpu
 os (build)                  : $build_os
@@ -403,10 +441,12 @@ SIMD                        : ${ac_SIMD}${SIMD_GEN_WIDTH_MSG}
 Threading                   : ${ac_openmp} 
 Communications type         : ${comms_type}
 Default precision           : ${ac_PRECISION}
+Software FP16 conversion    : ${ac_SFW_FP16}
 RNG choice                  : ${ac_RNG} 
 GMP                         : `if test "x$have_gmp" = xtrue; then echo yes; else echo no; fi`
 LAPACK                      : ${ac_LAPACK}
 FFTW                        : `if test "x$have_fftw" = xtrue; then echo yes; else echo no; fi`
+HDF5                        : `if test "x$have_hdf5" = xtrue; then echo yes; else echo no; fi`
 build DOXYGEN documentation : `if test "$DX_FLAG_doc" = '1'; then echo yes; else echo no; fi`
 ----- BUILD FLAGS -------------------------------------
 CXXFLAGS:

extras/Hadrons/Application.cc

@@ -0,0 +1,317 @@
+/*************************************************************************************
+
+Grid physics library, www.github.com/paboyle/Grid 
+
+Source file: extras/Hadrons/Application.cc
+
+Copyright (C) 2015
+Copyright (C) 2016
+
+Author: Antonin Portelli <antonin.portelli@me.com>
+
+This program is free software; you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation; either version 2 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License along
+with this program; if not, write to the Free Software Foundation, Inc.,
+51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+
+See the full license in the file "LICENSE" in the top level distribution directory
+*************************************************************************************/
+/*  END LEGAL */
+
+#include <Grid/Hadrons/Application.hpp>
+#include <Grid/Hadrons/GeneticScheduler.hpp>
+
+using namespace Grid;
+using namespace QCD;
+using namespace Hadrons;
+
+#define BIG_SEP "==============="
+#define SEP     "---------------"
+
+/******************************************************************************
+ *                       Application implementation                           *
+ ******************************************************************************/
+// constructors ////////////////////////////////////////////////////////////////
+Application::Application(void)
+{
+    LOG(Message) << "Modules available:" << std::endl;
+    auto list = ModuleFactory::getInstance().getBuilderList();
+    for (auto &m: list)
+    {
+        LOG(Message) << "  " << m << std::endl;
+    }
+    auto dim = GridDefaultLatt(), mpi = GridDefaultMpi(), loc(dim);
+    locVol_ = 1;
+    for (unsigned int d = 0; d < dim.size(); ++d)
+    {
+        loc[d]  /= mpi[d];
+        locVol_ *= loc[d];
+    }
+    LOG(Message) << "Global lattice: " << dim << std::endl;
+    LOG(Message) << "MPI partition : " << mpi << std::endl;
+    LOG(Message) << "Local lattice : " << loc << std::endl;
+}
+
+Application::Application(const Application::GlobalPar &par)
+: Application()
+{
+    setPar(par);
+}
+
+Application::Application(const std::string parameterFileName)
+: Application()
+{
+    parameterFileName_ = parameterFileName;
+}
+
+// environment shortcut ////////////////////////////////////////////////////////
+Environment & Application::env(void) const
+{
+    return Environment::getInstance();
+}
+
+// access //////////////////////////////////////////////////////////////////////
+void Application::setPar(const Application::GlobalPar &par)
+{
+    par_ = par;
+    env().setSeed(strToVec<int>(par_.seed));
+}
+
+const Application::GlobalPar & Application::getPar(void)
+{
+    return par_;
+}
+
+// execute /////////////////////////////////////////////////////////////////////
+void Application::run(void)
+{
+    if (!parameterFileName_.empty() and (env().getNModule() == 0))
+    {
+        parseParameterFile(parameterFileName_);
+    }
+    if (!scheduled_)
+    {
+        schedule();
+    }
+    printSchedule();
+    configLoop();
+}
+
+// parse parameter file ////////////////////////////////////////////////////////
+class ObjectId: Serializable
+{
+public:
+    GRID_SERIALIZABLE_CLASS_MEMBERS(ObjectId,
+                                    std::string, name,
+                                    std::string, type);
+};
+
+void Application::parseParameterFile(const std::string parameterFileName)
+{
+    XmlReader reader(parameterFileName);
+    GlobalPar par;
+    ObjectId  id;
+    
+    LOG(Message) << "Building application from '" << parameterFileName << "'..." << std::endl;
+    read(reader, "parameters", par);
+    setPar(par);
+    push(reader, "modules");
+    push(reader, "module");
+    do
+    {
+        read(reader, "id", id);
+        env().createModule(id.name, id.type, reader);
+    } while (reader.nextElement("module"));
+    pop(reader);
+    pop(reader);
+}
+
+void Application::saveParameterFile(const std::string parameterFileName)
+{
+    XmlWriter          writer(parameterFileName);
+    ObjectId           id;
+    const unsigned int nMod = env().getNModule();
+    
+    LOG(Message) << "Saving application to '" << parameterFileName << "'..." << std::endl;
+    write(writer, "parameters", getPar());
+    push(writer, "modules");
+    for (unsigned int i = 0; i < nMod; ++i)
+    {
+        push(writer, "module");
+        id.name = env().getModuleName(i);
+        id.type = env().getModule(i)->getRegisteredName();
+        write(writer, "id", id);
+        env().getModule(i)->saveParameters(writer, "options");
+        pop(writer);
+    }
+    pop(writer);
+    pop(writer);
+}
+
+// schedule computation ////////////////////////////////////////////////////////
+#define MEM_MSG(size)\
+sizeString((size)*locVol_) << " (" << sizeString(size)  << "/site)"
+
+#define DEFINE_MEMPEAK \
+auto memPeak = [this](const std::vector<unsigned int> &program)\
+{\
+    unsigned int memPeak;\
+    bool         msg;\
+    \
+    msg = HadronsLogMessage.isActive();\
+    HadronsLogMessage.Active(false);\
+    env().dryRun(true);\
+    memPeak = env().executeProgram(program);\
+    env().dryRun(false);\
+    env().freeAll();\
+    HadronsLogMessage.Active(true);\
+    \
+    return memPeak;\
+}
+
+void Application::schedule(void)
+{
+    DEFINE_MEMPEAK;
+    
+    // build module dependency graph
+    LOG(Message) << "Building module graph..." << std::endl;
+    auto graph = env().makeModuleGraph();
+    auto con = graph.getConnectedComponents();
+    
+    // constrained topological sort using a genetic algorithm
+    LOG(Message) << "Scheduling computation..." << std::endl;
+    LOG(Message) << "               #module= " << graph.size() << std::endl;
+    LOG(Message) << "       population size= " << par_.genetic.popSize << std::endl;
+    LOG(Message) << "       max. generation= " << par_.genetic.maxGen << std::endl;
+    LOG(Message) << "  max. cst. generation= " << par_.genetic.maxCstGen << std::endl;
+    LOG(Message) << "         mutation rate= " << par_.genetic.mutationRate << std::endl;
+    
+    unsigned int                               k = 0, gen, prevPeak, nCstPeak = 0;
+    std::random_device                         rd;
+    GeneticScheduler<unsigned int>::Parameters par;
+    
+    par.popSize      = par_.genetic.popSize;
+    par.mutationRate = par_.genetic.mutationRate;
+    par.seed         = rd();
+    memPeak_         = 0;
+    CartesianCommunicator::BroadcastWorld(0, &(par.seed), sizeof(par.seed));
+    for (unsigned int i = 0; i < con.size(); ++i)
+    {
+        GeneticScheduler<unsigned int> scheduler(con[i], memPeak, par);
+        
+        gen = 0;
+        do
+        {
+            LOG(Debug) << "Generation " << gen << ":" << std::endl;
+            scheduler.nextGeneration();
+            if (gen != 0)
+            {
+                if (prevPeak == scheduler.getMinValue())
+                {
+                    nCstPeak++;
+                }
+                else
+                {
+                    nCstPeak = 0;
+                }
+            }
+            
+            prevPeak = scheduler.getMinValue();
+            if (gen % 10 == 0)
+            {
+                LOG(Iterative) << "Generation " << gen << ": "
+                               << MEM_MSG(scheduler.getMinValue()) << std::endl;
+            }
+            
+            gen++;
+        } while ((gen < par_.genetic.maxGen)
+                 and (nCstPeak < par_.genetic.maxCstGen));
+        auto &t = scheduler.getMinSchedule();
+        if (scheduler.getMinValue() > memPeak_)
+        {
+            memPeak_ = scheduler.getMinValue();
+        }
+        for (unsigned int j = 0; j < t.size(); ++j)
+        {
+            program_.push_back(t[j]);
+        }
+    }
+    scheduled_ = true;
+}
+
+void Application::saveSchedule(const std::string filename)
+{
+    TextWriter               writer(filename);
+    std::vector<std::string> program;
+    
+    if (!scheduled_)
+    {
+        HADRON_ERROR("Computation not scheduled");
+    }
+    LOG(Message) << "Saving current schedule to '" << filename << "'..."
+                 << std::endl;
+    for (auto address: program_)
+    {
+        program.push_back(env().getModuleName(address));
+    }
+    write(writer, "schedule", program);
+}
+
+void Application::loadSchedule(const std::string filename)
+{
+    DEFINE_MEMPEAK;
+    
+    TextReader               reader(filename);
+    std::vector<std::string> program;
+    
+    LOG(Message) << "Loading schedule from '" << filename << "'..."
+                 << std::endl;
+    read(reader, "schedule", program);
+    program_.clear();
+    for (auto &name: program)
+    {
+        program_.push_back(env().getModuleAddress(name));
+    }
+    scheduled_ = true;
+    memPeak_   = memPeak(program_);
+}
+
+void Application::printSchedule(void)
+{
+    if (!scheduled_)
+    {
+        HADRON_ERROR("Computation not scheduled");
+    }
+    LOG(Message) << "Schedule (memory peak: " << MEM_MSG(memPeak_) << "):"
+                 << std::endl;
+    for (unsigned int i = 0; i < program_.size(); ++i)
+    {
+        LOG(Message) << std::setw(4) << i + 1 << ": "
+                     << env().getModuleName(program_[i]) << std::endl;
+    }
+}
+
+// loop on configurations //////////////////////////////////////////////////////
+void Application::configLoop(void)
+{
+    auto range = par_.trajCounter;
+    
+    for (unsigned int t = range.start; t < range.end; t += range.step)
+    {
+        LOG(Message) << BIG_SEP << " Starting measurement for trajectory " << t
+                     << " " << BIG_SEP << std::endl;
+        env().setTrajectory(t);
+        env().executeProgram(program_);
+    }
+    LOG(Message) << BIG_SEP << " End of measurement " << BIG_SEP << std::endl;
+    env().freeAll();
+}

extras/Hadrons/Application.hpp

@@ -0,0 +1,132 @@
+/*************************************************************************************
+
+Grid physics library, www.github.com/paboyle/Grid 
+
+Source file: extras/Hadrons/Application.hpp
+
+Copyright (C) 2015
+Copyright (C) 2016
+
+Author: Antonin Portelli <antonin.portelli@me.com>
+
+This program is free software; you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation; either version 2 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License along
+with this program; if not, write to the Free Software Foundation, Inc.,
+51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+
+See the full license in the file "LICENSE" in the top level distribution directory
+*************************************************************************************/
+/*  END LEGAL */
+
+#ifndef Hadrons_Application_hpp_
+#define Hadrons_Application_hpp_
+
+#include <Grid/Hadrons/Global.hpp>
+#include <Grid/Hadrons/Environment.hpp>
+#include <Grid/Hadrons/ModuleFactory.hpp>
+#include <Grid/Hadrons/Modules.hpp>
+
+BEGIN_HADRONS_NAMESPACE
+
+/******************************************************************************
+ *                         Main program manager                               *
+ ******************************************************************************/
+class Application
+{
+public:
+    class TrajRange: Serializable
+    {
+    public:
+        GRID_SERIALIZABLE_CLASS_MEMBERS(TrajRange,
+                                        unsigned int, start,
+                                        unsigned int, end,
+                                        unsigned int, step);
+    };
+    class GeneticPar: Serializable
+    {
+    public:
+        GeneticPar(void):
+            popSize{20}, maxGen{1000}, maxCstGen{100}, mutationRate{.1} {};
+    public:
+        GRID_SERIALIZABLE_CLASS_MEMBERS(GeneticPar,
+                                        unsigned int, popSize,
+                                        unsigned int, maxGen,
+                                        unsigned int, maxCstGen,
+                                        double      , mutationRate);
+    };
+    class GlobalPar: Serializable
+    {
+    public:
+        GRID_SERIALIZABLE_CLASS_MEMBERS(GlobalPar,
+                                        TrajRange,   trajCounter,
+                                        GeneticPar,  genetic,
+                                        std::string, seed);
+    };
+public:
+    // constructors
+    Application(void);
+    Application(const GlobalPar &par);
+    Application(const std::string parameterFileName);
+    // destructor
+    virtual ~Application(void) = default;
+    // access
+    void              setPar(const GlobalPar &par);
+    const GlobalPar & getPar(void);
+    // module creation
+    template <typename M>
+    void createModule(const std::string name);
+    template <typename M>
+    void createModule(const std::string name, const typename M::Par &par);
+    // execute
+    void run(void);
+    // XML parameter file I/O
+    void parseParameterFile(const std::string parameterFileName);
+    void saveParameterFile(const std::string parameterFileName);
+    // schedule computation
+    void schedule(void);
+    void saveSchedule(const std::string filename);
+    void loadSchedule(const std::string filename);
+    void printSchedule(void);
+    // loop on configurations
+    void configLoop(void);
+private:
+    // environment shortcut
+    Environment & env(void) const;
+private:
+    long unsigned int         locVol_;
+    std::string               parameterFileName_{""};
+    GlobalPar                 par_;
+    std::vector<unsigned int> program_;
+    Environment::Size         memPeak_;
+    bool                      scheduled_{false};
+};
+
+/******************************************************************************
+ *                     Application template implementation                    *
+ ******************************************************************************/
+// module creation /////////////////////////////////////////////////////////////
+template <typename M>
+void Application::createModule(const std::string name)
+{
+    env().createModule<M>(name);
+}
+
+template <typename M>
+void Application::createModule(const std::string name,
+                               const typename M::Par &par)
+{
+    env().createModule<M>(name, par);
+}
+
+END_HADRONS_NAMESPACE
+
+#endif // Hadrons_Application_hpp_

extras/Hadrons/Environment.cc

@@ -0,0 +1,743 @@
+/*************************************************************************************
+
+Grid physics library, www.github.com/paboyle/Grid 
+
+Source file: extras/Hadrons/Environment.cc
+
+Copyright (C) 2015
+Copyright (C) 2016
+
+Author: Antonin Portelli <antonin.portelli@me.com>
+
+This program is free software; you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation; either version 2 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License along
+with this program; if not, write to the Free Software Foundation, Inc.,
+51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+
+See the full license in the file "LICENSE" in the top level distribution directory
+*************************************************************************************/
+/*  END LEGAL */
+
+#include <Grid/Hadrons/Environment.hpp>
+#include <Grid/Hadrons/Module.hpp>
+#include <Grid/Hadrons/ModuleFactory.hpp>
+
+using namespace Grid;
+using namespace QCD;
+using namespace Hadrons;
+
+/******************************************************************************
+ *                       Environment implementation                           *
+ ******************************************************************************/
+// constructor /////////////////////////////////////////////////////////////////
+Environment::Environment(void)
+{
+    nd_ = GridDefaultLatt().size();
+    grid4d_.reset(SpaceTimeGrid::makeFourDimGrid(
+        GridDefaultLatt(), GridDefaultSimd(nd_, vComplex::Nsimd()),
+        GridDefaultMpi()));
+    gridRb4d_.reset(SpaceTimeGrid::makeFourDimRedBlackGrid(grid4d_.get()));
+    auto loc = getGrid()->LocalDimensions();
+    locVol_ = 1;
+    for (unsigned int d = 0; d < loc.size(); ++d)
+    {
+        locVol_ *= loc[d];
+    }
+    rng4d_.reset(new GridParallelRNG(grid4d_.get()));
+}
+
+// dry run /////////////////////////////////////////////////////////////////////
+void Environment::dryRun(const bool isDry)
+{
+    dryRun_ = isDry;
+}
+
+bool Environment::isDryRun(void) const
+{
+    return dryRun_;
+}
+
+// trajectory number ///////////////////////////////////////////////////////////
+void Environment::setTrajectory(const unsigned int traj)
+{
+    traj_ = traj;
+}
+
+unsigned int Environment::getTrajectory(void) const
+{
+    return traj_;
+}
+
+// grids ///////////////////////////////////////////////////////////////////////
+void Environment::createGrid(const unsigned int Ls)
+{
+    if (grid5d_.find(Ls) == grid5d_.end())
+    {
+        auto g = getGrid();
+        
+        grid5d_[Ls].reset(SpaceTimeGrid::makeFiveDimGrid(Ls, g));
+        gridRb5d_[Ls].reset(SpaceTimeGrid::makeFiveDimRedBlackGrid(Ls, g));
+    }
+}
+
+GridCartesian * Environment::getGrid(const unsigned int Ls) const
+{
+    try
+    {
+        if (Ls == 1)
+        {
+            return grid4d_.get();
+        }
+        else
+        {
+            return grid5d_.at(Ls).get();
+        }
+    }
+    catch(std::out_of_range &)
+    {
+        HADRON_ERROR("no grid with Ls= " << Ls);
+    }
+}
+
+GridRedBlackCartesian * Environment::getRbGrid(const unsigned int Ls) const
+{
+    try
+    {
+        if (Ls == 1)
+        {
+            return gridRb4d_.get();
+        }
+        else
+        {
+            return gridRb5d_.at(Ls).get();
+        }
+    }
+    catch(std::out_of_range &)
+    {
+        HADRON_ERROR("no red-black 5D grid with Ls= " << Ls);
+    }
+}
+
+unsigned int Environment::getNd(void) const
+{
+    return nd_;
+}
+
+// random number generator /////////////////////////////////////////////////////
+void Environment::setSeed(const std::vector<int> &seed)
+{
+    rng4d_->SeedFixedIntegers(seed);
+}
+
+GridParallelRNG * Environment::get4dRng(void) const
+{
+    return rng4d_.get();
+}
+
+// module management ///////////////////////////////////////////////////////////
+void Environment::pushModule(Environment::ModPt &pt)
+{
+    std::string name = pt->getName();
+    
+    if (!hasModule(name))
+    {
+        std::vector<unsigned int> inputAddress;
+        unsigned int              address;
+        ModuleInfo                m;
+        
+        m.data = std::move(pt);
+        m.type = typeIdPt(*m.data.get());
+        m.name = name;
+        auto input  = m.data->getInput();
+        for (auto &in: input)
+        {
+            if (!hasObject(in))
+            {
+                addObject(in , -1);
+            }
+            m.input.push_back(objectAddress_[in]);
+        }
+        auto output = m.data->getOutput();
+        module_.push_back(std::move(m));
+        address              = static_cast<unsigned int>(module_.size() - 1);
+        moduleAddress_[name] = address;
+        for (auto &out: output)
+        {
+            if (!hasObject(out))
+            {
+                addObject(out, address);
+            }
+            else
+            {
+                if (object_[objectAddress_[out]].module < 0)
+                {
+                    object_[objectAddress_[out]].module = address;
+                }
+                else
+                {
+                    HADRON_ERROR("object '" + out
+                                 + "' is already produced by module '"
+                                 + module_[object_[getObjectAddress(out)].module].name
+                                 + "' (while pushing module '" + name + "')");
+                }
+            }
+        }
+    }
+    else
+    {
+        HADRON_ERROR("module '" + name + "' already exists");
+    }
+}
+
+unsigned int Environment::getNModule(void) const
+{
+    return module_.size();
+}
+
+void Environment::createModule(const std::string name, const std::string type,
+                               XmlReader &reader)
+{
+    auto &factory = ModuleFactory::getInstance();
+    auto pt       = factory.create(type, name);
+    
+    pt->parseParameters(reader, "options");
+    pushModule(pt);
+}
+
+ModuleBase * Environment::getModule(const unsigned int address) const
+{
+    if (hasModule(address))
+    {
+        return module_[address].data.get();
+    }
+    else
+    {
+        HADRON_ERROR("no module with address " + std::to_string(address));
+    }
+}
+
+ModuleBase * Environment::getModule(const std::string name) const
+{
+    return getModule(getModuleAddress(name));
+}
+
+unsigned int Environment::getModuleAddress(const std::string name) const
+{
+    if (hasModule(name))
+    {
+        return moduleAddress_.at(name);
+    }
+    else
+    {
+        HADRON_ERROR("no module with name '" + name + "'");
+    }
+}
+
+std::string Environment::getModuleName(const unsigned int address) const
+{
+    if (hasModule(address))
+    {
+        return module_[address].name;
+    }
+    else
+    {
+        HADRON_ERROR("no module with address " + std::to_string(address));
+    }
+}
+
+std::string Environment::getModuleType(const unsigned int address) const
+{
+    if (hasModule(address))
+    {
+        return typeName(module_[address].type);
+    }
+    else
+    {
+        HADRON_ERROR("no module with address " + std::to_string(address));
+    }
+}
+
+std::string Environment::getModuleType(const std::string name) const
+{
+    return getModuleType(getModuleAddress(name));
+}
+
+bool Environment::hasModule(const unsigned int address) const
+{
+    return (address < module_.size());
+}
+
+bool Environment::hasModule(const std::string name) const
+{
+    return (moduleAddress_.find(name) != moduleAddress_.end());
+}
+
+Graph<unsigned int> Environment::makeModuleGraph(void) const
+{
+    Graph<unsigned int> moduleGraph;
+    
+    for (unsigned int i = 0; i < module_.size(); ++i)
+    {
+        moduleGraph.addVertex(i);
+        for (auto &j: module_[i].input)
+        {
+            moduleGraph.addEdge(object_[j].module, i);
+        }
+    }
+    
+    return moduleGraph;
+}
+
+#define BIG_SEP "==============="
+#define SEP     "---------------"
+#define MEM_MSG(size)\
+sizeString((size)*locVol_) << " (" << sizeString(size)  << "/site)"
+
+Environment::Size
+Environment::executeProgram(const std::vector<unsigned int> &p)
+{
+    Size                                memPeak = 0, sizeBefore, sizeAfter;
+    std::vector<std::set<unsigned int>> freeProg;
+    bool                                continueCollect, nothingFreed;
+    
+    // build garbage collection schedule
+    freeProg.resize(p.size());
+    for (unsigned int i = 0; i < object_.size(); ++i)
+    {
+        auto pred = [i, this](const unsigned int j)
+        {
+            auto &in = module_[j].input;
+            auto it  = std::find(in.begin(), in.end(), i);
+            
+            return (it != in.end()) or (j == object_[i].module);
+        };
+        auto it = std::find_if(p.rbegin(), p.rend(), pred);
+        if (it != p.rend())
+        {
+            freeProg[p.rend() - it - 1].insert(i);
+        }
+    }
+    
+    // program execution
+    for (unsigned int i = 0; i < p.size(); ++i)
+    {
+        // execute module
+        if (!isDryRun())
+        {
+            LOG(Message) << SEP << " Measurement step " << i+1 << "/"
+                         << p.size() << " (module '" << module_[p[i]].name
+                         << "') " << SEP << std::endl;
+        }
+        (*module_[p[i]].data)();
+        sizeBefore = getTotalSize();
+        // print used memory after execution
+        if (!isDryRun())
+        {
+            LOG(Message) << "Allocated objects: " << MEM_MSG(sizeBefore)
+                         << std::endl;
+        }
+        if (sizeBefore > memPeak)
+        {
+            memPeak = sizeBefore;
+        }
+        // garbage collection for step i
+        if (!isDryRun())
+        {
+            LOG(Message) << "Garbage collection..." << std::endl;
+        }
+        nothingFreed = true;
+        do
+        {
+            continueCollect = false;
+            auto toFree = freeProg[i];
+            for (auto &j: toFree)
+            {
+                // continue garbage collection while there are still
+                // objects without owners
+                continueCollect = continueCollect or !hasOwners(j);
+                if(freeObject(j))
+                {
+                    // if an object has been freed, remove it from
+                    // the garbage collection schedule
+                    freeProg[i].erase(j);
+                    nothingFreed = false;
+                }
+            }
+        } while (continueCollect);
+        // any remaining objects in step i garbage collection schedule
+        // is scheduled for step i + 1
+        if (i + 1 < p.size())
+        {
+            for (auto &j: freeProg[i])
+            {
+                freeProg[i + 1].insert(j);
+            }
+        }
+        // print used memory after garbage collection if necessary
+        if (!isDryRun())
+        {
+            sizeAfter = getTotalSize();
+            if (sizeBefore != sizeAfter)
+            {
+                LOG(Message) << "Allocated objects: " << MEM_MSG(sizeAfter)
+                             << std::endl;
+            }
+            else
+            {
+                LOG(Message) << "Nothing to free" << std::endl;
+            }
+        }
+    }
+    
+    return memPeak;
+}
+
+Environment::Size Environment::executeProgram(const std::vector<std::string> &p)
+{
+    std::vector<unsigned int> pAddress;
+    
+    for (auto &n: p)
+    {
+        pAddress.push_back(getModuleAddress(n));
+    }
+    
+    return executeProgram(pAddress);
+}
+
+// general memory management ///////////////////////////////////////////////////
+void Environment::addObject(const std::string name, const int moduleAddress)
+{
+    if (!hasObject(name))
+    {
+        ObjInfo info;
+        
+        info.name   = name;
+        info.module = moduleAddress;
+        object_.push_back(std::move(info));
+        objectAddress_[name] = static_cast<unsigned int>(object_.size() - 1);
+    }
+    else
+    {
+        HADRON_ERROR("object '" + name + "' already exists");
+    }
+}
+
+void Environment::registerObject(const unsigned int address,
+                                 const unsigned int size, const unsigned int Ls)
+{
+    if (!hasRegisteredObject(address))
+    {
+        if (hasObject(address))
+        {
+            object_[address].size         = size;
+            object_[address].Ls           = Ls;
+            object_[address].isRegistered = true;
+        }
+        else
+        {
+            HADRON_ERROR("no object with address " + std::to_string(address));
+        }
+    }
+    else
+    {
+        HADRON_ERROR("object with address " + std::to_string(address)
+                     + " already registered");
+    }
+}
+
+void Environment::registerObject(const std::string name,
+                                 const unsigned int size, const unsigned int Ls)
+{
+    if (!hasObject(name))
+    {
+        addObject(name);
+    }
+    registerObject(getObjectAddress(name), size, Ls);
+}
+
+unsigned int Environment::getObjectAddress(const std::string name) const
+{
+    if (hasObject(name))
+    {
+        return objectAddress_.at(name);
+    }
+    else
+    {
+        HADRON_ERROR("no object with name '" + name + "'");
+    }
+}
+
+std::string Environment::getObjectName(const unsigned int address) const
+{
+    if (hasObject(address))
+    {
+        return object_[address].name;
+    }
+    else
+    {
+        HADRON_ERROR("no object with address " + std::to_string(address));
+    }
+}
+
+std::string Environment::getObjectType(const unsigned int address) const
+{
+    if (hasRegisteredObject(address))
+    {
+        return typeName(object_[address].type);
+    }
+    else if (hasObject(address))
+    {
+        HADRON_ERROR("object with address " + std::to_string(address)
+                     + " exists but is not registered");
+    }
+    else
+    {
+        HADRON_ERROR("no object with address " + std::to_string(address));
+    }
+}
+
+std::string Environment::getObjectType(const std::string name) const
+{
+    return getObjectType(getObjectAddress(name));
+}
+
+Environment::Size Environment::getObjectSize(const unsigned int address) const
+{
+    if (hasRegisteredObject(address))
+    {
+        return object_[address].size;
+    }
+    else if (hasObject(address))
+    {
+        HADRON_ERROR("object with address " + std::to_string(address)
+                     + " exists but is not registered");
+    }
+    else
+    {
+        HADRON_ERROR("no object with address " + std::to_string(address));
+    }
+}
+
+Environment::Size Environment::getObjectSize(const std::string name) const
+{
+    return getObjectSize(getObjectAddress(name));
+}
+
+unsigned int Environment::getObjectLs(const unsigned int address) const
+{
+    if (hasRegisteredObject(address))
+    {
+        return object_[address].Ls;
+    }
+    else if (hasObject(address))
+    {
+        HADRON_ERROR("object with address " + std::to_string(address)
+                     + " exists but is not registered");
+    }
+    else
+    {
+        HADRON_ERROR("no object with address " + std::to_string(address));
+    }
+}
+
+unsigned int Environment::getObjectLs(const std::string name) const
+{
+    return getObjectLs(getObjectAddress(name));
+}
+
+bool Environment::hasObject(const unsigned int address) const
+{
+    return (address < object_.size());
+}
+
+bool Environment::hasObject(const std::string name) const
+{
+    auto it = objectAddress_.find(name);
+    
+    return ((it != objectAddress_.end()) and hasObject(it->second));
+}
+
+bool Environment::hasRegisteredObject(const unsigned int address) const
+{
+    if (hasObject(address))
+    {
+        return object_[address].isRegistered;
+    }
+    else
+    {
+        return false;
+    }
+}
+
+bool Environment::hasRegisteredObject(const std::string name) const
+{
+    if (hasObject(name))
+    {
+        return hasRegisteredObject(getObjectAddress(name));
+    }
+    else
+    {
+        return false;
+    }
+}
+
+bool Environment::hasCreatedObject(const unsigned int address) const
+{
+    if (hasObject(address))
+    {
+        return (object_[address].data != nullptr);
+    }
+    else
+    {
+        return false;
+    }
+}
+
+bool Environment::hasCreatedObject(const std::string name) const
+{
+    if (hasObject(name))
+    {
+        return hasCreatedObject(getObjectAddress(name));
+    }
+    else
+    {
+        return false;
+    }
+}
+
+bool Environment::isObject5d(const unsigned int address) const
+{
+    return (getObjectLs(address) > 1);
+}
+
+bool Environment::isObject5d(const std::string name) const
+{
+    return (getObjectLs(name) > 1);
+}
+
+Environment::Size Environment::getTotalSize(void) const
+{
+    Environment::Size size = 0;
+    
+    for (auto &o: object_)
+    {
+        if (o.isRegistered)
+        {
+            size += o.size;
+        }
+    }
+    
+    return size;
+}
+
+void Environment::addOwnership(const unsigned int owner,
+                               const unsigned int property)
+{
+    if (hasObject(property))
+    {
+        object_[property].owners.insert(owner);
+    }
+    else
+    {
+        HADRON_ERROR("no object with address " + std::to_string(property));
+    }
+    if (hasObject(owner))
+    {
+        object_[owner].properties.insert(property);
+    }
+    else
+    {
+        HADRON_ERROR("no object with address " + std::to_string(owner));
+    }
+}
+
+void Environment::addOwnership(const std::string owner,
+                               const std::string property)
+{
+    addOwnership(getObjectAddress(owner), getObjectAddress(property));
+}
+
+bool Environment::hasOwners(const unsigned int address) const
+{
+    
+    if (hasObject(address))
+    {
+        return (!object_[address].owners.empty());
+    }
+    else
+    {
+        HADRON_ERROR("no object with address " + std::to_string(address));
+    }
+}
+
+bool Environment::hasOwners(const std::string name) const
+{
+    return hasOwners(getObjectAddress(name));
+}
+
+bool Environment::freeObject(const unsigned int address)
+{
+    if (!hasOwners(address))
+    {
+        if (!isDryRun() and object_[address].isRegistered)
+        {
+            LOG(Message) << "Destroying object '" << object_[address].name
+                         << "'" << std::endl;
+        }
+        for (auto &p: object_[address].properties)
+        {
+            object_[p].owners.erase(address);
+        }
+        object_[address].size         = 0;
+        object_[address].Ls           = 0;
+        object_[address].isRegistered = false;
+        object_[address].type         = nullptr;
+        object_[address].owners.clear();
+        object_[address].properties.clear();
+        object_[address].data.reset(nullptr);
+        
+        return true;
+    }
+    else
+    {
+        return false;
+    }
+}
+
+bool Environment::freeObject(const std::string name)
+{
+    return freeObject(getObjectAddress(name));
+}
+
+void Environment::freeAll(void)
+{
+    for (unsigned int i = 0; i < object_.size(); ++i)
+    {
+        freeObject(i);
+    }
+}
+
+void Environment::printContent(void)
+{
+    LOG(Message) << "Modules: " << std::endl;
+    for (unsigned int i = 0; i < module_.size(); ++i)
+    {
+        LOG(Message) << std::setw(4) << i << ": "
+                     << getModuleName(i) << std::endl;
+    }
+    LOG(Message) << "Objects: " << std::endl;
+    for (unsigned int i = 0; i < object_.size(); ++i)
+    {
+        LOG(Message) << std::setw(4) << i << ": "
+                     << getObjectName(i) << std::endl;
+    }
+}

extras/Hadrons/Environment.hpp

@@ -0,0 +1,385 @@
+/*************************************************************************************
+
+Grid physics library, www.github.com/paboyle/Grid 
+
+Source file: extras/Hadrons/Environment.hpp
+
+Copyright (C) 2015
+Copyright (C) 2016
+
+Author: Antonin Portelli <antonin.portelli@me.com>
+
+This program is free software; you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation; either version 2 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License along
+with this program; if not, write to the Free Software Foundation, Inc.,
+51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+
+See the full license in the file "LICENSE" in the top level distribution directory
+*************************************************************************************/
+/*  END LEGAL */
+
+#ifndef Hadrons_Environment_hpp_
+#define Hadrons_Environment_hpp_
+
+#include <Grid/Hadrons/Global.hpp>
+#include <Grid/Hadrons/Graph.hpp>
+
+#ifndef SITE_SIZE_TYPE
+#define SITE_SIZE_TYPE unsigned int
+#endif
+
+BEGIN_HADRONS_NAMESPACE
+
+/******************************************************************************
+ *                         Global environment                                 *
+ ******************************************************************************/
+// forward declaration of Module
+class ModuleBase;
+
+class Object
+{
+public:
+    Object(void) = default;
+    virtual ~Object(void) = default;
+};
+
+template <typename T>
+class Holder: public Object
+{
+public:
+    Holder(void) = default;
+    Holder(T *pt);
+    virtual ~Holder(void) = default;
+    T &       get(void) const;
+    T *       getPt(void) const;
+    void      reset(T *pt);
+private:
+    std::unique_ptr<T> objPt_{nullptr};
+};
+
+class Environment
+{
+    SINGLETON(Environment);
+public:
+    typedef SITE_SIZE_TYPE                         Size;
+    typedef std::unique_ptr<ModuleBase>            ModPt;
+    typedef std::unique_ptr<GridCartesian>         GridPt;
+    typedef std::unique_ptr<GridRedBlackCartesian> GridRbPt;
+    typedef std::unique_ptr<GridParallelRNG>       RngPt;
+    typedef std::unique_ptr<LatticeBase>           LatticePt;
+private:
+    struct ModuleInfo
+    {
+        const std::type_info      *type{nullptr};
+        std::string               name;
+        ModPt                     data{nullptr};
+        std::vector<unsigned int> input;
+    };
+    struct ObjInfo
+    {
+        Size                    size{0};
+        unsigned int            Ls{0};
+        bool                    isRegistered{false};
+        const std::type_info    *type{nullptr};
+        std::string             name;
+        int                     module{-1};
+        std::set<unsigned int>  owners, properties;
+        std::unique_ptr<Object> data{nullptr};
+    };
+public:
+    // dry run
+    void                    dryRun(const bool isDry);
+    bool                    isDryRun(void) const;
+    // trajectory number
+    void                    setTrajectory(const unsigned int traj);
+    unsigned int            getTrajectory(void) const;
+    // grids
+    void                    createGrid(const unsigned int Ls);
+    GridCartesian *         getGrid(const unsigned int Ls = 1) const;
+    GridRedBlackCartesian * getRbGrid(const unsigned int Ls = 1) const;
+    unsigned int            getNd(void) const;
+    // random number generator
+    void                    setSeed(const std::vector<int> &seed);
+    GridParallelRNG *       get4dRng(void) const;
+    // module management
+    void                    pushModule(ModPt &pt);
+    template <typename M>
+    void                    createModule(const std::string name);
+    template <typename M>
+    void                    createModule(const std::string name,
+                                         const typename M::Par &par);
+    void                    createModule(const std::string name,
+                                         const std::string type,
+                                         XmlReader &reader);
+    unsigned int            getNModule(void) const;
+    ModuleBase *            getModule(const unsigned int address) const;
+    ModuleBase *            getModule(const std::string name) const;
+    template <typename M>
+    M *                     getModule(const unsigned int address) const;
+    template <typename M>
+    M *                     getModule(const std::string name) const;
+    unsigned int            getModuleAddress(const std::string name) const;
+    std::string             getModuleName(const unsigned int address) const;
+    std::string             getModuleType(const unsigned int address) const;
+    std::string             getModuleType(const std::string name) const;
+    bool                    hasModule(const unsigned int address) const;
+    bool                    hasModule(const std::string name) const;
+    Graph<unsigned int>     makeModuleGraph(void) const;
+    Size                    executeProgram(const std::vector<unsigned int> &p);
+    Size                    executeProgram(const std::vector<std::string> &p);
+    // general memory management
+    void                    addObject(const std::string name,
+                                      const int moduleAddress = -1);
+    void                    registerObject(const unsigned int address,
+                                           const unsigned int size,
+                                           const unsigned int Ls = 1);
+    void                    registerObject(const std::string name,
+                                           const unsigned int size,
+                                           const unsigned int Ls = 1);
+    template <typename T>
+    unsigned int            lattice4dSize(void) const;
+    template <typename T>
+    void                    registerLattice(const unsigned int address,
+                                            const unsigned int Ls = 1);
+    template <typename T>
+    void                    registerLattice(const std::string name,
+                                            const unsigned int Ls = 1);
+    template <typename T>
+    void                    setObject(const unsigned int address, T *object);
+    template <typename T>
+    void                    setObject(const std::string name, T *object);
+    template <typename T>
+    T *                     getObject(const unsigned int address) const;
+    template <typename T>
+    T *                     getObject(const std::string name) const;
+    template <typename T>
+    T *                     createLattice(const unsigned int address);
+    template <typename T>
+    T *                     createLattice(const std::string name);
+    unsigned int            getObjectAddress(const std::string name) const;
+    std::string             getObjectName(const unsigned int address) const;
+    std::string             getObjectType(const unsigned int address) const;
+    std::string             getObjectType(const std::string name) const;
+    Size                    getObjectSize(const unsigned int address) const;
+    Size                    getObjectSize(const std::string name) const;
+    unsigned int            getObjectLs(const unsigned int address) const;
+    unsigned int            getObjectLs(const std::string name) const;
+    bool                    hasObject(const unsigned int address) const;
+    bool                    hasObject(const std::string name) const;
+    bool                    hasRegisteredObject(const unsigned int address) const;
+    bool                    hasRegisteredObject(const std::string name) const;
+    bool                    hasCreatedObject(const unsigned int address) const;
+    bool                    hasCreatedObject(const std::string name) const;
+    bool                    isObject5d(const unsigned int address) const;
+    bool                    isObject5d(const std::string name) const;
+    Environment::Size       getTotalSize(void) const;
+    void                    addOwnership(const unsigned int owner,
+                                         const unsigned int property);
+    void                    addOwnership(const std::string owner,
+                                         const std::string property);
+    bool                    hasOwners(const unsigned int address) const;
+    bool                    hasOwners(const std::string name) const;
+    bool                    freeObject(const unsigned int address);
+    bool                    freeObject(const std::string name);
+    void                    freeAll(void);
+    void                    printContent(void);
+private:
+    // general
+    bool                                   dryRun_{false};
+    unsigned int                           traj_, locVol_;
+    // grids
+    GridPt                                 grid4d_;
+    std::map<unsigned int, GridPt>         grid5d_;
+    GridRbPt                               gridRb4d_;
+    std::map<unsigned int, GridRbPt>       gridRb5d_;
+    unsigned int                           nd_;
+    // random number generator
+    RngPt                                  rng4d_;
+    // module and related maps
+    std::vector<ModuleInfo>                module_;
+    std::map<std::string, unsigned int>    moduleAddress_;
+    // lattice store
+    std::map<unsigned int, LatticePt>      lattice_;
+    // object store
+    std::vector<ObjInfo>                   object_;
+    std::map<std::string, unsigned int>    objectAddress_;
+};
+
+/******************************************************************************
+ *                       Holder template implementation                       *
+ ******************************************************************************/
+// constructor /////////////////////////////////////////////////////////////////
+template <typename T>
+Holder<T>::Holder(T *pt)
+: objPt_(pt)
+{}
+
+// access //////////////////////////////////////////////////////////////////////
+template <typename T>
+T & Holder<T>::get(void) const
+{
+    return &objPt_.get();
+}
+
+template <typename T>
+T * Holder<T>::getPt(void) const
+{
+    return objPt_.get();
+}
+
+template <typename T>
+void Holder<T>::reset(T *pt)
+{
+    objPt_.reset(pt);
+}
+
+/******************************************************************************
+ *                     Environment template implementation                    *
+ ******************************************************************************/
+// module management ///////////////////////////////////////////////////////////
+template <typename M>
+void Environment::createModule(const std::string name)
+{
+    ModPt pt(new M(name));
+    
+    pushModule(pt);
+}
+
+template <typename M>
+void Environment::createModule(const std::string name,
+                               const typename M::Par &par)
+{
+    ModPt pt(new M(name));
+    
+    static_cast<M *>(pt.get())->setPar(par);
+    pushModule(pt);
+}
+
+template <typename M>
+M * Environment::getModule(const unsigned int address) const
+{
+    if (auto *pt = dynamic_cast<M *>(getModule(address)))
+    {
+        return pt;
+    }
+    else
+    {
+        HADRON_ERROR("module '" + module_[address].name
+                     + "' does not have type " + typeid(M).name()
+                     + "(object type: " + getModuleType(address) + ")");
+    }
+}
+
+template <typename M>
+M * Environment::getModule(const std::string name) const
+{
+    return getModule<M>(getModuleAddress(name));
+}
+
+template <typename T>
+unsigned int Environment::lattice4dSize(void) const
+{
+    return sizeof(typename T::vector_object)/getGrid()->Nsimd();
+}
+
+template <typename T>
+void Environment::registerLattice(const unsigned int address,
+                                  const unsigned int Ls)
+{
+    createGrid(Ls);
+    registerObject(address, Ls*lattice4dSize<T>(), Ls);
+}
+
+template <typename T>
+void Environment::registerLattice(const std::string name, const unsigned int Ls)
+{
+    createGrid(Ls);
+    registerObject(name, Ls*lattice4dSize<T>(), Ls);
+}
+
+template <typename T>
+void Environment::setObject(const unsigned int address, T *object)
+{
+    if (hasRegisteredObject(address))
+    {
+        object_[address].data.reset(new Holder<T>(object));
+        object_[address].type = &typeid(T);
+    }
+    else if (hasObject(address))
+    {
+        HADRON_ERROR("object with address " + std::to_string(address) +
+                     " exists but is not registered");
+    }
+    else
+    {
+        HADRON_ERROR("no object with address " + std::to_string(address));
+    }
+}
+
+template <typename T>
+void Environment::setObject(const std::string name, T *object)
+{
+    setObject(getObjectAddress(name), object);
+}
+
+template <typename T>
+T * Environment::getObject(const unsigned int address) const
+{
+    if (hasRegisteredObject(address))
+    {
+        if (auto h = dynamic_cast<Holder<T> *>(object_[address].data.get()))
+        {
+            return h->getPt();
+        }
+        else
+        {
+            HADRON_ERROR("object with address " + std::to_string(address) +
+                         " does not have type '" + typeid(T).name() +
+                         "' (has type '" + getObjectType(address) + "')");
+        }
+    }
+    else if (hasObject(address))
+    {
+        HADRON_ERROR("object with address " + std::to_string(address) +
+                     " exists but is not registered");
+    }
+    else
+    {
+        HADRON_ERROR("no object with address " + std::to_string(address));
+    }
+}
+
+template <typename T>
+T * Environment::getObject(const std::string name) const
+{
+    return getObject<T>(getObjectAddress(name));
+}
+
+template <typename T>
+T * Environment::createLattice(const unsigned int address)
+{
+    GridCartesian *g = getGrid(getObjectLs(address));
+    
+    setObject(address, new T(g));
+    
+    return getObject<T>(address);
+}
+
+template <typename T>
+T * Environment::createLattice(const std::string name)
+{
+    return createLattice<T>(getObjectAddress(name));
+}
+
+END_HADRONS_NAMESPACE
+
+#endif // Hadrons_Environment_hpp_

