Merge branch 'release/v0.6.0'

Double precision compile fix

.gitignore

@@ -9,7 +9,6 @@
 ################
 *~
 *#
-*.sublime-*
 
 # Precompiled Headers #
 #######################
@@ -48,9 +47,7 @@ Config.h.in
 config.log
 config.status
 .deps
-Make.inc
-eigen.inc
-Eigen.inc
+*.inc
 
 # http://www.gnu.org/software/autoconf #
 ########################################
@@ -105,15 +102,3 @@ 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

@@ -102,5 +102,5 @@ script:
     - ../configure --enable-precision=single --enable-simd=SSE4 --enable-comms=mpi-auto
     - make -j4
     - 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

@@ -1,12 +1,10 @@
 # additional include paths necessary to compile the C++ library
-SUBDIRS = lib benchmarks tests extras
+SUBDIRS = lib benchmarks tests
 
-include $(top_srcdir)/doxygen.inc
+.PHONY: tests
 
 tests: all
 	$(MAKE) -C tests tests
 
-.PHONY: tests doxygen-run doxygen-doc $(DX_PS_GOAL) $(DX_PDF_GOAL)
-
 AM_CXXFLAGS += -I$(top_builddir)/include
 ACLOCAL_AMFLAGS = -I m4

README.md

@@ -116,15 +116,13 @@ If you want to build all the tests at once just use `make tests`.
 - `--with-fftw=<path>`: look for FFTW in the UNIX prefix `<path>`
 - `--enable-lapack[=<path>]`: enable LAPACK support in Lanczos eigensolver. A UNIX prefix containing the library can be specified (optional).
 - `--enable-mkl[=<path>]`: use Intel MKL for FFT (and LAPACK if enabled) routines. A UNIX prefix containing the library can be specified (optional).
-- `--enable-numa`: enable NUMA first touch optimisation
+- `--enable-numa`: ???
 - `--enable-simd=<code>`: setup Grid for the SIMD target `<code>` (default: `GEN`). A list of possible SIMD targets is detailed in a section below.
-- `--enable-gen-simd-width=<size>`: select the size (in bytes) of the generic SIMD vector type (default: 32 bytes).
 - `--enable-precision={single|double}`: set the default precision (default: `double`).
 - `--enable-precision=<comm>`: Use `<comm>` for message passing (default: `none`). A list of possible SIMD targets is detailed in a section below.
 - `--enable-rng={ranlux48|mt19937}`: choose the RNG (default: `ranlux48 `).
 - `--disable-timers`: disable system dependent high-resolution timers.
 - `--enable-chroma`: enable Chroma regression tests.
-- `--enable-doxygen-doc`: enable the Doxygen documentation generation (build with `make doxygen-doc`)
 
 ### Possible communication interfaces
 
@@ -138,7 +136,7 @@ The following options can be use with the `--enable-comms=` option to target dif
 | `mpi3l[-auto]` | MPI communications using MPI 3 shared memory and leader model |
 | `shmem `       | Cray SHMEM communications                                     |
 
-For the MPI interfaces the optional `-auto` suffix instructs the `configure` scripts to determine all the necessary compilation and linking flags. This is done by extracting the informations from the MPI wrapper specified in the environment variable `MPICXX` (if not specified `configure` will scan though a list of default names). The `-auto` suffix is not supported by the Cray environment wrapper scripts. Use the standard versions instead.  
+For the MPI interfaces the optional `-auto` suffix instructs the `configure` scripts to determine all the necessary compilation and linking flags. This is done by extracting the informations from the MPI wrapper specified in the environment variable `MPICXX` (if not specified `configure` will scan though a list of default names).
 
 ### Possible SIMD types
 
@@ -167,7 +165,6 @@ Alternatively, some CPU codenames can be directly used:
 - We currently support AVX512 only for the Intel compiler. Support for GCC and clang will appear in future versions of Grid when the AVX512 support within GCC and clang will be more advanced.
 - For BG/Q only [bgclang](http://trac.alcf.anl.gov/projects/llvm-bgq) is supported. We do not presently plan to support more compilers for this platform.
 - BG/Q performances are currently rather poor. This is being investigated for future versions.
-- The vector size for the `GEN` target can be specified with the `configure` script option `--enable-gen-simd-width`.
 
 ### Build setup for Intel Knights Landing platform
 

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=24;
-  for(int lat=4;lat<=maxlat;lat+=4){
-    for(int Ls=8;Ls<=32;Ls*=2){
+  int maxlat=16;
+  for(int lat=4;lat<=maxlat;lat+=2){
+    for(int Ls=1;Ls<=16;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+=4){
-    for(int Ls=8;Ls<=32;Ls*=2){
+  for(int lat=4;lat<=maxlat;lat+=2){
+    for(int Ls=1;Ls<=16;Ls*=2){
 
       std::vector<int> latt_size  ({lat,lat,lat,lat});
 
@@ -194,14 +194,14 @@ int main (int argc, char ** argv)
   }  
 
 
-  Nloop=10;
+  Nloop=100;
   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+=4){
-    for(int Ls=8;Ls<=32;Ls*=2){
+  for(int lat=4;lat<=maxlat;lat+=2){
+    for(int Ls=1;Ls<=16;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+=4){
-    for(int Ls=8;Ls<=32;Ls*=2){
+  for(int lat=4;lat<=maxlat;lat+=2){
+    for(int Ls=1;Ls<=16;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::Algebra Gmu [] = {
-    Gamma::Algebra::GammaX,
-    Gamma::Algebra::GammaY,
-    Gamma::Algebra::GammaZ,
-    Gamma::Algebra::GammaT
+  Gamma::GammaMatrix Gmu [] = {
+    Gamma::GammaX,
+    Gamma::GammaY,
+    Gamma::GammaZ,
+    Gamma::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=16;
+  const int Ls=8;
   GridCartesian         * UGrid   = SpaceTimeGrid::makeFourDimGrid(GridDefaultLatt(), GridDefaultSimd(Nd,vComplex::Nsimd()),GridDefaultMpi());
   GridRedBlackCartesian * UrbGrid = SpaceTimeGrid::makeFourDimRedBlackGrid(UGrid);
   GridCartesian         * FGrid   = SpaceTimeGrid::makeFiveDimGrid(Ls,UGrid);
@@ -72,65 +72,34 @@ 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); 
-  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
+  random(RNG4,Umu);
 
-  ////////////////////////////////////
-  // Naive wilson implementation
-  ////////////////////////////////////
-  // replicate across fifth dimension
   LatticeGaugeField Umu5d(FGrid); 
-  std::vector<LatticeColourMatrix> U(4,FGrid);
+
+  // replicate across fifth dimension
   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)
   {
@@ -152,7 +121,6 @@ int main (int argc, char ** argv)
 
   RealD NP = UGrid->_Nprocessors;
 
-  std::cout << GridLogMessage << "Creating action operator " << std::endl;
   DomainWallFermionR Dw(Umu,*FGrid,*FrbGrid,*UGrid,*UrbGrid,mass,M5);
 
   std::cout << GridLogMessage<< "*****************************************************************" <<std::endl;
@@ -168,11 +136,10 @@ 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 =1000;
+  int ncall =100;
   if (1) {
     FGrid->Barrier();
     Dw.ZeroCounters();
-    Dw.Dhop(src,result,0);
     double t0=usecond();
     for(int i=0;i<ncall;i++){
       __SSC_START;
@@ -186,22 +153,12 @@ 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();
   }
@@ -226,12 +183,20 @@ int main (int argc, char ** argv)
 
     WilsonFermion5DR sDw(Umu,*sFGrid,*sFrbGrid,*sUGrid,*sUrbGrid,M5);
   
-    localConvert(src,ssrc);
+    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);
+    }}}}}
     std::cout<<GridLogMessage<< "src norms "<< norm2(src)<<" " <<norm2(ssrc)<<std::endl;
     FGrid->Barrier();
-    sDw.Dhop(ssrc,sresult,0);
-    sDw.ZeroCounters();
     double t0=usecond();
+    sDw.ZeroCounters();
     for(int i=0;i<ncall;i++){
       __SSC_START;
       sDw.Dhop(ssrc,sresult,0);
@@ -245,47 +210,46 @@ 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;
-
-    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);
-
-    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;
+    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 );
 
+
     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);
@@ -293,23 +257,33 @@ 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;
@@ -324,26 +298,22 @@ 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;
 
+      std::cout<<GridLogMessage << "sE norm diff   "<< norm2(ssrc_e)<< "  vec nrm"<<norm2(sr_e) <<std::endl;
       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<< "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;
+	std::cout<< ssrc << std::endl;
       }
-      assert(error<1.0e-4);
     }
+
+
   }
 
   if (1)
@@ -351,7 +321,7 @@ int main (int argc, char ** argv)
     ref = zero;
     for(int mu=0;mu<Nd;mu++){
 
-      //    ref =  src - Gamma(Gamma::Algebra::GammaX)* src ; // 1+gamma_x
+      //    ref =  src - Gamma(Gamma::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]; ;
@@ -365,19 +335,14 @@ int main (int argc, char ** argv)
     }
     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 dag result "<< norm2(result)<<std::endl;
-  std::cout<<GridLogMessage << "norm dag ref    "<< norm2(ref)<<std::endl;
+  std::cout<<GridLogMessage << "norm result "<< norm2(result)<<std::endl;
+  std::cout<<GridLogMessage << "norm ref    "<< norm2(ref)<<std::endl;
   err = ref-result; 
-  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;
-  }
+  std::cout<<GridLogMessage << "norm diff   "<< norm2(err)<<std::endl;
+  assert(norm2(err)<1.0e-4);
   LatticeFermion src_e (FrbGrid);
   LatticeFermion src_o (FrbGrid);
   LatticeFermion r_e   (FrbGrid);
@@ -385,18 +350,13 @@ 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;
@@ -409,7 +369,6 @@ 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);
@@ -437,19 +396,14 @@ int main (int argc, char ** argv)
 
   err = r_eo-result; 
   std::cout<<GridLogMessage << "norm diff   "<< norm2(err)<<std::endl;
-  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;
-  }
+  assert(norm2(err)<1.0e-4);
 
   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::Algebra Gmu [] = {
-    Gamma::Algebra::GammaX,
-    Gamma::Algebra::GammaY,
-    Gamma::Algebra::GammaZ,
-    Gamma::Algebra::GammaT
+  Gamma::GammaMatrix Gmu [] = {
+    Gamma::GammaX,
+    Gamma::GammaY,
+    Gamma::GammaZ,
+    Gamma::GammaT
   };
 
 void benchDw(std::vector<int> & L, int Ls, int threads, int report =0 );

benchmarks/Benchmark_memory_asynch.cc

@@ -66,8 +66,7 @@ int main (int argc, char ** argv)
 
     Vec tsum; tsum = zero;
 
-    GridParallelRNG          pRNG(&Grid);      
-    pRNG.SeedFixedIntegers(std::vector<int>({56,17,89,101}));
+    GridParallelRNG          pRNG(&Grid);      pRNG.SeedRandomDevice();
 
     std::vector<double> stop(threads);
     Vector<Vec> sum(threads);
@@ -78,7 +77,8 @@ int main (int argc, char ** argv)
     }
 
     double start=usecond();
-    parallel_for(int t=0;t<threads;t++){
+PARALLEL_FOR_LOOP
+    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.SeedFixedIntegers(std::vector<int>({45,12,81,9});
+      //      GridParallelRNG          pRNG(&Grid);      pRNG.SeedRandomDevice();
 
       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.SeedFixedIntegers(std::vector<int>({45,12,81,9});
+      //      GridParallelRNG          pRNG(&Grid);      pRNG.SeedRandomDevice();
 
       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.SeedFixedIntegers(std::vector<int>({45,12,81,9});
+      //      GridParallelRNG          pRNG(&Grid);      pRNG.SeedRandomDevice();
 
       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.SeedFixedIntegers(std::vector<int>({45,12,81,9});
+      //      GridParallelRNG          pRNG(&Grid);      pRNG.SeedRandomDevice();
       LatticeVec z(&Grid); //random(pRNG,z);
       LatticeVec x(&Grid); //random(pRNG,x);
       LatticeVec y(&Grid); //random(pRNG,y);

benchmarks/Benchmark_mooee.cc

@@ -1,222 +0,0 @@
-    /*************************************************************************************
-
-    Grid physics library, www.github.com/paboyle/Grid 
-
-    Source file: ./benchmarks/Benchmark_dwf.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);
-
-  int threads = GridThread::GetThreads();
-  std::cout<<GridLogMessage << "Grid is setup to use "<<threads<<" threads"<<std::endl;
-
-  std::vector<int> latt4 = GridDefaultLatt();
-  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);
-  GridRedBlackCartesian * FrbGrid = SpaceTimeGrid::makeFiveDimRedBlackGrid(Ls,UGrid);
-
-  std::cout << GridLogMessage << "Making Vec5d innermost grids"<<std::endl;
-  GridCartesian         * sUGrid   = SpaceTimeGrid::makeFourDimDWFGrid(GridDefaultLatt(),GridDefaultMpi());
-  GridRedBlackCartesian * sUrbGrid = SpaceTimeGrid::makeFourDimRedBlackGrid(sUGrid);
-  GridCartesian         * sFGrid   = SpaceTimeGrid::makeFiveDimDWFGrid(Ls,UGrid);
-  GridRedBlackCartesian * sFrbGrid = SpaceTimeGrid::makeFiveDimDWFRedBlackGrid(Ls,UGrid);
-
-  std::vector<int> seeds4({1,2,3,4});
-  std::vector<int> seeds5({5,6,7,8});
-
-  GridParallelRNG          RNG4(UGrid);  RNG4.SeedFixedIntegers(seeds4);
-  std::cout << GridLogMessage << "Seeded"<<std::endl;
-
-  LatticeGaugeField Umu(UGrid); SU3::HotConfiguration(RNG4,Umu);
-
-  std::cout << GridLogMessage << "made random gauge fields"<<std::endl;
-
-  RealD mass=0.1;
-  RealD M5  =1.8;
-  RealD NP = UGrid->_Nprocessors;
-
-
-  if (1)
-  {
-    const int ncall=1000;
-
-    std::cout << GridLogMessage<< "*********************************************************" <<std::endl;
-    std::cout << GridLogMessage<< "* Benchmarking DomainWallFermionR::Dhop "<<std::endl;
-    std::cout << GridLogMessage<< "*********************************************************" <<std::endl;
-
-    GridParallelRNG RNG5(FGrid);
-    LatticeFermion src(FGrid); random(RNG5,src);
-    LatticeFermion result(FGrid);
-
-    DomainWallFermionR Dw(Umu,*FGrid,*FrbGrid,*UGrid,*UrbGrid,mass,M5);
-    double t0,t1;
-
-    LatticeFermion r_eo(FGrid);
-    LatticeFermion src_e (FrbGrid);
-    LatticeFermion src_o (FrbGrid);
-    LatticeFermion r_e   (FrbGrid);
-    LatticeFermion r_o   (FrbGrid);
-    
-    pickCheckerboard(Even,src_e,src);
-    pickCheckerboard(Odd,src_o,src);
-    
-    setCheckerboard(r_eo,src_o);
-    setCheckerboard(r_eo,src_e);
-    
-    r_e = zero;
-    r_o = zero;
-
-
-#define BENCH_DW(A,in,out)			\
-    Dw.CayleyZeroCounters();			\
-    Dw. A (in,out);				\
-    FGrid->Barrier();				\
-    t0=usecond();				\
-    for(int i=0;i<ncall;i++){			\
-      Dw. A (in,out);				\
-    }						\
-    t1=usecond();				\
-    FGrid->Barrier();				\
-    Dw.CayleyReport();					\
-    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);				\
-    FGrid->Barrier();				\
-    t0=usecond();				\
-    for(int i=0;i<ncall;i++){			\
-      Dw. A (in,out,0);				\
-    }						\
-    t1=usecond();				\
-    FGrid->Barrier();				\
-    Dw.CayleyReport();					\
-    std::cout<<GridLogMessage << "Called " #A " "<< (t1-t0)/ncall<<" us"<<std::endl;\
-    std::cout<<GridLogMessage << "******************"<<std::endl;
-
-    BENCH_DW_MEO(Dhop    ,src,result);
-    BENCH_DW_MEO(DhopEO  ,src_o,r_e);
-    BENCH_DW(Meooe   ,src_o,r_e);
-    BENCH_DW(Mooee   ,src_o,r_o);
-    BENCH_DW(MooeeInv,src_o,r_o);
-
-  }
-
-  if (1)
-  {
-    const int ncall=1000;
-
-    std::cout << GridLogMessage<< "*********************************************************" <<std::endl;
-    std::cout << GridLogMessage<< "* Benchmarking DomainWallFermionVec5dR::Dhop "<<std::endl;
-    std::cout << GridLogMessage<< "*********************************************************" <<std::endl;
-
-    GridParallelRNG RNG5(sFGrid);
-    LatticeFermion src(sFGrid); random(RNG5,src);
-    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();
-
-    double t0,t1;
-
-    LatticeFermion r_eo(sFGrid);
-    LatticeFermion src_e (sFrbGrid);
-    LatticeFermion src_o (sFrbGrid);
-    LatticeFermion r_e   (sFrbGrid);
-    LatticeFermion r_o   (sFrbGrid);
-    
-    pickCheckerboard(Even,src_e,src);
-    pickCheckerboard(Odd,src_o,src);
-    
-    setCheckerboard(r_eo,src_o);
-    setCheckerboard(r_eo,src_e);
-    
-    r_e = zero;
-    r_o = zero;
-
-    BENCH_DW_MEO(Dhop    ,src,result);
-    BENCH_DW_MEO(DhopEO  ,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

@@ -1,134 +0,0 @@
-    /*************************************************************************************
-
-    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.SeedFixedIntegers(std::vector<int>({45,12,81,9});
+      //      GridParallelRNG          pRNG(&Grid);      pRNG.SeedRandomDevice();
 
       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.SeedFixedIntegers(std::vector<int>({45,12,81,9});
+      //      GridParallelRNG          pRNG(&Grid);      pRNG.SeedRandomDevice();
 
       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.SeedFixedIntegers(std::vector<int>({45,12,81,9});
+      //      GridParallelRNG          pRNG(&Grid);      pRNG.SeedRandomDevice();
 
       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.SeedFixedIntegers(std::vector<int>({45,12,81,9});
+      //      GridParallelRNG          pRNG(&Grid);      pRNG.SeedRandomDevice();
 
       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::Algebra Gmu [] = {
-    Gamma::Algebra::GammaX,
-    Gamma::Algebra::GammaY,
-    Gamma::Algebra::GammaZ,
-    Gamma::Algebra::GammaT
+  Gamma::GammaMatrix Gmu [] = {
+    Gamma::GammaX,
+    Gamma::GammaY,
+    Gamma::GammaZ,
+    Gamma::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.SeedFixedIntegers(std::vector<int>({45,12,81,9});
+  //  pRNG.SeedRandomDevice();
 
   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::Algebra::GammaX)* src ; // 1-gamma_x
+      //    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]; ;
@@ -159,7 +159,7 @@ int main (int argc, char ** argv)
     ref = zero;
     for(int mu=0;mu<Nd;mu++){
 
-      //    ref =  src - Gamma(Gamma::Algebra::GammaX)* src ; // 1+gamma_x
+      //    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]; ;

benchmarks/Benchmark_wilson_sweep.cc

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

benchmarks/Makefile.am

@@ -1,11 +1 @@
 include Make.inc
-
-simple: simple_su3_test.o simple_su3_expr.o simple_simd_test.o
-
-EXTRA_LIBRARIES = libsimple_su3_test.a libsimple_su3_expr.a libsimple_simd_test.a
-
-libsimple_su3_test_a_SOURCES = simple_su3_test.cc
-
-libsimple_su3_expr_a_SOURCES = simple_su3_expr.cc
-
-libsimple_simd_test_a_SOURCES = simple_simd_test.cc

benchmarks/simple_simd_test.cc

@@ -1,11 +0,0 @@
-#include <Grid/Grid.h>
-
-Grid::vRealD add(const Grid::vRealD &x, const Grid::vRealD &y)
-{
-	return x+y;
-}
-
-Grid::vRealD sub(const Grid::vRealD &x, const Grid::vRealD &y)
-{
-	return x-y;
-}

benchmarks/simple_su3_expr.cc

@@ -25,7 +25,7 @@ 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/Grid.h>
+#include <Grid.h>
 
 using namespace std;
 using namespace Grid;

benchmarks/simple_su3_test.cc

@@ -25,7 +25,7 @@ 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/Grid.h>
+#include <Grid.h>
 
 using namespace std;
 using namespace Grid;

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],[sed -i 's|PACKAGE_|GRID_|' lib/Config.h])
+AC_CONFIG_HEADERS([lib/Config.h])
 m4_ifdef([AM_SILENT_RULES], [AM_SILENT_RULES([yes])])
 
 ############### Checks for programs
@@ -99,13 +99,6 @@ 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])], 
@@ -152,25 +145,13 @@ 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
 
 ############### SIMD instruction selection
-AC_ARG_ENABLE([simd],[AC_HELP_STRING([--enable-simd=code],
+AC_ARG_ENABLE([simd],[AC_HELP_STRING([--enable-simd=<code>],
 	            [select SIMD target (cf. README.md)])], [ac_SIMD=${enable_simd}], [ac_SIMD=GEN])
 
-AC_ARG_ENABLE([gen-simd-width],
-            [AS_HELP_STRING([--enable-gen-simd-width=size],
-            [size (in bytes) of the generic SIMD vectors (default: 32)])],
-            [ac_gen_simd_width=$enable_gen_simd_width],
-            [ac_gen_simd_width=32])
-
 case ${ax_cv_cxx_compiler_vendor} in
   clang|gnu)
     case ${ac_SIMD} in
@@ -199,10 +180,7 @@ case ${ax_cv_cxx_compiler_vendor} in
         AC_DEFINE([AVX512],[1],[AVX512 intrinsics])
         SIMD_FLAGS='-march=knl';;
       GEN)
-        AC_DEFINE([GEN],[1],[generic vector code])
-        AC_DEFINE_UNQUOTED([GEN_SIMD_WIDTH],[$ac_gen_simd_width],
-                           [generic SIMD vector width (in bytes)])
-        SIMD_GEN_WIDTH_MSG=" (width= $ac_gen_simd_width)"
+        AC_DEFINE([GENERIC_VEC],[1],[generic vector code])
         SIMD_FLAGS='';;
       QPX|BGQ)
         AC_DEFINE([QPX],[1],[QPX intrinsics for BG/Q])
@@ -219,8 +197,8 @@ case ${ax_cv_cxx_compiler_vendor} in
         AC_DEFINE([AVX1],[1],[AVX intrinsics])
         SIMD_FLAGS='-mavx -xavx';;
       AVXFMA)
-        AC_DEFINE([AVXFMA],[1],[AVX intrinsics with FMA3])
-        SIMD_FLAGS='-mavx -fma';;
+        AC_DEFINE([AVXFMA],[1],[AVX intrinsics with FMA4])
+        SIMD_FLAGS='-mavx -mfma';;
       AVX2)
         AC_DEFINE([AVX2],[1],[AVX2 intrinsics])
         SIMD_FLAGS='-march=core-avx2 -xcore-avx2';;
@@ -234,10 +212,7 @@ case ${ax_cv_cxx_compiler_vendor} in
         AC_DEFINE([AVX512],[1],[AVX512 intrinsics for Knights Landing])
         SIMD_FLAGS='-xmic-avx512';;
       GEN)
-        AC_DEFINE([GEN],[1],[generic vector code])
-        AC_DEFINE_UNQUOTED([GEN_SIMD_WIDTH],[$ac_gen_simd_width],
-                           [generic SIMD vector width (in bytes)])
-        SIMD_GEN_WIDTH_MSG=" (width= $ac_gen_simd_width)"
+        AC_DEFINE([GENERIC_VEC],[1],[generic vector code])
         SIMD_FLAGS='';;
       *)
         AC_MSG_ERROR(["SIMD option ${ac_SIMD} not supported by the Intel compiler"]);;
@@ -303,7 +278,7 @@ esac
 case ${ac_COMMS} in
     *-auto)
         LX_FIND_MPI
-        if test "x$have_CXX_mpi" = 'xno'; then AC_MSG_ERROR(["The configure could not find the MPI compilation flags. N.B. The -auto mode is not supported by Cray wrappers. Use the non -auto version in this case."]); fi
+        if test "x$have_CXX_mpi" = 'xno'; then AC_MSG_ERROR(["MPI not found"]); fi
         AM_CXXFLAGS="$MPI_CXXFLAGS $AM_CXXFLAGS"
         AM_CFLAGS="$MPI_CFLAGS $AM_CFLAGS"
         AM_LDFLAGS="`echo $MPI_CXXLDFLAGS | sed -E 's/-l@<:@^ @:>@+//g'` $AM_LDFLAGS"
@@ -319,9 +294,9 @@ AM_CONDITIONAL(BUILD_COMMS_MPI3L, [ test "${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|sitmo],\
+AC_ARG_ENABLE([rng],[AC_HELP_STRING([--enable-rng=ranlux48|mt19937],\
 	            [Select Random Number Generator to be used])],\
-	            [ac_RNG=${enable_rng}],[ac_RNG=sitmo])
+	            [ac_RNG=${enable_rng}],[ac_RNG=ranlux48])
 
 case ${ac_RNG} in
      ranlux48)
@@ -330,9 +305,6 @@ 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]); 
      ;;
@@ -370,17 +342,12 @@ esac
 AM_CONDITIONAL(BUILD_CHROMA_REGRESSION,[ test "X${ac_CHROMA}X" == "XyesX" ])
 
 ############### Doxygen
-DX_DOXYGEN_FEATURE([OFF])
-DX_DOT_FEATURE([OFF])
-DX_HTML_FEATURE([ON])
-DX_CHM_FEATURE([OFF])
-DX_CHI_FEATURE([OFF])
-DX_MAN_FEATURE([OFF])
-DX_RTF_FEATURE([OFF])
-DX_XML_FEATURE([OFF])
-DX_PDF_FEATURE([OFF])
-DX_PS_FEATURE([OFF])
-DX_INIT_DOXYGEN([$PACKAGE_NAME], [doxygen.cfg])
+AC_PROG_DOXYGEN
+
+if test -n "$DOXYGEN"
+then
+AC_CONFIG_FILES([docs/doxy.cfg])
+fi
 
 ############### Ouput
 cwd=`pwd -P`; cd ${srcdir}; abs_srcdir=`pwd -P`; cd ${cwd}
@@ -397,14 +364,10 @@ 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 "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -419,7 +382,7 @@ os (target)                 : $target_os
 compiler vendor             : ${ax_cv_cxx_compiler_vendor}
 compiler version            : ${ax_cv_gxx_version}
 ----- BUILD OPTIONS -----------------------------------
-SIMD                        : ${ac_SIMD}${SIMD_GEN_WIDTH_MSG}
+SIMD                        : ${ac_SIMD}
 Threading                   : ${ac_openmp} 
 Communications type         : ${comms_type}
 Default precision           : ${ac_PRECISION}
@@ -427,8 +390,8 @@ 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 DOXYGEN documentation : `if test "x$enable_doc" = xyes; then echo yes; else echo no; fi`
+graphs and diagrams         : `if test "x$enable_dot" = xyes; then echo yes; else echo no; fi`
 ----- BUILD FLAGS -------------------------------------
 CXXFLAGS:
 `echo ${AM_CXXFLAGS} ${CXXFLAGS} | tr ' ' '\n' | sed 's/^-/    -/g'`

doxygen.inc

@@ -1,184 +0,0 @@
-# Copyright (C) 2004 Oren Ben-Kiki
-# This file is distributed under the same terms as the Automake macro files.
-
-# Generate automatic documentation using Doxygen. Goals and variables values
-# are controlled by the various DX_COND_??? conditionals set by autoconf.
-#
-# The provided goals are:
-# doxygen-doc: Generate all doxygen documentation.
-# doxygen-run: Run doxygen, which will generate some of the documentation
-#              (HTML, CHM, CHI, MAN, RTF, XML) but will not do the post
-#              processing required for the rest of it (PS, PDF, and some MAN).
-# doxygen-man: Rename some doxygen generated man pages.
-# doxygen-ps: Generate doxygen PostScript documentation.
-# doxygen-pdf: Generate doxygen PDF documentation.
-#
-# Note that by default these are not integrated into the automake goals. If
-# doxygen is used to generate man pages, you can achieve this integration by
-# setting man3_MANS to the list of man pages generated and then adding the
-# dependency:
-#
-#   $(man3_MANS): doxygen-doc
-#
-# This will cause make to run doxygen and generate all the documentation.
-#
-# The following variable is intended for use in Makefile.am:
-#
-# DX_CLEANFILES = everything to clean.
-#
-# This is usually added to MOSTLYCLEANFILES.
-
-## --------------------------------- ##
-## Format-independent Doxygen rules. ##
-## --------------------------------- ##
-
-if DX_COND_doc
-
-## ------------------------------- ##
-## Rules specific for HTML output. ##
-## ------------------------------- ##
-
-if DX_COND_html
-
-DX_CLEAN_HTML = @DX_DOCDIR@/html
-
-endif DX_COND_html
-
-## ------------------------------ ##
-## Rules specific for CHM output. ##
-## ------------------------------ ##
-
-if DX_COND_chm
-
-DX_CLEAN_CHM = @DX_DOCDIR@/chm
-
-if DX_COND_chi
-
-DX_CLEAN_CHI = @DX_DOCDIR@/@PACKAGE@.chi
-
-endif DX_COND_chi
-
-endif DX_COND_chm
-
-## ------------------------------ ##
-## Rules specific for MAN output. ##
-## ------------------------------ ##
-
-if DX_COND_man
-
-DX_CLEAN_MAN = @DX_DOCDIR@/man
-
-endif DX_COND_man
-
-## ------------------------------ ##
-## Rules specific for RTF output. ##
-## ------------------------------ ##
-
-if DX_COND_rtf
-
-DX_CLEAN_RTF = @DX_DOCDIR@/rtf
-
-endif DX_COND_rtf
-
-## ------------------------------ ##
-## Rules specific for XML output. ##
-## ------------------------------ ##
-
-if DX_COND_xml
-
-DX_CLEAN_XML = @DX_DOCDIR@/xml
-
-endif DX_COND_xml
-
-## ----------------------------- ##
-## Rules specific for PS output. ##
-## ----------------------------- ##
-
-if DX_COND_ps
-
-DX_CLEAN_PS = @DX_DOCDIR@/@PACKAGE@.ps
-
-DX_PS_GOAL = doxygen-ps
-
-doxygen-ps: @DX_DOCDIR@/@PACKAGE@.ps
-
-@DX_DOCDIR@/@PACKAGE@.ps: @DX_DOCDIR@/@PACKAGE@.tag
-	cd @DX_DOCDIR@/latex; \
-	rm -f *.aux *.toc *.idx *.ind *.ilg *.log *.out; \
-	$(DX_LATEX) refman.tex; \
-	$(MAKEINDEX_PATH) refman.idx; \
-	$(DX_LATEX) refman.tex; \
-	countdown=5; \
-	while $(DX_EGREP) 'Rerun (LaTeX|to get cross-references right)' \
-	                  refman.log > /dev/null 2>&1 \
-	   && test $$countdown -gt 0; do \
-	    $(DX_LATEX) refman.tex; \
-	    countdown=`expr $$countdown - 1`; \
-	done; \
-	$(DX_DVIPS) -o ../@PACKAGE@.ps refman.dvi
-
-endif DX_COND_ps
-
-## ------------------------------ ##
-## Rules specific for PDF output. ##
-## ------------------------------ ##
-
-if DX_COND_pdf
-
-DX_CLEAN_PDF = @DX_DOCDIR@/@PACKAGE@.pdf
-
-DX_PDF_GOAL = doxygen-pdf
-
-doxygen-pdf: @DX_DOCDIR@/@PACKAGE@.pdf
-
-@DX_DOCDIR@/@PACKAGE@.pdf: @DX_DOCDIR@/@PACKAGE@.tag
-	cd @DX_DOCDIR@/latex; \
-	rm -f *.aux *.toc *.idx *.ind *.ilg *.log *.out; \
-	$(DX_PDFLATEX) refman.tex; \
-	$(DX_MAKEINDEX) refman.idx; \
-	$(DX_PDFLATEX) refman.tex; \
-	countdown=5; \
-	while $(DX_EGREP) 'Rerun (LaTeX|to get cross-references right)' \
-	                  refman.log > /dev/null 2>&1 \
-	   && test $$countdown -gt 0; do \
-	    $(DX_PDFLATEX) refman.tex; \
-	    countdown=`expr $$countdown - 1`; \
-	done; \
-	mv refman.pdf ../@PACKAGE@.pdf
-
-endif DX_COND_pdf
-
-## ------------------------------------------------- ##
-## Rules specific for LaTeX (shared for PS and PDF). ##
-## ------------------------------------------------- ##
-
-if DX_COND_latex
-
-DX_CLEAN_LATEX = @DX_DOCDIR@/latex
-
-endif DX_COND_latex
-
-.INTERMEDIATE: doxygen-run $(DX_PS_GOAL) $(DX_PDF_GOAL)
-
-doxygen-run: @DX_DOCDIR@/@PACKAGE@.tag
-
-doxygen-doc: doxygen-run $(DX_PS_GOAL) $(DX_PDF_GOAL)
-
-@DX_DOCDIR@/@PACKAGE@.tag: $(DX_CONFIG) $(pkginclude_HEADERS)
-	rm -rf @DX_DOCDIR@
-	$(DX_ENV) $(DX_DOXYGEN) $(srcdir)/$(DX_CONFIG)
-
-DX_CLEANFILES = \
-    @DX_DOCDIR@/@PACKAGE@.tag \
-    -r \
-    $(DX_CLEAN_HTML) \
-    $(DX_CLEAN_CHM) \
-    $(DX_CLEAN_CHI) \
-    $(DX_CLEAN_MAN) \
-    $(DX_CLEAN_RTF) \
-    $(DX_CLEAN_XML) \
-    $(DX_CLEAN_PS) \
-    $(DX_CLEAN_PDF) \
-    $(DX_CLEAN_LATEX)
-
-endif DX_COND_doc