extras/Hadrons/Factory.hpp

@@ -0,0 +1,106 @@
+/*************************************************************************************
+
+Grid physics library, www.github.com/paboyle/Grid 
+
+Source file: extras/Hadrons/Factory.hpp
+
+Copyright (C) 2015
+Copyright (C) 2016
+
+Author: Antonin Portelli <antonin.portelli@me.com>
+
+This program is free software; you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation; either version 2 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License along
+with this program; if not, write to the Free Software Foundation, Inc.,
+51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+
+See the full license in the file "LICENSE" in the top level distribution directory
+*************************************************************************************/
+/*  END LEGAL */
+
+#ifndef Hadrons_Factory_hpp_
+#define Hadrons_Factory_hpp_
+
+#include <Grid/Hadrons/Global.hpp>
+
+BEGIN_HADRONS_NAMESPACE
+
+/******************************************************************************
+ *                        abstract factory class                              *
+ ******************************************************************************/
+template <typename T>
+class Factory
+{
+public:
+    typedef std::function<std::unique_ptr<T>(const std::string)> Func;
+public:
+    // constructor
+    Factory(void) = default;
+    // destructor
+    virtual ~Factory(void) = default;
+    // registration
+    void registerBuilder(const std::string type, const Func &f);
+    // get builder list
+    std::vector<std::string> getBuilderList(void) const;
+    // factory
+    std::unique_ptr<T> create(const std::string type,
+                              const std::string name) const;
+private:
+    std::map<std::string, Func> builder_;
+};
+
+/******************************************************************************
+ *                         template implementation                            *
+ ******************************************************************************/
+// registration ////////////////////////////////////////////////////////////////
+template <typename T>
+void Factory<T>::registerBuilder(const std::string type, const Func &f)
+{
+    builder_[type] = f;
+}
+
+// get module list /////////////////////////////////////////////////////////////
+template <typename T>
+std::vector<std::string> Factory<T>::getBuilderList(void) const
+{
+    std::vector<std::string> list;
+    
+    for (auto &b: builder_)
+    {
+        list.push_back(b.first);
+    }
+    
+    return list;
+}
+
+// factory /////////////////////////////////////////////////////////////////////
+template <typename T>
+std::unique_ptr<T> Factory<T>::create(const std::string type,
+                                      const std::string name) const
+{
+    Func func;
+    
+    try
+    {
+        func = builder_.at(type);
+    }
+    catch (std::out_of_range &)
+    {
+        HADRON_ERROR("object of type '" + type + "' unknown");
+    }
+    
+    return func(name);
+}
+
+END_HADRONS_NAMESPACE
+
+#endif // Hadrons_Factory_hpp_

extras/Hadrons/GeneticScheduler.hpp

@@ -0,0 +1,329 @@
+/*************************************************************************************
+
+Grid physics library, www.github.com/paboyle/Grid 
+
+Source file: extras/Hadrons/GeneticScheduler.hpp
+
+Copyright (C) 2015
+Copyright (C) 2016
+
+Author: Antonin Portelli <antonin.portelli@me.com>
+
+This program is free software; you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation; either version 2 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License along
+with this program; if not, write to the Free Software Foundation, Inc.,
+51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+
+See the full license in the file "LICENSE" in the top level distribution directory
+*************************************************************************************/
+/*  END LEGAL */
+
+#ifndef Hadrons_GeneticScheduler_hpp_
+#define Hadrons_GeneticScheduler_hpp_
+
+#include <Grid/Hadrons/Global.hpp>
+#include <Grid/Hadrons/Graph.hpp>
+
+BEGIN_HADRONS_NAMESPACE
+
+/******************************************************************************
+ *                   Scheduler based on a genetic algorithm                   *
+ ******************************************************************************/
+template <typename T>
+class GeneticScheduler
+{
+public:
+    typedef std::vector<T>                   Gene;
+    typedef std::pair<Gene *, Gene *>        GenePair;
+    typedef std::function<int(const Gene &)> ObjFunc;
+    struct Parameters
+    {
+        double       mutationRate;
+        unsigned int popSize, seed;
+    };
+public:
+    // constructor
+    GeneticScheduler(Graph<T> &graph, const ObjFunc &func,
+                     const Parameters &par);
+    // destructor
+    virtual ~GeneticScheduler(void) = default;
+    // access
+    const Gene & getMinSchedule(void);
+    int          getMinValue(void);
+    // breed a new generation
+    void nextGeneration(void);
+    // heuristic benchmarks
+    void benchmarkCrossover(const unsigned int nIt);
+    // print population
+    friend std::ostream & operator<<(std::ostream &out,
+                                     const GeneticScheduler<T> &s)
+    {
+        out << "[";
+        for (auto &p: s.population_)
+        {
+            out << p.first << ", ";
+        }
+        out << "\b\b]";
+        
+        return out;
+    }
+private:
+    // evolution steps
+    void initPopulation(void);
+    void doCrossover(void);
+    void doMutation(void);
+    // genetic operators
+    GenePair selectPair(void);
+    void     crossover(Gene &c1, Gene &c2, const Gene &p1, const Gene &p2);
+    void     mutation(Gene &m, const Gene &c);
+    
+private:
+    Graph<T>                 &graph_;
+    const ObjFunc            &func_;
+    const Parameters         par_;
+    std::multimap<int, Gene> population_;
+    std::mt19937             gen_;
+};
+
+/******************************************************************************
+ *                       template implementation                              *
+ ******************************************************************************/
+// constructor /////////////////////////////////////////////////////////////////
+template <typename T>
+GeneticScheduler<T>::GeneticScheduler(Graph<T> &graph, const ObjFunc &func,
+                                      const Parameters &par)
+: graph_(graph)
+, func_(func)
+, par_(par)
+{
+    gen_.seed(par_.seed);
+}
+
+// access //////////////////////////////////////////////////////////////////////
+template <typename T>
+const typename GeneticScheduler<T>::Gene &
+GeneticScheduler<T>::getMinSchedule(void)
+{
+    return population_.begin()->second;
+}
+
+template <typename T>
+int GeneticScheduler<T>::getMinValue(void)
+{
+    return population_.begin()->first;
+}
+
+// breed a new generation //////////////////////////////////////////////////////
+template <typename T>
+void GeneticScheduler<T>::nextGeneration(void)
+{
+    // random initialization of the population if necessary
+    if (population_.size() != par_.popSize)
+    {
+        initPopulation();
+    }
+    LOG(Debug) << "Starting population:\n" << *this << std::endl;
+    
+    // random mutations
+    //PARALLEL_FOR_LOOP
+    for (unsigned int i = 0; i < par_.popSize; ++i)
+    {
+        doMutation();
+    }
+    LOG(Debug) << "After mutations:\n" << *this << std::endl;
+    
+    // mating
+    //PARALLEL_FOR_LOOP
+    for (unsigned int i = 0; i < par_.popSize/2; ++i)
+    {
+        doCrossover();
+    }
+    LOG(Debug) << "After mating:\n" << *this << std::endl;
+    
+    // grim reaper
+    auto it = population_.begin();
+    
+    std::advance(it, par_.popSize);
+    population_.erase(it, population_.end());
+    LOG(Debug) << "After grim reaper:\n" << *this << std::endl;
+}
+
+// evolution steps /////////////////////////////////////////////////////////////
+template <typename T>
+void GeneticScheduler<T>::initPopulation(void)
+{
+    population_.clear();
+    for (unsigned int i = 0; i < par_.popSize; ++i)
+    {
+        auto p = graph_.topoSort(gen_);
+        
+        population_.insert(std::make_pair(func_(p), p));
+    }
+}
+
+template <typename T>
+void GeneticScheduler<T>::doCrossover(void)
+{
+    auto p = selectPair();
+    Gene &p1 = *(p.first), &p2 = *(p.second);
+    Gene c1, c2;
+    
+    crossover(c1, c2, p1, p2);
+    PARALLEL_CRITICAL
+    {
+        population_.insert(std::make_pair(func_(c1), c1));
+        population_.insert(std::make_pair(func_(c2), c2));
+    }
+}
+
+template <typename T>
+void GeneticScheduler<T>::doMutation(void)
+{
+    std::uniform_real_distribution<double>      mdis(0., 1.);
+    std::uniform_int_distribution<unsigned int> pdis(0, population_.size() - 1);
+    
+    if (mdis(gen_) < par_.mutationRate)
+    {
+        Gene m;
+        auto it = population_.begin();
+        
+        std::advance(it, pdis(gen_));
+        mutation(m, it->second);
+        PARALLEL_CRITICAL
+        {
+            population_.insert(std::make_pair(func_(m), m));
+        }
+    }
+}
+
+// genetic operators ///////////////////////////////////////////////////////////
+template <typename T>
+typename GeneticScheduler<T>::GenePair GeneticScheduler<T>::selectPair(void)
+{
+    std::vector<double> prob;
+    unsigned int        ind;
+    Gene                *p1, *p2;
+    
+    for (auto &c: population_)
+    {
+        prob.push_back(1./c.first);
+    }
+    do
+    {
+        double probCpy;
+        
+        std::discrete_distribution<unsigned int> dis1(prob.begin(), prob.end());
+        auto rIt = population_.begin();
+        ind = dis1(gen_);
+        std::advance(rIt, ind);
+        p1 = &(rIt->second);
+        probCpy   = prob[ind];
+        prob[ind] = 0.;
+        std::discrete_distribution<unsigned int> dis2(prob.begin(), prob.end());
+        rIt = population_.begin();
+        std::advance(rIt, dis2(gen_));
+        p2 = &(rIt->second);
+        prob[ind] = probCpy;
+    } while (p1 == p2);
+    
+    return std::make_pair(p1, p2);
+}
+
+template <typename T>
+void GeneticScheduler<T>::crossover(Gene &c1, Gene &c2, const Gene &p1,
+                                    const Gene &p2)
+{
+    Gene                                        buf;
+    std::uniform_int_distribution<unsigned int> dis(0, p1.size() - 1);
+    unsigned int                                cut = dis(gen_);
+    
+    c1.clear();
+    buf = p2;
+    for (unsigned int i = 0; i < cut; ++i)
+    {
+        c1.push_back(p1[i]);
+        buf.erase(std::find(buf.begin(), buf.end(), p1[i]));
+    }
+    for (unsigned int i = 0; i < buf.size(); ++i)
+    {
+        c1.push_back(buf[i]);
+    }
+    c2.clear();
+    buf = p2;
+    for (unsigned int i = cut; i < p1.size(); ++i)
+    {
+        buf.erase(std::find(buf.begin(), buf.end(), p1[i]));
+    }
+    for (unsigned int i = 0; i < buf.size(); ++i)
+    {
+        c2.push_back(buf[i]);
+    }
+    for (unsigned int i = cut; i < p1.size(); ++i)
+    {
+        c2.push_back(p1[i]);
+    }
+}
+
+template <typename T>
+void GeneticScheduler<T>::mutation(Gene &m, const Gene &c)
+{
+    Gene                                        buf;
+    std::uniform_int_distribution<unsigned int> dis(0, c.size() - 1);
+    unsigned int                                cut = dis(gen_);
+    Graph<T>                                    g1 = graph_, g2 = graph_;
+    
+    for (unsigned int i = 0; i < cut; ++i)
+    {
+        g1.removeVertex(c[i]);
+    }
+    for (unsigned int i = cut; i < c.size(); ++i)
+    {
+        g2.removeVertex(c[i]);
+    }
+    if (g1.size() > 0)
+    {
+        buf = g1.topoSort(gen_);
+    }
+    if (g2.size() > 0)
+    {
+        m = g2.topoSort(gen_);
+    }
+    for (unsigned int i = cut; i < c.size(); ++i)
+    {
+        m.push_back(buf[i - cut]);
+    }
+}
+
+template <typename T>
+void GeneticScheduler<T>::benchmarkCrossover(const unsigned int nIt)
+{
+    Gene   p1, p2, c1, c2;
+    double neg = 0., eq = 0., pos = 0., total;
+    int    improvement;
+    
+    LOG(Message) << "Benchmarking crossover..." << std::endl;
+    for (unsigned int i = 0; i < nIt; ++i)
+    {
+        p1 = graph_.topoSort(gen_);
+        p2 = graph_.topoSort(gen_);
+        crossover(c1, c2, p1, p2);
+        improvement = (func_(c1) + func_(c2) - func_(p1) - func_(p2))/2;
+        if (improvement < 0) neg++; else if (improvement == 0) eq++; else pos++;
+    }
+    total = neg + eq + pos;
+    LOG(Message) << "  -: " << neg/total << "  =: " << eq/total
+                 << "  +: " << pos/total << std::endl;
+}
+
+END_HADRONS_NAMESPACE
+
+#endif // Hadrons_GeneticScheduler_hpp_

extras/Hadrons/Global.cc

@@ -0,0 +1,82 @@
+/*************************************************************************************
+
+Grid physics library, www.github.com/paboyle/Grid 
+
+Source file: extras/Hadrons/Global.cc
+
+Copyright (C) 2015
+Copyright (C) 2016
+
+Author: Antonin Portelli <antonin.portelli@me.com>
+
+This program is free software; you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation; either version 2 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License along
+with this program; if not, write to the Free Software Foundation, Inc.,
+51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+
+See the full license in the file "LICENSE" in the top level distribution directory
+*************************************************************************************/
+/*  END LEGAL */
+
+#include <Grid/Hadrons/Global.hpp>
+
+using namespace Grid;
+using namespace QCD;
+using namespace Hadrons;
+
+HadronsLogger Hadrons::HadronsLogError(1,"Error");
+HadronsLogger Hadrons::HadronsLogWarning(1,"Warning");
+HadronsLogger Hadrons::HadronsLogMessage(1,"Message");
+HadronsLogger Hadrons::HadronsLogIterative(1,"Iterative");
+HadronsLogger Hadrons::HadronsLogDebug(1,"Debug");
+
+// pretty size formatting //////////////////////////////////////////////////////
+std::string Hadrons::sizeString(long unsigned int bytes)
+
+{
+    constexpr unsigned int bufSize = 256;
+    const char             *suffixes[7] = {"", "K", "M", "G", "T", "P", "E"};
+    char                   buf[256];
+    long unsigned int      s     = 0;
+    double                 count = bytes;
+    
+    while (count >= 1024 && s < 7)
+    {
+        s++;
+        count /= 1024;
+    }
+    if (count - floor(count) == 0.0)
+    {
+        snprintf(buf, bufSize, "%d %sB", (int)count, suffixes[s]);
+    }
+    else
+    {
+        snprintf(buf, bufSize, "%.1f %sB", count, suffixes[s]);
+    }
+    
+    return std::string(buf);
+}
+
+// type utilities //////////////////////////////////////////////////////////////
+constexpr unsigned int maxNameSize = 1024u;
+
+std::string Hadrons::typeName(const std::type_info *info)
+{
+    char        *buf;
+    std::string name;
+    
+    buf  = abi::__cxa_demangle(info->name(), nullptr, nullptr, nullptr);
+    name = buf;
+    free(buf);
+    
+    return name;
+}

extras/Hadrons/Global.hpp

@@ -0,0 +1,150 @@
+/*************************************************************************************
+
+Grid physics library, www.github.com/paboyle/Grid 
+
+Source file: extras/Hadrons/Global.hpp
+
+Copyright (C) 2015
+Copyright (C) 2016
+
+Author: Antonin Portelli <antonin.portelli@me.com>
+
+This program is free software; you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation; either version 2 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License along
+with this program; if not, write to the Free Software Foundation, Inc.,
+51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+
+See the full license in the file "LICENSE" in the top level distribution directory
+*************************************************************************************/
+/*  END LEGAL */
+
+#ifndef Hadrons_Global_hpp_
+#define Hadrons_Global_hpp_
+
+#include <set>
+#include <stack>
+#include <Grid/Grid.h>
+#include <cxxabi.h>
+
+#define BEGIN_HADRONS_NAMESPACE \
+namespace Grid {\
+using namespace QCD;\
+namespace Hadrons {\
+using Grid::operator<<;
+#define END_HADRONS_NAMESPACE }}
+
+#define BEGIN_MODULE_NAMESPACE(name)\
+namespace name {\
+using Grid::operator<<;
+#define END_MODULE_NAMESPACE }
+
+/* the 'using Grid::operator<<;' statement prevents a very nasty compilation
+ * error with GCC 5 (clang & GCC 6 compile fine without it).
+ */
+
+// FIXME: find a way to do that in a more general fashion
+#ifndef FIMPL
+#define FIMPL WilsonImplR
+#endif
+
+BEGIN_HADRONS_NAMESPACE
+
+// type aliases
+#define TYPE_ALIASES(FImpl, suffix)\
+typedef FermionOperator<FImpl>                       FMat##suffix;             \
+typedef typename FImpl::FermionField                 FermionField##suffix;     \
+typedef typename FImpl::PropagatorField              PropagatorField##suffix;  \
+typedef typename FImpl::SitePropagator               SitePropagator##suffix;   \
+typedef typename FImpl::DoubledGaugeField            DoubledGaugeField##suffix;\
+typedef std::function<void(FermionField##suffix &,                             \
+                      const FermionField##suffix &)> SolverFn##suffix;
+
+// logger
+class HadronsLogger: public Logger
+{
+public:
+    HadronsLogger(int on, std::string nm): Logger("Hadrons", on, nm,
+                                                  GridLogColours, "BLACK"){};
+};
+
+#define LOG(channel) std::cout << HadronsLog##channel
+#define HADRON_ERROR(msg)\
+LOG(Error) << msg << " (" << __FUNCTION__ << " at " << __FILE__ << ":"\
+           << __LINE__ << ")" << std::endl;\
+abort();
+
+#define DEBUG_VAR(var) LOG(Debug) << #var << "= " << (var) << std::endl;
+
+extern HadronsLogger HadronsLogError;
+extern HadronsLogger HadronsLogWarning;
+extern HadronsLogger HadronsLogMessage;
+extern HadronsLogger HadronsLogIterative;
+extern HadronsLogger HadronsLogDebug;
+
+// singleton pattern
+#define SINGLETON(name)\
+public:\
+    name(const name &e) = delete;\
+    void operator=(const name &e) = delete;\
+    static name & getInstance(void)\
+    {\
+        static name e;\
+        return e;\
+    }\
+private:\
+    name(void);
+
+#define SINGLETON_DEFCTOR(name)\
+public:\
+    name(const name &e) = delete;\
+    void operator=(const name &e) = delete;\
+    static name & getInstance(void)\
+    {\
+        static name e;\
+        return e;\
+    }\
+private:\
+    name(void) = default;
+
+// pretty size formating
+std::string sizeString(long unsigned int bytes);
+
+// type utilities
+template <typename T>
+const std::type_info * typeIdPt(const T &x)
+{
+    return &typeid(x);
+}
+
+std::string typeName(const std::type_info *info);
+
+template <typename T>
+const std::type_info * typeIdPt(void)
+{
+    return &typeid(T);
+}
+
+template <typename T>
+std::string typeName(const T &x)
+{
+    return typeName(typeIdPt(x));
+}
+
+template <typename T>
+std::string typeName(void)
+{
+    return typeName(typeIdPt<T>());
+}
+
+END_HADRONS_NAMESPACE
+
+#endif // Hadrons_Global_hpp_

extras/Hadrons/Graph.hpp

@@ -0,0 +1,760 @@
+/*************************************************************************************
+
+Grid physics library, www.github.com/paboyle/Grid 
+
+Source file: extras/Hadrons/Graph.hpp
+
+Copyright (C) 2015
+Copyright (C) 2016
+
+Author: Antonin Portelli <antonin.portelli@me.com>
+
+This program is free software; you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation; either version 2 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License along
+with this program; if not, write to the Free Software Foundation, Inc.,
+51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+
+See the full license in the file "LICENSE" in the top level distribution directory
+*************************************************************************************/
+/*  END LEGAL */
+
+#ifndef Hadrons_Graph_hpp_
+#define Hadrons_Graph_hpp_
+
+#include <Grid/Hadrons/Global.hpp>
+
+BEGIN_HADRONS_NAMESPACE
+
+/******************************************************************************
+ *                          Oriented graph class                              *
+ ******************************************************************************/
+// I/O for edges
+template <typename T>
+std::ostream & operator<<(std::ostream &out, const std::pair<T, T> &e)
+{
+    out << "\""  << e.first << "\" -> \"" << e.second << "\"";
+    
+    return out;
+}
+
+// main class
+template <typename T>
+class Graph
+{
+public:
+    typedef std::pair<T, T> Edge;
+public:
+    // constructor
+    Graph(void);
+    // destructor
+    virtual ~Graph(void) = default;
+    // access
+    void           addVertex(const T &value);
+    void           addEdge(const Edge &e);
+    void           addEdge(const T &start, const T &end);
+    std::vector<T> getVertices(void) const;
+    void           removeVertex(const T &value);
+    void           removeEdge(const Edge &e);
+    void           removeEdge(const T &start, const T &end);
+    unsigned int   size(void) const;
+    // tests
+    bool gotValue(const T &value) const;
+    // graph topological manipulations
+    std::vector<T>              getAdjacentVertices(const T &value) const;
+    std::vector<T>              getChildren(const T &value) const;
+    std::vector<T>              getParents(const T &value) const;
+    std::vector<T>              getRoots(void) const;
+    std::vector<Graph<T>>       getConnectedComponents(void) const;
+    std::vector<T>              topoSort(void);
+    template <typename Gen>
+    std::vector<T>              topoSort(Gen &gen);
+    std::vector<std::vector<T>> allTopoSort(void);
+    // I/O
+    friend std::ostream & operator<<(std::ostream &out, const Graph<T> &g)
+    {
+        out << "{";
+        for (auto &e: g.edgeSet_)
+        {
+            out << e << ", ";
+        }
+        if (g.edgeSet_.size() != 0)
+        {
+            out << "\b\b";
+        }
+        out << "}";
+        
+        return out;
+    }
+private:
+    // vertex marking
+    void      mark(const T &value, const bool doMark = true);
+    void      markAll(const bool doMark = true);
+    void      unmark(const T &value);
+    void      unmarkAll(void);
+    bool      isMarked(const T &value) const;
+    const T * getFirstMarked(const bool isMarked = true) const;
+    template <typename Gen>
+    const T * getRandomMarked(const bool isMarked, Gen &gen);
+    const T * getFirstUnmarked(void) const;
+    template <typename Gen>
+    const T * getRandomUnmarked(Gen &gen);
+    // prune marked/unmarked vertices
+    void removeMarked(const bool isMarked = true);
+    void removeUnmarked(void);
+    // depth-first search marking
+    void depthFirstSearch(void);
+    void depthFirstSearch(const T &root);
+private:
+    std::map<T, bool>  isMarked_;
+    std::set<Edge>     edgeSet_;
+};
+
+// build depedency matrix from topological sorts
+template <typename T>
+std::map<T, std::map<T, bool>>
+makeDependencyMatrix(const std::vector<std::vector<T>> &topSort);
+
+/******************************************************************************
+ *                       template implementation                              *
+ ******************************************************************************
+ * in all the following V is the number of vertex and E is the number of edge
+ * in the worst case E = V^2
+ */
+
+// constructor /////////////////////////////////////////////////////////////////
+template <typename T>
+Graph<T>::Graph(void)
+{}
+
+// access //////////////////////////////////////////////////////////////////////
+// complexity: log(V)
+template <typename T>
+void Graph<T>::addVertex(const T &value)
+{
+    isMarked_[value] = false;
+}
+
+// complexity: O(log(V))
+template <typename T>
+void Graph<T>::addEdge(const Edge &e)
+{
+    addVertex(e.first);
+    addVertex(e.second);
+    edgeSet_.insert(e);
+}
+
+// complexity: O(log(V))
+template <typename T>
+void Graph<T>::addEdge(const T &start, const T &end)
+{
+    addEdge(Edge(start, end));
+}
+
+template <typename T>
+std::vector<T> Graph<T>::getVertices(void) const
+{
+    std::vector<T> vertex;
+    
+    for (auto &v: isMarked_)
+    {
+        vertex.push_back(v.first);
+    }
+    
+    return vertex;
+}
+
+// complexity: O(V*log(V))
+template <typename T>
+void Graph<T>::removeVertex(const T &value)
+{
+    // remove vertex from the mark table
+    auto vIt = isMarked_.find(value);
+    
+    if (vIt != isMarked_.end())
+    {
+        isMarked_.erase(vIt);
+    }
+    else
+    {
+        HADRON_ERROR("vertex " << value << " does not exists");
+    }
+
+    // remove all edges containing the vertex
+    auto pred = [&value](const Edge &e)
+    {
+        return ((e.first == value) or (e.second == value));
+    };
+    auto eIt = find_if(edgeSet_.begin(), edgeSet_.end(), pred);
+    
+    while (eIt != edgeSet_.end())
+    {
+        edgeSet_.erase(eIt);
+        eIt = find_if(edgeSet_.begin(), edgeSet_.end(), pred);
+    }
+}
+
+// complexity: O(log(V))
+template <typename T>
+void Graph<T>::removeEdge(const Edge &e)
+{
+    auto eIt = edgeSet_.find(e);
+    
+    if (eIt != edgeSet_.end())
+    {
+        edgeSet_.erase(eIt);
+    }
+    else
+    {
+        HADRON_ERROR("edge "  << e << " does not exists");
+    }
+}
+
+// complexity: O(log(V))
+template <typename T>
+void Graph<T>::removeEdge(const T &start, const T &end)
+{
+    removeEdge(Edge(start, end));
+}
+
+// complexity: O(1)
+template <typename T>
+unsigned int Graph<T>::size(void) const
+{
+    return isMarked_.size();
+}
+
+// tests ///////////////////////////////////////////////////////////////////////
+// complexity: O(log(V))
+template <typename T>
+bool Graph<T>::gotValue(const T &value) const
+{
+    auto it = isMarked_.find(value);
+    
+    if (it == isMarked_.end())
+    {
+        return false;
+    }
+    else
+    {
+        return true;
+    }
+}
+
+// vertex marking //////////////////////////////////////////////////////////////
+// complexity: O(log(V))
+template <typename T>
+void Graph<T>::mark(const T &value, const bool doMark)
+{
+    if (gotValue(value))
+    {
+        isMarked_[value] = doMark;
+    }
+    else
+    {
+        HADRON_ERROR("vertex " << value << " does not exists");
+    }
+}
+
+// complexity: O(V*log(V))
+template <typename T>
+void Graph<T>::markAll(const bool doMark)
+{
+    for (auto &v: isMarked_)
+    {
+        mark(v.first, doMark);
+    }
+}
+
+// complexity: O(log(V))
+template <typename T>
+void Graph<T>::unmark(const T &value)
+{
+    mark(value, false);
+}
+
+// complexity: O(V*log(V))
+template <typename T>
+void Graph<T>::unmarkAll(void)
+{
+    markAll(false);
+}
+
+// complexity: O(log(V))
+template <typename T>
+bool Graph<T>::isMarked(const T &value) const
+{
+    if (gotValue(value))
+    {
+        return isMarked_.at(value);
+    }
+    else
+    {
+        HADRON_ERROR("vertex " << value << " does not exists");
+        
+        return false;
+    }
+}
+
+// complexity: O(log(V))
+template <typename T>
+const T * Graph<T>::getFirstMarked(const bool isMarked) const
+{
+    auto pred = [&isMarked](const std::pair<T, bool> &v)
+    {
+        return (v.second == isMarked);
+    };
+    auto vIt = std::find_if(isMarked_.begin(), isMarked_.end(), pred);
+    
+    if (vIt != isMarked_.end())
+    {
+        return &(vIt->first);
+    }
+    else
+    {
+        return nullptr;
+    }
+}
+
+// complexity: O(log(V))
+template <typename T>
+template <typename Gen>
+const T * Graph<T>::getRandomMarked(const bool isMarked, Gen &gen)
+{
+    auto pred = [&isMarked](const std::pair<T, bool> &v)
+    {
+        return (v.second == isMarked);
+    };
+    std::uniform_int_distribution<unsigned int> dis(0, size() - 1);
+    auto                                        rIt = isMarked_.begin();
+    
+    std::advance(rIt, dis(gen));
+    auto vIt = std::find_if(rIt, isMarked_.end(), pred);
+    if (vIt != isMarked_.end())
+    {
+        return &(vIt->first);
+    }
+    else
+    {
+        vIt = std::find_if(isMarked_.begin(), rIt, pred);
+        if (vIt != rIt)
+        {
+            return &(vIt->first);
+        }
+        else
+        {
+            return nullptr;
+        }
+    }
+}
+
+// complexity: O(log(V))
+template <typename T>
+const T * Graph<T>::getFirstUnmarked(void) const
+{
+    return getFirstMarked(false);
+}
+
+// complexity: O(log(V))
+template <typename T>
+template <typename Gen>
+const T * Graph<T>::getRandomUnmarked(Gen &gen)
+{
+    return getRandomMarked(false, gen);
+}
+
+// prune marked/unmarked vertices //////////////////////////////////////////////
+// complexity: O(V^2*log(V))
+template <typename T>
+void Graph<T>::removeMarked(const bool isMarked)
+{
+    auto isMarkedCopy = isMarked_;
+    
+    for (auto &v: isMarkedCopy)
+    {
+        if (v.second == isMarked)
+        {
+            removeVertex(v.first);
+        }
+    }
+}
+
+// complexity: O(V^2*log(V))
+template <typename T>
+void Graph<T>::removeUnmarked(void)
+{
+    removeMarked(false);
+}
+
+// depth-first search marking //////////////////////////////////////////////////
+// complexity: O(V*log(V))
+template <typename T>
+void Graph<T>::depthFirstSearch(void)
+{
+    depthFirstSearch(isMarked_.begin()->first);
+}
+
+// complexity: O(V*log(V))
+template <typename T>
+void Graph<T>::depthFirstSearch(const T &root)
+{
+    std::vector<T> adjacentVertex;
+    
+    mark(root);
+    adjacentVertex = getAdjacentVertices(root);
+    for (auto &v: adjacentVertex)
+    {
+        if (!isMarked(v))
+        {
+            depthFirstSearch(v);
+        }
+    }
+}
+
+// graph topological manipulations /////////////////////////////////////////////
+// complexity: O(V*log(V))
+template <typename T>
+std::vector<T> Graph<T>::getAdjacentVertices(const T &value) const
+{
+    std::vector<T> adjacentVertex;
+    
+    auto pred = [&value](const Edge &e)
+    {
+        return ((e.first == value) or (e.second == value));
+    };
+    auto eIt = find_if(edgeSet_.begin(), edgeSet_.end(), pred);
+    
+    while (eIt != edgeSet_.end())
+    {
+        if (eIt->first == value)
+        {
+            adjacentVertex.push_back((*eIt).second);
+        }
+        else if (eIt->second == value)
+        {
+            adjacentVertex.push_back((*eIt).first);
+        }
+        eIt = find_if(++eIt, edgeSet_.end(), pred);
+    }
+    
+    return adjacentVertex;
+}
+
+// complexity: O(V*log(V))
+template <typename T>
+std::vector<T> Graph<T>::getChildren(const T &value) const
+{
+    std::vector<T> child;
+    
+    auto pred = [&value](const Edge &e)
+    {
+        return (e.first == value);
+    };
+    auto eIt = find_if(edgeSet_.begin(), edgeSet_.end(), pred);
+    
+    while (eIt != edgeSet_.end())
+    {
+        child.push_back((*eIt).second);
+        eIt = find_if(++eIt, edgeSet_.end(), pred);
+    }
+    
+    return child;
+}
+
+// complexity: O(V*log(V))
+template <typename T>
+std::vector<T> Graph<T>::getParents(const T &value) const
+{
+    std::vector<T> parent;
+    
+    auto pred = [&value](const Edge &e)
+    {
+        return (e.second == value);
+    };
+    auto eIt = find_if(edgeSet_.begin(), edgeSet_.end(), pred);
+    
+    while (eIt != edgeSet_.end())
+    {
+        parent.push_back((*eIt).first);
+        eIt = find_if(++eIt, edgeSet_.end(), pred);
+    }
+    
+    return parent;
+}
+
+// complexity: O(V^2*log(V))
+template <typename T>
+std::vector<T> Graph<T>::getRoots(void) const
+{
+    std::vector<T> root;
+    
+    for (auto &v: isMarked_)
+    {
+        auto parent = getParents(v.first);
+        
+        if (parent.size() == 0)
+        {
+            root.push_back(v.first);
+        }
+    }
+    
+    return root;
+}
+
+// complexity: O(V^2*log(V))
+template <typename T>
+std::vector<Graph<T>> Graph<T>::getConnectedComponents(void) const
+{
+    std::vector<Graph<T>> res;
+    Graph<T>              copy(*this);
+    
+    while (copy.size() > 0)
+    {
+        copy.depthFirstSearch();
+        res.push_back(copy);
+        res.back().removeUnmarked();
+        res.back().unmarkAll();
+        copy.removeMarked();
+        copy.unmarkAll();
+    }
+    
+    return res;
+}
+
+// topological sort using a directed DFS algorithm
+// complexity: O(V*log(V))
+template <typename T>
+std::vector<T> Graph<T>::topoSort(void)
+{
+    std::stack<T>     buf;
+    std::vector<T>    res;
+    const T           *vPt;
+    std::map<T, bool> tmpMarked(isMarked_);
+
+    // visit function
+    std::function<void(const T &)> visit = [&](const T &v)
+    {
+        if (tmpMarked.at(v))
+        {
+            HADRON_ERROR("cannot topologically sort a cyclic graph");
+        }
+        if (!isMarked(v))
+        {
+            std::vector<T> child = getChildren(v);
+
+            tmpMarked[v] = true;
+            for (auto &c: child)
+            {
+                visit(c);
+            }
+            mark(v);
+            tmpMarked[v] = false;
+            buf.push(v);
+        }
+    };
+    
+    // reset temporary marks
+    for (auto &v: tmpMarked)
+    {
+        tmpMarked.at(v.first) = false;
+    }
+    
+    // loop on unmarked vertices
+    unmarkAll();
+    vPt = getFirstUnmarked();
+    while (vPt)
+    {
+        visit(*vPt);
+        vPt = getFirstUnmarked();
+    }
+    unmarkAll();
+    
+    // create result vector
+    while (!buf.empty())
+    {
+        res.push_back(buf.top());
+        buf.pop();
+    }
+    
+    return res;
+}
+
+// random version of the topological sort
+// complexity: O(V*log(V))
+template <typename T>
+template <typename Gen>
+std::vector<T> Graph<T>::topoSort(Gen &gen)
+{
+    std::stack<T>     buf;
+    std::vector<T>    res;
+    const T           *vPt;
+    std::map<T, bool> tmpMarked(isMarked_);
+    
+    // visit function
+    std::function<void(const T &)> visit = [&](const T &v)
+    {
+        if (tmpMarked.at(v))
+        {
+            HADRON_ERROR("cannot topologically sort a cyclic graph");
+        }
+        if (!isMarked(v))
+        {
+            std::vector<T> child = getChildren(v);
+            
+            tmpMarked[v] = true;
+            std::shuffle(child.begin(), child.end(), gen);
+            for (auto &c: child)
+            {
+                visit(c);
+            }
+            mark(v);
+            tmpMarked[v] = false;
+            buf.push(v);
+        }
+    };
+    
+    // reset temporary marks
+    for (auto &v: tmpMarked)
+    {
+        tmpMarked.at(v.first) = false;
+    }
+    
+    // loop on unmarked vertices
+    unmarkAll();
+    vPt = getRandomUnmarked(gen);
+    while (vPt)
+    {
+        visit(*vPt);
+        vPt = getRandomUnmarked(gen);
+    }
+    unmarkAll();
+    
+    // create result vector
+    while (!buf.empty())
+    {
+        res.push_back(buf.top());
+        buf.pop();
+    }
+    
+    return res;
+}
+
+// generate all possible topological sorts
+// Y. L. Varol & D. Rotem, Comput. J. 24(1), pp. 83–84, 1981
+// http://comjnl.oupjournals.org/cgi/doi/10.1093/comjnl/24.1.83
+// complexity: O(V*log(V)) (from the paper, but really ?)
+template <typename T>
+std::vector<std::vector<T>> Graph<T>::allTopoSort(void)
+{
+    std::vector<std::vector<T>>    res;
+    std::map<T, std::map<T, bool>> iMat;
+    
+    // create incidence matrix
+    for (auto &v1: isMarked_)
+    for (auto &v2: isMarked_)
+    {
+        iMat[v1.first][v2.first] = false;
+    }
+    for (auto &v: isMarked_)
+    {
+        auto cVec = getChildren(v.first);
+        
+        for (auto &c: cVec)
+        {
+            iMat[v.first][c] = true;
+        }
+    }
+    
+    // generate initial topological sort
+    res.push_back(topoSort());
+    
+    // generate all other topological sorts by permutation
+    std::vector<T>            p = res[0];
+    const unsigned int        n = size();
+    std::vector<unsigned int> loc(n);
+    unsigned int              i, k, k1;
+    T                         obj_k, obj_k1;
+    bool                      isFinal;
+    
+    for (unsigned int j = 0; j < n; ++j)
+    {
+        loc[j] = j;
+    }
+    i = 0;
+    while (i < n-1)
+    {
+        k      = loc[i];
+        k1     = k + 1;
+        obj_k  = p[k];
+        if (k1 >= n)
+        {
+            isFinal = true;
+            obj_k1  = obj_k;
+        }
+        else
+        {
+            isFinal = false;
+            obj_k1  = p[k1];
+        }
+        if (iMat[res[0][i]][obj_k1] or isFinal)
+        {
+            for (unsigned int l = k; l >= i + 1; --l)
+            {
+                p[l]   = p[l-1];
+            }
+            p[i]   = obj_k;
+            loc[i] = i;
+            i++;
+        }
+        else
+        {
+            p[k]   = obj_k1;
+            p[k1]  = obj_k;
+            loc[i] = k1;
+            i      = 0;
+            res.push_back(p);
+        }
+    }
+    
+    return res;
+}
+
+// build depedency matrix from topological sorts ///////////////////////////////
+// complexity: something like O(V^2*log(V!))
+template <typename T>
+std::map<T, std::map<T, bool>>
+makeDependencyMatrix(const std::vector<std::vector<T>> &topSort)
+{
+    std::map<T, std::map<T, bool>> m;
+    const std::vector<T>           &vList = topSort[0];
+    
+    for (auto &v1: vList)
+    for (auto &v2: vList)
+    {
+        bool dep = true;
+        
+        for (auto &t: topSort)
+        {
+            auto i1 = std::find(t.begin(), t.end(), v1);
+            auto i2 = std::find(t.begin(), t.end(), v2);
+            
+            dep = dep and (i1 - i2 > 0);
+            if (!dep) break;
+        }
+        m[v1][v2] = dep;
+    }
+    
+    return m;
+}
+
+END_HADRONS_NAMESPACE
+
+#endif // Hadrons_Graph_hpp_