extras/Hadrons/Application.cc

@@ -1,317 +0,0 @@
-/*************************************************************************************
-
-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

@@ -1,132 +0,0 @@
-/*************************************************************************************
-
-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

@@ -1,743 +0,0 @@
-/*************************************************************************************
-
-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

@@ -1,385 +0,0 @@
-/*************************************************************************************
-
-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

@@ -1,106 +0,0 @@
-/*************************************************************************************
-
-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

@@ -1,329 +0,0 @@
-/*************************************************************************************
-
-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

@@ -1,82 +0,0 @@
-/*************************************************************************************
-
-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

@@ -1,150 +0,0 @@
-/*************************************************************************************
-
-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

@@ -1,760 +0,0 @@
-/*************************************************************************************
-
-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

@@ -1,80 +0,0 @@
-/*************************************************************************************
-
-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

@@ -1,72 +0,0 @@
-/*************************************************************************************
-
-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

@@ -1,29 +0,0 @@
-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

@@ -1,71 +0,0 @@
-/*************************************************************************************
-
-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

@@ -1,198 +0,0 @@
-/*************************************************************************************
-
-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

@@ -1,49 +0,0 @@
-/*************************************************************************************
-
-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

@@ -1,40 +0,0 @@
-/*************************************************************************************
-
-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

@@ -1,134 +0,0 @@
-/*************************************************************************************
-
-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

@@ -1,126 +0,0 @@
-/*************************************************************************************
-
-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

@@ -1,131 +0,0 @@
-/*************************************************************************************
-
-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

@@ -1,137 +0,0 @@
-/*************************************************************************************
-
-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

@@ -1,78 +0,0 @@
-/*************************************************************************************
-
-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

@@ -1,73 +0,0 @@
-/*************************************************************************************
-
-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

@@ -1,69 +0,0 @@
-/*************************************************************************************
-
-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

@@ -1,66 +0,0 @@
-/*************************************************************************************
-
-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

@@ -1,69 +0,0 @@
-/*************************************************************************************
-
-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

@@ -1,66 +0,0 @@
-/*************************************************************************************
-
-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

@@ -1,132 +0,0 @@
-/*************************************************************************************
-
-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

@@ -1,135 +0,0 @@
-/*************************************************************************************
-
-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

@@ -1,163 +0,0 @@
-/*************************************************************************************
-
-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

@@ -1,151 +0,0 @@
-/*************************************************************************************
-
-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

@@ -1,185 +0,0 @@
-/*************************************************************************************
-
-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

@@ -1,39 +0,0 @@
-#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

@@ -1,40 +0,0 @@
-#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

@@ -1,40 +0,0 @@
-#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

@@ -1,44 +0,0 @@
-#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

@@ -1,81 +0,0 @@
-#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

@@ -1,85 +0,0 @@
-#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

@@ -1,31 +0,0 @@
-#!/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

@@ -1,28 +0,0 @@
-#!/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

@@ -1,12 +0,0 @@
-#!/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

@@ -1,19 +0,0 @@
-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

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

lib/Algorithms.h

@@ -42,14 +42,15 @@ 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/ImplicitlyRestartedLanczos.h>
+
 #include <Grid/algorithms/CoarsenedMatrix.h>
-#include <Grid/algorithms/FFT.h>
 
 // Eigen/lanczos
 // EigCg

lib/AlignedAllocator.h

@@ -42,32 +42,9 @@ 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: 
@@ -89,27 +66,27 @@ 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
-    if ( ptr == (_Tp *) NULL ) ptr = (_Tp *) _mm_malloc(bytes,128);
+    _Tp * ptr = (_Tp *) _mm_malloc(__n*sizeof(_Tp),128);
 #else
-    if ( ptr == (_Tp *) NULL ) ptr = (_Tp *) memalign(128,bytes);
+    _Tp * ptr = (_Tp *) memalign(128,__n*sizeof(_Tp));
 #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 __n) { 
-    size_type bytes = __n * sizeof(_Tp);
-    pointer __freeme = (pointer)PointerCache::Insert((void *)__p,bytes);
-
+  void deallocate(pointer __p, size_type) { 
 #ifdef HAVE_MM_MALLOC_H
-    if ( __freeme ) _mm_free((void *)__freeme); 
+    _mm_free((void *)__p); 
 #else
-    if ( __freeme ) free((void *)__freeme);
+    free((void *)__p);
 #endif
   }
   void construct(pointer __p, const _Tp& __val) { };

lib/FFT.h

@@ -244,11 +244,8 @@ namespace Grid {
             pokeLocalSite(s,pgbuf,cbuf);
           }
         }
-        if (p != processors[dim] - 1)
-        {
         result = Cshift(result,dim,L);
       }
-      }
       
       // Loop over orthog coords
       int NN=pencil_g.lSites();
@@ -290,10 +287,10 @@ namespace Grid {
           cgbuf = clbuf;
           cgbuf[dim] = clbuf[dim]+L*pc;
           peekLocalSite(s,pgbuf,cgbuf);
+          s = s * div;
           pokeLocalSite(s,result,clbuf);
         }
       }
-      result = result*div;
       
       // destroying plan
       FFTW<scalar>::fftw_destroy_plan(p);

lib/Grid.h

@@ -38,10 +38,52 @@ Author: paboyle <paboyle@ph.ed.ac.uk>
 #ifndef GRID_H
 #define GRID_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>
+///////////////////
+// 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/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>
+
+
 
 #endif

lib/GridCore.h

@@ -1,81 +0,0 @@
-    /*************************************************************************************
-
-    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/Hadrons

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

lib/Init.cc

@@ -41,13 +41,12 @@ Author: paboyle <paboyle@ph.ed.ac.uk>
 #include <signal.h>
 #include <iostream>
 #include <iterator>
+#include <Grid.h>
 #include <algorithm>
 #include <iterator>
 #include <cstdlib>
 #include <memory>
 
-#include <Grid/Grid.h>
-
 
 #include <fenv.h>
 #ifdef __APPLE__
@@ -220,57 +219,8 @@ void Grid_init(int *argc,char ***argv)
     CartesianCommunicator::MAX_MPI_SHM_BYTES = MB*1024*1024;
   }
 
-  if( GridCmdOptionExists(*argv,*argv+*argc,"--debug-signals") ){
-    Grid_debug_handler_init();
-  }
-
   CartesianCommunicator::Init(argc,argv);
 
-  if( !GridCmdOptionExists(*argv,*argv+*argc,"--debug-stdout") ){
-    Grid_quiesce_nodes();
-  } else { 
-    std::ostringstream fname;
-    fname<<"Grid.stdout.";
-    fname<<CartesianCommunicator::RankWorld();
-    freopen(fname.str().c_str(),"w",stdout);
-  }
-
-  ////////////////////////////////////
-  // Banner
-  ////////////////////////////////////
-  if ( CartesianCommunicator::RankWorld() == 0 ) { 
-    std::cout <<std::endl;
-    std::cout  << "__|__|__|__|__|__|__|__|__|__|__|__|__|__|__"<<std::endl; 
-    std::cout  << "__|__|__|__|__|__|__|__|__|__|__|__|__|__|__"<<std::endl; 
-    std::cout  << "__|_ |  |  |  |  |  |  |  |  |  |  |  | _|__"<<std::endl; 
-    std::cout  << "__|_                                    _|__"<<std::endl; 
-    std::cout  << "__|_   GGGG    RRRR    III    DDDD      _|__"<<std::endl;
-    std::cout  << "__|_  G        R   R    I     D   D     _|__"<<std::endl;
-    std::cout  << "__|_  G        R   R    I     D    D    _|__"<<std::endl;
-    std::cout  << "__|_  G  GG    RRRR     I     D    D    _|__"<<std::endl;
-    std::cout  << "__|_  G   G    R  R     I     D   D     _|__"<<std::endl;
-    std::cout  << "__|_   GGGG    R   R   III    DDDD      _|__"<<std::endl;
-    std::cout  << "__|_                                    _|__"<<std::endl; 
-    std::cout  << "__|__|__|__|__|__|__|__|__|__|__|__|__|__|__"<<std::endl; 
-    std::cout  << "__|__|__|__|__|__|__|__|__|__|__|__|__|__|__"<<std::endl; 
-    std::cout  << "  |  |  |  |  |  |  |  |  |  |  |  |  |  |  "<<std::endl; 
-    std::cout << std::endl;
-    std::cout << std::endl;
-    std::cout << "Copyright (C) 2015 Peter Boyle, Azusa Yamaguchi, Guido Cossu, Antonin Portelli and other authors"<<std::endl;
-    std::cout << std::endl;
-    std::cout << "This program is free software; you can redistribute it and/or modify"<<std::endl;
-    std::cout << "it under the terms of the GNU General Public License as published by"<<std::endl;
-    std::cout << "the Free Software Foundation; either version 2 of the License, or"<<std::endl;
-    std::cout << "(at your option) any later version."<<std::endl;
-    std::cout << std::endl;
-    std::cout << "This program is distributed in the hope that it will be useful,"<<std::endl;
-    std::cout << "but WITHOUT ANY WARRANTY; without even the implied warranty of"<<std::endl;
-    std::cout << "MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the"<<std::endl;
-    std::cout << "GNU General Public License for more details."<<std::endl;
-    std::cout << std::endl;
-  }
-
-
   ////////////////////////////////////
   // Logging
   ////////////////////////////////////
@@ -280,6 +230,9 @@ void Grid_init(int *argc,char ***argv)
   GridCmdOptionCSL(defaultLog,logstreams);
   GridLogConfigure(logstreams);
 
+  if( !GridCmdOptionExists(*argv,*argv+*argc,"--debug-stdout") ){
+    Grid_quiesce_nodes();
+  }
 
   if( GridCmdOptionExists(*argv,*argv+*argc,"--log") ){
     arg = GridCmdOptionPayload(*argv,*argv+*argc,"--log");
@@ -295,67 +248,94 @@ void Grid_init(int *argc,char ***argv)
     std::cout<<GridLogMessage<<"  --help : this message"<<std::endl;
     std::cout<<GridLogMessage<<std::endl;
     std::cout<<GridLogMessage<<"Geometry:"<<std::endl;
-    std::cout<<GridLogMessage<<std::endl;
     std::cout<<GridLogMessage<<"  --mpi n.n.n.n   : default MPI decomposition"<<std::endl;    
     std::cout<<GridLogMessage<<"  --threads n     : default number of OMP threads"<<std::endl;
     std::cout<<GridLogMessage<<"  --grid n.n.n.n  : default Grid size"<<std::endl;    
     std::cout<<GridLogMessage<<"  --shm  M        : allocate M megabytes of shared memory for comms"<<std::endl;    
     std::cout<<GridLogMessage<<std::endl;
     std::cout<<GridLogMessage<<"Verbose and debug:"<<std::endl;
-    std::cout<<GridLogMessage<<std::endl;
-    std::cout<<GridLogMessage<<"  --log list      : comma separated list from Error,Warning,Message,Performance,Iterative,Integrator,Debug,Colours"<<std::endl;
+    std::cout<<GridLogMessage<<"  --log list      : comma separted list of streams from Error,Warning,Message,Performance,Iterative,Integrator,Debug,Colours"<<std::endl;
     std::cout<<GridLogMessage<<"  --decomposition : report on default omp,mpi and simd decomposition"<<std::endl;    
     std::cout<<GridLogMessage<<"  --debug-signals : catch sigsegv and print a blame report"<<std::endl;
     std::cout<<GridLogMessage<<"  --debug-stdout  : print stdout from EVERY node"<<std::endl;    
     std::cout<<GridLogMessage<<"  --notimestamp   : suppress millisecond resolution stamps"<<std::endl;    
     std::cout<<GridLogMessage<<std::endl;
     std::cout<<GridLogMessage<<"Performance:"<<std::endl;
-    std::cout<<GridLogMessage<<std::endl;
-    std::cout<<GridLogMessage<<"  --comms-isend   : Asynchronous MPI calls; several dirs at a time "<<std::endl;    
-    std::cout<<GridLogMessage<<"  --comms-sendrecv: Synchronous MPI calls; one dirs at a time "<<std::endl;    
-    std::cout<<GridLogMessage<<"  --comms-overlap : Overlap comms with compute "<<std::endl;    
-    std::cout<<GridLogMessage<<std::endl;
     std::cout<<GridLogMessage<<"  --dslash-generic: Wilson kernel for generic Nc"<<std::endl;    
     std::cout<<GridLogMessage<<"  --dslash-unroll : Wilson kernel for Nc=3"<<std::endl;    
     std::cout<<GridLogMessage<<"  --dslash-asm    : Wilson kernel for AVX512"<<std::endl;    
-    std::cout<<GridLogMessage<<std::endl;
     std::cout<<GridLogMessage<<"  --lebesgue      : Cache oblivious Lebesgue curve/Morton order/Z-graph stencil looping"<<std::endl;    
     std::cout<<GridLogMessage<<"  --cacheblocking n.m.o.p : Hypercuboidal cache blocking"<<std::endl;    
     std::cout<<GridLogMessage<<std::endl;
     exit(EXIT_SUCCESS);
   }
 
+  ////////////////////////////////////
+  // Banner
+  ////////////////////////////////////
+
+  std::string COL_RED    = GridLogColours.colour["RED"];
+  std::string COL_PURPLE = GridLogColours.colour["PURPLE"];
+  std::string COL_BLACK  = GridLogColours.colour["BLACK"];
+  std::string COL_GREEN  = GridLogColours.colour["GREEN"];
+  std::string COL_BLUE   = GridLogColours.colour["BLUE"];
+  std::string COL_YELLOW = GridLogColours.colour["YELLOW"];
+  std::string COL_BACKGROUND = GridLogColours.colour["NORMAL"];
+  
+  std::cout <<std::endl;
+  std::cout <<COL_RED  << "__|__|__|__|__"<<             "|__|__|_"<<COL_PURPLE<<"_|__|__|"<<                "__|__|__|__|__"<<std::endl; 
+  std::cout <<COL_RED  << "__|__|__|__|__"<<             "|__|__|_"<<COL_PURPLE<<"_|__|__|"<<                "__|__|__|__|__"<<std::endl; 
+  std::cout <<COL_RED  << "__|_ |  |  |  "<<             "|  |  | "<<COL_PURPLE<<" |  |  |"<<                "  |  |  | _|__"<<std::endl; 
+  std::cout <<COL_RED  << "__|_          "<<             "        "<<COL_PURPLE<<"        "<<                "          _|__"<<std::endl; 
+  std::cout <<COL_RED  << "__|_  "<<COL_GREEN<<" GGGG   "<<COL_RED<<" RRRR   "<<COL_BLUE  <<" III    "<<COL_PURPLE<<"DDDD  "<<COL_PURPLE<<"    _|__"<<std::endl;
+  std::cout <<COL_RED  << "__|_  "<<COL_GREEN<<"G       "<<COL_RED<<" R   R  "<<COL_BLUE  <<"  I     "<<COL_PURPLE<<"D   D "<<COL_PURPLE<<"    _|__"<<std::endl;
+  std::cout <<COL_RED  << "__|_  "<<COL_GREEN<<"G       "<<COL_RED<<" R   R  "<<COL_BLUE  <<"  I     "<<COL_PURPLE<<"D    D"<<COL_PURPLE<<"    _|__"<<std::endl;
+  std::cout <<COL_BLUE << "__|_  "<<COL_GREEN<<"G  GG   "<<COL_RED<<" RRRR   "<<COL_BLUE  <<"  I     "<<COL_PURPLE<<"D    D"<<COL_GREEN <<"    _|__"<<std::endl;
+  std::cout <<COL_BLUE << "__|_  "<<COL_GREEN<<"G   G   "<<COL_RED<<" R  R   "<<COL_BLUE  <<"  I     "<<COL_PURPLE<<"D   D "<<COL_GREEN <<"    _|__"<<std::endl;
+  std::cout <<COL_BLUE << "__|_  "<<COL_GREEN<<" GGGG   "<<COL_RED<<" R   R  "<<COL_BLUE  <<" III    "<<COL_PURPLE<<"DDDD  "<<COL_GREEN <<"    _|__"<<std::endl;
+  std::cout <<COL_BLUE << "__|_          "<<             "        "<<COL_GREEN <<"        "<<                "          _|__"<<std::endl; 
+  std::cout <<COL_BLUE << "__|__|__|__|__"<<             "|__|__|_"<<COL_GREEN <<"_|__|__|"<<                "__|__|__|__|__"<<std::endl; 
+  std::cout <<COL_BLUE << "__|__|__|__|__"<<             "|__|__|_"<<COL_GREEN <<"_|__|__|"<<                "__|__|__|__|__"<<std::endl; 
+  std::cout <<COL_BLUE << "  |  |  |  |  "<<             "|  |  | "<<COL_GREEN <<" |  |  |"<<                "  |  |  |  |  "<<std::endl; 
+  std::cout << std::endl;
+  std::cout << std::endl;
+  std::cout <<COL_YELLOW<< std::endl;
+  std::cout << "Copyright (C) 2015 Peter Boyle, Azusa Yamaguchi, Guido Cossu, Antonin Portelli and other authors"<<std::endl;
+  std::cout << std::endl;
+  std::cout << "This program is free software; you can redistribute it and/or modify"<<std::endl;
+  std::cout << "it under the terms of the GNU General Public License as published by"<<std::endl;
+  std::cout << "the Free Software Foundation; either version 2 of the License, or"<<std::endl;
+  std::cout << "(at your option) any later version."<<std::endl;
+  std::cout << std::endl;
+  std::cout << "This program is distributed in the hope that it will be useful,"<<std::endl;
+  std::cout << "but WITHOUT ANY WARRANTY; without even the implied warranty of"<<std::endl;
+  std::cout << "MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the"<<std::endl;
+  std::cout << "GNU General Public License for more details."<<std::endl;
+  std::cout << COL_BACKGROUND <<std::endl;
+  std::cout << std::endl;
+
   ////////////////////////////////////
   // Debug and performance options
   ////////////////////////////////////
 
+
+  if( GridCmdOptionExists(*argv,*argv+*argc,"--debug-signals") ){
+    Grid_debug_handler_init();
+  }
   if( GridCmdOptionExists(*argv,*argv+*argc,"--dslash-unroll") ){
     QCD::WilsonKernelsStatic::Opt=QCD::WilsonKernelsStatic::OptHandUnroll;
-    QCD::StaggeredKernelsStatic::Opt=QCD::StaggeredKernelsStatic::OptHandUnroll;
   }
   if( GridCmdOptionExists(*argv,*argv+*argc,"--dslash-asm") ){
     QCD::WilsonKernelsStatic::Opt=QCD::WilsonKernelsStatic::OptInlineAsm;
-    QCD::StaggeredKernelsStatic::Opt=QCD::StaggeredKernelsStatic::OptInlineAsm;
   }
   if( GridCmdOptionExists(*argv,*argv+*argc,"--dslash-generic") ){
     QCD::WilsonKernelsStatic::Opt=QCD::WilsonKernelsStatic::OptGeneric;
-    QCD::StaggeredKernelsStatic::Opt=QCD::StaggeredKernelsStatic::OptGeneric;
-  }
-  if( GridCmdOptionExists(*argv,*argv+*argc,"--comms-overlap") ){
-    QCD::WilsonKernelsStatic::Comms = QCD::WilsonKernelsStatic::CommsAndCompute;
-  } else {
-    QCD::WilsonKernelsStatic::Comms = QCD::WilsonKernelsStatic::CommsThenCompute;
-  }
-  if( GridCmdOptionExists(*argv,*argv+*argc,"--comms-concurrent") ){
-    CartesianCommunicator::SetCommunicatorPolicy(CartesianCommunicator::CommunicatorPolicyConcurrent);
-  }
-  if( GridCmdOptionExists(*argv,*argv+*argc,"--comms-sequential") ){
-    CartesianCommunicator::SetCommunicatorPolicy(CartesianCommunicator::CommunicatorPolicySequential);
   }
   if( GridCmdOptionExists(*argv,*argv+*argc,"--lebesgue") ){
     LebesgueOrder::UseLebesgueOrder=1;
   }
 
+
   if( GridCmdOptionExists(*argv,*argv+*argc,"--cacheblocking") ){
     arg= GridCmdOptionPayload(*argv,*argv+*argc,"--cacheblocking");
     GridCmdOptionIntVector(arg,LebesgueOrder::Block);
@@ -393,25 +373,23 @@ void Grid_finalize(void)
   MPI_Finalize();
   Grid_unquiesce_nodes();
 #endif
-#if defined (GRID_COMMS_SHMEM)
-  shmem_finalize();
-#endif
 }
 
 void * Grid_backtrace_buffer[_NBACKTRACE];
 
 void Grid_sa_signal_handler(int sig,siginfo_t *si,void * ptr)
 {
-  fprintf(stderr,"Caught signal %d\n",si->si_signo);
-  fprintf(stderr,"  mem address %llx\n",(unsigned long long)si->si_addr);
-  fprintf(stderr,"         code %d\n",si->si_code);
+  printf("Caught signal %d\n",si->si_signo);
+  printf("  mem address %llx\n",(unsigned long long)si->si_addr);
+  printf("         code %d\n",si->si_code);
+
   // Linux/Posix
 #ifdef __linux__
   // And x86 64bit
 #ifdef __x86_64__
   ucontext_t * uc= (ucontext_t *)ptr;
   struct sigcontext *sc = (struct sigcontext *)&uc->uc_mcontext;
-  fprintf(stderr,"  instruction %llx\n",(unsigned long long)sc->rip);
+  printf("  instruction %llx\n",(unsigned long long)sc->rip);
 #define REG(A)  printf("  %s %lx\n",#A,sc-> A);
   REG(rdi);
   REG(rsi);
@@ -434,11 +412,7 @@ void Grid_sa_signal_handler(int sig,siginfo_t *si,void * ptr)
   REG(r15);
 #endif
 #endif
-  fflush(stderr);
-  BACKTRACEFP(stderr);
-  fprintf(stderr,"Called backtrace\n");
-  fflush(stdout);
-  fflush(stderr);
+  BACKTRACE();
   exit(0);
   return;
 };
@@ -451,11 +425,9 @@ void Grid_debug_handler_init(void)
   sa.sa_flags    = SA_SIGINFO;
   sigaction(SIGSEGV,&sa,NULL);
   sigaction(SIGTRAP,&sa,NULL);
-  sigaction(SIGBUS,&sa,NULL);
 
   feenableexcept( FE_INVALID|FE_OVERFLOW|FE_DIVBYZERO);
 
   sigaction(SIGFPE,&sa,NULL);
-  sigaction(SIGKILL,&sa,NULL);
 }
 }

lib/Log.cc

@@ -29,10 +29,9 @@ See the full license in the file "LICENSE" in the top level distribution
 directory
 *************************************************************************************/
 /*  END LEGAL */
-#include <Grid/GridCore.h>
+#include <Grid.h>
 
 #include <cxxabi.h>
-#include <memory>
 
 namespace Grid {
 

lib/Log.h

@@ -110,7 +110,7 @@ public:
   friend std::ostream& operator<< (std::ostream& stream, Logger& log){
 
     if ( log.active ) {
-      stream << log.background()<< std::setw(10) << std::left << log.topName << log.background()<< " : ";
+      stream << log.background()<< log.topName << log.background()<< " : ";
       stream << log.colour() <<std::setw(14) << std::left << log.name << log.background() << " : ";
       if ( log.timestamp ) {
 	StopWatch.Stop();

lib/Makefile.am

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

lib/Old/Tensor_peek.h

@@ -0,0 +1,154 @@
+    /*************************************************************************************
+
+    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

@@ -0,0 +1,127 @@
+    /*************************************************************************************
+
+    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/PerfCount.cc

@@ -26,8 +26,8 @@ Author: paboyle <paboyle@ph.ed.ac.uk>
     *************************************************************************************/
     /*  END LEGAL */
 
-#include <Grid/GridCore.h>
-#include <Grid/perfmon/PerfCount.h>
+#include <Grid.h>
+#include <PerfCount.h>
 
 namespace Grid {
 

lib/PerfCount.h

@@ -172,7 +172,7 @@ public:
     const char * name = PerformanceCounterConfigs[PCT].name;
     fd = perf_event_open(&pe, 0, -1, -1, 0); // pid 0, cpu -1 current process any cpu. group -1
     if (fd == -1) {
-      fprintf(stderr, "Error opening leader %llx for event %s\n",(long long) pe.config,name);
+      fprintf(stderr, "Error opening leader %llx for event %s\n", pe.config,name);
       perror("Error is");
     }
     int norm = PerformanceCounterConfigs[PCT].normalisation;
@@ -181,7 +181,7 @@ public:
     name = PerformanceCounterConfigs[norm].name;
     cyclefd = perf_event_open(&pe, 0, -1, -1, 0); // pid 0, cpu -1 current process any cpu. group -1
     if (cyclefd == -1) {
-      fprintf(stderr, "Error opening leader %llx for event %s\n",(long long) pe.config,name);
+      fprintf(stderr, "Error opening leader %llx for event %s\n", pe.config,name);
       perror("Error is");
     }
 #endif
@@ -205,13 +205,12 @@ public:
   void Stop(void) {
     count=0;
     cycles=0;
-    size_t ign;
 #ifdef __linux__
     if ( fd!= -1) {
       ::ioctl(fd, PERF_EVENT_IOC_DISABLE, 0);
       ::ioctl(cyclefd, PERF_EVENT_IOC_DISABLE, 0);
-      ign=::read(fd, &count, sizeof(long long));
-      ign=::read(cyclefd, &cycles, sizeof(long long));
+      ::read(fd, &count, sizeof(long long));
+      ::read(cyclefd, &cycles, sizeof(long long));
     }
     elapsed = cyclecount() - begin;
 #else

lib/Simd.h

@@ -172,8 +172,8 @@ namespace Grid {
 
 };
 
-#include <Grid/simd/Grid_vector_types.h>
-#include <Grid/simd/Grid_vector_unops.h>
+#include "simd/Grid_vector_types.h"
+#include "simd/Grid_vector_unops.h"
 
 namespace Grid {
   // Default precision

lib/Stat.cc

@@ -1,9 +1,11 @@
-#include <Grid/GridCore.h>
-#include <Grid/perfmon/PerfCount.h>
-#include <Grid/perfmon/Stat.h>
+#include <Grid.h>
+#include <PerfCount.h>
+#include <Stat.h>
+
 
 namespace Grid { 
 
+
 bool PmuStat::pmu_initialized=false;
 
 

lib/Stencil.h

@@ -28,8 +28,10 @@
  #ifndef GRID_STENCIL_H
  #define GRID_STENCIL_H
 
+ #include <thread>
+
  #include <Grid/stencil/Lebesgue.h>   // subdir aggregate
-#define NEW_XYZT_GATHER
+
  //////////////////////////////////////////////////////////////////////////////////////////
  // Must not lose sight that goal is to be able to construct really efficient
  // gather to a point stencil code. CSHIFT is not the best way, so need
@@ -68,48 +70,50 @@
 
 namespace Grid {
 
-///////////////////////////////////////////////////////////////////
-// Gather for when there *is* need to SIMD split with compression
-///////////////////////////////////////////////////////////////////
-void Gather_plane_table_compute (GridBase *grid,int dimension,int plane,int cbmask,
-					int off,std::vector<std::pair<int,int> > & table);
-
-template<class vobj,class cobj,class compressor> 
-void Gather_plane_simple_table (std::vector<std::pair<int,int> >& table,const Lattice<vobj> &rhs,cobj *buffer,compressor &compress, int off,int so)   __attribute__((noinline));
-
-template<class vobj,class cobj,class compressor> 
-void Gather_plane_simple_table (std::vector<std::pair<int,int> >& table,const Lattice<vobj> &rhs,cobj *buffer,compressor &compress, int off,int so)
+inline void Gather_plane_simple_table_compute (GridBase *grid,int dimension,int plane,int cbmask,
+					       int off,std::vector<std::pair<int,int> > & table)
 {
-  int num=table.size();
-  parallel_for(int i=0;i<num;i++){
-    vstream(buffer[off+table[i].first],compress(rhs._odata[so+table[i].second]));
+  table.resize(0);
+  int rd = grid->_rdimensions[dimension];
+
+  if ( !grid->CheckerBoarded(dimension) ) {
+    cbmask = 0x3;
+  }
+  int so= plane*grid->_ostride[dimension]; // base offset for start of plane 
+  int e1=grid->_slice_nblock[dimension];
+  int e2=grid->_slice_block[dimension];
+
+  int stride=grid->_slice_stride[dimension];
+  if ( cbmask == 0x3 ) { 
+    table.resize(e1*e2);
+    for(int n=0;n<e1;n++){
+      for(int b=0;b<e2;b++){
+	int o  = n*stride;
+	int bo = n*e2;
+	table[bo+b]=std::pair<int,int>(bo+b,o+b);
+      }
+    }
+  } else { 
+     int bo=0;
+     table.resize(e1*e2/2);
+     for(int n=0;n<e1;n++){
+       for(int b=0;b<e2;b++){
+	 int o  = n*stride;
+	 int ocb=1<<grid->CheckerBoardFromOindexTable(o+b);
+	 if ( ocb &cbmask ) {
+	   table[bo]=std::pair<int,int>(bo,o+b); bo++;
+	 }
+       }
+     }
   }
 }
 