extras/Hadrons/HadronsXmlRun.cc

@@ -0,0 +1,80 @@
+/*************************************************************************************
+
+Grid physics library, www.github.com/paboyle/Grid 
+
+Source file: extras/Hadrons/HadronsXmlRun.cc
+
+Copyright (C) 2015
+Copyright (C) 2016
+
+Author: Antonin Portelli <antonin.portelli@me.com>
+
+This program is free software; you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation; either version 2 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License along
+with this program; if not, write to the Free Software Foundation, Inc.,
+51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+
+See the full license in the file "LICENSE" in the top level distribution directory
+*************************************************************************************/
+/*  END LEGAL */
+
+#include <Grid/Hadrons/Application.hpp>
+
+using namespace Grid;
+using namespace QCD;
+using namespace Hadrons;
+
+int main(int argc, char *argv[])
+{
+    // parse command line
+    std::string parameterFileName, scheduleFileName = "";
+    
+    if (argc < 2)
+    {
+        std::cerr << "usage: " << argv[0] << " <parameter file> [<precomputed schedule>] [Grid options]";
+        std::cerr << std::endl;
+        std::exit(EXIT_FAILURE);
+    }
+    parameterFileName = argv[1];
+    if (argc > 2)
+    {
+        if (argv[2][0] != '-')
+        {
+            scheduleFileName = argv[2];
+        }
+    }
+    
+    // initialization
+    Grid_init(&argc, &argv);
+    HadronsLogError.Active(GridLogError.isActive());
+    HadronsLogWarning.Active(GridLogWarning.isActive());
+    HadronsLogMessage.Active(GridLogMessage.isActive());
+    HadronsLogIterative.Active(GridLogIterative.isActive());
+    HadronsLogDebug.Active(GridLogDebug.isActive());
+    LOG(Message) << "Grid initialized" << std::endl;
+    
+    // execution
+    Application application(parameterFileName);
+    
+    application.parseParameterFile(parameterFileName);
+    if (!scheduleFileName.empty())
+    {
+        application.loadSchedule(scheduleFileName);
+    }
+    application.run();
+    
+    // epilogue
+    LOG(Message) << "Grid is finalizing now" << std::endl;
+    Grid_finalize();
+    
+    return EXIT_SUCCESS;
+}

extras/Hadrons/HadronsXmlSchedule.cc

@@ -0,0 +1,72 @@
+/*************************************************************************************
+
+Grid physics library, www.github.com/paboyle/Grid 
+
+Source file: extras/Hadrons/HadronsXmlSchedule.cc
+
+Copyright (C) 2015
+Copyright (C) 2016
+
+Author: Antonin Portelli <antonin.portelli@me.com>
+
+This program is free software; you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation; either version 2 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License along
+with this program; if not, write to the Free Software Foundation, Inc.,
+51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+
+See the full license in the file "LICENSE" in the top level distribution directory
+*************************************************************************************/
+/*  END LEGAL */
+
+#include <Grid/Hadrons/Application.hpp>
+
+using namespace Grid;
+using namespace QCD;
+using namespace Hadrons;
+
+int main(int argc, char *argv[])
+{
+    // parse command line
+    std::string parameterFileName, scheduleFileName;
+    
+    if (argc < 3)
+    {
+        std::cerr << "usage: " << argv[0] << " <parameter file> <schedule output> [Grid options]";
+        std::cerr << std::endl;
+        std::exit(EXIT_FAILURE);
+    }
+    parameterFileName = argv[1];
+    scheduleFileName  = argv[2];
+    
+    // initialization
+    Grid_init(&argc, &argv);
+    HadronsLogError.Active(GridLogError.isActive());
+    HadronsLogWarning.Active(GridLogWarning.isActive());
+    HadronsLogMessage.Active(GridLogMessage.isActive());
+    HadronsLogIterative.Active(GridLogIterative.isActive());
+    HadronsLogDebug.Active(GridLogDebug.isActive());
+    LOG(Message) << "Grid initialized" << std::endl;
+    
+    // execution
+    Application application;
+    
+    application.parseParameterFile(parameterFileName);
+    application.schedule();
+    application.printSchedule();
+    application.saveSchedule(scheduleFileName);
+    
+    // epilogue
+    LOG(Message) << "Grid is finalizing now" << std::endl;
+    Grid_finalize();
+    
+    return EXIT_SUCCESS;
+}

extras/Hadrons/Makefile.am

@@ -0,0 +1,29 @@
+lib_LIBRARIES = libHadrons.a
+bin_PROGRAMS  = HadronsXmlRun HadronsXmlSchedule
+
+include modules.inc
+
+libHadrons_a_SOURCES = \
+    $(modules_cc)      \
+    Application.cc     \
+    Environment.cc     \
+    Global.cc          \
+    Module.cc
+libHadrons_adir = $(pkgincludedir)/Hadrons
+nobase_libHadrons_a_HEADERS = \
+	$(modules_hpp)            \
+	Application.hpp           \
+	Environment.hpp           \
+	Factory.hpp               \
+	GeneticScheduler.hpp      \
+	Global.hpp                \
+	Graph.hpp                 \
+	Module.hpp                \
+	Modules.hpp               \
+	ModuleFactory.hpp
+
+HadronsXmlRun_SOURCES = HadronsXmlRun.cc
+HadronsXmlRun_LDADD   = libHadrons.a -lGrid
+
+HadronsXmlSchedule_SOURCES = HadronsXmlSchedule.cc
+HadronsXmlSchedule_LDADD   = libHadrons.a -lGrid

extras/Hadrons/Module.cc

@@ -0,0 +1,71 @@
+/*************************************************************************************
+
+Grid physics library, www.github.com/paboyle/Grid 
+
+Source file: extras/Hadrons/Module.cc
+
+Copyright (C) 2015
+Copyright (C) 2016
+
+Author: Antonin Portelli <antonin.portelli@me.com>
+
+This program is free software; you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation; either version 2 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License along
+with this program; if not, write to the Free Software Foundation, Inc.,
+51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+
+See the full license in the file "LICENSE" in the top level distribution directory
+*************************************************************************************/
+/*  END LEGAL */
+
+#include <Grid/Hadrons/Module.hpp>
+
+using namespace Grid;
+using namespace QCD;
+using namespace Hadrons;
+
+/******************************************************************************
+ *                       ModuleBase implementation                            *
+ ******************************************************************************/
+// constructor /////////////////////////////////////////////////////////////////
+ModuleBase::ModuleBase(const std::string name)
+: name_(name)
+, env_(Environment::getInstance())
+{}
+
+// access //////////////////////////////////////////////////////////////////////
+std::string ModuleBase::getName(void) const
+{
+    return name_;
+}
+
+Environment & ModuleBase::env(void) const
+{
+    return env_;
+}
+
+// get factory registration name if available
+std::string ModuleBase::getRegisteredName(void)
+{
+    HADRON_ERROR("module '" + getName() + "' has a type not registered"
+                 + " in the factory");
+}
+
+// execution ///////////////////////////////////////////////////////////////////
+void ModuleBase::operator()(void)
+{
+    setup();
+    if (!env().isDryRun())
+    {
+        execute();
+    }
+}

extras/Hadrons/Module.hpp

@@ -0,0 +1,198 @@
+/*************************************************************************************
+
+Grid physics library, www.github.com/paboyle/Grid 
+
+Source file: extras/Hadrons/Module.hpp
+
+Copyright (C) 2015
+Copyright (C) 2016
+
+Author: Antonin Portelli <antonin.portelli@me.com>
+
+This program is free software; you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation; either version 2 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License along
+with this program; if not, write to the Free Software Foundation, Inc.,
+51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+
+See the full license in the file "LICENSE" in the top level distribution directory
+*************************************************************************************/
+/*  END LEGAL */
+
+#ifndef Hadrons_Module_hpp_
+#define Hadrons_Module_hpp_
+
+#include <Grid/Hadrons/Global.hpp>
+#include <Grid/Hadrons/Environment.hpp>
+
+BEGIN_HADRONS_NAMESPACE
+
+// module registration macros
+#define MODULE_REGISTER(mod, base)\
+class mod: public base\
+{\
+public:\
+    typedef base Base;\
+    using Base::Base;\
+    virtual std::string getRegisteredName(void)\
+    {\
+        return std::string(#mod);\
+    }\
+};\
+class mod##ModuleRegistrar\
+{\
+public:\
+    mod##ModuleRegistrar(void)\
+    {\
+        ModuleFactory &modFac = ModuleFactory::getInstance();\
+        modFac.registerBuilder(#mod, [&](const std::string name)\
+                              {\
+                                  return std::unique_ptr<mod>(new mod(name));\
+                              });\
+    }\
+};\
+static mod##ModuleRegistrar mod##ModuleRegistrarInstance;
+
+#define MODULE_REGISTER_NS(mod, base, ns)\
+class mod: public base\
+{\
+public:\
+    typedef base Base;\
+    using Base::Base;\
+    virtual std::string getRegisteredName(void)\
+    {\
+        return std::string(#ns "::" #mod);\
+    }\
+};\
+class ns##mod##ModuleRegistrar\
+{\
+public:\
+    ns##mod##ModuleRegistrar(void)\
+    {\
+        ModuleFactory &modFac = ModuleFactory::getInstance();\
+        modFac.registerBuilder(#ns "::" #mod, [&](const std::string name)\
+                              {\
+                                  return std::unique_ptr<ns::mod>(new ns::mod(name));\
+                              });\
+    }\
+};\
+static ns##mod##ModuleRegistrar ns##mod##ModuleRegistrarInstance;
+
+#define ARG(...) __VA_ARGS__
+
+/******************************************************************************
+ *                            Module class                                    *
+ ******************************************************************************/
+// base class
+class ModuleBase
+{
+public:
+    // constructor
+    ModuleBase(const std::string name);
+    // destructor
+    virtual ~ModuleBase(void) = default;
+    // access
+    std::string getName(void) const;
+    Environment &env(void) const;
+    // get factory registration name if available
+    virtual std::string getRegisteredName(void);
+    // dependencies/products
+    virtual std::vector<std::string> getInput(void) = 0;
+    virtual std::vector<std::string> getOutput(void) = 0;
+    // parse parameters
+    virtual void parseParameters(XmlReader &reader, const std::string name) = 0;
+    virtual void saveParameters(XmlWriter &writer, const std::string name) = 0;
+    // setup
+    virtual void setup(void) {};
+    // execution
+    void operator()(void);
+    virtual void execute(void) = 0;
+private:
+    std::string name_;
+    Environment &env_;
+};
+
+// derived class, templating the parameter class
+template <typename P>
+class Module: public ModuleBase
+{
+public:
+    typedef P Par;
+public:
+    // constructor
+    Module(const std::string name);
+    // destructor
+    virtual ~Module(void) = default;
+    // parse parameters
+    virtual void parseParameters(XmlReader &reader, const std::string name);
+    virtual void saveParameters(XmlWriter &writer, const std::string name);
+    // parameter access
+    const P & par(void) const;
+    void      setPar(const P &par);
+private:
+    P par_;
+};
+
+// no parameter type
+class NoPar {};
+
+template <>
+class Module<NoPar>: public ModuleBase
+{
+public:
+    // constructor
+    Module(const std::string name): ModuleBase(name) {};
+    // destructor
+    virtual ~Module(void) = default;
+    // parse parameters (do nothing)
+    virtual void parseParameters(XmlReader &reader, const std::string name) {};
+    virtual void saveParameters(XmlWriter &writer, const std::string name)
+    {
+        push(writer, "options");
+        pop(writer);
+    };
+};
+
+/******************************************************************************
+ *                           Template implementation                          *
+ ******************************************************************************/
+template <typename P>
+Module<P>::Module(const std::string name)
+: ModuleBase(name)
+{}
+
+template <typename P>
+void Module<P>::parseParameters(XmlReader &reader, const std::string name)
+{
+    read(reader, name, par_);
+}
+
+template <typename P>
+void Module<P>::saveParameters(XmlWriter &writer, const std::string name)
+{
+    write(writer, name, par_);
+}
+
+template <typename P>
+const P & Module<P>::par(void) const
+{
+    return par_;
+}
+
+template <typename P>
+void Module<P>::setPar(const P &par)
+{
+    par_ = par;
+}
+
+END_HADRONS_NAMESPACE
+
+#endif // Hadrons_Module_hpp_

extras/Hadrons/ModuleFactory.hpp

@@ -0,0 +1,49 @@
+/*************************************************************************************
+
+Grid physics library, www.github.com/paboyle/Grid 
+
+Source file: extras/Hadrons/ModuleFactory.hpp
+
+Copyright (C) 2015
+Copyright (C) 2016
+
+Author: Antonin Portelli <antonin.portelli@me.com>
+
+This program is free software; you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation; either version 2 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License along
+with this program; if not, write to the Free Software Foundation, Inc.,
+51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+
+See the full license in the file "LICENSE" in the top level distribution directory
+*************************************************************************************/
+/*  END LEGAL */
+
+#ifndef Hadrons_ModuleFactory_hpp_
+#define Hadrons_ModuleFactory_hpp_
+
+#include <Grid/Hadrons/Global.hpp>
+#include <Grid/Hadrons/Factory.hpp>
+#include <Grid/Hadrons/Module.hpp>
+
+BEGIN_HADRONS_NAMESPACE
+
+/******************************************************************************
+ *                            ModuleFactory                                   *
+ ******************************************************************************/
+class ModuleFactory: public Factory<ModuleBase>
+{
+    SINGLETON_DEFCTOR(ModuleFactory)
+};
+
+END_HADRONS_NAMESPACE
+
+#endif // Hadrons_ModuleFactory_hpp_

extras/Hadrons/Modules.hpp

@@ -0,0 +1,40 @@
+/*************************************************************************************
+
+Grid physics library, www.github.com/paboyle/Grid 
+
+Source file: extras/Hadrons/Modules.hpp
+
+Copyright (C) 2015
+Copyright (C) 2016
+
+Author: Antonin Portelli <antonin.portelli@me.com>
+
+This program is free software; you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation; either version 2 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License along
+with this program; if not, write to the Free Software Foundation, Inc.,
+51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+
+See the full license in the file "LICENSE" in the top level distribution directory
+*************************************************************************************/
+/*  END LEGAL */
+#include <Grid/Hadrons/Modules/MAction/DWF.hpp>
+#include <Grid/Hadrons/Modules/MAction/Wilson.hpp>
+#include <Grid/Hadrons/Modules/MContraction/Baryon.hpp>
+#include <Grid/Hadrons/Modules/MContraction/Meson.hpp>
+#include <Grid/Hadrons/Modules/MGauge/Load.hpp>
+#include <Grid/Hadrons/Modules/MGauge/Random.hpp>
+#include <Grid/Hadrons/Modules/MGauge/Unit.hpp>
+#include <Grid/Hadrons/Modules/MSolver/RBPrecCG.hpp>
+#include <Grid/Hadrons/Modules/MSource/Point.hpp>
+#include <Grid/Hadrons/Modules/MSource/SeqGamma.hpp>
+#include <Grid/Hadrons/Modules/MSource/Z2.hpp>
+#include <Grid/Hadrons/Modules/Quark.hpp>

extras/Hadrons/Modules/MAction/DWF.hpp

@@ -0,0 +1,134 @@
+/*************************************************************************************
+
+Grid physics library, www.github.com/paboyle/Grid 
+
+Source file: extras/Hadrons/Modules/MAction/DWF.hpp
+
+Copyright (C) 2015
+Copyright (C) 2016
+
+Author: Antonin Portelli <antonin.portelli@me.com>
+
+This program is free software; you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation; either version 2 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License along
+with this program; if not, write to the Free Software Foundation, Inc.,
+51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+
+See the full license in the file "LICENSE" in the top level distribution directory
+*************************************************************************************/
+/*  END LEGAL */
+
+#ifndef Hadrons_DWF_hpp_
+#define Hadrons_DWF_hpp_
+
+#include <Grid/Hadrons/Global.hpp>
+#include <Grid/Hadrons/Module.hpp>
+#include <Grid/Hadrons/ModuleFactory.hpp>
+
+BEGIN_HADRONS_NAMESPACE
+
+/******************************************************************************
+ *                     Domain wall quark action                               *
+ ******************************************************************************/
+BEGIN_MODULE_NAMESPACE(MAction)
+
+class DWFPar: Serializable
+{
+public:
+    GRID_SERIALIZABLE_CLASS_MEMBERS(DWFPar,
+                                    std::string, gauge,
+                                    unsigned int, Ls,
+                                    double      , mass,
+                                    double      , M5);
+};
+
+template <typename FImpl>
+class TDWF: public Module<DWFPar>
+{
+public:
+    TYPE_ALIASES(FImpl,);
+public:
+    // constructor
+    TDWF(const std::string name);
+    // destructor
+    virtual ~TDWF(void) = default;
+    // dependency relation
+    virtual std::vector<std::string> getInput(void);
+    virtual std::vector<std::string> getOutput(void);
+    // setup
+    virtual void setup(void);
+    // execution
+    virtual void execute(void);
+};
+
+MODULE_REGISTER_NS(DWF, TDWF<FIMPL>, MAction);
+
+/******************************************************************************
+ *                        DWF template implementation                         *
+ ******************************************************************************/
+// constructor /////////////////////////////////////////////////////////////////
+template <typename FImpl>
+TDWF<FImpl>::TDWF(const std::string name)
+: Module<DWFPar>(name)
+{}
+
+// dependencies/products ///////////////////////////////////////////////////////
+template <typename FImpl>
+std::vector<std::string> TDWF<FImpl>::getInput(void)
+{
+    std::vector<std::string> in = {par().gauge};
+    
+    return in;
+}
+
+template <typename FImpl>
+std::vector<std::string> TDWF<FImpl>::getOutput(void)
+{
+    std::vector<std::string> out = {getName()};
+    
+    return out;
+}
+
+// setup ///////////////////////////////////////////////////////////////////////
+template <typename FImpl>
+void TDWF<FImpl>::setup(void)
+{
+    unsigned int size;
+    
+    size = 2*env().template lattice4dSize<typename FImpl::DoubledGaugeField>();
+    env().registerObject(getName(), size, par().Ls);
+}
+
+// execution ///////////////////////////////////////////////////////////////////
+template <typename FImpl>
+void TDWF<FImpl>::execute(void)
+{
+    LOG(Message) << "Setting up domain wall fermion matrix with m= "
+                 << par().mass << ", M5= " << par().M5 << " and Ls= "
+                 << par().Ls << " using gauge field '" << par().gauge << "'"
+                 << std::endl;
+    env().createGrid(par().Ls);
+    auto &U      = *env().template getObject<LatticeGaugeField>(par().gauge);
+    auto &g4     = *env().getGrid();
+    auto &grb4   = *env().getRbGrid();
+    auto &g5     = *env().getGrid(par().Ls);
+    auto &grb5   = *env().getRbGrid(par().Ls);
+    FMat *fMatPt = new DomainWallFermion<FImpl>(U, g5, grb5, g4, grb4,
+                                                par().mass, par().M5);
+    env().setObject(getName(), fMatPt);
+}
+
+END_MODULE_NAMESPACE
+
+END_HADRONS_NAMESPACE
+
+#endif // Hadrons_DWF_hpp_

extras/Hadrons/Modules/MAction/Wilson.hpp

@@ -0,0 +1,126 @@
+/*************************************************************************************
+
+Grid physics library, www.github.com/paboyle/Grid 
+
+Source file: extras/Hadrons/Modules/MAction/Wilson.hpp
+
+Copyright (C) 2015
+Copyright (C) 2016
+
+Author: Antonin Portelli <antonin.portelli@me.com>
+
+This program is free software; you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation; either version 2 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License along
+with this program; if not, write to the Free Software Foundation, Inc.,
+51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+
+See the full license in the file "LICENSE" in the top level distribution directory
+*************************************************************************************/
+/*  END LEGAL */
+
+#ifndef Hadrons_Wilson_hpp_
+#define Hadrons_Wilson_hpp_
+
+#include <Grid/Hadrons/Global.hpp>
+#include <Grid/Hadrons/Module.hpp>
+#include <Grid/Hadrons/ModuleFactory.hpp>
+
+BEGIN_HADRONS_NAMESPACE
+
+/******************************************************************************
+ *                            TWilson quark action                            *
+ ******************************************************************************/
+BEGIN_MODULE_NAMESPACE(MAction)
+
+class WilsonPar: Serializable
+{
+public:
+    GRID_SERIALIZABLE_CLASS_MEMBERS(WilsonPar,
+                                    std::string, gauge,
+                                    double     , mass);
+};
+
+template <typename FImpl>
+class TWilson: public Module<WilsonPar>
+{
+public:
+    TYPE_ALIASES(FImpl,);
+public:
+    // constructor
+    TWilson(const std::string name);
+    // destructor
+    virtual ~TWilson(void) = default;
+    // dependencies/products
+    virtual std::vector<std::string> getInput(void);
+    virtual std::vector<std::string> getOutput(void);
+    // setup
+    virtual void setup(void);
+    // execution
+    virtual void execute(void);
+};
+
+MODULE_REGISTER_NS(Wilson, TWilson<FIMPL>, MAction);
+
+/******************************************************************************
+ *                     TWilson template implementation                        *
+ ******************************************************************************/
+// constructor /////////////////////////////////////////////////////////////////
+template <typename FImpl>
+TWilson<FImpl>::TWilson(const std::string name)
+: Module<WilsonPar>(name)
+{}
+
+// dependencies/products ///////////////////////////////////////////////////////
+template <typename FImpl>
+std::vector<std::string> TWilson<FImpl>::getInput(void)
+{
+    std::vector<std::string> in = {par().gauge};
+    
+    return in;
+}
+
+template <typename FImpl>
+std::vector<std::string> TWilson<FImpl>::getOutput(void)
+{
+    std::vector<std::string> out = {getName()};
+    
+    return out;
+}
+
+// setup ///////////////////////////////////////////////////////////////////////
+template <typename FImpl>
+void TWilson<FImpl>::setup(void)
+{
+    unsigned int size;
+    
+    size = 2*env().template lattice4dSize<typename FImpl::DoubledGaugeField>();
+    env().registerObject(getName(), size);
+}
+
+// execution ///////////////////////////////////////////////////////////////////
+template <typename FImpl>
+void TWilson<FImpl>::execute()
+{
+    LOG(Message) << "Setting up TWilson fermion matrix with m= " << par().mass
+                 << " using gauge field '" << par().gauge << "'" << std::endl;
+    auto &U      = *env().template getObject<LatticeGaugeField>(par().gauge);
+    auto &grid   = *env().getGrid();
+    auto &gridRb = *env().getRbGrid();
+    FMat *fMatPt = new WilsonFermion<FImpl>(U, grid, gridRb, par().mass);
+    env().setObject(getName(), fMatPt);
+}
+
+END_MODULE_NAMESPACE
+
+END_HADRONS_NAMESPACE
+
+#endif // Hadrons_Wilson_hpp_

extras/Hadrons/Modules/MContraction/Baryon.hpp

@@ -0,0 +1,131 @@
+/*************************************************************************************
+
+Grid physics library, www.github.com/paboyle/Grid 
+
+Source file: extras/Hadrons/Modules/MContraction/Baryon.hpp
+
+Copyright (C) 2015
+Copyright (C) 2016
+
+Author: Antonin Portelli <antonin.portelli@me.com>
+
+This program is free software; you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation; either version 2 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License along
+with this program; if not, write to the Free Software Foundation, Inc.,
+51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+
+See the full license in the file "LICENSE" in the top level distribution directory
+*************************************************************************************/
+/*  END LEGAL */
+
+#ifndef Hadrons_Baryon_hpp_
+#define Hadrons_Baryon_hpp_
+
+#include <Grid/Hadrons/Global.hpp>
+#include <Grid/Hadrons/Module.hpp>
+#include <Grid/Hadrons/ModuleFactory.hpp>
+
+BEGIN_HADRONS_NAMESPACE
+
+/******************************************************************************
+ *                               Baryon                                       *
+ ******************************************************************************/
+BEGIN_MODULE_NAMESPACE(MContraction)
+
+class BaryonPar: Serializable
+{
+public:
+    GRID_SERIALIZABLE_CLASS_MEMBERS(BaryonPar,
+                                    std::string, q1,
+                                    std::string, q2,
+                                    std::string, q3,
+                                    std::string, output);
+};
+
+template <typename FImpl1, typename FImpl2, typename FImpl3>
+class TBaryon: public Module<BaryonPar>
+{
+public:
+    TYPE_ALIASES(FImpl1, 1);
+    TYPE_ALIASES(FImpl2, 2);
+    TYPE_ALIASES(FImpl3, 3);
+    class Result: Serializable
+    {
+    public:
+        GRID_SERIALIZABLE_CLASS_MEMBERS(Result,
+                                        std::vector<std::vector<std::vector<Complex>>>, corr);
+    };
+public:
+    // constructor
+    TBaryon(const std::string name);
+    // destructor
+    virtual ~TBaryon(void) = default;
+    // dependency relation
+    virtual std::vector<std::string> getInput(void);
+    virtual std::vector<std::string> getOutput(void);
+    // execution
+    virtual void execute(void);
+};
+
+MODULE_REGISTER_NS(Baryon, ARG(TBaryon<FIMPL, FIMPL, FIMPL>), MContraction);
+
+/******************************************************************************
+ *                         TBaryon implementation                             *
+ ******************************************************************************/
+// constructor /////////////////////////////////////////////////////////////////
+template <typename FImpl1, typename FImpl2, typename FImpl3>
+TBaryon<FImpl1, FImpl2, FImpl3>::TBaryon(const std::string name)
+: Module<BaryonPar>(name)
+{}
+
+// dependencies/products ///////////////////////////////////////////////////////
+template <typename FImpl1, typename FImpl2, typename FImpl3>
+std::vector<std::string> TBaryon<FImpl1, FImpl2, FImpl3>::getInput(void)
+{
+    std::vector<std::string> input = {par().q1, par().q2, par().q3};
+    
+    return input;
+}
+
+template <typename FImpl1, typename FImpl2, typename FImpl3>
+std::vector<std::string> TBaryon<FImpl1, FImpl2, FImpl3>::getOutput(void)
+{
+    std::vector<std::string> out = {getName()};
+    
+    return out;
+}
+
+// execution ///////////////////////////////////////////////////////////////////
+template <typename FImpl1, typename FImpl2, typename FImpl3>
+void TBaryon<FImpl1, FImpl2, FImpl3>::execute(void)
+{
+    LOG(Message) << "Computing baryon contractions '" << getName() << "' using"
+                 << " quarks '" << par().q1 << "', '" << par().q2 << "', and '"
+                 << par().q3 << "'" << std::endl;
+    
+    XmlWriter             writer(par().output);
+    PropagatorField1      &q1 = *env().template getObject<PropagatorField1>(par().q1);
+    PropagatorField2      &q2 = *env().template getObject<PropagatorField2>(par().q2);
+    PropagatorField3      &q3 = *env().template getObject<PropagatorField3>(par().q2);
+    LatticeComplex        c(env().getGrid());
+    Result                result;
+    
+    // FIXME: do contractions
+    
+    write(writer, "meson", result);
+}
+
+END_MODULE_NAMESPACE
+
+END_HADRONS_NAMESPACE
+
+#endif // Hadrons_Baryon_hpp_

extras/Hadrons/Modules/MContraction/Meson.hpp

@@ -0,0 +1,137 @@
+/*************************************************************************************
+
+Grid physics library, www.github.com/paboyle/Grid 
+
+Source file: extras/Hadrons/Modules/MContraction/Meson.hpp
+
+Copyright (C) 2015
+Copyright (C) 2016
+
+Author: Antonin Portelli <antonin.portelli@me.com>
+
+This program is free software; you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation; either version 2 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License along
+with this program; if not, write to the Free Software Foundation, Inc.,
+51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+
+See the full license in the file "LICENSE" in the top level distribution directory
+*************************************************************************************/
+/*  END LEGAL */
+
+#ifndef Hadrons_Meson_hpp_
+#define Hadrons_Meson_hpp_
+
+#include <Grid/Hadrons/Global.hpp>
+#include <Grid/Hadrons/Module.hpp>
+#include <Grid/Hadrons/ModuleFactory.hpp>
+
+BEGIN_HADRONS_NAMESPACE
+
+/******************************************************************************
+ *                                TMeson                                       *
+ ******************************************************************************/
+BEGIN_MODULE_NAMESPACE(MContraction)
+
+class MesonPar: Serializable
+{
+public:
+    GRID_SERIALIZABLE_CLASS_MEMBERS(MesonPar,
+                                    std::string,    q1,
+                                    std::string,    q2,
+                                    std::string,    output,
+                                    Gamma::Algebra, gammaSource,
+                                    Gamma::Algebra, gammaSink);
+};
+
+template <typename FImpl1, typename FImpl2>
+class TMeson: public Module<MesonPar>
+{
+public:
+    TYPE_ALIASES(FImpl1, 1);
+    TYPE_ALIASES(FImpl2, 2);
+    class Result: Serializable
+    {
+    public:
+        GRID_SERIALIZABLE_CLASS_MEMBERS(Result, std::vector<Complex>, corr);
+    };
+public:
+    // constructor
+    TMeson(const std::string name);
+    // destructor
+    virtual ~TMeson(void) = default;
+    // dependencies/products
+    virtual std::vector<std::string> getInput(void);
+    virtual std::vector<std::string> getOutput(void);
+    // execution
+    virtual void execute(void);
+};
+
+MODULE_REGISTER_NS(Meson, ARG(TMeson<FIMPL, FIMPL>), MContraction);
+
+/******************************************************************************
+ *                           TMeson implementation                            *
+ ******************************************************************************/
+// constructor /////////////////////////////////////////////////////////////////
+template <typename FImpl1, typename FImpl2>
+TMeson<FImpl1, FImpl2>::TMeson(const std::string name)
+: Module<MesonPar>(name)
+{}
+
+// dependencies/products ///////////////////////////////////////////////////////
+template <typename FImpl1, typename FImpl2>
+std::vector<std::string> TMeson<FImpl1, FImpl2>::getInput(void)
+{
+    std::vector<std::string> input = {par().q1, par().q2};
+    
+    return input;
+}
+
+template <typename FImpl1, typename FImpl2>
+std::vector<std::string> TMeson<FImpl1, FImpl2>::getOutput(void)
+{
+    std::vector<std::string> output = {getName()};
+    
+    return output;
+}
+
+// execution ///////////////////////////////////////////////////////////////////
+template <typename FImpl1, typename FImpl2>
+void TMeson<FImpl1, FImpl2>::execute(void)
+{
+    LOG(Message) << "Computing meson contractions '" << getName() << "' using"
+                 << " quarks '" << par().q1 << "' and '" << par().q2 << "'"
+                 << std::endl;
+    
+    XmlWriter             writer(par().output);
+    PropagatorField1      &q1 = *env().template getObject<PropagatorField1>(par().q1);
+    PropagatorField2      &q2 = *env().template getObject<PropagatorField2>(par().q2);
+    LatticeComplex        c(env().getGrid());
+    Gamma                 gSrc(par().gammaSource), gSnk(par().gammaSink);
+    Gamma                 g5(Gamma::Algebra::Gamma5);
+    std::vector<TComplex> buf;
+    Result                result;
+    
+    c = trace(gSnk*q1*adj(gSrc)*g5*adj(q2)*g5);
+    sliceSum(c, buf, Tp);
+    result.corr.resize(buf.size());
+    for (unsigned int t = 0; t < buf.size(); ++t)
+    {
+        result.corr[t] = TensorRemove(buf[t]);
+    }
+    write(writer, "meson", result);
+}
+
+END_MODULE_NAMESPACE
+
+END_HADRONS_NAMESPACE
+
+#endif // Hadrons_Meson_hpp_

extras/Hadrons/Modules/MGauge/Load.cc

@@ -0,0 +1,78 @@
+/*************************************************************************************
+
+Grid physics library, www.github.com/paboyle/Grid 
+
+Source file: extras/Hadrons/Modules/MGauge/Load.cc
+
+Copyright (C) 2015
+Copyright (C) 2016
+
+Author: Antonin Portelli <antonin.portelli@me.com>
+
+This program is free software; you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation; either version 2 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License along
+with this program; if not, write to the Free Software Foundation, Inc.,
+51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+
+See the full license in the file "LICENSE" in the top level distribution directory
+*************************************************************************************/
+/*  END LEGAL */
+
+#include <Grid/Hadrons/Modules/MGauge/Load.hpp>
+
+using namespace Grid;
+using namespace Hadrons;
+using namespace MGauge;
+
+/******************************************************************************
+*                           TLoad implementation                               *
+******************************************************************************/
+// constructor /////////////////////////////////////////////////////////////////
+TLoad::TLoad(const std::string name)
+: Module<LoadPar>(name)
+{}
+
+// dependencies/products ///////////////////////////////////////////////////////
+std::vector<std::string> TLoad::getInput(void)
+{
+    std::vector<std::string> in;
+    
+    return in;
+}
+
+std::vector<std::string> TLoad::getOutput(void)
+{
+    std::vector<std::string> out = {getName()};
+    
+    return out;
+}
+
+// setup ///////////////////////////////////////////////////////////////////////
+void TLoad::setup(void)
+{
+    env().registerLattice<LatticeGaugeField>(getName());
+}
+
+// execution ///////////////////////////////////////////////////////////////////
+void TLoad::execute(void)
+{
+    NerscField  header;
+    std::string fileName = par().file + "."
+                           + std::to_string(env().getTrajectory());
+    
+    LOG(Message) << "Loading NERSC configuration from file '" << fileName
+                 << "'" << std::endl;
+    LatticeGaugeField &U = *env().createLattice<LatticeGaugeField>(getName());
+    NerscIO::readConfiguration(U, header, fileName);
+    LOG(Message) << "NERSC header:" << std::endl;
+    dump_nersc_header(header, LOG(Message));
+}

extras/Hadrons/Modules/MGauge/Load.hpp

@@ -0,0 +1,73 @@
+/*************************************************************************************
+
+Grid physics library, www.github.com/paboyle/Grid 
+
+Source file: extras/Hadrons/Modules/MGauge/Load.hpp
+
+Copyright (C) 2015
+Copyright (C) 2016
+
+Author: Antonin Portelli <antonin.portelli@me.com>
+
+This program is free software; you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation; either version 2 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License along
+with this program; if not, write to the Free Software Foundation, Inc.,
+51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+
+See the full license in the file "LICENSE" in the top level distribution directory
+*************************************************************************************/
+/*  END LEGAL */
+
+#ifndef Hadrons_Load_hpp_
+#define Hadrons_Load_hpp_
+
+#include <Grid/Hadrons/Global.hpp>
+#include <Grid/Hadrons/Module.hpp>
+#include <Grid/Hadrons/ModuleFactory.hpp>
+
+BEGIN_HADRONS_NAMESPACE
+
+/******************************************************************************
+ *                         Load a NERSC configuration                         *
+ ******************************************************************************/
+BEGIN_MODULE_NAMESPACE(MGauge)
+
+class LoadPar: Serializable
+{
+public:
+    GRID_SERIALIZABLE_CLASS_MEMBERS(LoadPar,
+                                    std::string, file);
+};
+
+class TLoad: public Module<LoadPar>
+{
+public:
+    // constructor
+    TLoad(const std::string name);
+    // destructor
+    virtual ~TLoad(void) = default;
+    // dependency relation
+    virtual std::vector<std::string> getInput(void);
+    virtual std::vector<std::string> getOutput(void);
+    // setup
+    virtual void setup(void);
+    // execution
+    virtual void execute(void);
+};
+
+MODULE_REGISTER_NS(Load, TLoad, MGauge);
+
+END_MODULE_NAMESPACE
+
+END_HADRONS_NAMESPACE
+
+#endif // Hadrons_Load_hpp_

extras/Hadrons/Modules/MGauge/Random.cc

@@ -0,0 +1,69 @@
+/*************************************************************************************
+
+Grid physics library, www.github.com/paboyle/Grid 
+
+Source file: extras/Hadrons/Modules/MGauge/Random.cc
+
+Copyright (C) 2015
+Copyright (C) 2016
+
+Author: Antonin Portelli <antonin.portelli@me.com>
+
+This program is free software; you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation; either version 2 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License along
+with this program; if not, write to the Free Software Foundation, Inc.,
+51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+
+See the full license in the file "LICENSE" in the top level distribution directory
+*************************************************************************************/
+/*  END LEGAL */
+
+#include <Grid/Hadrons/Modules/MGauge/Random.hpp>
+
+using namespace Grid;
+using namespace Hadrons;
+using namespace MGauge;
+
+/******************************************************************************
+*                           TRandom implementation                            *
+******************************************************************************/
+// constructor /////////////////////////////////////////////////////////////////
+TRandom::TRandom(const std::string name)
+: Module<NoPar>(name)
+{}
+
+// dependencies/products ///////////////////////////////////////////////////////
+std::vector<std::string> TRandom::getInput(void)
+{
+    return std::vector<std::string>();
+}
+
+std::vector<std::string> TRandom::getOutput(void)
+{
+    std::vector<std::string> out = {getName()};
+    
+    return out;
+}
+
+// setup ///////////////////////////////////////////////////////////////////////
+void TRandom::setup(void)
+{
+    env().registerLattice<LatticeGaugeField>(getName());
+}
+
+// execution ///////////////////////////////////////////////////////////////////
+void TRandom::execute(void)
+{
+    LOG(Message) << "Generating random gauge configuration" << std::endl;
+    LatticeGaugeField &U = *env().createLattice<LatticeGaugeField>(getName());
+    SU3::HotConfiguration(*env().get4dRng(), U);
+}

extras/Hadrons/Modules/MGauge/Random.hpp

@@ -0,0 +1,66 @@
+/*************************************************************************************
+
+Grid physics library, www.github.com/paboyle/Grid 
+
+Source file: extras/Hadrons/Modules/MGauge/Random.hpp
+
+Copyright (C) 2015
+Copyright (C) 2016
+
+Author: Antonin Portelli <antonin.portelli@me.com>
+
+This program is free software; you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation; either version 2 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License along
+with this program; if not, write to the Free Software Foundation, Inc.,
+51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+
+See the full license in the file "LICENSE" in the top level distribution directory
+*************************************************************************************/
+/*  END LEGAL */
+
+#ifndef Hadrons_Random_hpp_
+#define Hadrons_Random_hpp_
+
+#include <Grid/Hadrons/Global.hpp>
+#include <Grid/Hadrons/Module.hpp>
+#include <Grid/Hadrons/ModuleFactory.hpp>
+
+BEGIN_HADRONS_NAMESPACE
+
+/******************************************************************************
+ *                             Random gauge                                   *
+ ******************************************************************************/
+BEGIN_MODULE_NAMESPACE(MGauge)
+
+class TRandom: public Module<NoPar>
+{
+public:
+    // constructor
+    TRandom(const std::string name);
+    // destructor
+    virtual ~TRandom(void) = default;
+    // dependency relation
+    virtual std::vector<std::string> getInput(void);
+    virtual std::vector<std::string> getOutput(void);
+    // setup
+    virtual void setup(void);
+    // execution
+    virtual void execute(void);
+};
+
+MODULE_REGISTER_NS(Random, TRandom, MGauge);
+
+END_MODULE_NAMESPACE
+
+END_HADRONS_NAMESPACE
+
+#endif // Hadrons_Random_hpp_