-///////////////////////////////////////////////////////////////////
-// Gather for when there *is* need to SIMD split with compression
-///////////////////////////////////////////////////////////////////
-template<class cobj,class vobj,class compressor>
-void Gather_plane_exchange_table(const Lattice<vobj> &rhs,
-				 std::vector<cobj *> pointers,int dimension,int plane,int cbmask,compressor &compress,int type) __attribute__((noinline));
-
-template<class cobj,class vobj,class compressor>
-void Gather_plane_exchange_table(std::vector<std::pair<int,int> >& table,const Lattice<vobj> &rhs,
-				 std::vector<cobj *> pointers,int dimension,int plane,int cbmask,
-				 compressor &compress,int type)
+template<class vobj,class cobj,class compressor> void 
+Gather_plane_simple_table (std::vector<std::pair<int,int> >& table,const Lattice<vobj> &rhs,cobj *buffer,compressor &compress, int off,int so)
 {
-  assert( (table.size()&0x1)==0);
-  int num=table.size()/2;
-  int so  = plane*rhs._grid->_ostride[dimension]; // base offset for start of plane 
-  parallel_for(int j=0;j<num;j++){
-    //    buffer[off+table[i].first]=compress(rhs._odata[so+table[i].second]);
-    cobj temp1 =compress(rhs._odata[so+table[2*j].second]);
-    cobj temp2 =compress(rhs._odata[so+table[2*j+1].second]);
-    cobj temp3;
-    cobj temp4;
-    exchange(temp3,temp4,temp1,temp2,type);
-    vstream(pointers[0][j],temp3);
-    vstream(pointers[1][j],temp4);
+PARALLEL_FOR_LOOP     
+     for(int i=0;i<table.size();i++){
+       buffer[off+table[i].first]=compress(rhs._odata[so+table[i].second]);
      }
 }
 
@@ -121,8 +125,6 @@ struct StencilEntry {
   uint32_t _around_the_world; //256 bits, 32 bytes, 1/2 cacheline
 };
 
-//extern int dump;
-
 template<class vobj,class cobj>
 class CartesianStencil { // Stencil runs along coordinate axes only; NO diagonal fill in.
  public:
@@ -157,6 +159,7 @@ class CartesianStencil { // Stencil runs along coordinate axes only; NO diagonal
     p.to_rank  = to;
     p.from_rank= from;
     p.bytes    = bytes;
+    comms_bytes+=2.0*bytes;
     Packets.push_back(p);
   }
 
@@ -165,45 +168,36 @@ class CartesianStencil { // Stencil runs along coordinate axes only; NO diagonal
     reqs.resize(Packets.size());
     commtime-=usecond();
     for(int i=0;i<Packets.size();i++){
-      comms_bytes+=_grid->StencilSendToRecvFromBegin(reqs[i],
+	_grid->StencilSendToRecvFromBegin(reqs[i],
+					  Packets[i].send_buf,
+					  Packets[i].to_rank,
+					  Packets[i].recv_buf,
+					  Packets[i].from_rank,
+					  Packets[i].bytes);
+	/*
+      }else{
+	_grid->SendToRecvFromBegin(reqs[i],
 				   Packets[i].send_buf,
 				   Packets[i].to_rank,
 				   Packets[i].recv_buf,
 				   Packets[i].from_rank,
 				   Packets[i].bytes);
+      }
+	*/
     }
     commtime+=usecond();
   }
   void CommunicateComplete(std::vector<std::vector<CommsRequest_t> > &reqs)
   {
     commtime-=usecond();
+
     for(int i=0;i<Packets.size();i++){
+      //      if( ShmDirectCopy ) 
 	_grid->StencilSendToRecvFromComplete(reqs[i]);
+	//      else 
+	//	_grid->SendToRecvFromComplete(reqs[i]);
     }
-    _grid->StencilBarrier();// Synch shared memory on a single nodes
     commtime+=usecond();
-    /*
-    int dump=1;
-    if(dump){
-      for(int i=0;i<Packets.size();i++){
-	cobj * ptr  = (cobj *) Packets[i].recv_buf;
-	uint64_t num=Packets[i].bytes/sizeof(cobj);
-	  std::cout << " CommunicateComplete " << i<< " / " << Packets.size()<< " num " << num <<std::endl;
-	  std::stringstream ss;
-	  ss<<"recvbuf";
-	  for(int d=0;d<_grid->_ndimension;d++){
-	    ss<<"."<<_grid->_processor_coor[d];
-	  }
-	  ss<<"_mu_"<<i;
-	  std::string fname(ss.str());
-	  std::ofstream fout(fname);
-	  for(int k=0;k<num;k++) {
-	    fout << i<<" "<<k<<" "<<ptr[k]<<std::endl;
-	  }
-      }
-    }
-    dump =0;
-*/
   }
 
   ///////////////////////////////////////////
@@ -212,18 +206,14 @@ class CartesianStencil { // Stencil runs along coordinate axes only; NO diagonal
   struct Merge {
     cobj * mpointer;
     std::vector<scalar_object *> rpointers;
-    std::vector<cobj *> vpointers;
     Integer buffer_size;
     Integer packet_id;
-    Integer exchange;
-    Integer type;
   };
   
   std::vector<Merge> Mergers;
 
   void AddMerge(cobj *merge_p,std::vector<scalar_object *> &rpointers,Integer buffer_size,Integer packet_id) {
     Merge m;
-    m.exchange = 0;
     m.mpointer = merge_p;
     m.rpointers= rpointers;
     m.buffer_size = buffer_size;
@@ -231,48 +221,17 @@ class CartesianStencil { // Stencil runs along coordinate axes only; NO diagonal
     Mergers.push_back(m);
   }
 
-  void AddMergeNew(cobj *merge_p,std::vector<cobj *> &rpointers,Integer buffer_size,Integer packet_id,Integer type) {
-    Merge m;
-    m.exchange = 1;
-    m.type     = type;
-    m.mpointer = merge_p;
-    m.vpointers= rpointers;
-    m.buffer_size = buffer_size;
-    m.packet_id   = packet_id;
-    Mergers.push_back(m);
-  }
-
   void CommsMerge(void ) { 
 
     for(int i=0;i<Mergers.size();i++){	
+      
       mergetime-=usecond();
-
-      //      std::cout << "Merge " <<i << std::endl;
-      //      std::stringstream ss;
-      //      ss<<"mergebuf";
-      //      for(int d=0;d<_grid->_ndimension;d++){
-      //	ss<<"."<<_grid->_processor_coor[d];
-      //      }
-      //      ss<<"_m_"<<i;
-      //      std::string fname(ss.str());
-      //      std::ofstream fout(fname);
-
-      if ( Mergers[i].exchange == 0 ) { 
-	parallel_for(int o=0;o<Mergers[i].buffer_size;o++){
+PARALLEL_FOR_LOOP
+      for(int o=0;o<Mergers[i].buffer_size;o++){
 	merge1(Mergers[i].mpointer[o],Mergers[i].rpointers,o);
-	  //	fout<<o<<" "<<Mergers[i].mpointer[o]<<std::endl;
-	}
-      } else { 
-	parallel_for(int o=0;o<Mergers[i].buffer_size/2;o++){
-	  exchange(Mergers[i].mpointer[2*o],Mergers[i].mpointer[2*o+1],
-		   Mergers[i].vpointers[0][o],Mergers[i].vpointers[1][o],Mergers[i].type);
-	  //	  cobj temp1,temp2;
-	  //	  exchange(temp1,temp2,Mergers[i].vpointers[0][o],Mergers[i].vpointers[1][o],Mergers[i].type);
-	  //	  vstream(Mergers[i].mpointer[2*o],temp1);
-	  //	  vstream(Mergers[i].mpointer[2*o+1],temp2);
-	}
       }
       mergetime+=usecond();
+
     }
   }
 
@@ -336,8 +295,6 @@ class CartesianStencil { // Stencil runs along coordinate axes only; NO diagonal
   // depending on comms target
   cobj* u_recv_buf_p;
   cobj* u_send_buf_p;
-  std::vector<cobj *> new_simd_send_buf;
-  std::vector<cobj *> new_simd_recv_buf;
   std::vector<scalar_object *> u_simd_send_buf;
   std::vector<scalar_object *> u_simd_recv_buf;
 
@@ -384,11 +341,6 @@ class CartesianStencil { // Stencil runs along coordinate axes only; NO diagonal
   void Report(void) {
 #define PRINTIT(A)	\
  std::cout << GridLogMessage << " Stencil " << #A << " "<< A/calls<<std::endl;
-
-    RealD NP = _grid->_Nprocessors;
-    RealD NN = _grid->NodeCount();
-
-    _grid->GlobalSum(commtime);    commtime/=NP;
     if ( calls > 0. ) {
       std::cout << GridLogMessage << " Stencil calls "<<calls<<std::endl;
       PRINTIT(halogtime);
@@ -398,8 +350,7 @@ class CartesianStencil { // Stencil runs along coordinate axes only; NO diagonal
       if(comms_bytes>1.0){
 	PRINTIT(comms_bytes);
 	PRINTIT(commtime);
-	std::cout << GridLogMessage << " Stencil " << comms_bytes/commtime/1000. << " GB/s per rank"<<std::endl;
-	std::cout << GridLogMessage << " Stencil " << comms_bytes/commtime/1000.*NP/NN << " GB/s per node"<<std::endl;
+	std::cout << GridLogMessage << " Stencil " << comms_bytes/commtime/1000. << " GB/s "<<std::endl;
       }
       PRINTIT(jointime);
       PRINTIT(spintime);
@@ -443,9 +394,7 @@ class CartesianStencil { // Stencil runs along coordinate axes only; NO diagonal
       
       _checkerboard = checkerboard;
       
-      //////////////////////////
       // the permute type
-      //////////////////////////
       int simd_layout     = _grid->_simd_layout[dimension];
       int comm_dim        = _grid->_processors[dimension] >1 ;
       int splice_dim      = _grid->_simd_layout[dimension]>1 && (comm_dim);
@@ -455,11 +404,9 @@ class CartesianStencil { // Stencil runs along coordinate axes only; NO diagonal
       
       int sshift[2];
       
-      //////////////////////////
       // Underlying approach. For each local site build
       // up a table containing the npoint "neighbours" and whether they 
       // live in lattice or a comms buffer.
-      //////////////////////////
       if ( !comm_dim ) {
 	sshift[0] = _grid->CheckerBoardShiftForCB(_checkerboard,dimension,shift,Even);
 	sshift[1] = _grid->CheckerBoardShiftForCB(_checkerboard,dimension,shift,Odd);
@@ -470,11 +417,11 @@ class CartesianStencil { // Stencil runs along coordinate axes only; NO diagonal
 	  Local(point,dimension,shift,0x1);// if checkerboard is unfavourable take two passes
 	  Local(point,dimension,shift,0x2);// both with block stride loop iteration
 	}
-      } else { 
-	// All permute extract done in comms phase prior to Stencil application
+      } else { // All permute extract done in comms phase prior to Stencil application
 	//        So tables are the same whether comm_dim or splice_dim
 	sshift[0] = _grid->CheckerBoardShiftForCB(_checkerboard,dimension,shift,Even);
 	sshift[1] = _grid->CheckerBoardShiftForCB(_checkerboard,dimension,shift,Odd);
+	
 	if ( sshift[0] == sshift[1] ) {
 	  Comms(point,dimension,shift,0x3);
 	} else {
@@ -493,21 +440,13 @@ class CartesianStencil { // Stencil runs along coordinate axes only; NO diagonal
 
     u_simd_send_buf.resize(Nsimd);
     u_simd_recv_buf.resize(Nsimd);
-    new_simd_send_buf.resize(Nsimd);
-    new_simd_recv_buf.resize(Nsimd);
+
     u_send_buf_p=(cobj *)_grid->ShmBufferMalloc(_unified_buffer_size*sizeof(cobj));
     u_recv_buf_p=(cobj *)_grid->ShmBufferMalloc(_unified_buffer_size*sizeof(cobj));
-#ifdef NEW_XYZT_GATHER
-    for(int l=0;l<2;l++){
-      new_simd_recv_buf[l] = (cobj *)_grid->ShmBufferMalloc(_unified_buffer_size*sizeof(cobj));
-      new_simd_send_buf[l] = (cobj *)_grid->ShmBufferMalloc(_unified_buffer_size*sizeof(cobj));
-    }
-#else
     for(int l=0;l<Nsimd;l++){
       u_simd_recv_buf[l] = (scalar_object *)_grid->ShmBufferMalloc(_unified_buffer_size*sizeof(scalar_object));
       u_simd_send_buf[l] = (scalar_object *)_grid->ShmBufferMalloc(_unified_buffer_size*sizeof(scalar_object));
     }
-#endif
 
     PrecomputeByteOffsets();
   }
@@ -574,11 +513,9 @@ class CartesianStencil { // Stencil runs along coordinate axes only; NO diagonal
     assert(shift>=0);
     assert(shift<fd);
     
-    // done in reduced dims, so SIMD factored
-    int buffer_size = _grid->_slice_nblock[dimension]*_grid->_slice_block[dimension]; 
+    int buffer_size = _grid->_slice_nblock[dimension]*_grid->_slice_block[dimension]; // done in reduced dims, so SIMD factored
     
     _comm_buf_size[point] = buffer_size; // Size of _one_ plane. Multiple planes may be gathered and
-
     // send to one or more remote nodes.
     