extras/Hadrons/Modules/MGauge/Unit.cc

@@ -0,0 +1,69 @@
+/*************************************************************************************
+
+Grid physics library, www.github.com/paboyle/Grid 
+
+Source file: extras/Hadrons/Modules/MGauge/Unit.cc
+
+Copyright (C) 2015
+Copyright (C) 2016
+
+Author: Antonin Portelli <antonin.portelli@me.com>
+
+This program is free software; you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation; either version 2 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License along
+with this program; if not, write to the Free Software Foundation, Inc.,
+51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+
+See the full license in the file "LICENSE" in the top level distribution directory
+*************************************************************************************/
+/*  END LEGAL */
+
+#include <Grid/Hadrons/Modules/MGauge/Unit.hpp>
+
+using namespace Grid;
+using namespace Hadrons;
+using namespace MGauge;
+
+/******************************************************************************
+*                            TUnit implementation                             *
+******************************************************************************/
+// constructor /////////////////////////////////////////////////////////////////
+TUnit::TUnit(const std::string name)
+: Module<NoPar>(name)
+{}
+
+// dependencies/products ///////////////////////////////////////////////////////
+std::vector<std::string> TUnit::getInput(void)
+{
+    return std::vector<std::string>();
+}
+
+std::vector<std::string> TUnit::getOutput(void)
+{
+    std::vector<std::string> out = {getName()};
+    
+    return out;
+}
+
+// setup ///////////////////////////////////////////////////////////////////////
+void TUnit::setup(void)
+{
+    env().registerLattice<LatticeGaugeField>(getName());
+}
+
+// execution ///////////////////////////////////////////////////////////////////
+void TUnit::execute(void)
+{
+    LOG(Message) << "Creating unit gauge configuration" << std::endl;
+    LatticeGaugeField &U = *env().createLattice<LatticeGaugeField>(getName());
+    SU3::ColdConfiguration(*env().get4dRng(), U);
+}

extras/Hadrons/Modules/MGauge/Unit.hpp

@@ -0,0 +1,66 @@
+/*************************************************************************************
+
+Grid physics library, www.github.com/paboyle/Grid 
+
+Source file: extras/Hadrons/Modules/MGauge/Unit.hpp
+
+Copyright (C) 2015
+Copyright (C) 2016
+
+Author: Antonin Portelli <antonin.portelli@me.com>
+
+This program is free software; you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation; either version 2 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License along
+with this program; if not, write to the Free Software Foundation, Inc.,
+51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+
+See the full license in the file "LICENSE" in the top level distribution directory
+*************************************************************************************/
+/*  END LEGAL */
+
+#ifndef Hadrons_Unit_hpp_
+#define Hadrons_Unit_hpp_
+
+#include <Grid/Hadrons/Global.hpp>
+#include <Grid/Hadrons/Module.hpp>
+#include <Grid/Hadrons/ModuleFactory.hpp>
+
+BEGIN_HADRONS_NAMESPACE
+
+/******************************************************************************
+ *                              Unit gauge                                    *
+ ******************************************************************************/
+BEGIN_MODULE_NAMESPACE(MGauge)
+
+class TUnit: public Module<NoPar>
+{
+public:
+    // constructor
+    TUnit(const std::string name);
+    // destructor
+    virtual ~TUnit(void) = default;
+    // dependencies/products
+    virtual std::vector<std::string> getInput(void);
+    virtual std::vector<std::string> getOutput(void);
+    // setup
+    virtual void setup(void);
+    // execution
+    virtual void execute(void);
+};
+
+MODULE_REGISTER_NS(Unit, TUnit, MGauge);
+
+END_MODULE_NAMESPACE
+
+END_HADRONS_NAMESPACE
+
+#endif // Hadrons_Unit_hpp_

extras/Hadrons/Modules/MSolver/RBPrecCG.hpp

@@ -0,0 +1,132 @@
+/*************************************************************************************
+
+Grid physics library, www.github.com/paboyle/Grid 
+
+Source file: extras/Hadrons/Modules/MSolver/RBPrecCG.hpp
+
+Copyright (C) 2015
+Copyright (C) 2016
+
+Author: Antonin Portelli <antonin.portelli@me.com>
+
+This program is free software; you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation; either version 2 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License along
+with this program; if not, write to the Free Software Foundation, Inc.,
+51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+
+See the full license in the file "LICENSE" in the top level distribution directory
+*************************************************************************************/
+/*  END LEGAL */
+
+#ifndef Hadrons_RBPrecCG_hpp_
+#define Hadrons_RBPrecCG_hpp_
+
+#include <Grid/Hadrons/Global.hpp>
+#include <Grid/Hadrons/Module.hpp>
+#include <Grid/Hadrons/ModuleFactory.hpp>
+
+BEGIN_HADRONS_NAMESPACE
+
+/******************************************************************************
+ *                     Schur red-black preconditioned CG                      *
+ ******************************************************************************/
+BEGIN_MODULE_NAMESPACE(MSolver)
+
+class RBPrecCGPar: Serializable
+{
+public:
+    GRID_SERIALIZABLE_CLASS_MEMBERS(RBPrecCGPar,
+                                    std::string, action,
+                                    double     , residual);
+};
+
+template <typename FImpl>
+class TRBPrecCG: public Module<RBPrecCGPar>
+{
+public:
+    TYPE_ALIASES(FImpl,);
+public:
+    // constructor
+    TRBPrecCG(const std::string name);
+    // destructor
+    virtual ~TRBPrecCG(void) = default;
+    // dependencies/products
+    virtual std::vector<std::string> getInput(void);
+    virtual std::vector<std::string> getOutput(void);
+    // setup
+    virtual void setup(void);
+    // execution
+    virtual void execute(void);
+};
+
+MODULE_REGISTER_NS(RBPrecCG, TRBPrecCG<FIMPL>, MSolver);
+
+/******************************************************************************
+ *                      TRBPrecCG template implementation                     *
+ ******************************************************************************/
+// constructor /////////////////////////////////////////////////////////////////
+template <typename FImpl>
+TRBPrecCG<FImpl>::TRBPrecCG(const std::string name)
+: Module(name)
+{}
+
+// dependencies/products ///////////////////////////////////////////////////////
+template <typename FImpl>
+std::vector<std::string> TRBPrecCG<FImpl>::getInput(void)
+{
+    std::vector<std::string> in = {par().action};
+    
+    return in;
+}
+
+template <typename FImpl>
+std::vector<std::string> TRBPrecCG<FImpl>::getOutput(void)
+{
+    std::vector<std::string> out = {getName()};
+    
+    return out;
+}
+
+// setup ///////////////////////////////////////////////////////////////////////
+template <typename FImpl>
+void TRBPrecCG<FImpl>::setup(void)
+{
+    auto Ls = env().getObjectLs(par().action);
+    
+    env().registerObject(getName(), 0, Ls);
+    env().addOwnership(getName(), par().action);
+}
+
+// execution ///////////////////////////////////////////////////////////////////
+template <typename FImpl>
+void TRBPrecCG<FImpl>::execute(void)
+{
+    auto &mat   = *(env().template getObject<FMat>(par().action));
+    auto solver = [&mat, this](FermionField &sol, const FermionField &source)
+    {
+        ConjugateGradient<FermionField>           cg(par().residual, 10000);
+        SchurRedBlackDiagMooeeSolve<FermionField> schurSolver(cg);
+        
+        schurSolver(mat, source, sol);
+    };
+    
+    LOG(Message) << "setting up Schur red-black preconditioned CG for"
+                 << " action '" << par().action << "' with residual "
+                 << par().residual << std::endl;
+    env().setObject(getName(), new SolverFn(solver));
+}
+
+END_MODULE_NAMESPACE
+
+END_HADRONS_NAMESPACE
+
+#endif // Hadrons_RBPrecCG_hpp_

extras/Hadrons/Modules/MSource/Point.hpp

@@ -0,0 +1,135 @@
+/*************************************************************************************
+
+Grid physics library, www.github.com/paboyle/Grid 
+
+Source file: extras/Hadrons/Modules/MSource/Point.hpp
+
+Copyright (C) 2015
+Copyright (C) 2016
+
+Author: Antonin Portelli <antonin.portelli@me.com>
+
+This program is free software; you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation; either version 2 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License along
+with this program; if not, write to the Free Software Foundation, Inc.,
+51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+
+See the full license in the file "LICENSE" in the top level distribution directory
+*************************************************************************************/
+/*  END LEGAL */
+
+#ifndef Hadrons_Point_hpp_
+#define Hadrons_Point_hpp_
+
+#include <Grid/Hadrons/Global.hpp>
+#include <Grid/Hadrons/Module.hpp>
+#include <Grid/Hadrons/ModuleFactory.hpp>
+
+BEGIN_HADRONS_NAMESPACE
+
+/*
+ 
+ Point source
+ ------------
+ * src_x = delta_x,position
+ 
+ * options:
+ - position: space-separated integer sequence (e.g. "0 1 1 0")
+ 
+ */
+
+/******************************************************************************
+ *                                  TPoint                                     *
+ ******************************************************************************/
+BEGIN_MODULE_NAMESPACE(MSource)
+
+class PointPar: Serializable
+{
+public:
+    GRID_SERIALIZABLE_CLASS_MEMBERS(PointPar,
+                                    std::string, position);
+};
+
+template <typename FImpl>
+class TPoint: public Module<PointPar>
+{
+public:
+    TYPE_ALIASES(FImpl,);
+public:
+    // constructor
+    TPoint(const std::string name);
+    // destructor
+    virtual ~TPoint(void) = default;
+    // dependency relation
+    virtual std::vector<std::string> getInput(void);
+    virtual std::vector<std::string> getOutput(void);
+    // setup
+    virtual void setup(void);
+    // execution
+    virtual void execute(void);
+};
+
+MODULE_REGISTER_NS(Point, TPoint<FIMPL>, MSource);
+
+/******************************************************************************
+ *                       TPoint template implementation                       *
+ ******************************************************************************/
+// constructor /////////////////////////////////////////////////////////////////
+template <typename FImpl>
+TPoint<FImpl>::TPoint(const std::string name)
+: Module<PointPar>(name)
+{}
+
+// dependencies/products ///////////////////////////////////////////////////////
+template <typename FImpl>
+std::vector<std::string> TPoint<FImpl>::getInput(void)
+{
+    std::vector<std::string> in;
+    
+    return in;
+}
+
+template <typename FImpl>
+std::vector<std::string> TPoint<FImpl>::getOutput(void)
+{
+    std::vector<std::string> out = {getName()};
+    
+    return out;
+}
+
+// setup ///////////////////////////////////////////////////////////////////////
+template <typename FImpl>
+void TPoint<FImpl>::setup(void)
+{
+    env().template registerLattice<PropagatorField>(getName());
+}
+
+// execution ///////////////////////////////////////////////////////////////////
+template <typename FImpl>
+void TPoint<FImpl>::execute(void)
+{
+    std::vector<int> position = strToVec<int>(par().position);
+    typename SitePropagator::scalar_object id;
+    
+    LOG(Message) << "Creating point source at position [" << par().position
+                 << "]" << std::endl;
+    PropagatorField &src = *env().template createLattice<PropagatorField>(getName());
+    id  = 1.;
+    src = zero;
+    pokeSite(id, src, position);
+}
+
+END_MODULE_NAMESPACE
+
+END_HADRONS_NAMESPACE
+
+#endif // Hadrons_Point_hpp_

extras/Hadrons/Modules/MSource/SeqGamma.hpp

@@ -0,0 +1,163 @@
+/*************************************************************************************
+
+Grid physics library, www.github.com/paboyle/Grid 
+
+Source file: extras/Hadrons/Modules/MSource/SeqGamma.hpp
+
+Copyright (C) 2015
+Copyright (C) 2016
+
+Author: Antonin Portelli <antonin.portelli@me.com>
+
+This program is free software; you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation; either version 2 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License along
+with this program; if not, write to the Free Software Foundation, Inc.,
+51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+
+See the full license in the file "LICENSE" in the top level distribution directory
+*************************************************************************************/
+/*  END LEGAL */
+
+#ifndef Hadrons_SeqGamma_hpp_
+#define Hadrons_SeqGamma_hpp_
+
+#include <Grid/Hadrons/Global.hpp>
+#include <Grid/Hadrons/Module.hpp>
+#include <Grid/Hadrons/ModuleFactory.hpp>
+
+BEGIN_HADRONS_NAMESPACE
+
+/*
+ 
+ Sequential source
+ -----------------------------
+ * src_x = q_x * theta(x_3 - tA) * theta(tB - x_3) * gamma * exp(i x.mom)
+ 
+ * options:
+ - q: input propagator (string)
+ - tA: begin timeslice (integer)
+ - tB: end timesilce (integer)
+ - gamma: gamma product to insert (integer)
+ - mom: momentum insertion, space-separated float sequence (e.g ".1 .2 1. 0.")
+ 
+ */
+
+/******************************************************************************
+ *                         SeqGamma                                 *
+ ******************************************************************************/
+BEGIN_MODULE_NAMESPACE(MSource)
+
+class SeqGammaPar: Serializable
+{
+public:
+    GRID_SERIALIZABLE_CLASS_MEMBERS(SeqGammaPar,
+                                    std::string,    q,
+                                    unsigned int,   tA,
+                                    unsigned int,   tB,
+                                    Gamma::Algebra, gamma,
+                                    std::string,    mom);
+};
+
+template <typename FImpl>
+class TSeqGamma: public Module<SeqGammaPar>
+{
+public:
+    TYPE_ALIASES(FImpl,);
+public:
+    // constructor
+    TSeqGamma(const std::string name);
+    // destructor
+    virtual ~TSeqGamma(void) = default;
+    // dependency relation
+    virtual std::vector<std::string> getInput(void);
+    virtual std::vector<std::string> getOutput(void);
+    // setup
+    virtual void setup(void);
+    // execution
+    virtual void execute(void);
+};
+
+MODULE_REGISTER_NS(SeqGamma, TSeqGamma<FIMPL>, MSource);
+
+/******************************************************************************
+ *                         TSeqGamma implementation                           *
+ ******************************************************************************/
+// constructor /////////////////////////////////////////////////////////////////
+template <typename FImpl>
+TSeqGamma<FImpl>::TSeqGamma(const std::string name)
+: Module<SeqGammaPar>(name)
+{}
+
+// dependencies/products ///////////////////////////////////////////////////////
+template <typename FImpl>
+std::vector<std::string> TSeqGamma<FImpl>::getInput(void)
+{
+    std::vector<std::string> in = {par().q};
+    
+    return in;
+}
+
+template <typename FImpl>
+std::vector<std::string> TSeqGamma<FImpl>::getOutput(void)
+{
+    std::vector<std::string> out = {getName()};
+    
+    return out;
+}
+
+// setup ///////////////////////////////////////////////////////////////////////
+template <typename FImpl>
+void TSeqGamma<FImpl>::setup(void)
+{
+    env().template registerLattice<PropagatorField>(getName());
+}
+
+// execution ///////////////////////////////////////////////////////////////////
+template <typename FImpl>
+void TSeqGamma<FImpl>::execute(void)
+{
+    if (par().tA == par().tB)
+    {
+        LOG(Message) << "Generating gamma_" << par().gamma
+                     << " sequential source at t= " << par().tA << std::endl;
+    }
+    else
+    {
+        LOG(Message) << "Generating gamma_" << par().gamma
+                     << " sequential source for "
+                     << par().tA << " <= t <= " << par().tB << std::endl;
+    }
+    PropagatorField &src = *env().template createLattice<PropagatorField>(getName());
+    PropagatorField &q   = *env().template getObject<PropagatorField>(par().q);
+    Lattice<iScalar<vInteger>> t(env().getGrid());
+    LatticeComplex             ph(env().getGrid()), coor(env().getGrid());
+    Gamma                      g(par().gamma);
+    std::vector<Real>          p;
+    Complex                    i(0.0,1.0);
+    
+    p  = strToVec<Real>(par().mom);
+    ph = zero;
+    for(unsigned int mu = 0; mu < env().getNd(); mu++)
+    {
+        LatticeCoordinate(coor, mu);
+        ph = ph + p[mu]*coor;
+    }
+    ph = exp(i*ph);
+    LatticeCoordinate(t, Tp);
+    src = where((t >= par().tA) and (t <= par().tB), ph*(g*q), 0.*q);
+}
+
+END_MODULE_NAMESPACE
+
+END_HADRONS_NAMESPACE
+
+#endif // Hadrons_SeqGamma_hpp_

extras/Hadrons/Modules/MSource/Z2.hpp

@@ -0,0 +1,151 @@
+/*************************************************************************************
+
+Grid physics library, www.github.com/paboyle/Grid 
+
+Source file: extras/Hadrons/Modules/MSource/Z2.hpp
+
+Copyright (C) 2015
+Copyright (C) 2016
+
+Author: Antonin Portelli <antonin.portelli@me.com>
+
+This program is free software; you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation; either version 2 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License along
+with this program; if not, write to the Free Software Foundation, Inc.,
+51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+
+See the full license in the file "LICENSE" in the top level distribution directory
+*************************************************************************************/
+/*  END LEGAL */
+
+#ifndef Hadrons_Z2_hpp_
+#define Hadrons_Z2_hpp_
+
+#include <Grid/Hadrons/Global.hpp>
+#include <Grid/Hadrons/Module.hpp>
+#include <Grid/Hadrons/ModuleFactory.hpp>
+
+BEGIN_HADRONS_NAMESPACE
+
+/*
+ 
+ Z_2 stochastic source
+ -----------------------------
+ * src_x = eta_x * theta(x_3 - tA) * theta(tB - x_3)
+ 
+ the eta_x are independent uniform random numbers in {+/- 1 +/- i}
+ 
+ * options:
+ - tA: begin timeslice (integer)
+ - tB: end timesilce (integer)
+ 
+ */
+ 
+/******************************************************************************
+ *                          Z2 stochastic source                              *
+ ******************************************************************************/
+BEGIN_MODULE_NAMESPACE(MSource)
+
+class Z2Par: Serializable
+{
+public:
+    GRID_SERIALIZABLE_CLASS_MEMBERS(Z2Par,
+                                    unsigned int, tA,
+                                    unsigned int, tB);
+};
+
+template <typename FImpl>
+class TZ2: public Module<Z2Par>
+{
+public:
+    TYPE_ALIASES(FImpl,);
+public:
+    // constructor
+    TZ2(const std::string name);
+    // destructor
+    virtual ~TZ2(void) = default;
+    // dependency relation
+    virtual std::vector<std::string> getInput(void);
+    virtual std::vector<std::string> getOutput(void);
+    // setup
+    virtual void setup(void);
+    // execution
+    virtual void execute(void);
+};
+
+MODULE_REGISTER_NS(Z2, TZ2<FIMPL>, MSource);
+
+/******************************************************************************
+ *                       TZ2 template implementation                          *
+ ******************************************************************************/
+// constructor /////////////////////////////////////////////////////////////////
+template <typename FImpl>
+TZ2<FImpl>::TZ2(const std::string name)
+: Module<Z2Par>(name)
+{}
+
+// dependencies/products ///////////////////////////////////////////////////////
+template <typename FImpl>
+std::vector<std::string> TZ2<FImpl>::getInput(void)
+{
+    std::vector<std::string> in;
+    
+    return in;
+}
+
+template <typename FImpl>
+std::vector<std::string> TZ2<FImpl>::getOutput(void)
+{
+    std::vector<std::string> out = {getName()};
+    
+    return out;
+}
+
+// setup ///////////////////////////////////////////////////////////////////////
+template <typename FImpl>
+void TZ2<FImpl>::setup(void)
+{
+    env().template registerLattice<PropagatorField>(getName());
+}
+
+// execution ///////////////////////////////////////////////////////////////////
+template <typename FImpl>
+void TZ2<FImpl>::execute(void)
+{
+    Lattice<iScalar<vInteger>> t(env().getGrid());
+    LatticeComplex             eta(env().getGrid());
+    Complex                    shift(1., 1.);
+    
+    if (par().tA == par().tB)
+    {
+        LOG(Message) << "Generating Z_2 wall source at t= " << par().tA
+        << std::endl;
+    }
+    else
+    {
+        LOG(Message) << "Generating Z_2 band for " << par().tA << " <= t <= "
+        << par().tB << std::endl;
+    }
+    PropagatorField &src = *env().template createLattice<PropagatorField>(getName());
+    LatticeCoordinate(t, Tp);
+    bernoulli(*env().get4dRng(), eta);
+    eta = (2.*eta - shift)*(1./::sqrt(2.));
+    eta = where((t >= par().tA) and (t <= par().tB), eta, 0.*eta);
+    src = 1.;
+    src = src*eta;
+}
+
+END_MODULE_NAMESPACE
+
+END_HADRONS_NAMESPACE
+
+#endif // Hadrons_Z2_hpp_

extras/Hadrons/Modules/Quark.hpp

@@ -0,0 +1,185 @@
+/*************************************************************************************
+
+Grid physics library, www.github.com/paboyle/Grid 
+
+Source file: extras/Hadrons/Modules/Quark.hpp
+
+Copyright (C) 2015
+Copyright (C) 2016
+
+Author: Antonin Portelli <antonin.portelli@me.com>
+
+This program is free software; you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation; either version 2 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License along
+with this program; if not, write to the Free Software Foundation, Inc.,
+51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+
+See the full license in the file "LICENSE" in the top level distribution directory
+*************************************************************************************/
+/*  END LEGAL */
+
+#ifndef Hadrons_Quark_hpp_
+#define Hadrons_Quark_hpp_
+
+#include <Grid/Hadrons/Global.hpp>
+#include <Grid/Hadrons/Module.hpp>
+#include <Grid/Hadrons/ModuleFactory.hpp>
+
+BEGIN_HADRONS_NAMESPACE
+
+/******************************************************************************
+ *                               TQuark                                       *
+ ******************************************************************************/
+class QuarkPar: Serializable
+{
+public:
+    GRID_SERIALIZABLE_CLASS_MEMBERS(QuarkPar,
+                                    std::string, source,
+                                    std::string, solver);
+};
+
+template <typename FImpl>
+class TQuark: public Module<QuarkPar>
+{
+public:
+    TYPE_ALIASES(FImpl,);
+public:
+    // constructor
+    TQuark(const std::string name);
+    // destructor
+    virtual ~TQuark(void) = default;
+    // dependencies/products
+    virtual std::vector<std::string> getInput(void);
+    virtual std::vector<std::string> getOutput(void);
+    // setup
+    virtual void setup(void);
+    // execution
+    virtual void execute(void);
+private:
+    unsigned int Ls_;
+    SolverFn     *solver_{nullptr};
+};
+
+MODULE_REGISTER(Quark, TQuark<FIMPL>);
+
+/******************************************************************************
+ *                          TQuark implementation                             *
+ ******************************************************************************/
+// constructor /////////////////////////////////////////////////////////////////
+template <typename FImpl>
+TQuark<FImpl>::TQuark(const std::string name)
+: Module(name)
+{}
+
+// dependencies/products ///////////////////////////////////////////////////////
+template <typename FImpl>
+std::vector<std::string> TQuark<FImpl>::getInput(void)
+{
+    std::vector<std::string> in = {par().source, par().solver};
+    
+    return in;
+}
+
+template <typename FImpl>
+std::vector<std::string> TQuark<FImpl>::getOutput(void)
+{
+    std::vector<std::string> out = {getName(), getName() + "_5d"};
+    
+    return out;
+}
+
+// setup ///////////////////////////////////////////////////////////////////////
+template <typename FImpl>
+void TQuark<FImpl>::setup(void)
+{
+    Ls_ = env().getObjectLs(par().solver);
+    env().template registerLattice<PropagatorField>(getName());
+    if (Ls_ > 1)
+    {
+        env().template registerLattice<PropagatorField>(getName() + "_5d", Ls_);
+    }
+}
+
+// execution ///////////////////////////////////////////////////////////////////
+template <typename FImpl>
+void TQuark<FImpl>::execute(void)
+{
+    LOG(Message) << "Computing quark propagator '" << getName() << "'"
+                 << std::endl;
+    
+    FermionField    source(env().getGrid(Ls_)), sol(env().getGrid(Ls_)),
+                    tmp(env().getGrid());
+    std::string     propName = (Ls_ == 1) ? getName() : (getName() + "_5d");
+    PropagatorField &prop    = *env().template createLattice<PropagatorField>(propName);
+    PropagatorField &fullSrc = *env().template getObject<PropagatorField>(par().source);
+    SolverFn        &solver  = *env().template getObject<SolverFn>(par().solver);
+    if (Ls_ > 1)
+    {
+        env().template createLattice<PropagatorField>(getName());
+    }
+    
+    LOG(Message) << "Inverting using solver '" << par().solver
+                 << "' on source '" << par().source << "'" << std::endl;
+    for (unsigned int s = 0; s < Ns; ++s)
+    for (unsigned int c = 0; c < Nc; ++c)
+    {
+        LOG(Message) << "Inversion for spin= " << s << ", color= " << c
+        << std::endl;
+        // source conversion for 4D sources
+        if (!env().isObject5d(par().source))
+        {
+            if (Ls_ == 1)
+            {
+                PropToFerm(source, fullSrc, s, c);
+            }
+            else
+            {
+                source = zero;
+                PropToFerm(tmp, fullSrc, s, c);
+                InsertSlice(tmp, source, 0, 0);
+                InsertSlice(tmp, source, Ls_-1, 0);
+                axpby_ssp_pplus(source, 0., source, 1., source, 0, 0);
+                axpby_ssp_pminus(source, 0., source, 1., source, Ls_-1, Ls_-1);
+            }
+        }
+        // source conversion for 5D sources
+        else
+        {
+            if (Ls_ != env().getObjectLs(par().source))
+            {
+                HADRON_ERROR("Ls mismatch between quark action and source");
+            }
+            else
+            {
+                PropToFerm(source, fullSrc, s, c);
+            }
+        }
+        sol = zero;
+        solver(sol, source);
+        FermToProp(prop, sol, s, c);
+        // create 4D propagators from 5D one if necessary
+        if (Ls_ > 1)
+        {
+            PropagatorField &p4d =
+                *env().template getObject<PropagatorField>(getName());
+            
+            axpby_ssp_pminus(sol, 0., sol, 1., sol, 0, 0);
+            axpby_ssp_pplus(sol, 0., sol, 1., sol, 0, Ls_-1);
+            ExtractSlice(tmp, sol, 0, 0);
+            FermToProp(p4d, tmp, s, c);
+        }
+    }
+}
+
+END_HADRONS_NAMESPACE
+
+#endif // Hadrons_Quark_hpp_

extras/Hadrons/Modules/templates/Module.cc.template

@@ -0,0 +1,39 @@
+#include <Grid/Hadrons/Modules/___FILEBASENAME___.hpp>
+
+using namespace Grid;
+using namespace Hadrons;
+
+/******************************************************************************
+*                  T___FILEBASENAME___ implementation                             *
+******************************************************************************/
+// constructor /////////////////////////////////////////////////////////////////
+T___FILEBASENAME___::T___FILEBASENAME___(const std::string name)
+: Module<___FILEBASENAME___Par>(name)
+{}
+
+// dependencies/products ///////////////////////////////////////////////////////
+std::vector<std::string> T___FILEBASENAME___::getInput(void)
+{
+    std::vector<std::string> in;
+    
+    return in;
+}
+
+std::vector<std::string> T___FILEBASENAME___::getOutput(void)
+{
+    std::vector<std::string> out = {getName()};
+    
+    return out;
+}
+
+// setup ///////////////////////////////////////////////////////////////////////
+void T___FILEBASENAME___::setup(void)
+{
+
+}
+
+// execution ///////////////////////////////////////////////////////////////////
+void T___FILEBASENAME___::execute(void)
+{
+
+}

extras/Hadrons/Modules/templates/Module.hpp.template

@@ -0,0 +1,40 @@
+#ifndef Hadrons____FILEBASENAME____hpp_
+#define Hadrons____FILEBASENAME____hpp_
+
+#include <Grid/Hadrons/Global.hpp>
+#include <Grid/Hadrons/Module.hpp>
+#include <Grid/Hadrons/ModuleFactory.hpp>
+
+BEGIN_HADRONS_NAMESPACE
+
+/******************************************************************************
+ *                         ___FILEBASENAME___                                 *
+ ******************************************************************************/
+class ___FILEBASENAME___Par: Serializable
+{
+public:
+    GRID_SERIALIZABLE_CLASS_MEMBERS(___FILEBASENAME___Par, 
+                                    unsigned int, i);
+};
+
+class T___FILEBASENAME___: public Module<___FILEBASENAME___Par>
+{
+public:
+    // constructor
+    T___FILEBASENAME___(const std::string name);
+    // destructor
+    virtual ~T___FILEBASENAME___(void) = default;
+    // dependency relation
+    virtual std::vector<std::string> getInput(void);
+    virtual std::vector<std::string> getOutput(void);
+    // setup
+    virtual void setup(void);
+    // execution
+    virtual void execute(void);
+};
+
+MODULE_REGISTER(___FILEBASENAME___, T___FILEBASENAME___);
+
+END_HADRONS_NAMESPACE
+
+#endif // Hadrons____FILEBASENAME____hpp_

extras/Hadrons/Modules/templates/Module_in_NS.cc.template

@@ -0,0 +1,40 @@
+#include <Grid/Hadrons/Modules/___NAMESPACE___/___FILEBASENAME___.hpp>
+
+using namespace Grid;
+using namespace Hadrons;
+using namespace ___NAMESPACE___;
+
+/******************************************************************************
+*                  T___FILEBASENAME___ implementation                             *
+******************************************************************************/
+// constructor /////////////////////////////////////////////////////////////////
+T___FILEBASENAME___::T___FILEBASENAME___(const std::string name)
+: Module<___FILEBASENAME___Par>(name)
+{}
+
+// dependencies/products ///////////////////////////////////////////////////////
+std::vector<std::string> T___FILEBASENAME___::getInput(void)
+{
+    std::vector<std::string> in;
+    
+    return in;
+}
+
+std::vector<std::string> T___FILEBASENAME___::getOutput(void)
+{
+    std::vector<std::string> out = {getName()};
+    
+    return out;
+}
+
+// setup ///////////////////////////////////////////////////////////////////////
+void T___FILEBASENAME___::setup(void)
+{
+
+}
+
+// execution ///////////////////////////////////////////////////////////////////
+void T___FILEBASENAME___::execute(void)
+{
+
+}

extras/Hadrons/Modules/templates/Module_in_NS.hpp.template

@@ -0,0 +1,44 @@
+#ifndef Hadrons____FILEBASENAME____hpp_
+#define Hadrons____FILEBASENAME____hpp_
+
+#include <Grid/Hadrons/Global.hpp>
+#include <Grid/Hadrons/Module.hpp>
+#include <Grid/Hadrons/ModuleFactory.hpp>
+
+BEGIN_HADRONS_NAMESPACE
+
+/******************************************************************************
+ *                         ___FILEBASENAME___                                 *
+ ******************************************************************************/
+BEGIN_MODULE_NAMESPACE(___NAMESPACE___)
+
+class ___FILEBASENAME___Par: Serializable
+{
+public:
+    GRID_SERIALIZABLE_CLASS_MEMBERS(___FILEBASENAME___Par,
+                                    unsigned int, i);
+};
+
+class T___FILEBASENAME___: public Module<___FILEBASENAME___Par>
+{
+public:
+    // constructor
+    T___FILEBASENAME___(const std::string name);
+    // destructor
+    virtual ~T___FILEBASENAME___(void) = default;
+    // dependency relation
+    virtual std::vector<std::string> getInput(void);
+    virtual std::vector<std::string> getOutput(void);
+    // setup
+    virtual void setup(void);
+    // execution
+    virtual void execute(void);
+};
+
+MODULE_REGISTER_NS(___FILEBASENAME___, T___FILEBASENAME___, ___NAMESPACE___);
+
+END_MODULE_NAMESPACE
+
+END_HADRONS_NAMESPACE
+
+#endif // Hadrons____FILEBASENAME____hpp_

extras/Hadrons/Modules/templates/Module_tmp.hpp.template

@@ -0,0 +1,81 @@
+#ifndef Hadrons____FILEBASENAME____hpp_
+#define Hadrons____FILEBASENAME____hpp_
+
+#include <Grid/Hadrons/Global.hpp>
+#include <Grid/Hadrons/Module.hpp>
+#include <Grid/Hadrons/ModuleFactory.hpp>
+
+BEGIN_HADRONS_NAMESPACE
+
+/******************************************************************************
+ *                         ___FILEBASENAME___                                 *
+ ******************************************************************************/
+class ___FILEBASENAME___Par: Serializable
+{
+public:
+    GRID_SERIALIZABLE_CLASS_MEMBERS(___FILEBASENAME___Par,
+                                    unsigned int, i);
+};
+
+template <typename FImpl>
+class T___FILEBASENAME___: public Module<___FILEBASENAME___Par>
+{
+public:
+    // constructor
+    T___FILEBASENAME___(const std::string name);
+    // destructor
+    virtual ~T___FILEBASENAME___(void) = default;
+    // dependency relation
+    virtual std::vector<std::string> getInput(void);
+    virtual std::vector<std::string> getOutput(void);
+    // setup
+    virtual void setup(void);
+    // execution
+    virtual void execute(void);
+};
+
+MODULE_REGISTER(___FILEBASENAME___, T___FILEBASENAME___<FIMPL>);
+
+/******************************************************************************
+ *                 T___FILEBASENAME___ implementation                             *
+ ******************************************************************************/
+// constructor /////////////////////////////////////////////////////////////////
+template <typename FImpl>
+T___FILEBASENAME___<FImpl>::T___FILEBASENAME___(const std::string name)
+: Module<___FILEBASENAME___Par>(name)
+{}
+
+// dependencies/products ///////////////////////////////////////////////////////
+template <typename FImpl>
+std::vector<std::string> T___FILEBASENAME___<FImpl>::getInput(void)
+{
+    std::vector<std::string> in;
+    
+    return in;
+}
+
+template <typename FImpl>
+std::vector<std::string> T___FILEBASENAME___<FImpl>::getOutput(void)
+{
+    std::vector<std::string> out = {getName()};
+    
+    return out;
+}
+
+// setup ///////////////////////////////////////////////////////////////////////
+template <typename FImpl>
+void T___FILEBASENAME___<FImpl>::setup(void)
+{
+    
+}
+
+// execution ///////////////////////////////////////////////////////////////////
+template <typename FImpl>
+void T___FILEBASENAME___<FImpl>::execute(void)
+{
+    
+}
+
+END_HADRONS_NAMESPACE
+
+#endif // Hadrons____FILEBASENAME____hpp_

extras/Hadrons/Modules/templates/Module_tmp_in_NS.hpp.template

@@ -0,0 +1,85 @@
+#ifndef Hadrons____FILEBASENAME____hpp_
+#define Hadrons____FILEBASENAME____hpp_
+
+#include <Grid/Hadrons/Global.hpp>
+#include <Grid/Hadrons/Module.hpp>
+#include <Grid/Hadrons/ModuleFactory.hpp>
+
+BEGIN_HADRONS_NAMESPACE
+
+/******************************************************************************
+ *                         ___FILEBASENAME___                                 *
+ ******************************************************************************/
+BEGIN_MODULE_NAMESPACE(___NAMESPACE___)
+
+class ___FILEBASENAME___Par: Serializable
+{
+public:
+    GRID_SERIALIZABLE_CLASS_MEMBERS(___FILEBASENAME___Par,
+                                    unsigned int, i);
+};
+
+template <typename FImpl>
+class T___FILEBASENAME___: public Module<___FILEBASENAME___Par>
+{
+public:
+    // constructor
+    T___FILEBASENAME___(const std::string name);
+    // destructor
+    virtual ~T___FILEBASENAME___(void) = default;
+    // dependency relation
+    virtual std::vector<std::string> getInput(void);
+    virtual std::vector<std::string> getOutput(void);
+    // setup
+    virtual void setup(void);
+    // execution
+    virtual void execute(void);
+};
+
+MODULE_REGISTER_NS(___FILEBASENAME___, T___FILEBASENAME___<FIMPL>, ___NAMESPACE___);
+
+/******************************************************************************
+ *                 T___FILEBASENAME___ implementation                             *
+ ******************************************************************************/
+// constructor /////////////////////////////////////////////////////////////////
+template <typename FImpl>
+T___FILEBASENAME___<FImpl>::T___FILEBASENAME___(const std::string name)
+: Module<___FILEBASENAME___Par>(name)
+{}
+
+// dependencies/products ///////////////////////////////////////////////////////
+template <typename FImpl>
+std::vector<std::string> T___FILEBASENAME___<FImpl>::getInput(void)
+{
+    std::vector<std::string> in;
+    
+    return in;
+}
+
+template <typename FImpl>
+std::vector<std::string> T___FILEBASENAME___<FImpl>::getOutput(void)
+{
+    std::vector<std::string> out = {getName()};
+    
+    return out;
+}
+
+// setup ///////////////////////////////////////////////////////////////////////
+template <typename FImpl>
+void T___FILEBASENAME___<FImpl>::setup(void)
+{
+    
+}
+
+// execution ///////////////////////////////////////////////////////////////////
+template <typename FImpl>
+void T___FILEBASENAME___<FImpl>::execute(void)
+{
+    
+}
+
+END_MODULE_NAMESPACE
+
+END_HADRONS_NAMESPACE
+
+#endif // Hadrons____FILEBASENAME____hpp_

extras/Hadrons/add_module.sh

@@ -0,0 +1,31 @@
+#!/usr/bin/env bash
+
+if (( $# != 1 && $# != 2)); then
+    echo "usage: `basename $0` <module name> [<namespace>]" 1>&2
+    exit 1
+fi
+NAME=$1
+NS=$2
+
+if (( $# == 1 )); then
+	if [ -e "Modules/${NAME}.cc" ] || [ -e "Modules/${NAME}.hpp" ]; then
+	    echo "error: files Modules/${NAME}.* already exists" 1>&2
+	    exit 1
+	fi
+	sed "s/___FILEBASENAME___/${NAME}/g" Modules/templates/Module.cc.template > Modules/${NAME}.cc
+	sed "s/___FILEBASENAME___/${NAME}/g" Modules/templates/Module.hpp.template > Modules/${NAME}.hpp
+elif (( $# == 2 )); then
+	mkdir -p Modules/${NS}
+	if [ -e "Modules/${NS}/${NAME}.cc" ] || [ -e "Modules/${NS}/${NAME}.hpp" ]; then
+	    echo "error: files Modules/${NS}/${NAME}.* already exists" 1>&2
+	    exit 1
+	fi
+	TMPCC=".${NS}.${NAME}.tmp.cc"
+	TMPHPP=".${NS}.${NAME}.tmp.hpp"
+	sed "s/___FILEBASENAME___/${NAME}/g" Modules/templates/Module_in_NS.cc.template  > ${TMPCC}
+	sed "s/___FILEBASENAME___/${NAME}/g" Modules/templates/Module_in_NS.hpp.template > ${TMPHPP}
+	sed "s/___NAMESPACE___/${NS}/g" ${TMPCC}  > Modules/${NS}/${NAME}.cc
+	sed "s/___NAMESPACE___/${NS}/g" ${TMPHPP} > Modules/${NS}/${NAME}.hpp
+	rm -f ${TMPCC} ${TMPHPP}
+fi
+./make_module_list.sh

extras/Hadrons/add_module_template.sh

@@ -0,0 +1,28 @@
+#!/usr/bin/env bash
+
+if (( $# != 1 && $# != 2)); then
+    echo "usage: `basename $0` <module name> [<namespace>]" 1>&2
+    exit 1
+fi
+NAME=$1
+NS=$2
+
+if (( $# == 1 )); then
+	if [ -e "Modules/${NAME}.cc" ] || [ -e "Modules/${NAME}.hpp" ]; then
+	    echo "error: files Modules/${NAME}.* already exists" 1>&2
+	    exit 1
+	fi
+	sed "s/___FILEBASENAME___/${NAME}/g" Modules/templates/Module_tmp.hpp.template > Modules/${NAME}.hpp
+elif (( $# == 2 )); then
+	mkdir -p Modules/${NS}
+	if [ -e "Modules/${NS}/${NAME}.cc" ] || [ -e "Modules/${NS}/${NAME}.hpp" ]; then
+	    echo "error: files Modules/${NS}/${NAME}.* already exists" 1>&2
+	    exit 1
+	fi
+	TMPCC=".${NS}.${NAME}.tmp.cc"
+	TMPHPP=".${NS}.${NAME}.tmp.hpp"
+	sed "s/___FILEBASENAME___/${NAME}/g" Modules/templates/Module_tmp_in_NS.hpp.template > ${TMPHPP}
+	sed "s/___NAMESPACE___/${NS}/g" ${TMPHPP} > Modules/${NS}/${NAME}.hpp
+	rm -f ${TMPCC} ${TMPHPP}
+fi
+./make_module_list.sh

extras/Hadrons/make_module_list.sh

@@ -0,0 +1,12 @@
+#!/usr/bin/env bash
+
+echo 'modules_cc =\' > modules.inc
+find Modules -name '*.cc' -type f -print | sed 's/^/  /;$q;s/$/ \\/' >> modules.inc
+echo '' >> modules.inc
+echo 'modules_hpp =\' >> modules.inc
+find Modules -name '*.hpp' -type f -print | sed 's/^/  /;$q;s/$/ \\/' >> modules.inc
+echo '' >> modules.inc
+rm -f Modules.hpp
+for f in `find Modules -name '*.hpp'`; do
+	echo "#include <Grid/Hadrons/${f}>" >> Modules.hpp
+done

extras/Hadrons/modules.inc

@@ -0,0 +1,19 @@
+modules_cc =\
+  Modules/MGauge/Load.cc \
+  Modules/MGauge/Random.cc \
+  Modules/MGauge/Unit.cc
+
+modules_hpp =\
+  Modules/MAction/DWF.hpp \
+  Modules/MAction/Wilson.hpp \
+  Modules/MContraction/Baryon.hpp \
+  Modules/MContraction/Meson.hpp \
+  Modules/MGauge/Load.hpp \
+  Modules/MGauge/Random.hpp \
+  Modules/MGauge/Unit.hpp \
+  Modules/MSolver/RBPrecCG.hpp \
+  Modules/MSource/Point.hpp \
+  Modules/MSource/SeqGamma.hpp \
+  Modules/MSource/Z2.hpp \
+  Modules/Quark.hpp
+

extras/Makefile.am

@@ -0,0 +1 @@
+SUBDIRS = Hadrons

lib/Bitwise.h

@@ -1,76 +0,0 @@
-/*************************************************************************************
-
-Grid physics library, www.github.com/paboyle/Grid
-
-Source file: ./lib/Bitwise.h
-
-Copyright (C) 2016
-
-Author: Guido Cossu <guido.cossu@ed.ac.uk>
-
-This program is free software; you can redistribute it and/or modify
-it under the terms of the GNU General Public License as published by
-the Free Software Foundation; either version 2 of the License, or
-(at your option) any later version.
-
-This program is distributed in the hope that it will be useful,
-but WITHOUT ANY WARRANTY; without even the implied warranty of
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-GNU General Public License for more details.
-
-You should have received a copy of the GNU General Public License along
-with this program; if not, write to the Free Software Foundation, Inc.,
-51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
-
-See the full license in the file "LICENSE" in the top level distribution
-directory
-*************************************************************************************/
-/*  END LEGAL */
-#ifndef GRID_BITWISE_H
-#define GRID_BITWISE_H
-
-#include <cassert>
-#include <cfloat>
-#include <bitset>
-#include <climits>
-#include <Config.h>
-
-#ifdef GRID_DEFAULT_PRECISION_SINGLE
-#define GRID_REAL_BYTES 4
-#endif
-#ifdef GRID_DEFAULT_PRECISION_DOUBLE
-#define GRID_REAL_BYTES 8
-#endif
-
-
-namespace Grid {
-
-void show_binaryrep(const unsigned char* a, size_t size);
-
-template <typename T>
-void show_binaryrep(const T& a) {
-  const char* beg = reinterpret_cast<const char*>(&a);
-  const char* end = beg + sizeof(a);
-  unsigned int ctr = 0;
-  while (beg != end) {
-  	std::cout << std::bitset<CHAR_BIT>(*beg++) << ' ';
-  	ctr++;
-  	if (ctr % GRID_REAL_BYTES == 0) std::cout << '\n';
-  }
-  std::cout << '\n';
-}
-
-template <typename T>
-void bitwise_xor(T& l, T& r, unsigned char* xors) {
-  assert(sizeof(l) == sizeof(r));
-  unsigned char* org = reinterpret_cast<unsigned char*>(&l);
-  unsigned char* cur = reinterpret_cast<unsigned char*>(&r);
-  int words = sizeof(l) / sizeof(*org);
-  unsigned char result = 0;
-  for (int w = 0; w < words; w++) xors[w] = (org[w] ^ cur[w]);
-}
-
-}; // namespace 
-
-
-#endif

lib/Grid.h

@@ -38,53 +38,10 @@ Author: paboyle <paboyle@ph.ed.ac.uk>
 #ifndef GRID_H
 #define GRID_H
 
-///////////////////
-// Std C++ dependencies
-///////////////////
-#include <cassert>
-#include <complex>
-#include <vector>
-#include <iostream>
-#include <iomanip>
-#include <random>
-#include <functional>
-#include <stdio.h>
-#include <stdlib.h>
-#include <stdio.h>
-#include <signal.h>
-#include <ctime>
-#include <sys/time.h>
-#include <chrono>
-
-///////////////////
-// Grid headers
-///////////////////
-#include <Grid/serialisation/Serialisation.h>
-#include "Config.h"
-#include <Grid/Timer.h>
-#include <Grid/Bitwise.h>
-#include <Grid/PerfCount.h>
-#include <Grid/Log.h>
-#include <Grid/AlignedAllocator.h>
-#include <Grid/Simd.h>
-#include <Grid/Threads.h>
-#include <Grid/Lexicographic.h>
-#include <Grid/Init.h>
-#include <Grid/Communicator.h> 
-#include <Grid/Cartesian.h>    
-#include <Grid/Tensors.h>      
-#include <Grid/Lattice.h>      
-#include <Grid/Cshift.h>       
-#include <Grid/Stencil.h>      
-#include <Grid/Algorithms.h>   
-#include <Grid/parallelIO/BinaryIO.h>
-#include <Grid/FFT.h>
-
-#include <Grid/qcd/QCD.h>
-#include <Grid/parallelIO/NerscIO.h>
-#include <Grid/qcd/hmc/NerscCheckpointer.h>
-#include <Grid/qcd/hmc/HmcRunner.h>
-
-
+#include <Grid/GridCore.h>
+#include <Grid/GridQCDcore.h>
+#include <Grid/qcd/action/Action.h>
+#include <Grid/qcd/smearing/Smearing.h>
+#include <Grid/qcd/hmc/HMC_aggregate.h>
 
 #endif

lib/GridCore.h

@@ -0,0 +1,81 @@
+    /*************************************************************************************
+
+    Grid physics library, www.github.com/paboyle/Grid 
+
+    Source file: ./lib/Grid.h
+
+    Copyright (C) 2015
+
+Author: Peter Boyle <paboyle@ph.ed.ac.uk>
+Author: azusayamaguchi <ayamaguc@YAMAKAZE.local>
+Author: paboyle <paboyle@ph.ed.ac.uk>
+
+    This program is free software; you can redistribute it and/or modify
+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation; either version 2 of the License, or
+    (at your option) any later version.
+
+    This program is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+
+    You should have received a copy of the GNU General Public License along
+    with this program; if not, write to the Free Software Foundation, Inc.,
+    51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+
+    See the full license in the file "LICENSE" in the top level distribution directory
+    *************************************************************************************/
+    /*  END LEGAL */
+//
+//  Grid.h
+//  simd
+//
+//  Created by Peter Boyle on 09/05/2014.
+//  Copyright (c) 2014 University of Edinburgh. All rights reserved.
+//
+
+#ifndef GRID_BASE_H
+#define GRID_BASE_H
+
+///////////////////
+// Std C++ dependencies
+///////////////////
+#include <cassert>
+#include <complex>
+#include <vector>
+#include <iostream>
+#include <iomanip>
+#include <random>
+#include <functional>
+#include <stdio.h>
+#include <stdlib.h>
+#include <stdio.h>
+#include <signal.h>
+#include <ctime>
+#include <sys/time.h>
+#include <chrono>
+
+///////////////////
+// Grid headers
+///////////////////
+#include "Config.h"
+
+#include <Grid/perfmon/Timer.h>
+#include <Grid/perfmon/PerfCount.h>
+#include <Grid/log/Log.h>
+#include <Grid/allocator/AlignedAllocator.h>
+#include <Grid/simd/Simd.h>
+#include <Grid/serialisation/Serialisation.h>
+#include <Grid/threads/Threads.h>
+#include <Grid/util/Util.h>
+#include <Grid/communicator/Communicator.h> 
+#include <Grid/cartesian/Cartesian.h>    
+#include <Grid/tensors/Tensors.h>      
+#include <Grid/lattice/Lattice.h>      
+#include <Grid/cshift/Cshift.h>       
+#include <Grid/stencil/Stencil.h>      
+#include <Grid/parallelIO/BinaryIO.h>
+#include <Grid/algorithms/Algorithms.h>   
+
+#endif

lib/GridQCDcore.h

@@ -2,12 +2,12 @@
 
     Grid physics library, www.github.com/paboyle/Grid 
 
-    Source file: ./lib/qcd/hmc/HMC.cc
+    Source file: ./lib/Grid.h
 
     Copyright (C) 2015
 
 Author: Peter Boyle <paboyle@ph.ed.ac.uk>
-Author: neo <cossu@post.kek.jp>
+Author: azusayamaguchi <ayamaguc@YAMAKAZE.local>
 Author: paboyle <paboyle@ph.ed.ac.uk>
 
     This program is free software; you can redistribute it and/or modify
@@ -27,10 +27,16 @@ Author: paboyle <paboyle@ph.ed.ac.uk>
     See the full license in the file "LICENSE" in the top level distribution directory
     *************************************************************************************/
     /*  END LEGAL */
-#include <Grid.h>
+#ifndef GRID_QCD_CORE_H
+#define GRID_QCD_CORE_H
 
-namespace Grid{
-  namespace QCD{
+/////////////////////////
+// Core Grid QCD headers
+/////////////////////////
+#include <Grid/GridCore.h>
+#include <Grid/qcd/QCD.h>
+#include <Grid/qcd/spin/Spin.h>
+#include <Grid/qcd/utils/Utils.h>
+#include <Grid/qcd/representations/Representations.h>
 
-  }
-}
+#endif

lib/Hadrons

@@ -0,0 +1 @@
+../extras/Hadrons

lib/Makefile.am

@@ -1,4 +1,5 @@
 extra_sources=
+extra_headers=
 if BUILD_COMMS_MPI
   extra_sources+=communicator/Communicator_mpi.cc
   extra_sources+=communicator/Communicator_base.cc
@@ -24,6 +25,12 @@ if BUILD_COMMS_NONE
   extra_sources+=communicator/Communicator_base.cc
 endif
 
+if BUILD_HDF5
+  extra_sources+=serialisation/Hdf5IO.cc 
+  extra_headers+=serialisation/Hdf5IO.h
+  extra_headers+=serialisation/Hdf5Type.h
+endif
+
 #
 # Libraries
 #
@@ -32,6 +39,9 @@ include Eigen.inc
 
 lib_LIBRARIES = libGrid.a
 
-libGrid_a_SOURCES              = $(CCFILES) $(extra_sources)
+CCFILES += $(extra_sources)
+HFILES  += $(extra_headers)
+
+libGrid_a_SOURCES              = $(CCFILES)
 libGrid_adir                   = $(pkgincludedir)
 nobase_dist_pkginclude_HEADERS = $(HFILES) $(eigen_files) Config.h

lib/Old/Tensor_peek.h

@@ -1,154 +0,0 @@
-    /*************************************************************************************
-
-    Grid physics library, www.github.com/paboyle/Grid 
-
-    Source file: ./lib/Old/Tensor_peek.h
-
-    Copyright (C) 2015
-
-Author: Peter Boyle <paboyle@ph.ed.ac.uk>
-
-    This program is free software; you can redistribute it and/or modify
-    it under the terms of the GNU General Public License as published by
-    the Free Software Foundation; either version 2 of the License, or
-    (at your option) any later version.
-
-    This program is distributed in the hope that it will be useful,
-    but WITHOUT ANY WARRANTY; without even the implied warranty of
-    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-    GNU General Public License for more details.
-
-    You should have received a copy of the GNU General Public License along
-    with this program; if not, write to the Free Software Foundation, Inc.,
-    51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
-
-    See the full license in the file "LICENSE" in the top level distribution directory
-    *************************************************************************************/
-    /*  END LEGAL */
-#ifndef GRID_MATH_PEEK_H
-#define GRID_MATH_PEEK_H
-namespace Grid {
-
-//////////////////////////////////////////////////////////////////////////////
-// Peek on a specific index; returns a scalar in that index, tensor inherits rest
-//////////////////////////////////////////////////////////////////////////////
-// If we hit the right index, return scalar with no further recursion
-
-//template<int Level> inline ComplexF peekIndex(const ComplexF arg) { return arg;}
-//template<int Level> inline ComplexD peekIndex(const ComplexD arg) { return arg;}
-//template<int Level> inline RealF peekIndex(const RealF arg) { return arg;}
-//template<int Level> inline RealD peekIndex(const RealD arg) { return arg;}
-#if 0
-// Scalar peek, no indices
-template<int Level,class vtype,typename std::enable_if< iScalar<vtype>::TensorLevel == Level >::type * =nullptr> inline 
-  auto peekIndex(const iScalar<vtype> &arg) ->  iScalar<vtype> 
-{
-  return arg;
-}
-// Vector peek, one index
-template<int Level,class vtype,int N,typename std::enable_if< iScalar<vtype>::TensorLevel == Level >::type * =nullptr> inline 
-  auto peekIndex(const iVector<vtype,N> &arg,int i) -> iScalar<vtype> // Index matches
-{
-  iScalar<vtype> ret;                              // return scalar
-  ret._internal = arg._internal[i];
-  return ret;
-}
-// Matrix peek, two indices
-template<int Level,class vtype,int N,typename std::enable_if< iScalar<vtype>::TensorLevel == Level >::type * =nullptr> inline 
-  auto peekIndex(const iMatrix<vtype,N> &arg,int i,int j) ->  iScalar<vtype>
-{
-  iScalar<vtype> ret;                              // return scalar
-  ret._internal = arg._internal[i][j];
-  return ret;
-}
-
-/////////////
-// No match peek for scalar,vector,matrix must forward on either 0,1,2 args. Must have 9 routines with notvalue
-/////////////
-// scalar
-template<int Level,class vtype,typename std::enable_if< iScalar<vtype>::TensorLevel != Level >::type * =nullptr> inline 
-  auto peekIndex(const iScalar<vtype> &arg) -> iScalar<decltype(peekIndex<Level>(arg._internal))>
-{
-  iScalar<decltype(peekIndex<Level>(arg._internal))> ret;
-  ret._internal= peekIndex<Level>(arg._internal);
-  return ret;
-}
-template<int Level,class vtype, typename std::enable_if< iScalar<vtype>::TensorLevel != Level >::type * =nullptr> inline 
-  auto peekIndex(const iScalar<vtype> &arg,int i) ->  iScalar<decltype(peekIndex<Level>(arg._internal,i))> 
-{
-  iScalar<decltype(peekIndex<Level>(arg._internal,i))> ret;
-  ret._internal=peekIndex<Level>(arg._internal,i);
-  return ret;
-}
-template<int Level,class vtype, typename std::enable_if< iScalar<vtype>::TensorLevel != Level >::type * =nullptr> inline 
-  auto peekIndex(const iScalar<vtype> &arg,int i,int j) ->  iScalar<decltype(peekIndex<Level>(arg._internal,i,j))>
-{
-  iScalar<decltype(peekIndex<Level>(arg._internal,i,j))> ret;
-  ret._internal=peekIndex<Level>(arg._internal,i,j);
-  return ret;
-}
-// vector
-template<int Level,class vtype,int N, typename std::enable_if< iScalar<vtype>::TensorLevel != Level >::type * =nullptr> inline 
-auto peekIndex(const iVector<vtype,N> &arg) ->   iVector<decltype(peekIndex<Level>(arg._internal[0])),N>
-{
-  iVector<decltype(peekIndex<Level>(arg._internal[0])),N> ret;
-  for(int ii=0;ii<N;ii++){
-    ret._internal[ii]=peekIndex<Level>(arg._internal[ii]);
-  }
-  return ret;
-}
-template<int Level,class vtype,int N, typename std::enable_if< iScalar<vtype>::TensorLevel != Level >::type * =nullptr> inline 
-  auto peekIndex(const iVector<vtype,N> &arg,int i) ->  iVector<decltype(peekIndex<Level>(arg._internal[0],i)),N>
-{
-  iVector<decltype(peekIndex<Level>(arg._internal[0],i)),N> ret;
-  for(int ii=0;ii<N;ii++){
-    ret._internal[ii]=peekIndex<Level>(arg._internal[ii],i);
-  }
-  return ret;
-}
-template<int Level,class vtype,int N, typename std::enable_if< iScalar<vtype>::TensorLevel != Level >::type * =nullptr> inline 
-  auto peekIndex(const iVector<vtype,N> &arg,int i,int j) ->  iVector<decltype(peekIndex<Level>(arg._internal[0],i,j)),N> 
-{
-  iVector<decltype(peekIndex<Level>(arg._internal[0],i,j)),N> ret;
-  for(int ii=0;ii<N;ii++){
-    ret._internal[ii]=peekIndex<Level>(arg._internal[ii],i,j);
-  }
-  return ret;
-}
-
-// matrix
-template<int Level,class vtype,int N, typename std::enable_if< iScalar<vtype>::TensorLevel != Level >::type * =nullptr> inline 
-auto peekIndex(const iMatrix<vtype,N> &arg) ->   iMatrix<decltype(peekIndex<Level>(arg._internal[0][0])),N> 
-{
-  iMatrix<decltype(peekIndex<Level>(arg._internal[0][0])),N> ret;
-  for(int ii=0;ii<N;ii++){
-  for(int jj=0;jj<N;jj++){
-    ret._internal[ii][jj]=peekIndex<Level>(arg._internal[ii][jj]);// Could avoid this because peeking a scalar is dumb
-  }}
-  return ret;
-}
-template<int Level,class vtype,int N, typename std::enable_if< iScalar<vtype>::TensorLevel != Level >::type * =nullptr> inline 
-  auto peekIndex(const iMatrix<vtype,N> &arg,int i) ->   iMatrix<decltype(peekIndex<Level>(arg._internal[0][0],i)),N>
-{
-  iMatrix<decltype(peekIndex<Level>(arg._internal[0][0],i)),N> ret;
-  for(int ii=0;ii<N;ii++){
-  for(int jj=0;jj<N;jj++){
-    ret._internal[ii][jj]=peekIndex<Level>(arg._internal[ii][jj],i);
-  }}
-  return ret;
-}
-template<int Level,class vtype,int N, typename std::enable_if< iScalar<vtype>::TensorLevel != Level >::type * =nullptr> inline 
-  auto peekIndex(const iMatrix<vtype,N> &arg,int i,int j) ->   iMatrix<decltype(peekIndex<Level>(arg._internal[0][0],i,j)),N>
-{
-  iMatrix<decltype(peekIndex<Level>(arg._internal[0][0],i,j)),N> ret;
-  for(int ii=0;ii<N;ii++){
-  for(int jj=0;jj<N;jj++){
-    ret._internal[ii][jj]=peekIndex<Level>(arg._internal[ii][jj],i,j);
-  }}
-  return ret;
-}
-#endif
-
-
-}
-#endif

lib/Old/Tensor_poke.h

@@ -1,127 +0,0 @@
-    /*************************************************************************************
-
-    Grid physics library, www.github.com/paboyle/Grid 
-
-    Source file: ./lib/Old/Tensor_poke.h
-
-    Copyright (C) 2015
-
-Author: Peter Boyle <paboyle@ph.ed.ac.uk>
-
-    This program is free software; you can redistribute it and/or modify
-    it under the terms of the GNU General Public License as published by
-    the Free Software Foundation; either version 2 of the License, or
-    (at your option) any later version.
-
-    This program is distributed in the hope that it will be useful,
-    but WITHOUT ANY WARRANTY; without even the implied warranty of
-    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-    GNU General Public License for more details.
-
-    You should have received a copy of the GNU General Public License along
-    with this program; if not, write to the Free Software Foundation, Inc.,
-    51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
-
-    See the full license in the file "LICENSE" in the top level distribution directory
-    *************************************************************************************/
-    /*  END LEGAL */
-#ifndef GRID_MATH_POKE_H
-#define GRID_MATH_POKE_H
-namespace Grid {
-
-//////////////////////////////////////////////////////////////////////////////
-// Poke a specific index; 
-//////////////////////////////////////////////////////////////////////////////
-#if 0
-// Scalar poke
-template<int Level,class vtype,typename std::enable_if< iScalar<vtype>::TensorLevel == Level >::type * =nullptr> inline 
-  void pokeIndex(iScalar<vtype> &ret, const iScalar<vtype> &arg)
-{
-  ret._internal = arg._internal;
-}
-// Vector poke, one index
-template<int Level,class vtype,int N,typename std::enable_if< iScalar<vtype>::TensorLevel == Level >::type * =nullptr> inline 
-  void pokeIndex(iVector<vtype,N> &ret, const iScalar<vtype> &arg,int i)
-{
-  ret._internal[i] = arg._internal;
-}
-//Matrix poke, two indices
-template<int Level,class vtype,int N,typename std::enable_if< iScalar<vtype>::TensorLevel == Level >::type * =nullptr> inline 
-  void pokeIndex(iMatrix<vtype,N> &ret, const iScalar<vtype> &arg,int i,int j)
-{
-  ret._internal[i][j] = arg._internal;
-}
-
-/////////////
-// No match poke for scalar,vector,matrix must forward on either 0,1,2 args. Must have 9 routines with notvalue
-/////////////
-// scalar
-template<int Level,class vtype,typename std::enable_if< iScalar<vtype>::TensorLevel != Level >::type * =nullptr> inline 
-void pokeIndex(iScalar<vtype> &ret, const iScalar<decltype(peekIndex<Level>(ret._internal))>  &arg)
-{
-  pokeIndex<Level>(ret._internal,arg._internal);
-}
-template<int Level,class vtype,typename std::enable_if< iScalar<vtype>::TensorLevel != Level >::type * =nullptr> inline 
-  void pokeIndex(iScalar<vtype> &ret, const iScalar<decltype(peekIndex<Level>(ret._internal,0))> &arg, int i)
-		 
-{
-  pokeIndex<Level>(ret._internal,arg._internal,i);
-}
-template<int Level,class vtype,typename std::enable_if< iScalar<vtype>::TensorLevel != Level >::type * =nullptr> inline 
-  void pokeIndex(iScalar<vtype> &ret, const iScalar<decltype(peekIndex<Level>(ret._internal,0,0))> &arg,int i,int j)
-{
-  pokeIndex<Level>(ret._internal,arg._internal,i,j);
-}
-
-// Vector
-template<int Level,class vtype,int N,typename std::enable_if< iScalar<vtype>::TensorLevel != Level >::type * =nullptr> inline 
-  void pokeIndex(iVector<vtype,N> &ret, iVector<decltype(peekIndex<Level>(ret._internal)),N>  &arg)
-{
-  for(int ii=0;ii<N;ii++){
-    pokeIndex<Level>(ret._internal[ii],arg._internal[ii]);
-  }
-}
-template<int Level,class vtype,int N,typename std::enable_if< iScalar<vtype>::TensorLevel != Level >::type * =nullptr> inline 
-  void pokeIndex(iVector<vtype,N> &ret, const iVector<decltype(peekIndex<Level>(ret._internal,0)),N> &arg,int i)
-{
-  for(int ii=0;ii<N;ii++){
-    pokeIndex<Level>(ret._internal[ii],arg._internal[ii],i);
-  }
-}
-template<int Level,class vtype,int N,typename std::enable_if< iScalar<vtype>::TensorLevel != Level >::type * =nullptr> inline 
-  void pokeIndex(iVector<vtype,N> &ret, const iVector<decltype(peekIndex<Level>(ret._internal,0,0)),N> &arg,int i,int j)
-{
-  for(int ii=0;ii<N;ii++){
-    pokeIndex<Level>(ret._internal[ii],arg._internal[ii],i,j);
-  }
-}
-
-// Matrix
-template<int Level,class vtype,int N,typename std::enable_if< iScalar<vtype>::TensorLevel != Level >::type * =nullptr> inline 
-  void pokeIndex(iMatrix<vtype,N> &ret, const iMatrix<decltype(peekIndex<Level>(ret._internal)),N> &arg)		 
-{
-  for(int ii=0;ii<N;ii++){
-  for(int jj=0;jj<N;jj++){
-    pokeIndex<Level>(ret._internal[ii][jj],arg._internal[ii][jj]);
-  }}
-}
-template<int Level,class vtype,int N,typename std::enable_if< iScalar<vtype>::TensorLevel != Level >::type * =nullptr> inline 
-  void pokeIndex(iMatrix<vtype,N> &ret, const iMatrix<decltype(peekIndex<Level>(ret._internal,0)),N> &arg,int i)
-{
-  for(int ii=0;ii<N;ii++){
-  for(int jj=0;jj<N;jj++){
-    pokeIndex<Level>(ret._internal[ii][jj],arg._internal[ii][jj],i);
-  }}
-}
-template<int Level,class vtype,int N,typename std::enable_if< iScalar<vtype>::TensorLevel != Level >::type * =nullptr> inline 
-  void pokeIndex(iMatrix<vtype,N> &ret, const iMatrix<decltype(peekIndex<Level>(ret._internal,0,0)),N> &arg, int i,int j)
-{
-  for(int ii=0;ii<N;ii++){
-  for(int jj=0;jj<N;jj++){
-    pokeIndex<Level>(ret._internal[ii][jj],arg._internal[ii][jj],i,j);
-  }}
-}
-#endif
-
-}
-#endif

lib/algorithms/Algorithms.h

@@ -42,15 +42,14 @@ Author: Peter Boyle <paboyle@ph.ed.ac.uk>
 #include <Grid/algorithms/iterative/ConjugateResidual.h>
 #include <Grid/algorithms/iterative/NormalEquations.h>
 #include <Grid/algorithms/iterative/SchurRedBlack.h>
-
 #include <Grid/algorithms/iterative/ConjugateGradientMultiShift.h>
 #include <Grid/algorithms/iterative/ConjugateGradientMixedPrec.h>
 
 // Lanczos support
-#include <Grid/algorithms/iterative/MatrixUtils.h>
+//#include <Grid/algorithms/iterative/MatrixUtils.h>
 #include <Grid/algorithms/iterative/ImplicitlyRestartedLanczos.h>
-
 #include <Grid/algorithms/CoarsenedMatrix.h>
+#include <Grid/algorithms/FFT.h>
 
 // Eigen/lanczos
 // EigCg

lib/algorithms/CoarsenedMatrix.h

@@ -267,8 +267,7 @@ namespace Grid {
       SimpleCompressor<siteVector> compressor;
       Stencil.HaloExchange(in,compressor);
 
-PARALLEL_FOR_LOOP
-      for(int ss=0;ss<Grid()->oSites();ss++){
+      parallel_for(int ss=0;ss<Grid()->oSites();ss++){
         siteVector res = zero;
 	siteVector nbr;
 	int ptype;
@@ -380,8 +379,7 @@ PARALLEL_FOR_LOOP
 	  Subspace.ProjectToSubspace(oProj,oblock);
 	  //	  blockProject(iProj,iblock,Subspace.subspace);
 	  //	  blockProject(oProj,oblock,Subspace.subspace);
-PARALLEL_FOR_LOOP
-	  for(int ss=0;ss<Grid()->oSites();ss++){
+	  parallel_for(int ss=0;ss<Grid()->oSites();ss++){
 	    for(int j=0;j<nbasis;j++){
 	      if( disp!= 0 ) {
 		A[p]._odata[ss](j,i) = oProj._odata[ss](j);
@@ -427,7 +425,7 @@ PARALLEL_FOR_LOOP
 	A[p]=zero;
       }
 
-      GridParallelRNG  RNG(Grid()); RNG.SeedRandomDevice();
+      GridParallelRNG  RNG(Grid()); RNG.SeedFixedIntegers(std::vector<int>({55,72,19,17,34}));
       Lattice<iScalar<CComplex> > val(Grid()); random(RNG,val);
 
       Complex one(1.0);

lib/algorithms/approx/MultiShiftFunction.cc

@@ -25,7 +25,7 @@ Author: Azusa Yamaguchi <ayamaguc@staffmail.ed.ac.uk>
     See the full license in the file "LICENSE" in the top level distribution directory
     *************************************************************************************/
     /*  END LEGAL */
-#include <Grid.h>
+#include <Grid/GridCore.h>
 
 namespace Grid {
 double MultiShiftFunction::approx(double x)

lib/algorithms/approx/Remez.cc

@@ -20,7 +20,7 @@
 #include<iomanip>
 #include<cassert>
 
-#include<algorithms/approx/Remez.h>
+#include<Grid/algorithms/approx/Remez.h>
 
 // Constructor
 AlgRemez::AlgRemez(double lower, double upper, long precision) 

lib/algorithms/iterative/BlockConjugateGradient.h

@@ -0,0 +1,366 @@
+/*************************************************************************************
+
+Grid physics library, www.github.com/paboyle/Grid
+
+Source file: ./lib/algorithms/iterative/BlockConjugateGradient.h
+
+Copyright (C) 2017
+
+Author: Azusa Yamaguchi <ayamaguc@staffmail.ed.ac.uk>
+Author: Peter Boyle <paboyle@ph.ed.ac.uk>
+
+This program is free software; you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation; either version 2 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License along
+with this program; if not, write to the Free Software Foundation, Inc.,
+51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+
+See the full license in the file "LICENSE" in the top level distribution
+directory
+*************************************************************************************/
+/*  END LEGAL */
+#ifndef GRID_BLOCK_CONJUGATE_GRADIENT_H
+#define GRID_BLOCK_CONJUGATE_GRADIENT_H
+
+
+namespace Grid {
+
+//////////////////////////////////////////////////////////////////////////
+// Block conjugate gradient. Dimension zero should be the block direction
+//////////////////////////////////////////////////////////////////////////
+template <class Field>
+class BlockConjugateGradient : public OperatorFunction<Field> {
+ public:
+
+  typedef typename Field::scalar_type scomplex;
+
+  const int blockDim = 0;
+
+  int Nblock;
+  bool ErrorOnNoConverge;  // throw an assert when the CG fails to converge.
+                           // Defaults true.
+  RealD Tolerance;
+  Integer MaxIterations;
+  Integer IterationsToComplete; //Number of iterations the CG took to finish. Filled in upon completion
+  
+  BlockConjugateGradient(RealD tol, Integer maxit, bool err_on_no_conv = true)
+    : Tolerance(tol),
+    MaxIterations(maxit),
+    ErrorOnNoConverge(err_on_no_conv){};
+
+void operator()(LinearOperatorBase<Field> &Linop, const Field &Src, Field &Psi) 
+{
+  int Orthog = 0; // First dimension is block dim
+  Nblock = Src._grid->_fdimensions[Orthog];
+
+  std::cout<<GridLogMessage<<" Block Conjugate Gradient : Orthog "<<Orthog<<" Nblock "<<Nblock<<std::endl;
+
+  Psi.checkerboard = Src.checkerboard;
+  conformable(Psi, Src);
+
+  Field P(Src);
+  Field AP(Src);
+  Field R(Src);
+  
+  Eigen::MatrixXcd m_pAp    = Eigen::MatrixXcd::Identity(Nblock,Nblock);
+  Eigen::MatrixXcd m_pAp_inv= Eigen::MatrixXcd::Identity(Nblock,Nblock);
+  Eigen::MatrixXcd m_rr     = Eigen::MatrixXcd::Zero(Nblock,Nblock);
+  Eigen::MatrixXcd m_rr_inv = Eigen::MatrixXcd::Zero(Nblock,Nblock);
+
+  Eigen::MatrixXcd m_alpha      = Eigen::MatrixXcd::Zero(Nblock,Nblock);
+  Eigen::MatrixXcd m_beta   = Eigen::MatrixXcd::Zero(Nblock,Nblock);
+
+  // Initial residual computation & set up
+  std::vector<RealD> residuals(Nblock);
+  std::vector<RealD> ssq(Nblock);
+
+  sliceNorm(ssq,Src,Orthog);
+  RealD sssum=0;
+  for(int b=0;b<Nblock;b++) sssum+=ssq[b];
+
+  sliceNorm(residuals,Src,Orthog);
+  for(int b=0;b<Nblock;b++){ assert(std::isnan(residuals[b])==0); }
+
+  sliceNorm(residuals,Psi,Orthog);
+  for(int b=0;b<Nblock;b++){ assert(std::isnan(residuals[b])==0); }
+
+  // Initial search dir is guess
+  Linop.HermOp(Psi, AP);
+  
+
+  /************************************************************************
+   * Block conjugate gradient (Stephen Pickles, thesis 1995, pp 71, O Leary 1980)
+   ************************************************************************
+   * O'Leary : R = B - A X
+   * O'Leary : P = M R ; preconditioner M = 1
+   * O'Leary : alpha = PAP^{-1} RMR
+   * O'Leary : beta  = RMR^{-1}_old RMR_new
+   * O'Leary : X=X+Palpha
+   * O'Leary : R_new=R_old-AP alpha
+   * O'Leary : P=MR_new+P beta
+   */
+
+  R = Src - AP;  
+  P = R;
+  sliceInnerProductMatrix(m_rr,R,R,Orthog);
+
+  GridStopWatch sliceInnerTimer;
+  GridStopWatch sliceMaddTimer;
+  GridStopWatch MatrixTimer;
+  GridStopWatch SolverTimer;
+  SolverTimer.Start();
+
+  int k;
+  for (k = 1; k <= MaxIterations; k++) {
+
+    RealD rrsum=0;
+    for(int b=0;b<Nblock;b++) rrsum+=real(m_rr(b,b));
+
+    std::cout << GridLogIterative << "\titeration "<<k<<" rr_sum "<<rrsum<<" ssq_sum "<< sssum
+	      <<" / "<<std::sqrt(rrsum/sssum) <<std::endl;
+
+    MatrixTimer.Start();
+    Linop.HermOp(P, AP);
+    MatrixTimer.Stop();
+
+    // Alpha
+    sliceInnerTimer.Start();
+    sliceInnerProductMatrix(m_pAp,P,AP,Orthog);
+    sliceInnerTimer.Stop();
+    m_pAp_inv = m_pAp.inverse();
+    m_alpha   = m_pAp_inv * m_rr ;
+
+    // Psi, R update
+    sliceMaddTimer.Start();
+    sliceMaddMatrix(Psi,m_alpha, P,Psi,Orthog);     // add alpha *  P to psi
+    sliceMaddMatrix(R  ,m_alpha,AP,  R,Orthog,-1.0);// sub alpha * AP to resid
+    sliceMaddTimer.Stop();
+
+    // Beta
+    m_rr_inv = m_rr.inverse();
+    sliceInnerTimer.Start();
+    sliceInnerProductMatrix(m_rr,R,R,Orthog);
+    sliceInnerTimer.Stop();
+    m_beta = m_rr_inv *m_rr;
+
+    // Search update
+    sliceMaddTimer.Start();
+    sliceMaddMatrix(AP,m_beta,P,R,Orthog);
+    sliceMaddTimer.Stop();
+    P= AP;
+
+    /*********************
+     * convergence monitor
+     *********************
+     */
+    RealD max_resid=0;
+    for(int b=0;b<Nblock;b++){
+      RealD rr = real(m_rr(b,b))/ssq[b];
+      if ( rr > max_resid ) max_resid = rr;
+    }
+    
+    if ( max_resid < Tolerance*Tolerance ) { 
+
+      SolverTimer.Stop();
+
+      std::cout << GridLogMessage<<"BlockCG converged in "<<k<<" iterations"<<std::endl;
+      for(int b=0;b<Nblock;b++){
+	std::cout << GridLogMessage<< "\t\tblock "<<b<<" resid "<< std::sqrt(real(m_rr(b,b))/ssq[b])<<std::endl;
+      }
+      std::cout << GridLogMessage<<"\tMax residual is "<<std::sqrt(max_resid)<<std::endl;
+
+      Linop.HermOp(Psi, AP);
+      AP = AP-Src;
+      std::cout << GridLogMessage <<"\tTrue residual is " << std::sqrt(norm2(AP)/norm2(Src)) <<std::endl;
+
+      std::cout << GridLogMessage << "Time Breakdown "<<std::endl;
+      std::cout << GridLogMessage << "\tElapsed    " << SolverTimer.Elapsed()     <<std::endl;
+      std::cout << GridLogMessage << "\tMatrix     " << MatrixTimer.Elapsed()     <<std::endl;
+      std::cout << GridLogMessage << "\tInnerProd  " << sliceInnerTimer.Elapsed() <<std::endl;
+      std::cout << GridLogMessage << "\tMaddMatrix " << sliceMaddTimer.Elapsed()  <<std::endl;
+	    
+      IterationsToComplete = k;
+      return;
+    }
+
+  }
+  std::cout << GridLogMessage << "BlockConjugateGradient did NOT converge" << std::endl;
+
+  if (ErrorOnNoConverge) assert(0);
+  IterationsToComplete = k;
+}
+};
+
+
+//////////////////////////////////////////////////////////////////////////
+// multiRHS conjugate gradient. Dimension zero should be the block direction
+//////////////////////////////////////////////////////////////////////////
+template <class Field>
+class MultiRHSConjugateGradient : public OperatorFunction<Field> {
+ public:
+
+  typedef typename Field::scalar_type scomplex;
+
+  const int blockDim = 0;
+
+  int Nblock;
+  bool ErrorOnNoConverge;  // throw an assert when the CG fails to converge.
+                           // Defaults true.
+  RealD Tolerance;
+  Integer MaxIterations;
+  Integer IterationsToComplete; //Number of iterations the CG took to finish. Filled in upon completion
+  
+   MultiRHSConjugateGradient(RealD tol, Integer maxit, bool err_on_no_conv = true)
+    : Tolerance(tol),
+    MaxIterations(maxit),
+    ErrorOnNoConverge(err_on_no_conv){};
+
+void operator()(LinearOperatorBase<Field> &Linop, const Field &Src, Field &Psi) 
+{
+  int Orthog = 0; // First dimension is block dim
+  Nblock = Src._grid->_fdimensions[Orthog];
+
+  std::cout<<GridLogMessage<<"MultiRHS Conjugate Gradient : Orthog "<<Orthog<<" Nblock "<<Nblock<<std::endl;
+
+  Psi.checkerboard = Src.checkerboard;
+  conformable(Psi, Src);
+
+  Field P(Src);
+  Field AP(Src);
+  Field R(Src);
+  
+  std::vector<ComplexD> v_pAp(Nblock);
+  std::vector<RealD> v_rr (Nblock);
+  std::vector<RealD> v_rr_inv(Nblock);
+  std::vector<RealD> v_alpha(Nblock);
+  std::vector<RealD> v_beta(Nblock);
+
+  // Initial residual computation & set up
+  std::vector<RealD> residuals(Nblock);
+  std::vector<RealD> ssq(Nblock);
+
+  sliceNorm(ssq,Src,Orthog);
+  RealD sssum=0;
+  for(int b=0;b<Nblock;b++) sssum+=ssq[b];
+
+  sliceNorm(residuals,Src,Orthog);
+  for(int b=0;b<Nblock;b++){ assert(std::isnan(residuals[b])==0); }
+
+  sliceNorm(residuals,Psi,Orthog);
+  for(int b=0;b<Nblock;b++){ assert(std::isnan(residuals[b])==0); }
+
+  // Initial search dir is guess
+  Linop.HermOp(Psi, AP);
+
+  R = Src - AP;  
+  P = R;
+  sliceNorm(v_rr,R,Orthog);
+
+  GridStopWatch sliceInnerTimer;
+  GridStopWatch sliceMaddTimer;
+  GridStopWatch sliceNormTimer;
+  GridStopWatch MatrixTimer;
+  GridStopWatch SolverTimer;
+
+  SolverTimer.Start();
+  int k;
+  for (k = 1; k <= MaxIterations; k++) {
+
+    RealD rrsum=0;
+    for(int b=0;b<Nblock;b++) rrsum+=real(v_rr[b]);
+
+    std::cout << GridLogIterative << "\titeration "<<k<<" rr_sum "<<rrsum<<" ssq_sum "<< sssum
+	      <<" / "<<std::sqrt(rrsum/sssum) <<std::endl;
+
+    MatrixTimer.Start();
+    Linop.HermOp(P, AP);
+    MatrixTimer.Stop();
+
+    // Alpha
+    //    sliceInnerProductVectorTest(v_pAp_test,P,AP,Orthog);
+    sliceInnerTimer.Start();
+    sliceInnerProductVector(v_pAp,P,AP,Orthog);
+    sliceInnerTimer.Stop();
+    for(int b=0;b<Nblock;b++){
+      //      std::cout << " "<< v_pAp[b]<<" "<< v_pAp_test[b]<<std::endl;
+      v_alpha[b] = v_rr[b]/real(v_pAp[b]);
+    }
+
+    // Psi, R update
+    sliceMaddTimer.Start();
+    sliceMaddVector(Psi,v_alpha, P,Psi,Orthog);     // add alpha *  P to psi
+    sliceMaddVector(R  ,v_alpha,AP,  R,Orthog,-1.0);// sub alpha * AP to resid
+    sliceMaddTimer.Stop();
+
+    // Beta
+    for(int b=0;b<Nblock;b++){
+      v_rr_inv[b] = 1.0/v_rr[b];
+    }
+    sliceNormTimer.Start();
+    sliceNorm(v_rr,R,Orthog);
+    sliceNormTimer.Stop();
+    for(int b=0;b<Nblock;b++){
+      v_beta[b] = v_rr_inv[b] *v_rr[b];
+    }
+
+    // Search update
+    sliceMaddTimer.Start();
+    sliceMaddVector(P,v_beta,P,R,Orthog);
+    sliceMaddTimer.Stop();
+
+    /*********************
+     * convergence monitor
+     *********************
+     */
+    RealD max_resid=0;
+    for(int b=0;b<Nblock;b++){
+      RealD rr = v_rr[b]/ssq[b];
+      if ( rr > max_resid ) max_resid = rr;
+    }
+    
+    if ( max_resid < Tolerance*Tolerance ) { 
+
+      SolverTimer.Stop();
+
+      std::cout << GridLogMessage<<"MultiRHS solver converged in " <<k<<" iterations"<<std::endl;
+      for(int b=0;b<Nblock;b++){
+	std::cout << GridLogMessage<< "\t\tBlock "<<b<<" resid "<< std::sqrt(v_rr[b]/ssq[b])<<std::endl;
+      }
+      std::cout << GridLogMessage<<"\tMax residual is "<<std::sqrt(max_resid)<<std::endl;
+
+      Linop.HermOp(Psi, AP);
+      AP = AP-Src;
+      std::cout <<GridLogMessage << "\tTrue residual is " << std::sqrt(norm2(AP)/norm2(Src)) <<std::endl;
+
+      std::cout << GridLogMessage << "Time Breakdown "<<std::endl;
+      std::cout << GridLogMessage << "\tElapsed    " << SolverTimer.Elapsed()     <<std::endl;
+      std::cout << GridLogMessage << "\tMatrix     " << MatrixTimer.Elapsed()     <<std::endl;
+      std::cout << GridLogMessage << "\tInnerProd  " << sliceInnerTimer.Elapsed() <<std::endl;
+      std::cout << GridLogMessage << "\tNorm       " << sliceNormTimer.Elapsed() <<std::endl;
+      std::cout << GridLogMessage << "\tMaddMatrix " << sliceMaddTimer.Elapsed()  <<std::endl;
+
+
+      IterationsToComplete = k;
+      return;
+    }
+
+  }
+  std::cout << GridLogMessage << "MultiRHSConjugateGradient did NOT converge" << std::endl;
+
+  if (ErrorOnNoConverge) assert(0);
+  IterationsToComplete = k;
+}
+};
+
+
+
+}
+#endif

lib/algorithms/iterative/ConjugateGradient.h

@@ -9,7 +9,6 @@ Copyright (C) 2015
 Author: Azusa Yamaguchi <ayamaguc@staffmail.ed.ac.uk>
 Author: Peter Boyle <paboyle@ph.ed.ac.uk>
 Author: paboyle <paboyle@ph.ed.ac.uk>
-Author: Guido Cossu <guido.cossu@ed.ac.uk>
 