     int cb= (cbmask==0x2)? Odd : Even;
@@ -741,10 +678,13 @@ class CartesianStencil { // Stencil runs along coordinate axes only; NO diagonal
     calls++;
     Mergers.resize(0);
     Packets.resize(0);
+    _grid->StencilBarrier();
     HaloGather(source,compress);
     this->CommunicateBegin(reqs);
+    _grid->StencilBarrier();
     this->CommunicateComplete(reqs);
-    CommsMerge(); 
+    _grid->StencilBarrier();
+    CommsMerge(); // spins
   }
   
   template<class compressor> void HaloGatherDir(const Lattice<vobj> &source,compressor &compress,int point,int & face_idx)
@@ -775,13 +715,7 @@ class CartesianStencil { // Stencil runs along coordinate axes only; NO diagonal
       if ( sshift[0] == sshift[1] ) {
 	if (splice_dim) {
 	  splicetime-=usecond();
-	  //	  GatherSimd(source,dimension,shift,0x3,compress,face_idx);
-	  //	  std::cout << "GatherSimdNew"<<std::endl;
-#ifdef NEW_XYZT_GATHER
-	  GatherSimdNew(source,dimension,shift,0x3,compress,face_idx);
-#else 
 	  GatherSimd(source,dimension,shift,0x3,compress,face_idx);
-#endif
 	  splicetime+=usecond();
 	} else { 
 	  nosplicetime-=usecond();
@@ -791,14 +725,8 @@ class CartesianStencil { // Stencil runs along coordinate axes only; NO diagonal
       } else {
 	if(splice_dim){
 	  splicetime-=usecond();
-	  //	  std::cout << "GatherSimdNew2calls"<<std::endl;
-#ifdef NEW_XYZT_GATHER
-	  GatherSimdNew(source,dimension,shift,0x1,compress,face_idx);// if checkerboard is unfavourable take two passes
-	  GatherSimdNew(source,dimension,shift,0x2,compress,face_idx);// both with block stride loop iteration
-#else 
 	  GatherSimd(source,dimension,shift,0x1,compress,face_idx);// if checkerboard is unfavourable take two passes
 	  GatherSimd(source,dimension,shift,0x2,compress,face_idx);// both with block stride loop iteration
-#endif
 	  splicetime+=usecond();
 	} else {
 	  nosplicetime-=usecond();
@@ -813,8 +741,6 @@ class CartesianStencil { // Stencil runs along coordinate axes only; NO diagonal
   template<class compressor>
   void HaloGather(const Lattice<vobj> &source,compressor &compress)
   {
-    _grid->StencilBarrier();// Synch shared memory on a single nodes
-
     // conformable(source._grid,_grid);
     assert(source._grid==_grid);
     halogtime-=usecond();
@@ -875,12 +801,12 @@ class CartesianStencil { // Stencil runs along coordinate axes only; NO diagonal
 	if ( !face_table_computed ) {
 	  t_table-=usecond();
 	  face_table.resize(face_idx+1);
-	  Gather_plane_table_compute ((GridBase *)_grid,dimension,sx,cbmask,u_comm_offset,face_table[face_idx]);
-	  //	  std::cout << " face table size "<<face_idx <<" " <<  face_table[face_idx].size() <<" computed buffer size "<< words <<
-	  //		    " bytes = " << bytes <<std::endl;
+	  Gather_plane_simple_table_compute ((GridBase *)_grid,dimension,sx,cbmask,u_comm_offset,
+					     face_table[face_idx]);
 	  t_table+=usecond();
 	}
 	
+	
 	int rank           = _grid->_processor;
 	int recv_from_rank;
 	int xmit_to_rank;
@@ -892,12 +818,15 @@ class CartesianStencil { // Stencil runs along coordinate axes only; NO diagonal
 	/////////////////////////////////////////////////////////
 	// try the direct copy if possible
 	/////////////////////////////////////////////////////////
+
+
 	cobj *send_buf = (cobj *)_grid->ShmBufferTranslate(xmit_to_rank,u_recv_buf_p);
 	if ( send_buf==NULL ) { 
 	  send_buf = u_send_buf_p;
 	}
-	
+	//	std::cout << " send_bufs  "<<std::hex<< send_buf <<" ubp "<<u_send_buf_p <<std::dec<<std::endl;
 	t_data-=usecond();
+	assert(u_send_buf_p!=NULL);
 	assert(send_buf!=NULL);
 	Gather_plane_simple_table         (face_table[face_idx],rhs,send_buf,compress,u_comm_offset,so);  face_idx++;
 	t_data+=usecond();
@@ -947,8 +876,6 @@ class CartesianStencil { // Stencil runs along coordinate axes only; NO diagonal
     std::vector<scalar_object *> rpointers(Nsimd);
     std::vector<scalar_object *> spointers(Nsimd);
     
-    //    std::cout << "GatherSimd " << dimension << " shift "<<shift<<std::endl;
-
     ///////////////////////////////////////////
     // Work out what to send where
     ///////////////////////////////////////////
@@ -975,10 +902,10 @@ class CartesianStencil { // Stencil runs along coordinate axes only; NO diagonal
 
 	for(int i=0;i<Nsimd;i++){
 	  
-	  // FIXME -  This logic is hard coded to simd_layout==2 and not allowing >2
-	  //	  for(int w=0;w<buffer_size;w++){
-	  //	    std::cout << "GatherSimd<"<<Nsimd<<"> : lane " << i <<" elem "<<w<<" "<< u_simd_send_buf[i ][u_comm_offset+w]<<std::endl;
-	  //	  }
+	  // FIXME 
+	  // This logic is hard coded to simd_layout ==2 and not allowing >2
+	  //		std::cout << "GatherSimd : lane 1st elem " << i << u_simd_send_buf[i ][u_comm_offset]<<std::endl;
+	  
 	  int inner_bit = (Nsimd>>(permute_type+1));
 	  int ic= (i&inner_bit)? 1:0;
 	  
@@ -1003,9 +930,8 @@ class CartesianStencil { // Stencil runs along coordinate axes only; NO diagonal
 	    
 	    _grid->ShiftedRanks(dimension,nbr_proc,xmit_to_rank,recv_from_rank); 
  
-	    // shm == receive pointer         if offnode
-	    // shm == Translate[send pointer] if on node -- my view of his send pointer
 	    scalar_object *shm = (scalar_object *) _grid->ShmBufferTranslate(recv_from_rank,sp);
+	    //	    if ((ShmDirectCopy==0)||(shm==NULL)) { 
 	    if (shm==NULL) { 
 	      shm = rp;
 	    } 
@@ -1030,133 +956,6 @@ class CartesianStencil { // Stencil runs along coordinate axes only; NO diagonal
     }
   }
   
-
-  template<class compressor>
-  void  GatherSimdNew(const Lattice<vobj> &rhs,int dimension,int shift,int cbmask,compressor &compress,int & face_idx)
-  {
-    const int Nsimd = _grid->Nsimd();
-
-    const int maxl =2;// max layout in a direction
-    int fd = _grid->_fdimensions[dimension];
-    int rd = _grid->_rdimensions[dimension];
-    int ld = _grid->_ldimensions[dimension];
-    int pd              = _grid->_processors[dimension];
-    int simd_layout     = _grid->_simd_layout[dimension];
-    int comm_dim        = _grid->_processors[dimension] >1 ;
-    assert(comm_dim==1);
-    // This will not work with a rotate dim
-    assert(simd_layout==maxl);
-    assert(shift>=0);
-    assert(shift<fd);
-
-    int permute_type=_grid->PermuteType(dimension);
-    //    std::cout << "SimdNew permute type "<<permute_type<<std::endl;
-
-    ///////////////////////////////////////////////
-    // Simd direction uses an extract/merge pair
-    ///////////////////////////////////////////////
-    int buffer_size = _grid->_slice_nblock[dimension]*_grid->_slice_block[dimension];
-    int words = sizeof(cobj)/sizeof(vector_type);
-    
-    assert(cbmask==0x3); // Fixme think there is a latent bug if not true
-    
-    int reduced_buffer_size = buffer_size;
-    if (cbmask != 0x3) reduced_buffer_size=buffer_size>>1;
-
-    int bytes = (reduced_buffer_size*sizeof(cobj))/simd_layout;
-    assert(bytes*simd_layout == reduced_buffer_size*sizeof(cobj));
-
-    std::vector<cobj *> rpointers(maxl);
-    std::vector<cobj *> spointers(maxl);
-
-    ///////////////////////////////////////////
-    // Work out what to send where
-    ///////////////////////////////////////////
-    
-    int cb    = (cbmask==0x2)? Odd : Even;
-    int sshift= _grid->CheckerBoardShiftForCB(rhs.checkerboard,dimension,shift,cb);
-    
-    // loop over outer coord planes orthog to dim
-    for(int x=0;x<rd;x++){       
-      
-      int any_offnode = ( ((x+sshift)%fd) >= rd );
-
-      if ( any_offnode ) {
-
-	
-	for(int i=0;i<maxl;i++){       
-	  spointers[i] = (cobj *) &new_simd_send_buf[i][u_comm_offset];
-	}
-	
-	int sx   = (x+sshift)%rd;
-
-	//	if ( cbmask==0x3 ) { 
-	//	  std::vector<std::pair<int,int> > table;
-	t_table-=usecond();
-	if ( !face_table_computed ) {
-	  face_table.resize(face_idx+1);
-	  Gather_plane_table_compute ((GridBase *)_grid,dimension,sx,cbmask,u_comm_offset,face_table[face_idx]);
-	  //	  std::cout << " face table size "<<face_idx <<" " <<  face_table[face_idx].size() <<" computed buffer size "<< reduced_buffer_size <<
-	  //		    " bytes = "<<bytes <<std::endl;
-	}
-	t_table+=usecond();
-	gathermtime-=usecond();
-	Gather_plane_exchange_table(face_table[face_idx],rhs,spointers,dimension,sx,cbmask,compress,permute_type);  face_idx++;
-	gathermtime+=usecond();
-      
-	//spointers[0] -- low
-	//spointers[1] -- high
-
-	for(int i=0;i<maxl;i++){
-
-	  int my_coor  = rd*i + x;            // self explanatory
-	  int nbr_coor = my_coor+sshift;      // self explanatory
-
-	  int nbr_proc = ((nbr_coor)/ld) % pd;// relative shift in processors
-	  int nbr_lcoor= (nbr_coor%ld);       // local plane coor on neighbour node
-	  int nbr_ic   = (nbr_lcoor)/rd;      // inner coord of peer simd lane "i"
-	  int nbr_ox   = (nbr_lcoor%rd);      // outer coord of peer "x"
-
-	  int nbr_plane = nbr_ic;
-	  assert (sx == nbr_ox);
-
-	  auto rp = &new_simd_recv_buf[i        ][u_comm_offset];
-	  auto sp = &new_simd_send_buf[nbr_plane][u_comm_offset];
-
-	  if(nbr_proc){
-
-	    int recv_from_rank;
-	    int xmit_to_rank;
-	    
-	    _grid->ShiftedRanks(dimension,nbr_proc,xmit_to_rank,recv_from_rank); 
- 
-	    // shm == receive pointer         if offnode
-	    // shm == Translate[send pointer] if on node -- my view of his send pointer
-	    cobj *shm = (cobj *) _grid->ShmBufferTranslate(recv_from_rank,sp);
-	    if (shm==NULL) { 
-	      shm = rp;
-	    }
-
-	    // if Direct, StencilSendToRecvFrom will suppress copy to a peer on node
-	    // assuming above pointer flip
-	    AddPacket((void *)sp,(void *)rp,xmit_to_rank,recv_from_rank,bytes);
-
-	    rpointers[i] = shm;
-	    
-	  } else { 
-	    
-	    rpointers[i] = sp;
-	    
-	  }
-	}
-
-	AddMergeNew(&u_recv_buf_p[u_comm_offset],rpointers,reduced_buffer_size,Packets.size()-1,permute_type);
-
-	u_comm_offset     +=buffer_size;
-      }
-    }
-  }
-  
 };
 }
 #endif

lib/Threads.h

@@ -37,23 +37,22 @@ Author: paboyle <paboyle@ph.ed.ac.uk>
 
 #ifdef GRID_OMP
 #include <omp.h>
-
+#ifdef GRID_NUMA
 #define PARALLEL_FOR_LOOP        _Pragma("omp parallel for schedule(static)")
 #define PARALLEL_FOR_LOOP_INTERN _Pragma("omp for schedule(static)")
+#else
+#define PARALLEL_FOR_LOOP        _Pragma("omp parallel for schedule(runtime)")
+#define PARALLEL_FOR_LOOP_INTERN _Pragma("omp for schedule(runtime)")
+#endif
 #define PARALLEL_NESTED_LOOP2 _Pragma("omp parallel for collapse(2)")
 #define PARALLEL_REGION       _Pragma("omp parallel")
-#define PARALLEL_CRITICAL     _Pragma("omp critical")
 #else
 #define PARALLEL_FOR_LOOP
 #define PARALLEL_FOR_LOOP_INTERN
 #define PARALLEL_NESTED_LOOP2
 #define PARALLEL_REGION
-#define PARALLEL_CRITICAL
 #endif
 
-#define parallel_for       PARALLEL_FOR_LOOP for
-#define parallel_for_nest2 PARALLEL_NESTED_LOOP2 for
-
 namespace Grid {
 
   // Introduce a class to gain deterministic bit reproducible reduction.

lib/algorithms/CoarsenedMatrix.h

@@ -267,7 +267,8 @@ namespace Grid {
       SimpleCompressor<siteVector> compressor;
       Stencil.HaloExchange(in,compressor);
 
-      parallel_for(int ss=0;ss<Grid()->oSites();ss++){
+PARALLEL_FOR_LOOP
+      for(int ss=0;ss<Grid()->oSites();ss++){
         siteVector res = zero;
 	siteVector nbr;
 	int ptype;
@@ -379,7 +380,8 @@ namespace Grid {
 	  Subspace.ProjectToSubspace(oProj,oblock);
 	  //	  blockProject(iProj,iblock,Subspace.subspace);
 	  //	  blockProject(oProj,oblock,Subspace.subspace);
-	  parallel_for(int ss=0;ss<Grid()->oSites();ss++){
+PARALLEL_FOR_LOOP
+	  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);
@@ -425,7 +427,7 @@ namespace Grid {
 	A[p]=zero;
       }
 
-      GridParallelRNG  RNG(Grid()); RNG.SeedFixedIntegers(std::vector<int>({55,72,19,17,34}));
+      GridParallelRNG  RNG(Grid()); RNG.SeedRandomDevice();
       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/GridCore.h>
+#include <Grid.h>
 
 namespace Grid {
 double MultiShiftFunction::approx(double x)

lib/algorithms/approx/Remez.cc

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

lib/algorithms/iterative/ConjugateGradient.h

@@ -45,8 +45,6 @@ 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
-  
   ConjugateGradient(RealD tol, Integer maxit, bool err_on_no_conv = true)
       : Tolerance(tol),
         MaxIterations(maxit),
@@ -157,14 +155,13 @@ class ConjugateGradient : public OperatorFunction<Field> {
         std::cout << std::endl;
 
         if (ErrorOnNoConverge) assert(true_residual / Tolerance < 10000.0);
-	IterationsToComplete = k;	
+
         return;
       }
     }
     std::cout << GridLogMessage << "ConjugateGradient did NOT converge"
               << std::endl;
     if (ErrorOnNoConverge) assert(0);
-    IterationsToComplete = k;
   }
 };
 }

lib/algorithms/iterative/ConjugateGradientMixedPrec.h

@@ -35,7 +35,6 @@ 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
@@ -43,16 +42,12 @@ 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), InnerTolerance(tol), MaxInnerIterations(maxinnerit), MaxOuterIterations(maxouterit), SinglePrecGrid(_sp_grid),
+      Tolerance(tol), MaxInnerIterations(maxinnerit), MaxOuterIterations(maxouterit), SinglePrecGrid(_sp_grid),
       OuterLoopNormMult(100.), guesser(NULL){ };
 
     void useGuesser(LinearFunction<FieldF> &g){
@@ -60,8 +55,6 @@ namespace Grid {
     }
   
     void operator() (const FieldD &src_d_in, FieldD &sol_d){
-      TotalInnerIterations = 0;
-	
       GridStopWatch TotalTimer;
       TotalTimer.Start();
     
@@ -81,7 +74,7 @@ namespace Grid {
       FieldD src_d(DoublePrecGrid);
       src_d = src_d_in; //source for next inner iteration, computed from residual during operation
     
-      RealD inner_tol = InnerTolerance;
+      RealD inner_tol = Tolerance;
     
       FieldF src_f(SinglePrecGrid);
       src_f.checkerboard = cb;
@@ -96,9 +89,7 @@ namespace Grid {
 