 This program is free software; you can redistribute it and/or modify
 it under the terms of the GNU General Public License as published by
@@ -34,21 +33,6 @@ directory
 
 namespace Grid {
 
-struct CG_state {
-  bool do_repro;
-  std::vector<RealD> residuals;
-
-  CG_state() {reset();}
-
-  void reset(){
-    do_repro = false;
-    residuals.clear();
-  }
-};
-
-
-enum CGexec_mode{ Default, ReproducibilityTest };
-
 /////////////////////////////////////////////////////////////
 // Base classes for iterative processes based on operators
 // single input vec, single output vec.
@@ -61,30 +45,12 @@ class ConjugateGradient : public OperatorFunction<Field> {
                            // Defaults true.
   RealD Tolerance;
   Integer MaxIterations;
+  Integer IterationsToComplete; //Number of iterations the CG took to finish. Filled in upon completion
   
-  // Reproducibility controls
-  bool ReproTest;
-  CG_state CGState; //to check reproducibility by repeating the CG
-  ReproducibilityState<typename Field::vector_object> ReprTest; // for the inner proucts
-
-  // Constructor
-  ConjugateGradient(RealD tol, Integer maxit, CGexec_mode Mode = Default)
-    : Tolerance(tol),MaxIterations(maxit){
-    switch(Mode)
-    {
-      case Default  : 
-      ErrorOnNoConverge = true;
-      ReproTest = false;
-      case ReproducibilityTest :
-      ErrorOnNoConverge = false;
-      ReproTest = true; 
-    }
-  };
-
-  void set_reproducibility_interval(unsigned int interval){
-    ReprTest.interval = interval;
-  }
-
+  ConjugateGradient(RealD tol, Integer maxit, bool err_on_no_conv = true)
+      : Tolerance(tol),
+        MaxIterations(maxit),
+        ErrorOnNoConverge(err_on_no_conv){};
 
   void operator()(LinearOperatorBase<Field> &Linop, const Field &src,
                   Field &psi) {
@@ -96,37 +62,28 @@ class ConjugateGradient : public OperatorFunction<Field> {
     Field p(src);
     Field mmp(src);
     Field r(src);
-    Field psi_start(psi);// save for the repro test
-
-    if (CGState.do_repro && ReproTest)
-        std::cout << GridLogMessage << "Starting reproducibility test, full check every "
-                  << ReprTest.interval << " calls" << std::endl;
-
-    if(!ReprTest.do_check)
-        ReprTest.reset();
-    ReprTest.enable_reprocheck=ReproTest;
-
-
 
     // Initial residual computation & set up
-    RealD guess = norm2(psi, ReprTest);
+    RealD guess = norm2(psi);
     assert(std::isnan(guess) == 0);
 
-    Linop.HermOpAndNorm(psi, mmp, d, b);// eventually split this for the norm check
+    
+    Linop.HermOpAndNorm(psi, mmp, d, b);
+    
 
     r = src - mmp;
     p = r;
 
-    a = norm2(p, ReprTest);
+    a = norm2(p);
     cp = a;
-    ssq = norm2(src, ReprTest);
+    ssq = norm2(src);
 
-    std::cout << GridLogIterative << "ConjugateGradient: guess " << guess << std::endl;
-    std::cout << GridLogIterative << "ConjugateGradient:   src " << ssq << std::endl;
-    std::cout << GridLogIterative << "ConjugateGradient:    mp " << d << std::endl;
-    std::cout << GridLogIterative << "ConjugateGradient:   mmp " << b << std::endl;
-    std::cout << GridLogIterative << "ConjugateGradient:  cp,r " << cp << std::endl;
-    std::cout << GridLogIterative << "ConjugateGradient:     p " << a << std::endl;
+    std::cout << GridLogIterative << std::setprecision(4) << "ConjugateGradient: guess " << guess << std::endl;
+    std::cout << GridLogIterative << std::setprecision(4) << "ConjugateGradient:   src " << ssq << std::endl;
+    std::cout << GridLogIterative << std::setprecision(4) << "ConjugateGradient:    mp " << d << std::endl;
+    std::cout << GridLogIterative << std::setprecision(4) << "ConjugateGradient:   mmp " << b << std::endl;
+    std::cout << GridLogIterative << std::setprecision(4) << "ConjugateGradient:  cp,r " << cp << std::endl;
+    std::cout << GridLogIterative << std::setprecision(4) << "ConjugateGradient:     p " << a << std::endl;
 
     RealD rsq = Tolerance * Tolerance * ssq;
 
@@ -136,8 +93,7 @@ class ConjugateGradient : public OperatorFunction<Field> {
     }
 
     std::cout << GridLogIterative << std::setprecision(4)
-              << "ConjugateGradient: k=0 residual " << cp << " target " << rsq
-              << std::endl;
+              << "ConjugateGradient: k=0 residual " << cp << " target " << rsq << std::endl;
 
     GridStopWatch LinalgTimer;
     GridStopWatch MatrixTimer;
@@ -146,10 +102,10 @@ class ConjugateGradient : public OperatorFunction<Field> {
     SolverTimer.Start();
     int k;
     for (k = 1; k <= MaxIterations; k++) {
-      c = cp;// old residual
+      c = cp;
 
       MatrixTimer.Start();
-      Linop.HermOpAndNorm(p, mmp, d, qq);// mmp = Ap, d=pAp
+      Linop.HermOpAndNorm(p, mmp, d, qq);
       MatrixTimer.Stop();
 
       LinalgTimer.Start();
@@ -157,31 +113,14 @@ class ConjugateGradient : public OperatorFunction<Field> {
       //  ComplexD dck  = innerProduct(p,mmp);
 
       a = c / d;
-      b_pred = a * (a * qq - d) / c;// a check
+      b_pred = a * (a * qq - d) / c;
 
-
-      axpy(r, -a, mmp, r);// new residual r = r_old - a * Ap
-      cp = norm2(r, ReprTest); // bookkeeping this norm
-      if (ReproTest && !CGState.do_repro) {
-        CGState.residuals.push_back(cp);  // save residuals state
-                std::cout << GridLogIterative << "ReproTest: Saving state" << std::endl;
-        }
-      if (ReproTest && CGState.do_repro){
-        // check that the residual agrees with the previous run
-        std::cout << GridLogIterative << "ReproTest: Checking state k=" << k << std::endl;
-        if (cp != CGState.residuals[k-1]){
-                std::cout << GridLogMessage << "Failing reproducibility test";
-                std::cout << GridLogMessage << " at k=" << k << std::endl;
-                std::cout << GridLogMessage << "saved residual = " << CGState.residuals[k-1] 
-                        << " cp = " << cp << std::endl;
-                exit(1);  // exit after the first failure
-        }
-      }
+      cp = axpy_norm(r, -a, mmp, r);
       b = cp / c;
 
       // Fuse these loops ; should be really easy
-      psi = a * p + psi; // update solution
-      p = p * b + r;  // update search direction
+      psi = a * p + psi;
+      p = p * b + r;
 
       LinalgTimer.Stop();
       std::cout << GridLogIterative << "ConjugateGradient: Iteration " << k
@@ -199,41 +138,27 @@ class ConjugateGradient : public OperatorFunction<Field> {
         RealD resnorm = sqrt(norm2(p));
         RealD true_residual = resnorm / srcnorm;
 
-        std::cout << GridLogMessage
-                  << "ConjugateGradient: Converged on iteration " << k << std::endl;
-        std::cout << GridLogMessage << "Computed residual " << sqrt(cp / ssq)
-                  << " true residual " << true_residual << " target "
-                  << Tolerance << std::endl;
-        std::cout << GridLogMessage << "Time elapsed: Iterations "
-                  << SolverTimer.Elapsed() << " Matrix  "
-                  << MatrixTimer.Elapsed() << " Linalg "
-                  << LinalgTimer.Elapsed();
-        std::cout << std::endl;
+        std::cout << GridLogMessage << "ConjugateGradient Converged on iteration " << k << std::endl;
+        std::cout << GridLogMessage << "\tComputed residual " << sqrt(cp / ssq)<<std::endl;
+	std::cout << GridLogMessage << "\tTrue residual " << true_residual<<std::endl;
+	std::cout << GridLogMessage << "\tTarget " << Tolerance << std::endl;
+
+        std::cout << GridLogMessage << "Time breakdown "<<std::endl;
+	std::cout << GridLogMessage << "\tElapsed    " << SolverTimer.Elapsed() <<std::endl;
+	std::cout << GridLogMessage << "\tMatrix     " << MatrixTimer.Elapsed() <<std::endl;
+	std::cout << GridLogMessage << "\tLinalg     " << LinalgTimer.Elapsed() <<std::endl;
 
         if (ErrorOnNoConverge) assert(true_residual / Tolerance < 10000.0);
 
-        if (! (CGState.do_repro && ReproTest)){
-                CGState.do_repro = true;
-                ReprTest.do_check = true;
-                ReprTest.reset_counter();
-                this->operator()(Linop, src, psi_start);// run the repro test
-                if (ReprTest.success)
-                	std::cout << GridLogMessage << "Reproducibility test passed" << std::endl;
-                else{
-                	std::cout << GridLogMessage << "Reproducibility test failed" << std::endl;
-                	exit(1);
-                }
-        }
+	IterationsToComplete = k;	
 
-        // Clear state
-        CGState.reset();
-        ReprTest.reset();
         return;
       }
     }
     std::cout << GridLogMessage << "ConjugateGradient did NOT converge"
               << std::endl;
     if (ErrorOnNoConverge) assert(0);
+    IterationsToComplete = k;
   }
 };
 }

lib/algorithms/iterative/ConjugateGradientMixedPrec.h

@@ -35,6 +35,7 @@ namespace Grid {
   class MixedPrecisionConjugateGradient : public LinearFunction<FieldD> {
   public:                                                
     RealD   Tolerance;
+    RealD   InnerTolerance; //Initial tolerance for inner CG. Defaults to Tolerance but can be changed
     Integer MaxInnerIterations;
     Integer MaxOuterIterations;
     GridBase* SinglePrecGrid; //Grid for single-precision fields
@@ -42,12 +43,16 @@ namespace Grid {
     LinearOperatorBase<FieldF> &Linop_f;
     LinearOperatorBase<FieldD> &Linop_d;
 
+    Integer TotalInnerIterations; //Number of inner CG iterations
+    Integer TotalOuterIterations; //Number of restarts
+    Integer TotalFinalStepIterations; //Number of CG iterations in final patch-up step
+
     //Option to speed up *inner single precision* solves using a LinearFunction that produces a guess
     LinearFunction<FieldF> *guesser;
     
     MixedPrecisionConjugateGradient(RealD tol, Integer maxinnerit, Integer maxouterit, GridBase* _sp_grid, LinearOperatorBase<FieldF> &_Linop_f, LinearOperatorBase<FieldD> &_Linop_d) :
       Linop_f(_Linop_f), Linop_d(_Linop_d),
-      Tolerance(tol), MaxInnerIterations(maxinnerit), MaxOuterIterations(maxouterit), SinglePrecGrid(_sp_grid),
+      Tolerance(tol), InnerTolerance(tol), MaxInnerIterations(maxinnerit), MaxOuterIterations(maxouterit), SinglePrecGrid(_sp_grid),
       OuterLoopNormMult(100.), guesser(NULL){ };
 
     void useGuesser(LinearFunction<FieldF> &g){
@@ -55,6 +60,8 @@ namespace Grid {
     }
   
     void operator() (const FieldD &src_d_in, FieldD &sol_d){
+      TotalInnerIterations = 0;
+	
       GridStopWatch TotalTimer;
       TotalTimer.Start();
     
@@ -74,7 +81,7 @@ namespace Grid {
       FieldD src_d(DoublePrecGrid);
       src_d = src_d_in; //source for next inner iteration, computed from residual during operation
     
-      RealD inner_tol = Tolerance;
+      RealD inner_tol = InnerTolerance;
     
       FieldF src_f(SinglePrecGrid);
       src_f.checkerboard = cb;
@@ -89,7 +96,9 @@ namespace Grid {
 
       GridStopWatch PrecChangeTimer;
     
-      for(Integer outer_iter = 0; outer_iter < MaxOuterIterations; outer_iter++){
+      Integer &outer_iter = TotalOuterIterations; //so it will be equal to the final iteration count
+      
+      for(outer_iter = 0; outer_iter < MaxOuterIterations; outer_iter++){
 	//Compute double precision rsd and also new RHS vector.
 	Linop_d.HermOp(sol_d, tmp_d);
 	RealD norm = axpy_norm(src_d, -1., tmp_d, src_d_in); //src_d is residual vector
@@ -117,6 +126,7 @@ namespace Grid {
 	InnerCGtimer.Start();
 	CG_f(Linop_f, src_f, sol_f);
 	InnerCGtimer.Stop();
+	TotalInnerIterations += CG_f.IterationsToComplete;
       
 	//Convert sol back to double and add to double prec solution
 	PrecChangeTimer.Start();
@@ -131,9 +141,11 @@ namespace Grid {
     
       ConjugateGradient<FieldD> CG_d(Tolerance, MaxInnerIterations);
       CG_d(Linop_d, src_d_in, sol_d);
+      TotalFinalStepIterations = CG_d.IterationsToComplete;
 
       TotalTimer.Stop();
-      std::cout<<GridLogMessage<<"MixedPrecisionConjugateGradient: Total " << TotalTimer.Elapsed() << " Precision change " << PrecChangeTimer.Elapsed() << " Inner CG total " << InnerCGtimer.Elapsed() << std::endl;
+      std::cout<<GridLogMessage<<"MixedPrecisionConjugateGradient: Inner CG iterations " << TotalInnerIterations << " Restarts " << TotalOuterIterations << " Final CG iterations " << TotalFinalStepIterations << std::endl;
+      std::cout<<GridLogMessage<<"MixedPrecisionConjugateGradient: Total time " << TotalTimer.Elapsed() << " Precision change " << PrecChangeTimer.Elapsed() << " Inner CG total " << InnerCGtimer.Elapsed() << std::endl;
     }
   };
 

lib/algorithms/iterative/ImplicitlyRestartedLanczos.h

@@ -30,6 +30,7 @@ Author: paboyle <paboyle@ph.ed.ac.uk>
 #define GRID_IRL_H
 
 #include <string.h> //memset
+
 #ifdef USE_LAPACK
 void LAPACK_dstegr(char *jobz, char *range, int *n, double *d, double *e,
                    double *vl, double *vu, int *il, int *iu, double *abstol,
@@ -37,8 +38,9 @@ void LAPACK_dstegr(char *jobz, char *range, int *n, double *d, double *e,
                    double *work, int *lwork, int *iwork, int *liwork,
                    int *info);
 #endif
-#include "DenseMatrix.h"
-#include "EigenSort.h"
+
+#include <Grid/algorithms/densematrix/DenseMatrix.h>
+#include <Grid/algorithms/iterative/EigenSort.h>
 
 namespace Grid {
 
@@ -59,7 +61,7 @@ public:
 
     int Nstop;   // Number of evecs checked for convergence
     int Nk;      // Number of converged sought
-    int Np;      // Np -- Number of spare vecs in krylov space
+    int Np;      // Np -- Number of spare vecs in kryloc space
     int Nm;      // Nm -- total number of vectors
 
     RealD eresid;
@@ -1088,8 +1090,6 @@ static void Lock(DenseMatrix<T> &H, 	// Hess mtx
 		 int dfg,
 		 bool herm)
 {	
-
-
   //ForceTridiagonal(H);
 
   int M = H.dim;
@@ -1122,7 +1122,6 @@ static void Lock(DenseMatrix<T> &H, 	// Hess mtx
   AH = Hermitian(QQ)*AH;
   AH = AH*QQ;
 
-
   for(int i=con;i<M;i++){
     for(int j=con;j<M;j++){
       Q[i][j]=QQ[i-con][j-con];

lib/algorithms/iterative/Matrix.h

@@ -1,453 +0,0 @@
-    /*************************************************************************************
-
-    Grid physics library, www.github.com/paboyle/Grid 
-
-    Source file: ./lib/algorithms/iterative/Matrix.h
-
-    Copyright (C) 2015
-
-Author: Peter Boyle <paboyle@ph.ed.ac.uk>
-
-    This program is free software; you can redistribute it and/or modify
-    it under the terms of the GNU General Public License as published by
-    the Free Software Foundation; either version 2 of the License, or
-    (at your option) any later version.
-
-    This program is distributed in the hope that it will be useful,
-    but WITHOUT ANY WARRANTY; without even the implied warranty of
-    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-    GNU General Public License for more details.
-
-    You should have received a copy of the GNU General Public License along
-    with this program; if not, write to the Free Software Foundation, Inc.,
-    51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
-
-    See the full license in the file "LICENSE" in the top level distribution directory
-    *************************************************************************************/
-    /*  END LEGAL */
-#ifndef MATRIX_H
-#define MATRIX_H
-
-#include <cstdlib>
-#include <string>
-#include <cmath>
-#include <vector>
-#include <iostream>
-#include <iomanip>
-#include <complex>
-#include <typeinfo>
-#include <Grid.h>
-
-
-/** Sign function **/
-template <class T> T sign(T p){return ( p/abs(p) );}
-
-/////////////////////////////////////////////////////////////////////////////////////////////////////////
-///////////////////// Hijack STL containers for our wicked means /////////////////////////////////////////
-/////////////////////////////////////////////////////////////////////////////////////////////////////////
-template<class T> using Vector = Vector<T>;
-template<class T> using Matrix = Vector<Vector<T> >;
-
-template<class T> void Resize(Vector<T > & vec, int N) { vec.resize(N); }
-
-template<class T> void Resize(Matrix<T > & mat, int N, int M) { 
-  mat.resize(N);
-  for(int i=0;i<N;i++){
-    mat[i].resize(M);
-  }
-}
-template<class T> void Size(Vector<T> & vec, int &N) 
-{ 
-  N= vec.size();
-}
-template<class T> void Size(Matrix<T> & mat, int &N,int &M) 
-{ 
-  N= mat.size();
-  M= mat[0].size();
-}
-template<class T> void SizeSquare(Matrix<T> & mat, int &N) 
-{ 
-  int M; Size(mat,N,M);
-  assert(N==M);
-}
-template<class T> void SizeSame(Matrix<T> & mat1,Matrix<T> &mat2, int &N1,int &M1) 
-{ 
-  int N2,M2;
-  Size(mat1,N1,M1);
-  Size(mat2,N2,M2);
-  assert(N1==N2);
-  assert(M1==M2);
-}
-
-//*****************************************
-//*	(Complex) Vector operations	*
-//*****************************************
-
-/**Conj of a Vector **/
-template <class T> Vector<T> conj(Vector<T> p){
-	Vector<T> q(p.size());
-	for(int i=0;i<p.size();i++){q[i] = conj(p[i]);}
-	return q;
-}
-
-/** Norm of a Vector**/
-template <class T> T norm(Vector<T> p){
-	T sum = 0;
-	for(int i=0;i<p.size();i++){sum = sum + p[i]*conj(p[i]);}
-	return abs(sqrt(sum));
-}
-
-/** Norm squared of a Vector **/
-template <class T> T norm2(Vector<T> p){
-	T sum = 0;
-	for(int i=0;i<p.size();i++){sum = sum + p[i]*conj(p[i]);}
-	return abs((sum));
-}
-
-/** Sum elements of a Vector **/
-template <class T> T trace(Vector<T> p){
-	T sum = 0;
-	for(int i=0;i<p.size();i++){sum = sum + p[i];}
-	return sum;
-}
-
-/** Fill a Vector with constant c **/
-template <class T> void Fill(Vector<T> &p, T c){
-	for(int i=0;i<p.size();i++){p[i] = c;}
-}
-/** Normalize a Vector **/
-template <class T> void normalize(Vector<T> &p){
-	T m = norm(p);
-	if( abs(m) > 0.0) for(int i=0;i<p.size();i++){p[i] /= m;}
-}
-/** Vector by scalar **/
-template <class T, class U> Vector<T> times(Vector<T> p, U s){
-	for(int i=0;i<p.size();i++){p[i] *= s;}
-	return p;
-}
-template <class T, class U> Vector<T> times(U s, Vector<T> p){
-	for(int i=0;i<p.size();i++){p[i] *= s;}
-	return p;
-}
-/** inner product of a and b = conj(a) . b **/
-template <class T> T inner(Vector<T> a, Vector<T> b){
-	T m = 0.;
-	for(int i=0;i<a.size();i++){m = m + conj(a[i])*b[i];}
-	return m;
-}
-/** sum of a and b = a + b **/
-template <class T> Vector<T> add(Vector<T> a, Vector<T> b){
-	Vector<T> m(a.size());
-	for(int i=0;i<a.size();i++){m[i] = a[i] + b[i];}
-	return m;
-}
-/** sum of a and b = a - b **/
-template <class T> Vector<T> sub(Vector<T> a, Vector<T> b){
-	Vector<T> m(a.size());
-	for(int i=0;i<a.size();i++){m[i] = a[i] - b[i];}
-	return m;
-}
-
-/** 
- *********************************
- *	Matrices	         *
- *********************************
- **/
-
-template<class T> void Fill(Matrix<T> & mat, T&val) { 
-  int N,M;
-  Size(mat,N,M);
-  for(int i=0;i<N;i++){
-  for(int j=0;j<M;j++){
-    mat[i][j] = val;
-  }}
-}
-
-/** Transpose of a matrix **/
-Matrix<T> Transpose(Matrix<T> & mat){
-  int N,M;
-  Size(mat,N,M);
-  Matrix C; Resize(C,M,N);
-  for(int i=0;i<M;i++){
-  for(int j=0;j<N;j++){
-    C[i][j] = mat[j][i];
-  }} 
-  return C;
-}
-/** Set Matrix to unit matrix **/
-template<class T> void Unity(Matrix<T> &mat){
-  int N;  SizeSquare(mat,N);
-  for(int i=0;i<N;i++){
-    for(int j=0;j<N;j++){
-      if ( i==j ) A[i][j] = 1;
-      else        A[i][j] = 0;
-    } 
-  } 
-}
-/** Add C * I to matrix **/
-template<class T>
-void PlusUnit(Matrix<T> & A,T c){
-  int dim;  SizeSquare(A,dim);
-  for(int i=0;i<dim;i++){A[i][i] = A[i][i] + c;} 
-}
-
-/** return the Hermitian conjugate of matrix **/
-Matrix<T> HermitianConj(Matrix<T> &mat){
-
-  int dim; SizeSquare(mat,dim);
-
-  Matrix<T> C; Resize(C,dim,dim);
-
-  for(int i=0;i<dim;i++){
-    for(int j=0;j<dim;j++){
-      C[i][j] = conj(mat[j][i]);
-    } 
-  } 
-  return C;
-}
-
-/** return diagonal entries as a Vector **/
-Vector<T> diag(Matrix<T> &A)
-{
-  int dim; SizeSquare(A,dim);
-  Vector<T> d; Resize(d,dim);
-
-  for(int i=0;i<dim;i++){
-    d[i] = A[i][i];
-  }
-  return d;
-}
-
-/** Left multiply by a Vector **/
-Vector<T> operator *(Vector<T> &B,Matrix<T> &A)
-{
-  int K,M,N; 
-  Size(B,K);
-  Size(A,M,N);
-  assert(K==M);
-  
-  Vector<T> C; Resize(C,N);
-
-  for(int j=0;j<N;j++){
-    T sum = 0.0;
-    for(int i=0;i<M;i++){
-      sum += B[i] * A[i][j];
-    }
-    C[j] =  sum;
-  }
-  return C; 
-}
-
-/** return 1/diagonal entries as a Vector **/
-Vector<T> inv_diag(Matrix<T> & A){
-  int dim; SizeSquare(A,dim);
-  Vector<T> d; Resize(d,dim);
-  for(int i=0;i<dim;i++){
-    d[i] = 1.0/A[i][i];
-  }
-  return d;
-}
-/** Matrix Addition **/
-inline Matrix<T> operator + (Matrix<T> &A,Matrix<T> &B)
-{
-  int N,M  ; SizeSame(A,B,N,M);
-  Matrix C; Resize(C,N,M);
-  for(int i=0;i<N;i++){
-    for(int j=0;j<M;j++){
-      C[i][j] = A[i][j] +  B[i][j];
-    } 
-  } 
-  return C;
-} 
-/** Matrix Subtraction **/
-inline Matrix<T> operator- (Matrix<T> & A,Matrix<T> &B){
-  int N,M  ; SizeSame(A,B,N,M);
-  Matrix C; Resize(C,N,M);
-  for(int i=0;i<N;i++){
-  for(int j=0;j<M;j++){
-    C[i][j] = A[i][j] -  B[i][j];
-  }}
-  return C;
-} 
-
-/** Matrix scalar multiplication **/
-inline Matrix<T> operator* (Matrix<T> & A,T c){
-  int N,M; Size(A,N,M);
-  Matrix C; Resize(C,N,M);
-  for(int i=0;i<N;i++){
-  for(int j=0;j<M;j++){
-    C[i][j] = A[i][j]*c;
-  }} 
-  return C;
-} 
-/** Matrix Matrix multiplication **/
-inline Matrix<T> operator* (Matrix<T> &A,Matrix<T> &B){
-  int K,L,N,M;
-  Size(A,K,L);
-  Size(B,N,M); assert(L==N);
-  Matrix C; Resize(C,K,M);
-
-  for(int i=0;i<K;i++){
-    for(int j=0;j<M;j++){
-      T sum = 0.0;
-      for(int k=0;k<N;k++) sum += A[i][k]*B[k][j];
-      C[i][j] =sum;
-    }
-  }
-  return C; 
-} 
-/** Matrix Vector multiplication **/
-inline Vector<T> operator* (Matrix<T> &A,Vector<T> &B){
-  int M,N,K;
-  Size(A,N,M);
-  Size(B,K); assert(K==M);
-  Vector<T> C; Resize(C,N);
-  for(int i=0;i<N;i++){
-    T sum = 0.0;
-    for(int j=0;j<M;j++) sum += A[i][j]*B[j];
-    C[i] =  sum;
-  }
-  return C; 
-} 
-
-/** Some version of Matrix norm **/
-/*
-inline T Norm(){ // this is not a usual L2 norm
-    T norm = 0;
-    for(int i=0;i<dim;i++){
-      for(int j=0;j<dim;j++){
-	norm += abs(A[i][j]);
-    }}
-    return norm;
-  }
-*/
-
-/** Some version of Matrix norm **/
-template<class T> T LargestDiag(Matrix<T> &A)
-{
-  int dim ; SizeSquare(A,dim); 
-
-  T ld = abs(A[0][0]);
-  for(int i=1;i<dim;i++){
-    T cf = abs(A[i][i]);
-    if(abs(cf) > abs(ld) ){ld = cf;}
-  }
-  return ld;
-}
-
-/** Look for entries on the leading subdiagonal that are smaller than 'small' **/
-template <class T,class U> int Chop_subdiag(Matrix<T> &A,T norm, int offset, U small)
-{
-  int dim; SizeSquare(A,dim);
-  for(int l = dim - 1 - offset; l >= 1; l--) {             		
-    if((U)abs(A[l][l - 1]) < (U)small) {
-      A[l][l-1]=(U)0.0;
-      return l;
-    }
-  }
-  return 0;
-}
-
-/** Look for entries on the leading subdiagonal that are smaller than 'small' **/
-template <class T,class U> int Chop_symm_subdiag(Matrix<T> & A,T norm, int offset, U small) 
-{
-  int dim; SizeSquare(A,dim);
-  for(int l = dim - 1 - offset; l >= 1; l--) {
-    if((U)abs(A[l][l - 1]) < (U)small) {
-      A[l][l - 1] = (U)0.0;
-      A[l - 1][l] = (U)0.0;
-      return l;
-    }
-  }
-  return 0;
-}
-/**Assign a submatrix to a larger one**/
-template<class T>
-void AssignSubMtx(Matrix<T> & A,int row_st, int row_end, int col_st, int col_end, Matrix<T> &S)
-{
-  for(int i = row_st; i<row_end; i++){
-    for(int j = col_st; j<col_end; j++){
-      A[i][j] = S[i - row_st][j - col_st];
-    }
-  }
-}
-
-/**Get a square submatrix**/
-template <class T>
-Matrix<T> GetSubMtx(Matrix<T> &A,int row_st, int row_end, int col_st, int col_end)
-{
-  Matrix<T> H; Resize(row_end - row_st,col_end-col_st);
-
-  for(int i = row_st; i<row_end; i++){
-  for(int j = col_st; j<col_end; j++){
-    H[i-row_st][j-col_st]=A[i][j];
-  }}
-  return H;
-}
-  
- /**Assign a submatrix to a larger one NB remember Vector Vectors are transposes of the matricies they represent**/
-template<class T>
-void AssignSubMtx(Matrix<T> & A,int row_st, int row_end, int col_st, int col_end, Matrix<T> &S)
-{
-  for(int i = row_st; i<row_end; i++){
-  for(int j = col_st; j<col_end; j++){
-    A[i][j] = S[i - row_st][j - col_st];
-  }}
-}
-  
-/** compute b_i A_ij b_j **/ // surprised no Conj
-template<class T> T proj(Matrix<T> A, Vector<T> B){
-  int dim; SizeSquare(A,dim);
-  int dimB; Size(B,dimB);
-  assert(dimB==dim);
-  T C = 0;
-  for(int i=0;i<dim;i++){
-    T sum = 0.0;
-    for(int j=0;j<dim;j++){
-      sum += A[i][j]*B[j];
-    }
-    C +=  B[i]*sum; // No conj?
-  }
-  return C; 
-}
-
-
-/*
- *************************************************************
- *
- * Matrix Vector products
- *
- *************************************************************
- */
-// Instead make a linop and call my CG;
-
-/// q -> q Q
-template <class T,class Fermion> void times(Vector<Fermion> &q, Matrix<T> &Q)
-{
-  int M; SizeSquare(Q,M);
-  int N; Size(q,N); 
-  assert(M==N);
-
-  times(q,Q,N);
-}
-
-/// q -> q Q
-template <class T> void times(multi1d<LatticeFermion> &q, Matrix<T> &Q, int N)
-{
-  GridBase *grid = q[0]._grid;
-  int M; SizeSquare(Q,M);
-  int K; Size(q,K); 
-  assert(N<M);
-  assert(N<K);
-  Vector<Fermion> S(N,grid );
-  for(int j=0;j<N;j++){
-    S[j] = zero;
-    for(int k=0;k<N;k++){
-      S[j] = S[j] +  q[k]* Q[k][j]; 
-    }
-  }
-  for(int j=0;j<q.size();j++){
-    q[j] = S[j];
-  }
-}
-#endif

lib/algorithms/iterative/TODO

@@ -1,15 +0,0 @@
-- ConjugateGradientMultiShift
-- MCR
-
-- Potentially Useful Boost libraries
-
-- MultiArray
-- Aligned allocator; memory pool
-- Remez -- Mike or Boost?
-- Multiprecision
-- quaternians
-- Tokenize
-- Serialization
-- Regex
-- Proto (ET)
-- uBlas

lib/algorithms/iterative/bisec.c

@@ -1,122 +0,0 @@
-#include <math.h>
-#include <stdlib.h>
-#include <vector>
-
-struct Bisection {
-
-static void get_eig2(int row_num,std::vector<RealD> &ALPHA,std::vector<RealD> &BETA, std::vector<RealD> & eig)
-{
-  int i,j;
-  std::vector<RealD> evec1(row_num+3);
-  std::vector<RealD> evec2(row_num+3);
-  RealD eps2;
-  ALPHA[1]=0.;
-  BETHA[1]=0.;
-  for(i=0;i<row_num-1;i++) {
-    ALPHA[i+1] = A[i*(row_num+1)].real();
-    BETHA[i+2] = A[i*(row_num+1)+1].real();
-  }
-  ALPHA[row_num] = A[(row_num-1)*(row_num+1)].real();
-  bisec(ALPHA,BETHA,row_num,1,row_num,1e-10,1e-10,evec1,eps2);
-  bisec(ALPHA,BETHA,row_num,1,row_num,1e-16,1e-16,evec2,eps2);
-
-  // Do we really need to sort here?
-  int begin=1;
-  int end = row_num;
-  int swapped=1;
-  while(swapped) {
-    swapped=0;
-    for(i=begin;i<end;i++){
-      if(mag(evec2[i])>mag(evec2[i+1]))	{
-	swap(evec2+i,evec2+i+1);
-	swapped=1;
-      }
-    }
-    end--;
-    for(i=end-1;i>=begin;i--){
-      if(mag(evec2[i])>mag(evec2[i+1]))	{
-	swap(evec2+i,evec2+i+1);
-	swapped=1;
-      }
-    }
-    begin++;
-  }
-
-  for(i=0;i<row_num;i++){
-    for(j=0;j<row_num;j++) {
-      if(i==j) H[i*row_num+j]=evec2[i+1];
-      else H[i*row_num+j]=0.;
-    }
-  }
-}
-
-static void bisec(std::vector<RealD> &c,   
-		  std::vector<RealD> &b,
-		  int n,
-		  int m1,
-		  int m2,
-		  RealD eps1,
-		  RealD relfeh,
-		  std::vector<RealD> &x,
-		  RealD &eps2)
-{
-  std::vector<RealD> wu(n+2);
-
-  RealD h,q,x1,xu,x0,xmin,xmax; 
-  int i,a,k;
-
-  b[1]=0.0;
-  xmin=c[n]-fabs(b[n]);
-  xmax=c[n]+fabs(b[n]);
-  for(i=1;i<n;i++){
-    h=fabs(b[i])+fabs(b[i+1]);
-    if(c[i]+h>xmax) xmax= c[i]+h;
-    if(c[i]-h<xmin) xmin= c[i]-h;
-  }
-  xmax *=2.;
-
-  eps2=relfeh*((xmin+xmax)>0.0 ? xmax : -xmin);
-  if(eps1<=0.0) eps1=eps2;
-  eps2=0.5*eps1+7.0*(eps2);
-  x0=xmax;
-  for(i=m1;i<=m2;i++){
-    x[i]=xmax;
-    wu[i]=xmin;
-  }
-
-  for(k=m2;k>=m1;k--){
-    xu=xmin;
-    i=k;
-    do{
-      if(xu<wu[i]){
-	xu=wu[i];
-	i=m1-1;
-      }
-      i--;
-    }while(i>=m1);
-    if(x0>x[k]) x0=x[k];
-    while((x0-xu)>2*relfeh*(fabs(xu)+fabs(x0))+eps1){
-      x1=(xu+x0)/2;
-
-      a=0;
-      q=1.0;
-      for(i=1;i<=n;i++){
-	q=c[i]-x1-((q!=0.0)? b[i]*b[i]/q:fabs(b[i])/relfeh);
-	if(q<0) a++;
-      }
-      //			printf("x1=%e a=%d\n",x1,a);
-      if(a<k){
-	if(a<m1){
-	  xu=x1;
-	  wu[m1]=x1;
-	}else {
-	  xu=x1;
-	  wu[a+1]=x1;
-	  if(x[a]>x1) x[a]=x1;
-	}
-      }else x0=x1;
-    }
-    x[k]=(x0+xu)/2;
-  }
-}
-}

lib/algorithms/iterative/get_eig.c

@@ -1 +0,0 @@
-

lib/allocator/AlignedAllocator.cc

@@ -0,0 +1,66 @@
+
+
+
+#include <Grid/GridCore.h>
+
+namespace Grid {
+
+int PointerCache::victim;
+
+  PointerCache::PointerCacheEntry PointerCache::Entries[PointerCache::Ncache];
+
+void *PointerCache::Insert(void *ptr,size_t bytes) {
+
+  if (bytes < 4096 ) return NULL;
+
+#ifdef GRID_OMP
+  assert(omp_in_parallel()==0);
+#endif 
+
+  void * ret = NULL;
+  int v = -1;
+
+  for(int e=0;e<Ncache;e++) {
+    if ( Entries[e].valid==0 ) {
+      v=e; 
+      break;
+    }
+  }
+
+  if ( v==-1 ) {
+    v=victim;
+    victim = (victim+1)%Ncache;
+  }
+
+  if ( Entries[v].valid ) {
+    ret = Entries[v].address;
+    Entries[v].valid = 0;
+    Entries[v].address = NULL;
+    Entries[v].bytes = 0;
+  }
+
+  Entries[v].address=ptr;
+  Entries[v].bytes  =bytes;
+  Entries[v].valid  =1;
+
+  return ret;
+}
+
+void *PointerCache::Lookup(size_t bytes) {
+
+ if (bytes < 4096 ) return NULL;
+
+#ifdef _OPENMP
+  assert(omp_in_parallel()==0);
+#endif 
+
+  for(int e=0;e<Ncache;e++){
+    if ( Entries[e].valid && ( Entries[e].bytes == bytes ) ) {
+      Entries[e].valid = 0;
+      return Entries[e].address;
+    }
+  }
+  return NULL;
+}
+
+}

lib/allocator/AlignedAllocator.h

@@ -1,4 +1,4 @@
-    /*************************************************************************************
+/*************************************************************************************
 