       GridStopWatch PrecChangeTimer;
     
-      Integer &outer_iter = TotalOuterIterations; //so it will be equal to the final iteration count
-      
-      for(outer_iter = 0; outer_iter < MaxOuterIterations; outer_iter++){
+      for(Integer 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
@@ -126,7 +117,6 @@ 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();
@@ -141,11 +131,9 @@ 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: 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;
+      std::cout<<GridLogMessage<<"MixedPrecisionConjugateGradient: Total " << TotalTimer.Elapsed() << " Precision change " << PrecChangeTimer.Elapsed() << " Inner CG total " << InnerCGtimer.Elapsed() << std::endl;
     }
   };
 

lib/algorithms/iterative/ImplicitlyRestartedLanczos.h

@@ -31,16 +31,11 @@ Author: paboyle <paboyle@ph.ed.ac.uk>
 
 #include <string.h> //memset
 #ifdef USE_LAPACK
-#ifdef USE_MKL
-#include<mkl_lapack.h>
-#else
 void LAPACK_dstegr(char *jobz, char *range, int *n, double *d, double *e,
                    double *vl, double *vu, int *il, int *iu, double *abstol,
                    int *m, double *w, double *z, int *ldz, int *isuppz,
                    double *work, int *lwork, int *iwork, int *liwork,
                    int *info);
-//#include <lapacke/lapacke.h>
-#endif
 #endif
 #include "DenseMatrix.h"
 #include "EigenSort.h"
@@ -67,13 +62,12 @@ public:
     int Np;      // Np -- Number of spare vecs in kryloc space
     int Nm;      // Nm -- total number of vectors
 
-
-    RealD OrthoTime;
-
     RealD eresid;
 
     SortEigen<Field> _sort;
 
+//    GridCartesian &_fgrid;
+
     LinearOperatorBase<Field> &_Linop;
 
     OperatorFunction<Field>   &_poly;
@@ -130,23 +124,23 @@ public:
 
       GridBase *grid = evec[0]._grid;
       Field w(grid);
-      std::cout<<GridLogMessage << "RitzMatrix "<<std::endl;
+      std::cout << "RitzMatrix "<<std::endl;
       for(int i=0;i<k;i++){
 	_poly(_Linop,evec[i],w);
-	std::cout<<GridLogMessage << "["<<i<<"] ";
+	std::cout << "["<<i<<"] ";
 	for(int j=0;j<k;j++){
 	  ComplexD in = innerProduct(evec[j],w);
 	  if ( fabs((double)i-j)>1 ) { 
 	    if (abs(in) >1.0e-9 )  { 
-	      std::cout<<GridLogMessage<<"oops"<<std::endl;
+	      std::cout<<"oops"<<std::endl;
 	      abort();
 	    } else 
-	      std::cout<<GridLogMessage << " 0 ";
+	      std::cout << " 0 ";
 	  } else { 
-	    std::cout<<GridLogMessage << " "<<in<<" ";
+	    std::cout << " "<<in<<" ";
 	  }
 	}
-	std::cout<<GridLogMessage << std::endl;
+	std::cout << std::endl;
       }
     }
 
@@ -180,10 +174,10 @@ public:
       RealD beta = normalise(w); // 6. βk+1 := ∥wk∥2. If βk+1 = 0 then Stop
                                  // 7. vk+1 := wk/βk+1
 
-	std::cout<<GridLogMessage << "alpha = " << zalph << " beta "<<beta<<std::endl;
+//	std::cout << "alpha = " << zalph << " beta "<<beta<<std::endl;
       const RealD tiny = 1.0e-20;
       if ( beta < tiny ) { 
-	std::cout<<GridLogMessage << " beta is tiny "<<beta<<std::endl;
+	std::cout << " beta is tiny "<<beta<<std::endl;
      }
       lmd[k] = alph;
       lme[k]  = beta;
@@ -259,7 +253,6 @@ public:
     }
 
 #ifdef USE_LAPACK
-#define LAPACK_INT long long
     void diagonalize_lapack(DenseVector<RealD>& lmd,
 		     DenseVector<RealD>& lme, 
 		     int N1,
@@ -269,7 +262,7 @@ public:
   const int size = Nm;
 //  tevals.resize(size);
 //  tevecs.resize(size);
-  LAPACK_INT NN = N1;
+  int NN = N1;
   double evals_tmp[NN];
   double evec_tmp[NN][NN];
   memset(evec_tmp[0],0,sizeof(double)*NN*NN);
@@ -283,19 +276,19 @@ public:
         if (i==j) evals_tmp[i] = lmd[i];
         if (j==(i-1)) EE[j] = lme[j];
       }
-  LAPACK_INT evals_found;
-  LAPACK_INT lwork = ( (18*NN) > (1+4*NN+NN*NN)? (18*NN):(1+4*NN+NN*NN)) ;
-  LAPACK_INT liwork =  3+NN*10 ;
-  LAPACK_INT iwork[liwork];
+  int evals_found;
+  int lwork = ( (18*NN) > (1+4*NN+NN*NN)? (18*NN):(1+4*NN+NN*NN)) ;
+  int liwork =  3+NN*10 ;
+  int iwork[liwork];
   double work[lwork];
-  LAPACK_INT isuppz[2*NN];
+  int isuppz[2*NN];
   char jobz = 'V'; // calculate evals & evecs
   char range = 'I'; // calculate all evals
   //    char range = 'A'; // calculate all evals
   char uplo = 'U'; // refer to upper half of original matrix
   char compz = 'I'; // Compute eigenvectors of tridiagonal matrix
   int ifail[NN];
-  long long info;
+  int info;
 //  int total = QMP_get_number_of_nodes();
 //  int node = QMP_get_node_number();
 //  GridBase *grid = evec[0]._grid;
@@ -303,18 +296,14 @@ public:
   int node = grid->_processor;
   int interval = (NN/total)+1;
   double vl = 0.0, vu = 0.0;
-  LAPACK_INT il = interval*node+1 , iu = interval*(node+1);
+  int il = interval*node+1 , iu = interval*(node+1);
   if (iu > NN)  iu=NN;
   double tol = 0.0;
     if (1) {
       memset(evals_tmp,0,sizeof(double)*NN);
       if ( il <= NN){
         printf("total=%d node=%d il=%d iu=%d\n",total,node,il,iu);
-#ifdef USE_MKL
-        dstegr(&jobz, &range, &NN,
-#else
         LAPACK_dstegr(&jobz, &range, &NN,
-#endif
             (double*)DD, (double*)EE,
             &vl, &vu, &il, &iu, // these four are ignored if second parameteris 'A'
             &tol, // tolerance
@@ -346,7 +335,6 @@ public:
       lmd [NN-1-i]=evals_tmp[i];
   }
 }
-#undef LAPACK_INT 
 #endif
 
 
@@ -377,14 +365,12 @@ public:
 //	diagonalize_lapack(lmd2,lme2,Nm2,Nm,Qt,grid);
 #endif
 
-      int Niter = 10000*N1;
+      int Niter = 100*N1;
       int kmin = 1;
       int kmax = N2;
       // (this should be more sophisticated)
 
-      for(int iter=0; ; ++iter){
-      if ( (iter+1)%(100*N1)==0) 
-      std::cout<<GridLogMessage << "[QL method] Not converged - iteration "<<iter+1<<"\n";
+      for(int iter=0; iter<Niter; ++iter){
 
 	// determination of 2x2 leading submatrix
 	RealD dsub = lmd[kmax-1]-lmd[kmax-2];
@@ -413,11 +399,11 @@ public:
         _sort.push(lmd3,N2);
         _sort.push(lmd2,N2);
          for(int k=0; k<N2; ++k){
-	    if (fabs(lmd2[k] - lmd3[k]) >SMALL)  std::cout<<GridLogMessage <<"lmd(qr) lmd(lapack) "<< k << ": " << lmd2[k] <<" "<< lmd3[k] <<std::endl;
-//	    if (fabs(lme2[k] - lme[k]) >SMALL)  std::cout<<GridLogMessage <<"lme(qr)-lme(lapack) "<< k << ": " << lme2[k] - lme[k] <<std::endl;
+	    if (fabs(lmd2[k] - lmd3[k]) >SMALL)  std::cout <<"lmd(qr) lmd(lapack) "<< k << ": " << lmd2[k] <<" "<< lmd3[k] <<std::endl;
+//	    if (fabs(lme2[k] - lme[k]) >SMALL)  std::cout <<"lme(qr)-lme(lapack) "<< k << ": " << lme2[k] - lme[k] <<std::endl;
 	  }
          for(int k=0; k<N1*N1; ++k){
-//	    if (fabs(Qt2[k] - Qt[k]) >SMALL)  std::cout<<GridLogMessage <<"Qt(qr)-Qt(lapack) "<< k << ": " << Qt2[k] - Qt[k] <<std::endl;
+//	    if (fabs(Qt2[k] - Qt[k]) >SMALL)  std::cout <<"Qt(qr)-Qt(lapack) "<< k << ": " << Qt2[k] - Qt[k] <<std::endl;
 	}
     }
 #endif
@@ -432,7 +418,7 @@ public:
 	  }
 	}
       }
-      std::cout<<GridLogMessage << "[QL method] Error - Too many iteration: "<<Niter<<"\n";
+      std::cout << "[QL method] Error - Too many iteration: "<<Niter<<"\n";
       abort();
     }
 
@@ -449,7 +435,6 @@ public:
 		       DenseVector<Field>& evec,
 		       int k)
     {
-      double t0=-usecond()/1e6;
       typedef typename Field::scalar_type MyComplex;
       MyComplex ip;
 
@@ -468,8 +453,6 @@ public:
 	w = w - ip * evec[j];
       }
       normalise(w);
-      t0+=usecond()/1e6;
-      OrthoTime +=t0;
     }
 
     void setUnit_Qt(int Nm, DenseVector<RealD> &Qt) {
@@ -503,10 +486,10 @@ until convergence
 	GridBase *grid = evec[0]._grid;
 	assert(grid == src._grid);
 
-	std::cout<<GridLogMessage << " -- Nk = " << Nk << " Np = "<< Np << std::endl;
-	std::cout<<GridLogMessage << " -- Nm = " << Nm << std::endl;
-	std::cout<<GridLogMessage << " -- size of eval   = " << eval.size() << std::endl;
-	std::cout<<GridLogMessage << " -- size of evec  = " << evec.size() << std::endl;
+	std::cout << " -- Nk = " << Nk << " Np = "<< Np << std::endl;
+	std::cout << " -- Nm = " << Nm << std::endl;
+	std::cout << " -- size of eval   = " << eval.size() << std::endl;
+	std::cout << " -- size of evec  = " << evec.size() << std::endl;
 	
 	assert(Nm == evec.size() && Nm == eval.size());
 	
@@ -517,7 +500,6 @@ until convergence
 	DenseVector<int>   Iconv(Nm);
 
 	DenseVector<Field>  B(Nm,grid); // waste of space replicating
-//	DenseVector<Field>  Btemp(Nm,grid); // waste of space replicating
 	
 	Field f(grid);
 	Field v(grid);
@@ -533,48 +515,35 @@ until convergence
 	// (uniform vector) Why not src??
 	//	evec[0] = 1.0;
 	evec[0] = src;
-	std:: cout<<GridLogMessage <<"norm2(src)= " << norm2(src)<<std::endl;
+	std:: cout <<"norm2(src)= " << norm2(src)<<std::endl;
 // << src._grid  << std::endl;
 	normalise(evec[0]);
-	std:: cout<<GridLogMessage <<"norm2(evec[0])= " << norm2(evec[0]) <<std::endl;
+	std:: cout <<"norm2(evec[0])= " << norm2(evec[0]) <<std::endl;
 // << evec[0]._grid << std::endl;
 	
 	// Initial Nk steps
-	OrthoTime=0.;
-	double t0=usecond()/1e6;
 	for(int k=0; k<Nk; ++k) step(eval,lme,evec,f,Nm,k);
-	double t1=usecond()/1e6;
-	std::cout<<GridLogMessage <<"IRL::Initial steps: "<<t1-t0<< "seconds"<<std::endl; t0=t1;
-	std::cout<<GridLogMessage <<"IRL::Initial steps:OrthoTime "<<OrthoTime<< "seconds"<<std::endl;
-//	std:: cout<<GridLogMessage <<"norm2(evec[1])= " << norm2(evec[1]) << std::endl;
-//	std:: cout<<GridLogMessage <<"norm2(evec[2])= " << norm2(evec[2]) << std::endl;
+//	std:: cout <<"norm2(evec[1])= " << norm2(evec[1]) << std::endl;
+//	std:: cout <<"norm2(evec[2])= " << norm2(evec[2]) << std::endl;
 	RitzMatrix(evec,Nk);
-	t1=usecond()/1e6;
-	std::cout<<GridLogMessage <<"IRL::RitzMatrix: "<<t1-t0<< "seconds"<<std::endl; t0=t1;
 	for(int k=0; k<Nk; ++k){
-//	std:: cout<<GridLogMessage <<"eval " << k << " " <<eval[k] << std::endl;
-//	std:: cout<<GridLogMessage <<"lme " << k << " " << lme[k] << std::endl;
+//	std:: cout <<"eval " << k << " " <<eval[k] << std::endl;
+//	std:: cout <<"lme " << k << " " << lme[k] << std::endl;
 	}
 
 	// Restarting loop begins
 	for(int iter = 0; iter<Niter; ++iter){
 
-	  std::cout<<GridLogMessage<<"\n Restart iteration = "<< iter << std::endl;
+	  std::cout<<"\n Restart iteration = "<< iter << std::endl;
 
 	  // 
 	  // Rudy does a sort first which looks very different. Getting fed up with sorting out the algo defs.
 	  // We loop over 
 	  //
-	OrthoTime=0.;
 	  for(int k=Nk; k<Nm; ++k) step(eval,lme,evec,f,Nm,k);
-	t1=usecond()/1e6;
-	std::cout<<GridLogMessage <<"IRL:: "<<Np <<" steps: "<<t1-t0<< "seconds"<<std::endl; t0=t1;
-	std::cout<<GridLogMessage <<"IRL::Initial steps:OrthoTime "<<OrthoTime<< "seconds"<<std::endl;
 	  f *= lme[Nm-1];
 
 	  RitzMatrix(evec,k2);
-	t1=usecond()/1e6;
-	std::cout<<GridLogMessage <<"IRL:: RitzMatrix: "<<t1-t0<< "seconds"<<std::endl; t0=t1;
 	  
 	  // getting eigenvalues
 	  for(int k=0; k<Nm; ++k){
@@ -583,27 +552,18 @@ until convergence
 	  }
 	  setUnit_Qt(Nm,Qt);
 	  diagonalize(eval2,lme2,Nm,Nm,Qt,grid);
-	t1=usecond()/1e6;
-	std::cout<<GridLogMessage <<"IRL:: diagonalize: "<<t1-t0<< "seconds"<<std::endl; t0=t1;
 
 	  // sorting
 	  _sort.push(eval2,Nm);
-	t1=usecond()/1e6;
-	std::cout<<GridLogMessage <<"IRL:: eval sorting: "<<t1-t0<< "seconds"<<std::endl; t0=t1;
 	  
 	  // Implicitly shifted QR transformations
 	  setUnit_Qt(Nm,Qt);
-	  for(int ip=0; ip<k2; ++ip){
-	std::cout<<GridLogMessage << "eval "<< ip << " "<< eval2[ip] << std::endl;
-	}
 	  for(int ip=k2; ip<Nm; ++ip){ 
-	std::cout<<GridLogMessage << "qr_decomp "<< ip << " "<< eval2[ip] << std::endl;
+	std::cout << "qr_decomp "<< ip << " "<< eval2[ip] << std::endl;
 	    qr_decomp(eval,lme,Nm,Nm,Qt,eval2[ip],k1,Nm);
 		