     Grid physics library, www.github.com/paboyle/Grid 
 
@@ -42,9 +42,32 @@ Author: Peter Boyle <paboyle@ph.ed.ac.uk>
 
 namespace Grid {
 
+  class PointerCache {
+  private:
+
+    static const int Ncache=8;
+    static int victim;
+
+    typedef struct { 
+      void *address;
+      size_t bytes;
+      int valid;
+    } PointerCacheEntry;
+    
+    static PointerCacheEntry Entries[Ncache];
+
+  public:
+
+
+    static void *Insert(void *ptr,size_t bytes) ;
+    static void *Lookup(size_t bytes) ;
+
+  };
+
 ////////////////////////////////////////////////////////////////////
 // A lattice of something, but assume the something is SIMDized.
 ////////////////////////////////////////////////////////////////////
+
 template<typename _Tp>
 class alignedAllocator {
 public: 
@@ -66,27 +89,27 @@ public:
 
   pointer allocate(size_type __n, const void* _p= 0)
   { 
+    size_type bytes = __n*sizeof(_Tp);
+
+    _Tp *ptr = (_Tp *) PointerCache::Lookup(bytes);
+    
 #ifdef HAVE_MM_MALLOC_H
-    _Tp * ptr = (_Tp *) _mm_malloc(__n*sizeof(_Tp),128);
+    if ( ptr == (_Tp *) NULL ) ptr = (_Tp *) _mm_malloc(bytes,128);
 #else
-    _Tp * ptr = (_Tp *) memalign(128,__n*sizeof(_Tp));
+    if ( ptr == (_Tp *) NULL ) ptr = (_Tp *) memalign(128,bytes);
 #endif
 
-    _Tp tmp;
-#ifdef GRID_NUMA
-#pragma omp parallel for schedule(static)
-  for(int i=0;i<__n;i++){
-    ptr[i]=tmp;
-  }
-#endif 
     return ptr;
   }
 
-  void deallocate(pointer __p, size_type) { 
+  void deallocate(pointer __p, size_type __n) { 
+    size_type bytes = __n * sizeof(_Tp);
+    pointer __freeme = (pointer)PointerCache::Insert((void *)__p,bytes);
+
 #ifdef HAVE_MM_MALLOC_H
-    _mm_free((void *)__p); 
+    if ( __freeme ) _mm_free((void *)__freeme); 
 #else
-    free((void *)__p);
+    if ( __freeme ) free((void *)__freeme);
 #endif
   }
   void construct(pointer __p, const _Tp& __val) { };

lib/cartesian/Cartesian_base.h

@@ -52,7 +52,7 @@ public:
 
     // Physics Grid information.
     std::vector<int> _simd_layout;// Which dimensions get relayed out over simd lanes.
-    std::vector<int> _fdimensions;// Global dimensions of array prior to cb removal
+    std::vector<int> _fdimensions;// (full) Global dimensions of array prior to cb removal
     std::vector<int> _gdimensions;// Global dimensions of array after cb removal
     std::vector<int> _ldimensions;// local dimensions of array with processor images removed
     std::vector<int> _rdimensions;// Reduced local dimensions with simd lane images and processor images removed 
@@ -77,7 +77,7 @@ public:
     // GridCartesian / GridRedBlackCartesian
     ////////////////////////////////////////////////////////////////
     virtual int CheckerBoarded(int dim)=0;
-    virtual int CheckerBoard(std::vector<int> &site)=0;
+    virtual int CheckerBoard(const std::vector<int> &site)=0;
     virtual int CheckerBoardDestination(int source_cb,int shift,int dim)=0;
     virtual int CheckerBoardShift(int source_cb,int dim,int shift,int osite)=0;
     virtual int CheckerBoardShiftForCB(int source_cb,int dim,int shift,int cb)=0;
@@ -121,7 +121,6 @@ public:
       Lexicographic::CoorFromIndex(coor,Oindex,_rdimensions);
     }
 
-
     //////////////////////////////////////////////////////////
     // SIMD lane addressing
     //////////////////////////////////////////////////////////
@@ -178,9 +177,11 @@ public:
     // Global addressing
     ////////////////////////////////////////////////////////////////
     void GlobalIndexToGlobalCoor(int gidx,std::vector<int> &gcoor){
+      assert(gidx< gSites());
       Lexicographic::CoorFromIndex(gcoor,gidx,_gdimensions);
     }
     void LocalIndexToLocalCoor(int lidx,std::vector<int> &lcoor){
+      assert(lidx<lSites());
       Lexicographic::CoorFromIndex(lcoor,lidx,_ldimensions);
     }
     void GlobalCoorToGlobalIndex(const std::vector<int> & gcoor,int & gidx){
@@ -207,16 +208,16 @@ public:
       std::vector<int> lcoor;
       GlobalCoorToProcessorCoorLocalCoor(pcoor,lcoor,gcoor);
       rank = RankFromProcessorCoor(pcoor);
-
+      /*
       std::vector<int> cblcoor(lcoor);
       for(int d=0;d<cblcoor.size();d++){
 	if( this->CheckerBoarded(d) ) {
 	  cblcoor[d] = lcoor[d]/2;
 	}
       }
-
-      i_idx= iIndex(cblcoor);// this does not imply divide by 2 on checker dim
-      o_idx= oIndex(lcoor);  // this implies divide by 2 on checkerdim
+      */
+      i_idx= iIndex(lcoor);
+      o_idx= oIndex(lcoor);
     }
 
     void RankIndexToGlobalCoor(int rank, int o_idx, int i_idx , std::vector<int> &gcoor)

lib/cartesian/Cartesian_full.h

@@ -49,7 +49,7 @@ public:
     virtual int CheckerBoarded(int dim){
       return 0;
     }
-    virtual int CheckerBoard(std::vector<int> &site){
+    virtual int CheckerBoard(const std::vector<int> &site){
         return 0;
     }
     virtual int CheckerBoardDestination(int cb,int shift,int dim){

lib/cartesian/Cartesian_red_black.h

@@ -49,7 +49,7 @@ public:
       if( dim==_checker_dim) return 1;
       else return 0;
     }
-    virtual int CheckerBoard(std::vector<int> &site){
+    virtual int CheckerBoard(const std::vector<int> &site){
       int linear=0;
       assert(site.size()==_ndimension);
       for(int d=0;d<_ndimension;d++){ 

lib/communicator/Communicator_base.cc

@@ -25,7 +25,8 @@ Author: Peter Boyle <paboyle@ph.ed.ac.uk>
     See the full license in the file "LICENSE" in the top level distribution directory
     *************************************************************************************/
     /*  END LEGAL */
-#include "Grid.h"
+#include <Grid/GridCore.h>
+
 namespace Grid {
 
 ///////////////////////////////////////////////////////////////
@@ -33,6 +34,7 @@ namespace Grid {
 ///////////////////////////////////////////////////////////////
 void *              CartesianCommunicator::ShmCommBuf;
 uint64_t            CartesianCommunicator::MAX_MPI_SHM_BYTES   = 128*1024*1024; 
+CartesianCommunicator::CommunicatorPolicy_t  CartesianCommunicator::CommunicatorPolicy= CartesianCommunicator::CommunicatorPolicyConcurrent;
 
 /////////////////////////////////
 // Alloc, free shmem region
@@ -65,7 +67,6 @@ const std::vector<int> & CartesianCommunicator::ThisProcessorCoor(void) { return
 const std::vector<int> & CartesianCommunicator::ProcessorGrid(void)     { return _processors; };
 int                      CartesianCommunicator::ProcessorCount(void)    { return _Nprocessors; };
 
-
 ////////////////////////////////////////////////////////////////////////////////
 // very VERY rarely (Log, serial RNG) we need world without a grid
 ////////////////////////////////////////////////////////////////////////////////
@@ -89,14 +90,17 @@ void CartesianCommunicator::GlobalSumVector(ComplexD *c,int N)
 
 #if !defined( GRID_COMMS_MPI3) && !defined (GRID_COMMS_MPI3L)
 
-void CartesianCommunicator::StencilSendToRecvFromBegin(std::vector<CommsRequest_t> &list,
-                                                       void *xmit,
-                                                       int xmit_to_rank,
-                                                       void *recv,
-                                                       int recv_from_rank,
-                                                       int bytes)
+int                      CartesianCommunicator::NodeCount(void)    { return ProcessorCount();};
+
+double CartesianCommunicator::StencilSendToRecvFromBegin(std::vector<CommsRequest_t> &list,
+						       void *xmit,
+						       int xmit_to_rank,
+						       void *recv,
+						       int recv_from_rank,
+						       int bytes)
 {
   SendToRecvFromBegin(list,xmit,xmit_to_rank,recv,recv_from_rank,bytes);
+  return 2.0*bytes;
 }
 void CartesianCommunicator::StencilSendToRecvFromComplete(std::vector<CommsRequest_t> &waitall)
 {

lib/communicator/Communicator_base.h

@@ -68,8 +68,6 @@ class CartesianCommunicator {
   static MPI_Comm communicator_world;
          MPI_Comm communicator;
   typedef MPI_Request CommsRequest_t;
-  static char name[MPI_MAX_PROCESSOR_NAME]; // processing node physical name
-  static int length; 
 #else 
   typedef int CommsRequest_t;
 #endif
@@ -118,6 +116,12 @@ class CartesianCommunicator {
   // Implemented in Communicator_base.C
   /////////////////////////////////
   static void * ShmCommBuf;
+
+  // Isend/Irecv/Wait, or Sendrecv blocking
+  enum CommunicatorPolicy_t { CommunicatorPolicyConcurrent, CommunicatorPolicySequential };
+  static CommunicatorPolicy_t CommunicatorPolicy;
+  static void SetCommunicatorPolicy(CommunicatorPolicy_t policy ) { CommunicatorPolicy = policy; }
+
   size_t heap_top;
   size_t heap_bytes;
 
@@ -150,8 +154,8 @@ class CartesianCommunicator {
   const std::vector<int> & ThisProcessorCoor(void) ;
   const std::vector<int> & ProcessorGrid(void)     ;
   int                      ProcessorCount(void)    ;
+  int                      NodeCount(void)    ;
 
-  void        		 PrintRankInfo(void)     ;
   ////////////////////////////////////////////////////////////////////////////////
   // very VERY rarely (Log, serial RNG) we need world without a grid
   ////////////////////////////////////////////////////////////////////////////////
@@ -203,7 +207,7 @@ class CartesianCommunicator {
   
   void SendToRecvFromComplete(std::vector<CommsRequest_t> &waitall);
 
-  void StencilSendToRecvFromBegin(std::vector<CommsRequest_t> &list,
+  double StencilSendToRecvFromBegin(std::vector<CommsRequest_t> &list,
 				  void *xmit,
 				  int xmit_to_rank,
 				  void *recv,

lib/communicator/Communicator_mpi.cc

@@ -25,7 +25,9 @@ Author: Peter Boyle <paboyle@ph.ed.ac.uk>
     See the full license in the file "LICENSE" in the top level distribution directory
     *************************************************************************************/
     /*  END LEGAL */
-#include "Grid.h"
+#include <Grid/GridCore.h>
+#include <Grid/GridQCDcore.h>
+#include <Grid/qcd/action/ActionCore.h>
 #include <mpi.h>
 
 namespace Grid {
@@ -35,19 +37,19 @@ namespace Grid {
 // Info that is setup once and indept of cartesian layout
 ///////////////////////////////////////////////////////////////////////////////////////////////////
 MPI_Comm CartesianCommunicator::communicator_world;
-char CartesianCommunicator::name[MPI_MAX_PROCESSOR_NAME]; // processing node physical name
-int CartesianCommunicator::length; 
 
 // Should error check all MPI calls.
 void CartesianCommunicator::Init(int *argc, char ***argv) {
   int flag;
+  int provided;
   MPI_Initialized(&flag); // needed to coexist with other libs apparently
   if ( !flag ) {
-    MPI_Init(argc,argv);
+    MPI_Init_thread(argc,argv,MPI_THREAD_MULTIPLE,&provided);
+    if ( provided != MPI_THREAD_MULTIPLE ) {
+      QCD::WilsonKernelsStatic::Comms = QCD::WilsonKernelsStatic::CommsThenCompute;
+    }
   }
   MPI_Comm_dup (MPI_COMM_WORLD,&communicator_world);
-
-  MPI_Get_processor_name(name, &length);
   ShmInitGeneric();
 }
 
@@ -156,24 +158,34 @@ void CartesianCommunicator::SendToRecvFromBegin(std::vector<CommsRequest_t> &lis
 						int from,
 						int bytes)
 {
-  MPI_Request xrq;
-  MPI_Request rrq;
-  int rank = _processor;
+  int myrank = _processor;
   int ierr;
-  ierr =MPI_Isend(xmit, bytes, MPI_CHAR,dest,_processor,communicator,&xrq);
-  ierr|=MPI_Irecv(recv, bytes, MPI_CHAR,from,from,communicator,&rrq);
+  if ( CommunicatorPolicy == CommunicatorPolicyConcurrent ) { 
+    MPI_Request xrq;
+    MPI_Request rrq;
 
-  assert(ierr==0);
+    ierr =MPI_Irecv(recv, bytes, MPI_CHAR,from,from,communicator,&rrq);
+    ierr|=MPI_Isend(xmit, bytes, MPI_CHAR,dest,_processor,communicator,&xrq);
     
-  list.push_back(xrq);
-  list.push_back(rrq);
+    assert(ierr==0);
+    list.push_back(xrq);
+    list.push_back(rrq);
+  } else { 
+    // Give the CPU to MPI immediately; can use threads to overlap optionally
+    ierr=MPI_Sendrecv(xmit,bytes,MPI_CHAR,dest,myrank,
+		      recv,bytes,MPI_CHAR,from, from,
+		      communicator,MPI_STATUS_IGNORE);
+    assert(ierr==0);
+  }
 }
 void CartesianCommunicator::SendToRecvFromComplete(std::vector<CommsRequest_t> &list)
 {
-  int nreq=list.size();
-  std::vector<MPI_Status> status(nreq);
-  int ierr = MPI_Waitall(nreq,&list[0],&status[0]);
-  assert(ierr==0);
+  if ( CommunicatorPolicy == CommunicatorPolicyConcurrent ) { 
+    int nreq=list.size();
+    std::vector<MPI_Status> status(nreq);
+    int ierr = MPI_Waitall(nreq,&list[0],&status[0]);
+    assert(ierr==0);
+  }
 }
 
 void CartesianCommunicator::Barrier(void)
@@ -210,10 +222,5 @@ void CartesianCommunicator::BroadcastWorld(int root,void* data, int bytes)
   assert(ierr==0);
 }
 
-void CartesianCommunicator::PrintRankInfo(){
-    std::cout << "Grid: Rank "<< _processor << "  -  Physical node name: " << name << std::endl;
 }
 
-
-}// end of namespace
-

lib/communicator/Communicator_mpi3.cc

@@ -1,4 +1,4 @@
-    /*************************************************************************************
+/*************************************************************************************
 
     Grid physics library, www.github.com/paboyle/Grid 
 
@@ -25,9 +25,23 @@ Author: Peter Boyle <paboyle@ph.ed.ac.uk>
     See the full license in the file "LICENSE" in the top level distribution directory
     *************************************************************************************/
     /*  END LEGAL */
-#include "Grid.h"
+#include <Grid/GridCore.h>
+
 #include <mpi.h>
 
+#include <semaphore.h>
+#include <fcntl.h>
+#include <unistd.h>
+#include <limits.h>
+#include <sys/types.h>
+#include <sys/ipc.h>
+#include <sys/shm.h>
+#include <sys/mman.h>
+//#include <zlib.h>
+#ifndef SHM_HUGETLB
+#define SHM_HUGETLB 04000
+#endif
+
 namespace Grid {
 
 ///////////////////////////////////////////////////////////////////////////////////////////////////
@@ -50,6 +64,10 @@ std::vector<int> CartesianCommunicator::GroupRanks;
 std::vector<int> CartesianCommunicator::MyGroup;
 std::vector<void *> CartesianCommunicator::ShmCommBufs;
 
+int CartesianCommunicator::NodeCount(void)    { return GroupSize;};
+
+
+#undef FORCE_COMMS
 void *CartesianCommunicator::ShmBufferSelf(void)
 {
   return ShmCommBufs[ShmRank];
@@ -57,6 +75,9 @@ void *CartesianCommunicator::ShmBufferSelf(void)
 void *CartesianCommunicator::ShmBuffer(int rank)
 {
   int gpeer = GroupRanks[rank];
+#ifdef FORCE_COMMS
+  return NULL;
+#endif
   if (gpeer == MPI_UNDEFINED){
     return NULL;
   } else { 
@@ -65,7 +86,13 @@ void *CartesianCommunicator::ShmBuffer(int rank)
 }
 void *CartesianCommunicator::ShmBufferTranslate(int rank,void * local_p)
 {
+  static int count =0;
   int gpeer = GroupRanks[rank];
+  assert(gpeer!=ShmRank); // never send to self
+  assert(rank!=WorldRank);// never send to self
+#ifdef FORCE_COMMS
+  return NULL;
+#endif
   if (gpeer == MPI_UNDEFINED){
     return NULL;
   } else { 
@@ -76,16 +103,27 @@ void *CartesianCommunicator::ShmBufferTranslate(int rank,void * local_p)
 }
 
 void CartesianCommunicator::Init(int *argc, char ***argv) {
+
   int flag;
+  int provided;
+  //  mtrace();
+
   MPI_Initialized(&flag); // needed to coexist with other libs apparently
   if ( !flag ) {
-    MPI_Init(argc,argv);
+    MPI_Init_thread(argc,argv,MPI_THREAD_MULTIPLE,&provided);
+    assert (provided == MPI_THREAD_MULTIPLE);
   }
 
+  Grid_quiesce_nodes();
+
   MPI_Comm_dup (MPI_COMM_WORLD,&communicator_world);
   MPI_Comm_rank(communicator_world,&WorldRank);
   MPI_Comm_size(communicator_world,&WorldSize);
 
+  if ( WorldRank == 0 ) {
+    std::cout << GridLogMessage<< "Initialising MPI "<< WorldRank <<"/"<<WorldSize <<std::endl;
+  }
+
   /////////////////////////////////////////////////////////////////////
   // Split into groups that can share memory
   /////////////////////////////////////////////////////////////////////
@@ -131,7 +169,6 @@ void CartesianCommunicator::Init(int *argc, char ***argv) {
   ///////////////////////////////////////////////////////////////////
   int ierr=MPI_Allreduce(MPI_IN_PLACE,&leaders_1hot[0],WorldSize,MPI_INT,MPI_SUM,communicator_world);
   assert(ierr==0);
-  
   ///////////////////////////////////////////////////////////////////
   // find the group leaders world rank
   ///////////////////////////////////////////////////////////////////
@@ -141,7 +178,6 @@ void CartesianCommunicator::Init(int *argc, char ***argv) {
       leaders_group[group++] = l;
     }
   }
-  
   ///////////////////////////////////////////////////////////////////
   // Identify the rank of the group in which I (and my leader) live
   ///////////////////////////////////////////////////////////////////
@@ -152,39 +188,114 @@ void CartesianCommunicator::Init(int *argc, char ***argv) {
     }
   }
   assert(GroupRank!=-1);
-  
   //////////////////////////////////////////////////////////////////////////////////////////////////////////
   // allocate the shared window for our group
   //////////////////////////////////////////////////////////////////////////////////////////////////////////
+  MPI_Barrier(ShmComm);
 
   ShmCommBuf = 0;
-  ierr = MPI_Win_allocate_shared(MAX_MPI_SHM_BYTES,1,MPI_INFO_NULL,ShmComm,&ShmCommBuf,&ShmWindow);
-  assert(ierr==0);
-  // KNL hack -- force to numa-domain 1 in flat
-#if 0
-  //#include <numaif.h>
-  for(uint64_t page=0;page<MAX_MPI_SHM_BYTES;page+=4096){
-    void *pages = (void *) ( page + ShmCommBuf );
-    int status;
-    int flags=MPOL_MF_MOVE_ALL;
-    int nodes=1; // numa domain == MCDRAM
-    unsigned long count=1;
-    ierr= move_pages(0,count, &pages,&nodes,&status,flags);
-    if (ierr && (page==0)) perror("numa relocate command failed");
-  }
-#endif
-  MPI_Win_lock_all (MPI_MODE_NOCHECK, ShmWindow);
-  
-  /////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
-  // Plan: allocate a fixed SHM region. Scratch that is just used via some scheme during stencil comms, with no allocate free.
-  /////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
   ShmCommBufs.resize(ShmSize);
-  for(int r=0;r<ShmSize;r++){
-    MPI_Aint sz;
-    int dsp_unit;
-    MPI_Win_shared_query (ShmWindow, r, &sz, &dsp_unit, &ShmCommBufs[r]);
+
+#if 1
+  char shm_name [NAME_MAX];
+  if ( ShmRank == 0 ) {
+    for(int r=0;r<ShmSize;r++){
+
+      size_t size = CartesianCommunicator::MAX_MPI_SHM_BYTES;
+
+      sprintf(shm_name,"/Grid_mpi3_shm_%d_%d",GroupRank,r);
+
+      shm_unlink(shm_name);
+      int fd=shm_open(shm_name,O_RDWR|O_CREAT,0666);
+      if ( fd < 0 ) {	perror("failed shm_open");	assert(0);      }
+      ftruncate(fd, size);
+
+      void * ptr =  mmap(NULL,size, PROT_READ | PROT_WRITE, MAP_SHARED, fd, 0);
+      if ( ptr == MAP_FAILED ) {       perror("failed mmap");      assert(0);    }
+      assert(((uint64_t)ptr&0x3F)==0);
+      ShmCommBufs[r] =ptr;
+      
+    }
   }
 
+  MPI_Barrier(ShmComm);
+
+  if ( ShmRank != 0 ) { 
+    for(int r=0;r<ShmSize;r++){
+      size_t size = CartesianCommunicator::MAX_MPI_SHM_BYTES ;
+    
+      sprintf(shm_name,"/Grid_mpi3_shm_%d_%d",GroupRank,r);
+
+      int fd=shm_open(shm_name,O_RDWR,0666);
+      if ( fd<0 ) {	perror("failed shm_open");	assert(0);      }
+
+      void * ptr =  mmap(NULL,size, PROT_READ | PROT_WRITE, MAP_SHARED, fd, 0);
+      if ( ptr == MAP_FAILED ) {       perror("failed mmap");      assert(0);    }
+      assert(((uint64_t)ptr&0x3F)==0);
+      ShmCommBufs[r] =ptr;
+    }
+  }
+
+#else
+  std::vector<int> shmids(ShmSize);
+
+  if ( ShmRank == 0 ) {
+    for(int r=0;r<ShmSize;r++){
+      size_t size = CartesianCommunicator::MAX_MPI_SHM_BYTES;
+      key_t key   = 0x4545 + r;
+      if ((shmids[r]= shmget(key,size, SHM_HUGETLB | IPC_CREAT | SHM_R | SHM_W)) < 0) {
+	int errsv = errno;
+	printf("Errno %d\n",errsv);
+	perror("shmget");
+	exit(1);
+      }
+      printf("shmid: 0x%x\n", shmids[r]);
+    }
+  }
+  MPI_Barrier(ShmComm);
+  MPI_Bcast(&shmids[0],ShmSize*sizeof(int),MPI_BYTE,0,ShmComm);
+  MPI_Barrier(ShmComm);
+
+  for(int r=0;r<ShmSize;r++){
+    ShmCommBufs[r] = (uint64_t *)shmat(shmids[r], NULL,0);
+    if (ShmCommBufs[r] == (uint64_t *)-1) {
+      perror("Shared memory attach failure");
+      shmctl(shmids[r], IPC_RMID, NULL);
+      exit(2);
+    }
+    printf("shmaddr: %p\n", ShmCommBufs[r]);
+  }
+  MPI_Barrier(ShmComm);
+  // Mark for clean up
+  for(int r=0;r<ShmSize;r++){
+    shmctl(shmids[r], IPC_RMID,(struct shmid_ds *)NULL);
+  }
+  MPI_Barrier(ShmComm);
+
+#endif
+  ShmCommBuf         = ShmCommBufs[ShmRank];
+
+  MPI_Barrier(ShmComm);
+  if ( ShmRank == 0 ) {
+    for(int r=0;r<ShmSize;r++){
+      uint64_t * check = (uint64_t *) ShmCommBufs[r];
+      check[0] = GroupRank;
+      check[1] = r;
+      check[2] = 0x5A5A5A;
+    }
+  }
+
+  MPI_Barrier(ShmComm);
+  for(int r=0;r<ShmSize;r++){
+    uint64_t * check = (uint64_t *) ShmCommBufs[r];
+    
+    assert(check[0]==GroupRank);
+    assert(check[1]==r);
+    assert(check[2]==0x5A5A5A);
+
+  }
+  MPI_Barrier(ShmComm);
+
   //////////////////////////////////////////////////////////////////////////////////////////////////////////
   // Verbose for now
   //////////////////////////////////////////////////////////////////////////////////////////////////////////
@@ -192,7 +303,7 @@ void CartesianCommunicator::Init(int *argc, char ***argv) {
     std::cout<<GridLogMessage<< "Grid MPI-3 configuration: detected ";
     std::cout<< WorldSize << " Ranks " ;
     std::cout<< GroupSize << " Nodes " ;
-    std::cout<<  ShmSize  << " with ranks-per-node "<<std::endl;
+    std::cout<< " with "<< ShmSize  << " ranks-per-node "<<std::endl;
     
     std::cout<<GridLogMessage     <<"Grid MPI-3 configuration: allocated shared memory region of size ";
     std::cout<<std::hex << MAX_MPI_SHM_BYTES <<" ShmCommBuf address = "<<ShmCommBuf << std::dec<<std::endl;
@@ -207,7 +318,6 @@ void CartesianCommunicator::Init(int *argc, char ***argv) {
       if(g!=ShmSize-1) std::cout<<",";
       else std::cout<<"}"<<std::endl;
     }
-
   }
   
   for(int g=0;g<GroupSize;g++){
@@ -216,7 +326,7 @@ void CartesianCommunicator::Init(int *argc, char ***argv) {
       if ( (ShmRank == 0) && (GroupRank==g) ) {
 	std::cout<<MyGroup[r];
 	if(r<ShmSize-1) std::cout<<",";
-	else std::cout<<"}"<<std::endl;
+	else std::cout<<"}"<<std::endl<<std::flush;
       }
       MPI_Barrier(communicator_world);
     }
@@ -225,14 +335,12 @@ void CartesianCommunicator::Init(int *argc, char ***argv) {
   assert(ShmSetup==0);  ShmSetup=1;
 }
 
-
 ////////////////////////////////////////////////////////////////////////////////////////////////////////////
 // Want to implement some magic ... Group sub-cubes into those on same node
 ////////////////////////////////////////////////////////////////////////////////////////////////////////////
-void CartesianCommunicator::ShiftedRanks(int dim,int shift,int &source,int &dest)
+void CartesianCommunicator::ShiftedRanks(int dim,int shift,int &dest,int &source)
 {
-  std::vector<int> coor = _processor_coor;
-
+  std::vector<int> coor = _processor_coor; // my coord
   assert(std::abs(shift) <_processors[dim]);
 
   coor[dim] = (_processor_coor[dim] + shift + _processors[dim])%_processors[dim];
@@ -242,26 +350,30 @@ void CartesianCommunicator::ShiftedRanks(int dim,int shift,int &source,int &dest
   coor[dim] = (_processor_coor[dim] - shift + _processors[dim])%_processors[dim];
   Lexicographic::IndexFromCoor(coor,dest,_processors);
   dest = LexicographicToWorldRank[dest];
-}
+
+}// rank is world rank.
+
 int CartesianCommunicator::RankFromProcessorCoor(std::vector<int> &coor)
 {
   int rank;
   Lexicographic::IndexFromCoor(coor,rank,_processors);
   rank = LexicographicToWorldRank[rank];
   return rank;
-}
+}// rank is world rank
+
 void  CartesianCommunicator::ProcessorCoorFromRank(int rank, std::vector<int> &coor)
 {
-  Lexicographic::CoorFromIndex(coor,rank,_processors);
-  rank = LexicographicToWorldRank[rank];
+  int lr=-1;
+  for(int r=0;r<WorldSize;r++){// map world Rank to lexico and then to coor
+    if( LexicographicToWorldRank[r]==rank) lr = r;
+  }
+  assert(lr!=-1);
+  Lexicographic::CoorFromIndex(coor,lr,_processors);
 }
-
 CartesianCommunicator::CartesianCommunicator(const std::vector<int> &processors)
 { 
   int ierr;
-
   communicator=communicator_world;
-
   _ndimension = processors.size();
 
   ////////////////////////////////////////////////////////////////
@@ -280,19 +392,17 @@ CartesianCommunicator::CartesianCommunicator(const std::vector<int> &processors)
   // Identify subblock of ranks on node spreading across dims
   // in a maximally symmetrical way
   ////////////////////////////////////////////////////////////////
-  int dim = 0;
-  
   std::vector<int> WorldDims = processors;
 
-  ShmDims.resize(_ndimension,1);
+  ShmDims.resize  (_ndimension,1);
   GroupDims.resize(_ndimension);
-    
-  ShmCoor.resize(_ndimension);
+  ShmCoor.resize  (_ndimension);
   GroupCoor.resize(_ndimension);
   WorldCoor.resize(_ndimension);
 
+  int dim = 0;
   for(int l2=0;l2<log2size;l2++){
-    while ( WorldDims[dim] / ShmDims[dim] <= 1 ) dim=(dim+1)%_ndimension;
+    while ( (WorldDims[dim] / ShmDims[dim]) <= 1 ) dim=(dim+1)%_ndimension;
     ShmDims[dim]*=2;
     dim=(dim+1)%_ndimension;
   }
@@ -304,6 +414,29 @@ CartesianCommunicator::CartesianCommunicator(const std::vector<int> &processors)
     GroupDims[d] = WorldDims[d]/ShmDims[d];
   }
 
+  ////////////////////////////////////////////////////////////////
+  // Verbose
+  ////////////////////////////////////////////////////////////////
+#if 0
+  std::cout<< GridLogMessage << "MPI-3 usage "<<std::endl;
+  std::cout<< GridLogMessage << "SHM   ";
+  for(int d=0;d<_ndimension;d++){
+    std::cout<< ShmDims[d] <<" ";
+  }
+  std::cout<< std::endl;
+
+  std::cout<< GridLogMessage << "Group ";
+  for(int d=0;d<_ndimension;d++){
+    std::cout<< GroupDims[d] <<" ";
+  }
+  std::cout<< std::endl;
+
+  std::cout<< GridLogMessage<<"World ";
+  for(int d=0;d<_ndimension;d++){
+    std::cout<< WorldDims[d] <<" ";
+  }
+  std::cout<< std::endl;
+#endif
   ////////////////////////////////////////////////////////////////
   // Check processor counts match
   ////////////////////////////////////////////////////////////////
@@ -317,29 +450,57 @@ CartesianCommunicator::CartesianCommunicator(const std::vector<int> &processors)
       
   ////////////////////////////////////////////////////////////////
   // Establish mapping between lexico physics coord and WorldRank
-  // 
   ////////////////////////////////////////////////////////////////
-  LexicographicToWorldRank.resize(WorldSize,0);
   Lexicographic::CoorFromIndex(GroupCoor,GroupRank,GroupDims);
   Lexicographic::CoorFromIndex(ShmCoor,ShmRank,ShmDims);
   for(int d=0;d<_ndimension;d++){
     WorldCoor[d] = GroupCoor[d]*ShmDims[d]+ShmCoor[d];
   }
   _processor_coor = WorldCoor;
-
-  int lexico;
-  Lexicographic::IndexFromCoor(WorldCoor,lexico,WorldDims);
-  LexicographicToWorldRank[lexico]=WorldRank;
-  _processor = lexico;
+  _processor      = WorldRank;
 
   ///////////////////////////////////////////////////////////////////
   // global sum Lexico to World mapping
   ///////////////////////////////////////////////////////////////////
+  int lexico;
+  LexicographicToWorldRank.resize(WorldSize,0);
+  Lexicographic::IndexFromCoor(WorldCoor,lexico,WorldDims);
+  LexicographicToWorldRank[lexico] = WorldRank;
   ierr=MPI_Allreduce(MPI_IN_PLACE,&LexicographicToWorldRank[0],WorldSize,MPI_INT,MPI_SUM,communicator);
   assert(ierr==0);
 
-};
+  for(int i=0;i<WorldSize;i++){
 
+    int wr = LexicographicToWorldRank[i];
+    //    int wr = i;
+
+    std::vector<int> coor(_ndimension);
+    ProcessorCoorFromRank(wr,coor); // from world rank
+    int ck = RankFromProcessorCoor(coor);
+    assert(ck==wr);
+
+    if ( wr == WorldRank ) { 
+      for(int j=0;j<coor.size();j++) {
+	assert(coor[j] == _processor_coor[j]);
+      }
+    }
+    /*
+    std::cout << GridLogMessage<< " Lexicographic "<<i;
+    std::cout << " MPI rank      "<<wr;
+    std::cout << " Coor          ";
+    for(int j=0;j<coor.size();j++) std::cout << coor[j];
+    std::cout<< std::endl;
+    */
+    /////////////////////////////////////////////////////
+    // Check everyone agrees on everyone elses coords
+    /////////////////////////////////////////////////////
+    std::vector<int> mcoor = coor;
+    this->Broadcast(0,(void *)&mcoor[0],mcoor.size()*sizeof(int));
+    for(int d = 0 ; d< _ndimension; d++) {
+      assert(coor[d] == mcoor[d]);
+    }
+  }
+};
 void CartesianCommunicator::GlobalSum(uint32_t &u){
   int ierr=MPI_Allreduce(MPI_IN_PLACE,&u,1,MPI_UINT32_T,MPI_SUM,communicator);
   assert(ierr==0);
@@ -367,8 +528,6 @@ void CartesianCommunicator::GlobalSumVector(double *d,int N)
   int ierr = MPI_Allreduce(MPI_IN_PLACE,d,N,MPI_DOUBLE,MPI_SUM,communicator);
   assert(ierr==0);
 }
-
-
 // Basic Halo comms primitive
 void CartesianCommunicator::SendToRecvFrom(void *xmit,
 					   int dest,
@@ -377,10 +536,14 @@ void CartesianCommunicator::SendToRecvFrom(void *xmit,
 					   int bytes)
 {
   std::vector<CommsRequest_t> reqs(0);
+  //    unsigned long  xcrc = crc32(0L, Z_NULL, 0);
+  //    unsigned long  rcrc = crc32(0L, Z_NULL, 0);
+  //    xcrc = crc32(xcrc,(unsigned char *)xmit,bytes);
   SendToRecvFromBegin(reqs,xmit,dest,recv,from,bytes);
   SendToRecvFromComplete(reqs);
+  //    rcrc = crc32(rcrc,(unsigned char *)recv,bytes);
+  //    printf("proc %d SendToRecvFrom %d bytes %lx %lx\n",_processor,bytes,xcrc,rcrc);
 }
-
 void CartesianCommunicator::SendRecvPacket(void *xmit,
 					   void *recv,
 					   int sender,
@@ -397,7 +560,6 @@ void CartesianCommunicator::SendRecvPacket(void *xmit,
     MPI_Recv(recv, bytes, MPI_CHAR,sender,tag,communicator,&stat);
   }
 }
-
 // Basic Halo comms primitive
 void CartesianCommunicator::SendToRecvFromBegin(std::vector<CommsRequest_t> &list,
 						void *xmit,
@@ -406,95 +568,29 @@ void CartesianCommunicator::SendToRecvFromBegin(std::vector<CommsRequest_t> &lis
 						int from,
 						int bytes)
 {
-#if 0
-  this->StencilBarrier();
-
-  MPI_Request xrq;
-  MPI_Request rrq;
-  
-  static int sequence;
-
+  int myrank = _processor;
   int ierr;
-  int tag;
-  int check;
 
-  assert(dest != _processor);
-  assert(from != _processor);
+  if ( CommunicatorPolicy == CommunicatorPolicyConcurrent ) { 
+    MPI_Request xrq;
+    MPI_Request rrq;
 
-  int gdest = GroupRanks[dest];
-  int gfrom = GroupRanks[from];
-  int gme   = GroupRanks[_processor];
+    ierr =MPI_Irecv(recv, bytes, MPI_CHAR,from,from,communicator,&rrq);
+    ierr|=MPI_Isend(xmit, bytes, MPI_CHAR,dest,_processor,communicator,&xrq);
     
-  sequence++;
-  
-  char *from_ptr = (char *)ShmCommBufs[ShmRank];
-
-  int small = (bytes<MAX_MPI_SHM_BYTES);
-
-  typedef uint64_t T;
-  int words = bytes/sizeof(T);
-
-  assert(((size_t)bytes &(sizeof(T)-1))==0);
-  assert(gme == ShmRank);
-
-  if ( small && (gdest !=MPI_UNDEFINED) ) {
-
-    char *to_ptr   = (char *)ShmCommBufs[gdest];
-
-    assert(gme != gdest);
-
-    T *ip = (T *)xmit;
-    T *op = (T *)to_ptr;
-PARALLEL_FOR_LOOP 
-    for(int w=0;w<words;w++) {
-      op[w]=ip[w];
-    }
-
-    bcopy(&_processor,&to_ptr[bytes],sizeof(_processor));
-    bcopy(&  sequence,&to_ptr[bytes+4],sizeof(sequence));
-  } else { 
-    ierr =MPI_Isend(xmit, bytes, MPI_CHAR,dest,_processor,communicator,&xrq);
     assert(ierr==0);
     list.push_back(xrq);
-  }
-
-  this->StencilBarrier();
-  
-  if (small && (gfrom !=MPI_UNDEFINED) ) {
-    T *ip = (T *)from_ptr;
-    T *op = (T *)recv;
-PARALLEL_FOR_LOOP 
-    for(int w=0;w<words;w++) {
-      op[w]=ip[w];
-    }
-    bcopy(&from_ptr[bytes]  ,&tag  ,sizeof(tag));
-    bcopy(&from_ptr[bytes+4],&check,sizeof(check));
-    assert(check==sequence);
-    assert(tag==from);
-  } else { 
-    ierr=MPI_Irecv(recv, bytes, MPI_CHAR,from,from,communicator,&rrq);
-    assert(ierr==0);
     list.push_back(rrq);
+  } else { 
+    // Give the CPU to MPI immediately; can use threads to overlap optionally
+    ierr=MPI_Sendrecv(xmit,bytes,MPI_CHAR,dest,myrank,
+		      recv,bytes,MPI_CHAR,from, from,
+		      communicator,MPI_STATUS_IGNORE);
+    assert(ierr==0);
   }
-
-  this->StencilBarrier();
-
-#else
-  MPI_Request xrq;
-  MPI_Request rrq;
-  int rank = _processor;
-  int ierr;
-  ierr =MPI_Isend(xmit, bytes, MPI_CHAR,dest,_processor,communicator,&xrq);
-  ierr|=MPI_Irecv(recv, bytes, MPI_CHAR,from,from,communicator,&rrq);
-  
-  assert(ierr==0);
-
-  list.push_back(xrq);
-  list.push_back(rrq);
-#endif
 }
 
-void CartesianCommunicator::StencilSendToRecvFromBegin(std::vector<CommsRequest_t> &list,
+double CartesianCommunicator::StencilSendToRecvFromBegin(std::vector<CommsRequest_t> &list,
 						       void *xmit,
 						       int dest,
 						       void *recv,
@@ -505,57 +601,63 @@ void CartesianCommunicator::StencilSendToRecvFromBegin(std::vector<CommsRequest_
   MPI_Request rrq;
 
   int ierr;
-
-  assert(dest != _processor);
-  assert(from != _processor);
-  
   int gdest = GroupRanks[dest];
   int gfrom = GroupRanks[from];
   int gme   = GroupRanks[_processor];
 
-  assert(gme == ShmRank);
+  assert(dest != _processor);
+  assert(from != _processor);
+  assert(gme  == ShmRank);
+  double off_node_bytes=0.0;
+
+#ifdef FORCE_COMMS
+  gdest = MPI_UNDEFINED;
+  gfrom = MPI_UNDEFINED;
+#endif
+  if ( gfrom ==MPI_UNDEFINED) {
+    ierr=MPI_Irecv(recv, bytes, MPI_CHAR,from,from,communicator,&rrq);
+    assert(ierr==0);
+    list.push_back(rrq);
+    off_node_bytes+=bytes;
+  }
 
   if ( gdest == MPI_UNDEFINED ) {
     ierr =MPI_Isend(xmit, bytes, MPI_CHAR,dest,_processor,communicator,&xrq);
     assert(ierr==0);
     list.push_back(xrq);
+    off_node_bytes+=bytes;
   }
 
-  if ( gfrom ==MPI_UNDEFINED) {
-    ierr=MPI_Irecv(recv, bytes, MPI_CHAR,from,from,communicator,&rrq);
-    assert(ierr==0);
-    list.push_back(rrq);
+  if ( CommunicatorPolicy == CommunicatorPolicySequential ) { 
+    this->StencilSendToRecvFromComplete(list);
   }
 
+  return off_node_bytes;
 }
-
-
-void CartesianCommunicator::StencilSendToRecvFromComplete(std::vector<CommsRequest_t> &list)
+void CartesianCommunicator::StencilSendToRecvFromComplete(std::vector<CommsRequest_t> &waitall)
 {
-  SendToRecvFromComplete(list);
+  SendToRecvFromComplete(waitall);
 }
-
 void CartesianCommunicator::StencilBarrier(void)
 {
-  MPI_Win_sync (ShmWindow);   
   MPI_Barrier  (ShmComm);
-  MPI_Win_sync (ShmWindow);   
 }
-
 void CartesianCommunicator::SendToRecvFromComplete(std::vector<CommsRequest_t> &list)
 {
   int nreq=list.size();
+
+  if (nreq==0) return;
+
   std::vector<MPI_Status> status(nreq);
   int ierr = MPI_Waitall(nreq,&list[0],&status[0]);
   assert(ierr==0);
+  list.resize(0);
 }
-
 void CartesianCommunicator::Barrier(void)
 {
   int ierr = MPI_Barrier(communicator);
   assert(ierr==0);
 }
-
 void CartesianCommunicator::Broadcast(int root,void* data, int bytes)
 {
   int ierr=MPI_Bcast(data,
@@ -565,7 +667,11 @@ void CartesianCommunicator::Broadcast(int root,void* data, int bytes)
 		     communicator);
   assert(ierr==0);
 }
-
+int CartesianCommunicator::RankWorld(void){ 
+  int r; 
+  MPI_Comm_rank(communicator_world,&r);
+  return r;
+}
 void CartesianCommunicator::BroadcastWorld(int root,void* data, int bytes)
 {
   int ierr= MPI_Bcast(data,
@@ -576,10 +682,5 @@ void CartesianCommunicator::BroadcastWorld(int root,void* data, int bytes)
   assert(ierr==0);
 }
 
-  void CartesianCommunicator::PrintRankInfo(){
-    std::cout << "Grid: Rank "<< _processor << "  -  Physical node name: " << name << std::endl;
-  }
-
-  
 }
 

lib/communicator/Communicator_mpi3_leader.cc

@@ -27,6 +27,7 @@ Author: Peter Boyle <paboyle@ph.ed.ac.uk>
     /*  END LEGAL */
 #include "Grid.h"
 #include <mpi.h>
+//#include <numaif.h>
 
 ////////////////////////////////////////////////////////////////////////////////////////////////////////////////
 /// Workarounds:
@@ -42,19 +43,27 @@ Author: Peter Boyle <paboyle@ph.ed.ac.uk>
 #include <fcntl.h>
 #include <unistd.h>
 #include <limits.h>
-
 typedef sem_t *Grid_semaphore;
 
+
+#error  /*THis is deprecated*/
+
+#if 0 
 #define SEM_INIT(S)      S = sem_open(sem_name,0,0600,0); assert ( S != SEM_FAILED );
 #define SEM_INIT_EXCL(S) sem_unlink(sem_name); S = sem_open(sem_name,O_CREAT|O_EXCL,0600,0); assert ( S != SEM_FAILED );
 #define SEM_POST(S) assert ( sem_post(S) == 0 ); 
 #define SEM_WAIT(S) assert ( sem_wait(S) == 0 );
-
+#else
+#define SEM_INIT(S)      ;
+#define SEM_INIT_EXCL(S) ;
+#define SEM_POST(S) ;
+#define SEM_WAIT(S) ;
+#endif
 #include <sys/mman.h>
 
 namespace Grid {
 
-enum { COMMAND_ISEND, COMMAND_IRECV, COMMAND_WAITALL };
+enum { COMMAND_ISEND, COMMAND_IRECV, COMMAND_WAITALL, COMMAND_SENDRECV };
 
 struct Descriptor {
   uint64_t buf;
@@ -62,6 +71,12 @@ struct Descriptor {
   int rank;
   int tag;
   int command;
+  uint64_t xbuf;
+  uint64_t rbuf;
+  int xtag;
+  int rtag;
+  int src;
+  int dest;
   MPI_Request request;
 };
 
@@ -94,18 +109,14 @@ public:
 
   void SemInit(void) {
     sprintf(sem_name,"/Grid_mpi3_sem_head_%d",universe_rank);
-    //    printf("SEM_NAME: %s \n",sem_name);
     SEM_INIT(sem_head);
     sprintf(sem_name,"/Grid_mpi3_sem_tail_%d",universe_rank);
-    //    printf("SEM_NAME: %s \n",sem_name);
     SEM_INIT(sem_tail);
   }  
   void SemInitExcl(void) {
     sprintf(sem_name,"/Grid_mpi3_sem_head_%d",universe_rank);
-    //    printf("SEM_INIT_EXCL: %s \n",sem_name);
     SEM_INIT_EXCL(sem_head);
     sprintf(sem_name,"/Grid_mpi3_sem_tail_%d",universe_rank);
-    //    printf("SEM_INIT_EXCL: %s \n",sem_name);
     SEM_INIT_EXCL(sem_tail);
   }  
   void WakeUpDMA(void) { 
@@ -125,6 +136,13 @@ public:
     while(1){
       WaitForCommand();
       //      std::cout << "Getting command "<<std::endl;
+#if 0
+      _mm_monitor((void *)&state->head,0,0);
+      int s=state->start;
+      if ( s != state->head ) {
+	_mm_mwait(0,0);
+      }
+#endif
       Event();
     }
   }
@@ -132,6 +150,7 @@ public:
   int Event (void) ;
 
   uint64_t QueueCommand(int command,void *buf, int bytes, int hashtag, MPI_Comm comm,int u_rank) ;
+  void QueueSendRecv(void *xbuf, void *rbuf, int bytes, int xtag, int rtag, MPI_Comm comm,int dest,int src) ;
 
   void WaitAll() {
     //    std::cout << "Queueing WAIT command  "<<std::endl;
@@ -141,7 +160,7 @@ public:
     //    std::cout << "Waiting from semaphore "<<std::endl;
     WaitForComplete();
     //    std::cout << "Checking FIFO is empty "<<std::endl;
-    assert ( state->tail == state->head );
+    while ( state->tail != state->head );
   }
 };
 
@@ -196,6 +215,12 @@ public:
     //    std::cout << "Waking up DMA "<< slave<<std::endl;
   };
 
+  static void QueueSendRecv(int slave,void *xbuf, void *rbuf, int bytes, int xtag, int rtag, MPI_Comm comm,int dest,int src) 
+  {
+    Slaves[slave].QueueSendRecv(xbuf,rbuf,bytes,xtag,rtag,comm,dest,src);
+    Slaves[slave].WakeUpDMA();
+  }
+
   static void QueueRecv(int slave, void *buf, int bytes, int tag, MPI_Comm comm,int rank) {
     //    std::cout<< " Queueing recv "<< bytes<< " slave "<< slave << " from comm "<<rank  <<std::endl;
     Slaves[slave].QueueCommand(COMMAND_IRECV,buf,bytes,tag,comm,rank);
@@ -226,6 +251,28 @@ public:
     return;
   };
 
+  static void QueueRoundRobinSendRecv(void *xbuf, void *rbuf, int bytes, int xtag, int rtag, MPI_Comm comm,int dest,int src) {
+    uint8_t * cxbuf = (uint8_t *) xbuf;
+    uint8_t * crbuf = (uint8_t *) rbuf;
+    static int rrp=0;
+    int procs = VerticalSize-1;
+    int myoff=0;
+    int mywork=bytes;
+    QueueSendRecv(rrp+1,&cxbuf[myoff],&crbuf[myoff],mywork,xtag,rtag,comm,dest,src);
+    rrp = rrp+1;
+    if ( rrp == (VerticalSize-1) ) rrp = 0;
+  }
+
+  static void QueueMultiplexedSendRecv(void *xbuf, void *rbuf, int bytes, int xtag, int rtag, MPI_Comm comm,int dest,int src) {
+    uint8_t * cxbuf = (uint8_t *) xbuf;
+    uint8_t * crbuf = (uint8_t *) rbuf;
+    int mywork, myoff, procs;
+    procs = VerticalSize-1;
+    for(int s=0;s<procs;s++) {
+      GetWork(bytes,s,mywork,myoff,procs);
+      QueueSendRecv(s+1,&cxbuf[myoff],&crbuf[myoff],mywork,xtag,rtag,comm,dest,src);
+    }
+  };
   static void QueueMultiplexedSend(void *buf, int bytes, int tag, MPI_Comm comm,int rank) {
     uint8_t * cbuf = (uint8_t *) buf;
     int mywork, myoff, procs;
@@ -275,6 +322,7 @@ std::vector<void *>            MPIoffloadEngine::VerticalShmBufs;
 std::vector<std::vector<int> > MPIoffloadEngine::UniverseRanks;
 std::vector<int>               MPIoffloadEngine::UserCommunicatorToWorldRanks; 
 
+int CartesianCommunicator::NodeCount(void)    { return HorizontalSize;};
 int MPIoffloadEngine::ShmSetup = 0;
 
 void MPIoffloadEngine::CommunicatorInit (MPI_Comm &communicator_world,
@@ -370,12 +418,22 @@ void MPIoffloadEngine::CommunicatorInit (MPI_Comm &communicator_world,
       ftruncate(fd, size);
 
       VerticalShmBufs[r] = mmap(NULL,size, PROT_READ | PROT_WRITE, MAP_SHARED, fd, 0);
-
       if ( VerticalShmBufs[r] == MAP_FAILED ) { 
 	perror("failed mmap");
 	assert(0);
       }
 
+      /*
+      for(uint64_t page=0;page<size;page+=4096){
+	void *pages = (void *) ( page + (uint64_t)VerticalShmBufs[r] );
+	int status;
+	int flags=MPOL_MF_MOVE_ALL;
+	int nodes=1; // numa domain == MCDRAM
+	unsigned long count=1;
+	ierr= move_pages(0,count, &pages,&nodes,&status,flags);
+	if (ierr && (page==0)) perror("numa relocate command failed");
+      }
+      */
       uint64_t * check = (uint64_t *) VerticalShmBufs[r];
       check[0] = WorldRank;
       check[1] = r;
@@ -404,7 +462,7 @@ void MPIoffloadEngine::CommunicatorInit (MPI_Comm &communicator_world,
     uint64_t * check = (uint64_t *) VerticalShmBufs[r];
     assert(check[0]== WorldRank);
     assert(check[1]== r);
-    std::cerr<<"SHM "<<r<<" " <<VerticalShmBufs[r]<<std::endl;
+    //    std::cerr<<"SHM "<<r<<" " <<VerticalShmBufs[r]<<std::endl;
   }
   }
 #endif
@@ -542,6 +600,8 @@ int Slave::Event (void) {
   static int head_last;
   static int start_last;
   int ierr;
+  MPI_Status stat;
+  static int i=0;
 
   ////////////////////////////////////////////////////
   // Try to advance the start pointers
@@ -550,11 +610,6 @@ int Slave::Event (void) {
   if ( s != state->head ) {
     switch ( state->Descrs[s].command ) {
     case COMMAND_ISEND:
-      /*
-            std::cout<< " Send "<<s << " ptr "<< state<<" "<< state->Descrs[s].buf<< "["<<state->Descrs[s].bytes<<"]"
-      	       << " to " << state->Descrs[s].rank<< " tag" << state->Descrs[s].tag
-       << " Comm " << MPIoffloadEngine::communicator_universe<< " me " <<universe_rank<< std::endl;
-      */
       ierr = MPI_Isend((void *)(state->Descrs[s].buf+base), 
 		       state->Descrs[s].bytes, 
 		       MPI_CHAR,
@@ -568,11 +623,6 @@ int Slave::Event (void) {
       break;
 
     case COMMAND_IRECV:
-      /*
-      std::cout<< " Recv "<<s << " ptr "<< state<<" "<< state->Descrs[s].buf<< "["<<state->Descrs[s].bytes<<"]"
-	       << " from " << state->Descrs[s].rank<< " tag" << state->Descrs[s].tag
-	       << " Comm " << MPIoffloadEngine::communicator_universe<< " me "<< universe_rank<< std::endl;
-      */
       ierr=MPI_Irecv((void *)(state->Descrs[s].buf+base), 
 		     state->Descrs[s].bytes, 
 		     MPI_CHAR,
@@ -588,10 +638,32 @@ int Slave::Event (void) {
       return 1;
       break;
 
+    case COMMAND_SENDRECV:
+
+      //      fprintf(stderr,"Sendrecv ->%d %d : <-%d %d \n",state->Descrs[s].dest, state->Descrs[s].xtag+i*10,state->Descrs[s].src, state->Descrs[s].rtag+i*10);
+
+      ierr=MPI_Sendrecv((void *)(state->Descrs[s].xbuf+base), state->Descrs[s].bytes, MPI_CHAR, state->Descrs[s].dest, state->Descrs[s].xtag+i*10,
+			(void *)(state->Descrs[s].rbuf+base), state->Descrs[s].bytes, MPI_CHAR, state->Descrs[s].src , state->Descrs[s].rtag+i*10,
+			MPIoffloadEngine::communicator_universe,MPI_STATUS_IGNORE);
+
+      assert(ierr==0);
+
+      //      fprintf(stderr,"Sendrecv done %d %d\n",ierr,i);
+      //      MPI_Barrier(MPIoffloadEngine::HorizontalComm);
+      //      fprintf(stderr,"Barrier\n");
+      i++;
+
+      state->start = PERI_PLUS(s);
+
+      return 1;
+      break;
+
     case COMMAND_WAITALL:
 
       for(int t=state->tail;t!=s; t=PERI_PLUS(t) ){
-	MPI_Wait((MPI_Request *)&state->Descrs[t].request,MPI_STATUS_IGNORE);
+	if ( state->Descrs[t].command != COMMAND_SENDRECV ) {
+	  MPI_Wait((MPI_Request *)&state->Descrs[t].request,MPI_STATUS_IGNORE);
+	}
       };
       s=PERI_PLUS(s);
       state->start = s;
@@ -613,6 +685,45 @@ int Slave::Event (void) {
   // External interaction with the queue
   //////////////////////////////////////////////////////////////////////////////
   
+void Slave::QueueSendRecv(void *xbuf, void *rbuf, int bytes, int xtag, int rtag, MPI_Comm comm,int dest,int src) 
+{
+  int head =state->head;
+  int next = PERI_PLUS(head);
+  
+  // Set up descriptor
+  int worldrank;
+  int hashtag;
+  MPI_Comm    communicator;
+  MPI_Request request;
+  uint64_t relative;
+  
+  relative = (uint64_t)xbuf - base;
+  state->Descrs[head].xbuf    = relative;
+  
+  relative= (uint64_t)rbuf - base;
+  state->Descrs[head].rbuf    = relative;
+  
+  state->Descrs[head].bytes  = bytes;
+  
+  MPIoffloadEngine::MapCommRankToWorldRank(hashtag,worldrank,xtag,comm,dest);
+  state->Descrs[head].dest   = MPIoffloadEngine::UniverseRanks[worldrank][vertical_rank];
+  state->Descrs[head].xtag    = hashtag;
+  
+  MPIoffloadEngine::MapCommRankToWorldRank(hashtag,worldrank,rtag,comm,src);
+  state->Descrs[head].src    = MPIoffloadEngine::UniverseRanks[worldrank][vertical_rank];
+  state->Descrs[head].rtag    = hashtag;
+  
+  state->Descrs[head].command= COMMAND_SENDRECV;
+  
+  // Block until FIFO has space
+  while( state->tail==next );
+  
+  // Msync on weak order architectures
+  
+  // Advance pointer
+  state->head = next;
+  
+};
 uint64_t Slave::QueueCommand(int command,void *buf, int bytes, int tag, MPI_Comm comm,int commrank) 
 {
   /////////////////////////////////////////
@@ -812,19 +923,22 @@ void CartesianCommunicator::StencilSendToRecvFromBegin(std::vector<CommsRequest_
   assert( (recv_i >= shm) && (recv_i+bytes <= shm+MAX_MPI_SHM_BYTES) );
   assert(from!=_processor);
   assert(dest!=_processor);
-  MPIoffloadEngine::QueueMultiplexedSend(xmit,bytes,_processor,communicator,dest);
-  MPIoffloadEngine::QueueMultiplexedRecv(recv,bytes,from,communicator,from);
-}
 
+  MPIoffloadEngine::QueueMultiplexedSendRecv(xmit,recv,bytes,_processor,from,communicator,dest,from);
+
+  //MPIoffloadEngine::QueueRoundRobinSendRecv(xmit,recv,bytes,_processor,from,communicator,dest,from);
+
+  //MPIoffloadEngine::QueueMultiplexedSend(xmit,bytes,_processor,communicator,dest);
+  //MPIoffloadEngine::QueueMultiplexedRecv(recv,bytes,from,communicator,from);
+}
 
 void CartesianCommunicator::StencilSendToRecvFromComplete(std::vector<CommsRequest_t> &list)
 {
   MPIoffloadEngine::WaitAll();
+  //this->Barrier();
 }
 
-void CartesianCommunicator::StencilBarrier(void)
-{
-}
+void CartesianCommunicator::StencilBarrier(void) { }
 
 void CartesianCommunicator::SendToRecvFromComplete(std::vector<CommsRequest_t> &list)
 {
@@ -869,9 +983,6 @@ void *CartesianCommunicator::ShmBufferTranslate(int rank,void * local_p) {
   return NULL;
 }
 
-  void CartesianCommunicator::PrintRankInfo(){
-    std::cout << "Grid: Rank "<< _processor << "  -  Physical node name: " << name << std::endl;
-  }
 
 };
 

lib/communicator/Communicator_none.cc

@@ -25,7 +25,8 @@ Author: Peter Boyle <paboyle@ph.ed.ac.uk>
     See the full license in the file "LICENSE" in the top level distribution directory
     *************************************************************************************/
     /*  END LEGAL */
-#include "Grid.h"
+#include <Grid/GridCore.h>
+
 namespace Grid {
 
 ///////////////////////////////////////////////////////////////////////////////////////////////////
@@ -37,11 +38,6 @@ void CartesianCommunicator::Init(int *argc, char *** arv)
   ShmInitGeneric();
 }
 
-void CartesianCommunicator::PrintRankInfo(){
-    std::cout << GridLogMessage << "No Rank Info available" << std::endl;
-}
-
-
 CartesianCommunicator::CartesianCommunicator(const std::vector<int> &processors)
 {
   _processors = processors;
@@ -65,10 +61,10 @@ void CartesianCommunicator::GlobalSum(uint64_t &){}
 void CartesianCommunicator::GlobalSumVector(double *,int N){}
 
 void CartesianCommunicator::SendRecvPacket(void *xmit,
-                                           void *recv,
-                                           int xmit_to_rank,
-                                           int recv_from_rank,
-                                           int bytes)
+					   void *recv,
+					   int xmit_to_rank,
+					   int recv_from_rank,
+					   int bytes)
 {
   assert(0);
 }
@@ -76,22 +72,23 @@ void CartesianCommunicator::SendRecvPacket(void *xmit,
 
 // Basic Halo comms primitive -- should never call in single node
 void CartesianCommunicator::SendToRecvFrom(void *xmit,
-                                           int dest,
-                                           void *recv,
-                                           int from,
-                                           int bytes)
+					   int dest,
+					   void *recv,
+					   int from,
+					   int bytes)
 {
   assert(0);
 }
 void CartesianCommunicator::SendToRecvFromBegin(std::vector<CommsRequest_t> &list,
-                                                void *xmit,
-                                                int dest,
-                                                void *recv,
-                                                int from,
-                                                int bytes)
+						void *xmit,
+						int dest,
+						void *recv,
+						int from,
+						int bytes)
 {
   assert(0);
 }
+
 void CartesianCommunicator::SendToRecvFromComplete(std::vector<CommsRequest_t> &list)
 {
   assert(0);
@@ -102,7 +99,7 @@ void CartesianCommunicator::Barrier(void){}
 void CartesianCommunicator::Broadcast(int root,void* data, int bytes) {}
 void CartesianCommunicator::BroadcastWorld(int root,void* data, int bytes) { }
 int  CartesianCommunicator::RankFromProcessorCoor(std::vector<int> &coor) {  return 0;}
-void CartesianCommunicator::ProcessorCoorFromRank(int rank, std::vector<int> &coor){ coor = _processor_coor ;}
+void CartesianCommunicator::ProcessorCoorFromRank(int rank, std::vector<int> &coor){  coor = _processor_coor; }
 void CartesianCommunicator::ShiftedRanks(int dim,int shift,int &source,int &dest)
 {
   source =0;

lib/communicator/Communicator_shmem.cc

@@ -25,8 +25,9 @@ Author: Peter Boyle <paboyle@ph.ed.ac.uk>
     See the full license in the file "LICENSE" in the top level distribution directory
     *************************************************************************************/
     /*  END LEGAL */
-#include "Grid.h"
+#include <Grid/Grid.h>
 #include <mpp/shmem.h>
+#include <array>
 
 namespace Grid {
 
@@ -51,7 +52,7 @@ typedef struct HandShake_t {
 } HandShake;
 
 std::array<long,_SHMEM_REDUCE_SYNC_SIZE> make_psync_init(void) {
-  array<long,_SHMEM_REDUCE_SYNC_SIZE> ret;
+  std::array<long,_SHMEM_REDUCE_SYNC_SIZE> ret;
   ret.fill(SHMEM_SYNC_VALUE);
   return ret;
 }
@@ -109,7 +110,7 @@ void CartesianCommunicator::GlobalSum(uint32_t &u){
 
   source = u;
   dest   = 0;
-  shmem_longlong_sum_to_all(&dest,&source,1,0,0,_Nprocessors,llwrk,psync);
+  shmem_longlong_sum_to_all(&dest,&source,1,0,0,_Nprocessors,llwrk,psync.data());
   shmem_barrier_all(); // necessary?
   u = dest;
 }
@@ -125,7 +126,7 @@ void CartesianCommunicator::GlobalSum(uint64_t &u){
 
   source = u;
   dest   = 0;
-  shmem_longlong_sum_to_all(&dest,&source,1,0,0,_Nprocessors,llwrk,psync);
+  shmem_longlong_sum_to_all(&dest,&source,1,0,0,_Nprocessors,llwrk,psync.data());
   shmem_barrier_all(); // necessary?
   u = dest;
 }
@@ -137,7 +138,8 @@ void CartesianCommunicator::GlobalSum(float &f){
 
   source = f;
   dest   =0.0;
-  shmem_float_sum_to_all(&dest,&source,1,0,0,_Nprocessors,llwrk,psync);
+  shmem_float_sum_to_all(&dest,&source,1,0,0,_Nprocessors,llwrk,psync.data());
+  shmem_barrier_all();
   f = dest;
 }
 void CartesianCommunicator::GlobalSumVector(float *f,int N)
@@ -148,14 +150,16 @@ void CartesianCommunicator::GlobalSumVector(float *f,int N)
   static std::array<long,_SHMEM_REDUCE_SYNC_SIZE> psync =  psync_init;
 
   if ( shmem_addr_accessible(f,_processor)  ){
-    shmem_float_sum_to_all(f,f,N,0,0,_Nprocessors,llwrk,psync);
+    shmem_float_sum_to_all(f,f,N,0,0,_Nprocessors,llwrk,psync.data());
+    shmem_barrier_all();
     return;
   }
 
   for(int i=0;i<N;i++){
     dest   =0.0;
     source = f[i];
-    shmem_float_sum_to_all(&dest,&source,1,0,0,_Nprocessors,llwrk,psync);
+    shmem_float_sum_to_all(&dest,&source,1,0,0,_Nprocessors,llwrk,psync.data());
+    shmem_barrier_all();
     f[i] = dest;
   }
 }
@@ -168,7 +172,8 @@ void CartesianCommunicator::GlobalSum(double &d)
 
   source = d;
   dest   = 0;
-  shmem_double_sum_to_all(&dest,&source,1,0,0,_Nprocessors,llwrk,psync);
+  shmem_double_sum_to_all(&dest,&source,1,0,0,_Nprocessors,llwrk,psync.data());
+  shmem_barrier_all();
   d = dest;
 }
 void CartesianCommunicator::GlobalSumVector(double *d,int N)
@@ -180,14 +185,16 @@ void CartesianCommunicator::GlobalSumVector(double *d,int N)
 
 
   if ( shmem_addr_accessible(d,_processor)  ){
-    shmem_double_sum_to_all(d,d,N,0,0,_Nprocessors,llwrk,psync);
+    shmem_double_sum_to_all(d,d,N,0,0,_Nprocessors,llwrk,psync.data());
+    shmem_barrier_all();
     return;
   }
 
   for(int i=0;i<N;i++){
     source = d[i];
     dest   =0.0;
-    shmem_double_sum_to_all(&dest,&source,1,0,0,_Nprocessors,llwrk,psync);
+    shmem_double_sum_to_all(&dest,&source,1,0,0,_Nprocessors,llwrk,psync.data());
+    shmem_barrier_all();
     d[i] = dest;
   }
 }
@@ -282,11 +289,13 @@ void CartesianCommunicator::SendToRecvFromBegin(std::vector<CommsRequest_t> &lis
   SHMEM_VET(recv);
   //  shmem_putmem_nb(recv,xmit,bytes,dest,NULL);
   shmem_putmem(recv,xmit,bytes,dest);
+
+  if ( CommunicatorPolicy == CommunicatorPolicySequential ) shmem_barrier_all(); 
 }
 void CartesianCommunicator::SendToRecvFromComplete(std::vector<CommsRequest_t> &list)
 {
   //  shmem_quiet();      // I'm done
-  shmem_barrier_all();// He's done too
+  if( CommunicatorPolicy == CommunicatorPolicyConcurrent ) shmem_barrier_all();// He's done too
 }
 void CartesianCommunicator::Barrier(void)
 {
@@ -301,13 +310,13 @@ void CartesianCommunicator::Broadcast(int root,void* data, int bytes)
   int words = bytes/4;
 
   if ( shmem_addr_accessible(data,_processor)  ){
-    shmem_broadcast32(data,data,words,root,0,0,shmem_n_pes(),psync);
+    shmem_broadcast32(data,data,words,root,0,0,shmem_n_pes(),psync.data());
     return;
   }
 
   for(int w=0;w<words;w++){
     word = array[w];
-    shmem_broadcast32((void *)&word,(void *)&word,1,root,0,0,shmem_n_pes(),psync);
+    shmem_broadcast32((void *)&word,(void *)&word,1,root,0,0,shmem_n_pes(),psync.data());
     if ( shmem_my_pe() != root ) {
       array[w] = word;
     }
@@ -325,7 +334,7 @@ void CartesianCommunicator::BroadcastWorld(int root,void* data, int bytes)
 
   for(int w=0;w<words;w++){
     word = array[w];
-    shmem_broadcast32((void *)&word,(void *)&word,1,root,0,0,shmem_n_pes(),psync);
+    shmem_broadcast32((void *)&word,(void *)&word,1,root,0,0,shmem_n_pes(),psync.data());
     if ( shmem_my_pe() != root ) {
       array[w]= word;
     }
@@ -333,9 +342,9 @@ void CartesianCommunicator::BroadcastWorld(int root,void* data, int bytes)
   }
 }
   
-  void CartesianCommunicator::PrintRankInfo(){
-    std::cout << GridLogMessage << "SHMEM: Rank Info not implemented yet" << std::endl;
-  }
+int CartesianCommunicator::RankWorld(void){ 
+  return shmem_my_pe();
+}
 
 }
 

lib/cshift/Cshift_common.h

@@ -1,5 +1,4 @@
-
-    /*************************************************************************************
+/*************************************************************************************
 
     Grid physics library, www.github.com/paboyle/Grid 
 
@@ -31,21 +30,11 @@ Author: Peter Boyle <paboyle@ph.ed.ac.uk>
 
 namespace Grid {
 
-template<class vobj>
-class SimpleCompressor {
-public:
-  void Point(int) {};
-
-  vobj operator() (const vobj &arg) {
-    return arg;
-  }
-};
-
 ///////////////////////////////////////////////////////////////////
-// Gather for when there is no need to SIMD split with compression
+// Gather for when there is no need to SIMD split 
 ///////////////////////////////////////////////////////////////////
-template<class vobj,class cobj,class compressor> void 
-Gather_plane_simple (const Lattice<vobj> &rhs,commVector<cobj> &buffer,int dimension,int plane,int cbmask,compressor &compress, int off=0)
+template<class vobj> void 
+Gather_plane_simple (const Lattice<vobj> &rhs,commVector<vobj> &buffer,int dimension,int plane,int cbmask, int off=0)
 {
   int rd = rhs._grid->_rdimensions[dimension];
 
@@ -53,19 +42,17 @@ Gather_plane_simple (const Lattice<vobj> &rhs,commVector<cobj> &buffer,int dimen
     cbmask = 0x3;
   }
   
-  int so  = plane*rhs._grid->_ostride[dimension]; // base offset for start of plane 
-  
+  int so=plane*rhs._grid->_ostride[dimension]; // base offset for start of plane 
   int e1=rhs._grid->_slice_nblock[dimension];
   int e2=rhs._grid->_slice_block[dimension];
 
   int stride=rhs._grid->_slice_stride[dimension];
   if ( cbmask == 0x3 ) { 
-PARALLEL_NESTED_LOOP2
-    for(int n=0;n<e1;n++){
+    parallel_for_nest2(int n=0;n<e1;n++){
       for(int b=0;b<e2;b++){
 	int o  = n*stride;
 	int bo = n*e2;
-	buffer[off+bo+b]=compress(rhs._odata[so+o+b]);
+	buffer[off+bo+b]=rhs._odata[so+o+b];
       }
     }
   } else { 
@@ -74,25 +61,23 @@ PARALLEL_NESTED_LOOP2
      for(int n=0;n<e1;n++){
        for(int b=0;b<e2;b++){
 	 int o  = n*stride;
-	 int ocb=1<<rhs._grid->CheckerBoardFromOindexTable(o+b);
+	 int ocb=1<<rhs._grid->CheckerBoardFromOindex(o+b);
 	 if ( ocb &cbmask ) {
 	   table.push_back(std::pair<int,int> (bo++,o+b));
 	 }
        }
      }
-PARALLEL_FOR_LOOP     
-     for(int i=0;i<table.size();i++){
-       buffer[off+table[i].first]=compress(rhs._odata[so+table[i].second]);
+     parallel_for(int i=0;i<table.size();i++){
+       buffer[off+table[i].first]=rhs._odata[so+table[i].second];
      }
   }
 }
 
-
 ///////////////////////////////////////////////////////////////////
-// Gather for when there *is* need to SIMD split with compression
+// Gather for when there *is* need to SIMD split 
 ///////////////////////////////////////////////////////////////////
-template<class cobj,class vobj,class compressor> void 
-Gather_plane_extract(const Lattice<vobj> &rhs,std::vector<typename cobj::scalar_object *> pointers,int dimension,int plane,int cbmask,compressor &compress)
+template<class vobj> void 
+Gather_plane_extract(const Lattice<vobj> &rhs,std::vector<typename vobj::scalar_object *> pointers,int dimension,int plane,int cbmask)
 {
   int rd = rhs._grid->_rdimensions[dimension];
 
@@ -105,57 +90,40 @@ Gather_plane_extract(const Lattice<vobj> &rhs,std::vector<typename cobj::scalar_
   int e1=rhs._grid->_slice_nblock[dimension];
   int e2=rhs._grid->_slice_block[dimension];
   int n1=rhs._grid->_slice_stride[dimension];
-  int n2=rhs._grid->_slice_block[dimension];
+
   if ( cbmask ==0x3){
-PARALLEL_NESTED_LOOP2
-    for(int n=0;n<e1;n++){
+    parallel_for_nest2(int n=0;n<e1;n++){
       for(int b=0;b<e2;b++){
 
 	int o      =   n*n1;
-	int offset = b+n*n2;
-	cobj temp =compress(rhs._odata[so+o+b]);
+	int offset = b+n*e2;
 	
-	extract<cobj>(temp,pointers,offset);
+	vobj temp =rhs._odata[so+o+b];
+	extract<vobj>(temp,pointers,offset);
 
       }
     }
   } else { 
 
-    assert(0); //Fixme think this is buggy
-
-    for(int n=0;n<e1;n++){
+    // Case of SIMD split AND checker dim cannot currently be hit, except in 
+    // Test_cshift_red_black code.
+    std::cout << " Dense packed buffer WARNING " <<std::endl;
+    parallel_for_nest2(int n=0;n<e1;n++){
       for(int b=0;b<e2;b++){
-	int o=n*rhs._grid->_slice_stride[dimension];
+
+	int o=n*n1;
 	int ocb=1<<rhs._grid->CheckerBoardFromOindex(o+b);
-	int offset = b+n*rhs._grid->_slice_block[dimension];
+	int offset = b+n*e2;
 
 	if ( ocb & cbmask ) {
-	  cobj temp =compress(rhs._odata[so+o+b]);
-	  extract<cobj>(temp,pointers,offset);
+	  vobj temp =rhs._odata[so+o+b];
+	  extract<vobj>(temp,pointers,offset);
 	}
       }
     }
   }
 }
 
-//////////////////////////////////////////////////////
-// Gather for when there is no need to SIMD split
-//////////////////////////////////////////////////////
-template<class vobj> void Gather_plane_simple (const Lattice<vobj> &rhs,commVector<vobj> &buffer, int dimension,int plane,int cbmask)
-{
-  SimpleCompressor<vobj> dontcompress;
-  Gather_plane_simple (rhs,buffer,dimension,plane,cbmask,dontcompress);
-}
-
-//////////////////////////////////////////////////////
-// Gather for when there *is* need to SIMD split
-//////////////////////////////////////////////////////
-template<class vobj> void Gather_plane_extract(const Lattice<vobj> &rhs,std::vector<typename vobj::scalar_object *> pointers,int dimension,int plane,int cbmask)
-{
-  SimpleCompressor<vobj> dontcompress;
-  Gather_plane_extract<vobj,vobj,decltype(dontcompress)>(rhs,pointers,dimension,plane,cbmask,dontcompress);
-}
-
 //////////////////////////////////////////////////////
 // Scatter for when there is no need to SIMD split
 //////////////////////////////////////////////////////
@@ -171,10 +139,10 @@ template<class vobj> void Scatter_plane_simple (Lattice<vobj> &rhs,commVector<vo
     
   int e1=rhs._grid->_slice_nblock[dimension];
   int e2=rhs._grid->_slice_block[dimension];
+  int stride=rhs._grid->_slice_stride[dimension];
   
   if ( cbmask ==0x3 ) {
-PARALLEL_NESTED_LOOP2
-    for(int n=0;n<e1;n++){
+    parallel_for_nest2(int n=0;n<e1;n++){
       for(int b=0;b<e2;b++){
 	int o   =n*rhs._grid->_slice_stride[dimension];
 	int bo  =n*rhs._grid->_slice_block[dimension];
@@ -182,24 +150,28 @@ PARALLEL_NESTED_LOOP2
       }
     }
   } else { 
+    std::vector<std::pair<int,int> > table;
     int bo=0;
     for(int n=0;n<e1;n++){
       for(int b=0;b<e2;b++){
 	int o   =n*rhs._grid->_slice_stride[dimension];
-	int bo  =n*rhs._grid->_slice_block[dimension];
 	int ocb=1<<rhs._grid->CheckerBoardFromOindex(o+b);// Could easily be a table lookup
 	if ( ocb & cbmask ) {
-	  rhs._odata[so+o+b]=buffer[bo++];
+	  table.push_back(std::pair<int,int> (so+o+b,bo++));
 	}
       }
     }
+    parallel_for(int i=0;i<table.size();i++){
+       //       std::cout << "Rcv"<< table[i].first << " " << table[i].second << " " <<buffer[table[i].second]<<std::endl;
+       rhs._odata[table[i].first]=buffer[table[i].second];
+     }
   }
 }
 
 //////////////////////////////////////////////////////
 // Scatter for when there *is* need to SIMD split
 //////////////////////////////////////////////////////
- template<class vobj,class cobj> void Scatter_plane_merge(Lattice<vobj> &rhs,std::vector<cobj *> pointers,int dimension,int plane,int cbmask)
+template<class vobj> void Scatter_plane_merge(Lattice<vobj> &rhs,std::vector<typename vobj::scalar_object *> pointers,int dimension,int plane,int cbmask)
 {
   int rd = rhs._grid->_rdimensions[dimension];
 
@@ -213,8 +185,7 @@ PARALLEL_NESTED_LOOP2
   int e2=rhs._grid->_slice_block[dimension];
 
   if(cbmask ==0x3 ) {
-PARALLEL_NESTED_LOOP2
-    for(int n=0;n<e1;n++){
+    parallel_for_nest2(int n=0;n<e1;n++){
       for(int b=0;b<e2;b++){
 	int o      = n*rhs._grid->_slice_stride[dimension];
 	int offset = b+n*rhs._grid->_slice_block[dimension];
@@ -222,7 +193,11 @@ PARALLEL_NESTED_LOOP2
       }
     }
   } else { 
-    assert(0); // think this is buggy FIXME
+
+    // Case of SIMD split AND checker dim cannot currently be hit, except in 
+    // Test_cshift_red_black code.
+    //    std::cout << "Scatter_plane merge assert(0); think this is buggy FIXME "<< std::endl;// think this is buggy FIXME
+    std::cout<<" Unthreaded warning -- buffer is not densely packed ??"<<std::endl;
     for(int n=0;n<e1;n++){
       for(int b=0;b<e2;b++){
 	int o      = n*rhs._grid->_slice_stride[dimension];
@@ -254,8 +229,7 @@ template<class vobj> void Copy_plane(Lattice<vobj>& lhs,const Lattice<vobj> &rhs
   int e2=rhs._grid->_slice_block[dimension];
   int stride = rhs._grid->_slice_stride[dimension];
   if(cbmask == 0x3 ){
-PARALLEL_NESTED_LOOP2
-    for(int n=0;n<e1;n++){
+    parallel_for_nest2(int n=0;n<e1;n++){
       for(int b=0;b<e2;b++){
  
         int o =n*stride+b;
@@ -264,8 +238,7 @@ PARALLEL_NESTED_LOOP2
       }
     }
   } else { 
-PARALLEL_NESTED_LOOP2
-    for(int n=0;n<e1;n++){
+    parallel_for_nest2(int n=0;n<e1;n++){
       for(int b=0;b<e2;b++){
  
         int o =n*stride+b;
@@ -295,8 +268,8 @@ template<class vobj> void Copy_plane_permute(Lattice<vobj>& lhs,const Lattice<vo
   int e1=rhs._grid->_slice_nblock[dimension];
   int e2=rhs._grid->_slice_block [dimension];
   int stride = rhs._grid->_slice_stride[dimension];
-PARALLEL_NESTED_LOOP2
-  for(int n=0;n<e1;n++){
+
+  parallel_for_nest2(int n=0;n<e1;n++){
   for(int b=0;b<e2;b++){
 
       int o  =n*stride;
@@ -338,8 +311,8 @@ template<class vobj> Lattice<vobj> Cshift_local(Lattice<vobj> &ret,const Lattice
   // Map to always positive shift modulo global full dimension.
   shift = (shift+fd)%fd;
 
-  ret.checkerboard = grid->CheckerBoardDestination(rhs.checkerboard,shift,dimension);
   // the permute type
+  ret.checkerboard = grid->CheckerBoardDestination(rhs.checkerboard,shift,dimension);
   int permute_dim =grid->PermuteDim(dimension);
   int permute_type=grid->PermuteType(dimension);
   int permute_type_dist;
@@ -348,7 +321,6 @@ template<class vobj> Lattice<vobj> Cshift_local(Lattice<vobj> &ret,const Lattice
 
     int o   = 0;
     int bo  = x * grid->_ostride[dimension];
-    
     int cb= (cbmask==0x2)? Odd : Even;
 
     int sshift = grid->CheckerBoardShiftForCB(rhs.checkerboard,dimension,shift,cb);
@@ -361,9 +333,23 @@ template<class vobj> Lattice<vobj> Cshift_local(Lattice<vobj> &ret,const Lattice
     // wrap is whether sshift > rd.
     //  num is sshift mod rd.
     // 
+    //  shift 7
+    //
+    //  XoXo YcYc 
+    //  oXoX cYcY
+    //  XoXo YcYc
+    //  oXoX cYcY
+    //
+    //  sshift -- 
+    //
+    //  XX YY ; 3
+    //  XX YY ; 0
+    //  XX YY ; 3
+    //  XX YY ; 0
+    //
     int permute_slice=0;
     if(permute_dim){
-      int wrap = sshift/rd;
+      int wrap = sshift/rd; wrap=wrap % ly;
       int  num = sshift%rd;
 
       if ( x< rd-num ) permute_slice=wrap;
@@ -375,7 +361,6 @@ template<class vobj> Lattice<vobj> Cshift_local(Lattice<vobj> &ret,const Lattice
       } else {
 	permute_type_dist = permute_type;
       }
-      
     }
 
     if ( permute_slice ) Copy_plane_permute(ret,rhs,dimension,x,sx,cbmask,permute_type_dist);