 	}
-	t1=usecond()/1e6;
-	std::cout<<GridLogMessage <<"IRL::qr_decomp: "<<t1-t0<< "seconds"<<std::endl; t0=t1;
-if (0) {  
+    
 	  for(int i=0; i<(Nk+1); ++i) B[i] = 0.0;
 	  
 	  for(int j=k1-1; j<k2+1; ++j){
@@ -611,30 +571,6 @@ if (0) {
 	    B[j].checkerboard = evec[k].checkerboard;
 	      B[j] += Qt[k+Nm*j] * evec[k];
 	    }
-	  }
-	t1=usecond()/1e6;
-	std::cout<<GridLogMessage <<"IRL::QR Rotate: "<<t1-t0<< "seconds"<<std::endl; t0=t1;
-}
-
-if (1) {
-	for(int i=0; i<(Nk+1); ++i) {
-		B[i] = 0.0;
-	  	B[i].checkerboard = evec[0].checkerboard;
-	}
-
-	int j_block = 24; int k_block=24;
-PARALLEL_FOR_LOOP
-	for(int ss=0;ss < grid->oSites();ss++){
-	for(int jj=k1-1; jj<k2+1; jj += j_block)
-	for(int kk=0; kk<Nm; kk += k_block)
-	for(int j=jj; (j<(k2+1)) && j<(jj+j_block); ++j){
-	for(int k=kk; (k<Nm) && k<(kk+k_block) ; ++k){
-	    B[j]._odata[ss] +=Qt[k+Nm*j] * evec[k]._odata[ss]; 
-	}
-	}
-	}
-	t1=usecond()/1e6;
-	std::cout<<GridLogMessage <<"IRL::QR rotation: "<<t1-t0<< "seconds"<<std::endl; t0=t1;
 	  }
 	  for(int j=k1-1; j<k2+1; ++j) evec[j] = B[j];
 
@@ -643,7 +579,7 @@ PARALLEL_FOR_LOOP
 	  f += lme[k2-1] * evec[k2];
 	  beta_k = norm2(f);
 	  beta_k = sqrt(beta_k);
-	  std::cout<<GridLogMessage<<" beta(k) = "<<beta_k<<std::endl;
+	  std::cout<<" beta(k) = "<<beta_k<<std::endl;
 
 	  RealD betar = 1.0/beta_k;
 	  evec[k2] = betar * f;
@@ -656,10 +592,7 @@ PARALLEL_FOR_LOOP
 	  }
 	  setUnit_Qt(Nm,Qt);
 	  diagonalize(eval2,lme2,Nk,Nm,Qt,grid);
-	t1=usecond()/1e6;
-	std::cout<<GridLogMessage <<"IRL::diagonalize: "<<t1-t0<< "seconds"<<std::endl; t0=t1;
 	  
-if (0) {
 	  for(int k = 0; k<Nk; ++k) B[k]=0.0;
 	  
 	  for(int j = 0; j<Nk; ++j){
@@ -667,34 +600,12 @@ if (0) {
 	    B[j].checkerboard = evec[k].checkerboard;
 	      B[j] += Qt[k+j*Nm] * evec[k];
 	    }
-	    std::cout<<GridLogMessage << "norm(B["<<j<<"])="<<norm2(B[j])<<std::endl;
-	  }
-	t1=usecond()/1e6;
-	std::cout<<GridLogMessage <<"IRL::Convergence rotation: "<<t1-t0<< "seconds"<<std::endl; t0=t1;
-}
-if (1) {
-	for(int i=0; i<(Nk+1); ++i) {
-		B[i] = 0.0;
-	  	B[i].checkerboard = evec[0].checkerboard;
-	}
-
-	int j_block = 24; int k_block=24;
-PARALLEL_FOR_LOOP
-	for(int ss=0;ss < grid->oSites();ss++){
-	for(int jj=0; jj<Nk; jj += j_block)
-	for(int kk=0; kk<Nk; kk += k_block)
-	for(int j=jj; (j<Nk) && j<(jj+j_block); ++j){
-	for(int k=kk; (k<Nk) && k<(kk+k_block) ; ++k){
-	    B[j]._odata[ss] +=Qt[k+Nm*j] * evec[k]._odata[ss]; 
-	}
-	}
-	}
-	t1=usecond()/1e6;
-	std::cout<<GridLogMessage <<"IRL::convergence rotation : "<<t1-t0<< "seconds"<<std::endl; t0=t1;
+//	    std::cout << "norm(B["<<j<<"])="<<norm2(B[j])<<std::endl;
 	  }
+//	_sort.push(eval2,B,Nk);
 
 	  Nconv = 0;
-	  //	  std::cout<<GridLogMessage << std::setiosflags(std::ios_base::scientific);
+	  //	  std::cout << std::setiosflags(std::ios_base::scientific);
 	  for(int i=0; i<Nk; ++i){
 
 //	    _poly(_Linop,B[i],v);
@@ -702,16 +613,14 @@ PARALLEL_FOR_LOOP
 	    
 	    RealD vnum = real(innerProduct(B[i],v)); // HermOp.
 	    RealD vden = norm2(B[i]);
-	    RealD vv0 = norm2(v);
 	    eval2[i] = vnum/vden;
 	    v -= eval2[i]*B[i];
 	    RealD vv = norm2(v);
 	    
 	    std::cout.precision(13);
-	    std::cout<<GridLogMessage << "[" << std::setw(3)<< std::setiosflags(std::ios_base::right) <<i<<"] ";
+	    std::cout << "[" << std::setw(3)<< std::setiosflags(std::ios_base::right) <<i<<"] ";
 	    std::cout << "eval = "<<std::setw(25)<< std::setiosflags(std::ios_base::left)<< eval2[i];
-	    std::cout<<"|H B[i] - eval[i]B[i]|^2 "<< std::setw(25)<< std::setiosflags(std::ios_base::right)<< vv;
-	    std::cout<<" "<< vnum/(sqrt(vden)*sqrt(vv0)) << std::endl;
+	    std::cout <<" |H B[i] - eval[i]B[i]|^2 "<< std::setw(25)<< std::setiosflags(std::ios_base::right)<< vv<< std::endl;
 	    
 	// change the criteria as evals are supposed to be sorted, all evals smaller(larger) than Nstop should have converged
 	    if((vv<eresid*eresid) && (i == Nconv) ){
@@ -720,19 +629,17 @@ PARALLEL_FOR_LOOP
 	    }
 
 	  }  // i-loop end
-	  //	  std::cout<<GridLogMessage << std::resetiosflags(std::ios_base::scientific);
-	t1=usecond()/1e6;
-	std::cout<<GridLogMessage <<"IRL::convergence testing: "<<t1-t0<< "seconds"<<std::endl; t0=t1;
+	  //	  std::cout << std::resetiosflags(std::ios_base::scientific);
 
 
-	  std::cout<<GridLogMessage<<" #modes converged: "<<Nconv<<std::endl;
+	  std::cout<<" #modes converged: "<<Nconv<<std::endl;
 
 	  if( Nconv>=Nstop ){
 	    goto converged;
 	  }
 	} // end of iter loop
 	
-	std::cout<<GridLogMessage<<"\n NOT converged.\n";
+	std::cout<<"\n NOT converged.\n";
 	abort();
 	
       converged:
@@ -745,10 +652,10 @@ PARALLEL_FOR_LOOP
        }
       _sort.push(eval,evec,Nconv);
 
-      std::cout<<GridLogMessage << "\n Converged\n Summary :\n";
-      std::cout<<GridLogMessage << " -- Iterations  = "<< Nconv  << "\n";
-      std::cout<<GridLogMessage << " -- beta(k)     = "<< beta_k << "\n";
-      std::cout<<GridLogMessage << " -- Nconv       = "<< Nconv  << "\n";
+      std::cout << "\n Converged\n Summary :\n";
+      std::cout << " -- Iterations  = "<< Nconv  << "\n";
+      std::cout << " -- beta(k)     = "<< beta_k << "\n";
+      std::cout << " -- Nconv       = "<< Nconv  << "\n";
      }
 
     /////////////////////////////////////////////////
@@ -771,25 +678,25 @@ PARALLEL_FOR_LOOP
 	}
       }
 
-      std::cout<<GridLogMessage<<"Lanczos_Factor start/end " <<start <<"/"<<end<<std::endl;
+      std::cout<<"Lanczos_Factor start/end " <<start <<"/"<<end<<std::endl;
 
       // Starting from scratch, bq[0] contains a random vector and |bq[0]| = 1
       int first;
       if(start == 0){
 
-	std::cout<<GridLogMessage << "start == 0\n"; //TESTING
+	std::cout << "start == 0\n"; //TESTING
 
 	_poly(_Linop,bq[0],bf);
 
 	alpha = real(innerProduct(bq[0],bf));//alpha =  bq[0]^dag A bq[0]
 
-	std::cout<<GridLogMessage << "alpha = " << alpha << std::endl;
+	std::cout << "alpha = " << alpha << std::endl;
 	
 	bf = bf - alpha * bq[0];  //bf =  A bq[0] - alpha bq[0]
 
 	H[0][0]=alpha;
 
-	std::cout<<GridLogMessage << "Set H(0,0) to " << H[0][0] << std::endl;
+	std::cout << "Set H(0,0) to " << H[0][0] << std::endl;
 
 	first = 1;
 
@@ -809,19 +716,19 @@ PARALLEL_FOR_LOOP
 
 	beta = 0;sqbt = 0;
 
-	std::cout<<GridLogMessage << "cont is true so setting beta to zero\n";
+	std::cout << "cont is true so setting beta to zero\n";
 
       }	else {
 
 	beta = norm2(bf);
 	sqbt = sqrt(beta);
 
-	std::cout<<GridLogMessage << "beta = " << beta << std::endl;
+	std::cout << "beta = " << beta << std::endl;
       }
 
       for(int j=first;j<end;j++){
 
-	std::cout<<GridLogMessage << "Factor j " << j <<std::endl;
+	std::cout << "Factor j " << j <<std::endl;
 
 	if(cont){ // switches to factoring; understand start!=0 and initial bf value is right.
 	  bq[j] = bf; cont = false;
@@ -844,7 +751,7 @@ PARALLEL_FOR_LOOP
 
 	beta = fnorm;
 	sqbt = sqrt(beta);
-	std::cout<<GridLogMessage << "alpha = " << alpha << " fnorm = " << fnorm << '\n';
+	std::cout << "alpha = " << alpha << " fnorm = " << fnorm << '\n';
 
 	///Iterative refinement of orthogonality V = [ bq[0]  bq[1]  ...  bq[M] ]
 	int re = 0;
@@ -879,8 +786,8 @@ PARALLEL_FOR_LOOP
 	  bck = sqrt( nmbex );
 	  re++;
 	}
-	std::cout<<GridLogMessage << "Iteratively refined orthogonality, changes alpha\n";
-	if(re > 1) std::cout<<GridLogMessage << "orthagonality refined " << re << " times" <<std::endl;
+	std::cout << "Iteratively refined orthogonality, changes alpha\n";
+	if(re > 1) std::cout << "orthagonality refined " << re << " times" <<std::endl;
 	H[j][j]=alpha;
       }
 
@@ -895,13 +802,11 @@ PARALLEL_FOR_LOOP
 
     void ImplicitRestart(int TM, DenseVector<RealD> &evals,  DenseVector<DenseVector<RealD> > &evecs, DenseVector<Field> &bq, Field &bf, int cont)
     {
-      std::cout<<GridLogMessage << "ImplicitRestart begin. Eigensort starting\n";
+      std::cout << "ImplicitRestart begin. Eigensort starting\n";
 
       DenseMatrix<RealD> H; Resize(H,Nm,Nm);
 
-#ifndef USE_LAPACK
       EigenSort(evals, evecs);
-#endif
 
       ///Assign shifts
       int K=Nk;
@@ -924,15 +829,15 @@ PARALLEL_FOR_LOOP
       /// Shifted H defines a new K step Arnoldi factorization
       RealD  beta = H[ff][ff-1]; 
       RealD  sig  = Q[TM - 1][ff - 1];
-      std::cout<<GridLogMessage << "beta = " << beta << " sig = " << real(sig) <<std::endl;
+      std::cout << "beta = " << beta << " sig = " << real(sig) <<std::endl;
 
-      std::cout<<GridLogMessage << "TM = " << TM << " ";
-      std::cout<<GridLogMessage << norm2(bq[0]) << " -- before" <<std::endl;
+      std::cout << "TM = " << TM << " ";
+      std::cout << norm2(bq[0]) << " -- before" <<std::endl;
 
       /// q -> q Q
       times_real(bq, Q, TM);
 
-      std::cout<<GridLogMessage << norm2(bq[0]) << " -- after " << ff <<std::endl;
+      std::cout << norm2(bq[0]) << " -- after " << ff <<std::endl;
       bf =  beta* bq[ff] + sig* bf;
 
       /// Do the rest of the factorization
@@ -956,7 +861,7 @@ PARALLEL_FOR_LOOP
       int ff = Lanczos_Factor(0, M, cont, bq,bf,H); // 0--M to begin with
 
       if(ff < M) {
-	std::cout<<GridLogMessage << "Krylov: aborting ff "<<ff <<" "<<M<<std::endl;
+	std::cout << "Krylov: aborting ff "<<ff <<" "<<M<<std::endl;
 	abort(); // Why would this happen?
       }
 
@@ -965,7 +870,7 @@ PARALLEL_FOR_LOOP
 
       for(int it = 0; it < Niter && (converged < Nk); ++it) {
 
-	std::cout<<GridLogMessage << "Krylov: Iteration --> " << it << std::endl;
+	std::cout << "Krylov: Iteration --> " << it << std::endl;
 	int lock_num = lock ? converged : 0;
 	DenseVector<RealD> tevals(M - lock_num );
 	DenseMatrix<RealD> tevecs; Resize(tevecs,M - lock_num,M - lock_num);
@@ -981,7 +886,7 @@ PARALLEL_FOR_LOOP
       Wilkinson<RealD>(H, evals, evecs, small); 
       //      Check();
 
-      std::cout<<GridLogMessage << "Done  "<<std::endl;
+      std::cout << "Done  "<<std::endl;
 
     }
 
@@ -1046,7 +951,7 @@ PARALLEL_FOR_LOOP
 		  DenseVector<RealD> &tevals, DenseVector<DenseVector<RealD> > &tevecs, 
 		  int lock, int converged)
     {
-      std::cout<<GridLogMessage << "Converged " << converged << " so far." << std::endl;
+      std::cout << "Converged " << converged << " so far." << std::endl;
       int lock_num = lock ? converged : 0;
       int M = Nm;
 
@@ -1061,9 +966,7 @@ PARALLEL_FOR_LOOP
       RealD small=1.0e-16;
       Wilkinson<RealD>(AH, tevals, tevecs, small);
 
-#ifndef USE_LAPACK
       EigenSort(tevals, tevecs);
-#endif
 
       RealD resid_nrm=  norm2(bf);
 
@@ -1074,7 +977,7 @@ PARALLEL_FOR_LOOP
 	RealD diff = 0;
 	diff = abs( tevecs[i][Nm - 1 - lock_num] ) * resid_nrm;
 
-	std::cout<<GridLogMessage << "residual estimate " << SS-1-i << " " << diff << " of (" << tevals[i] << ")" << std::endl;
+	std::cout << "residual estimate " << SS-1-i << " " << diff << " of (" << tevals[i] << ")" << std::endl;
 
 	if(diff < converged) {
 
@@ -1090,13 +993,13 @@ PARALLEL_FOR_LOOP
 	    lock_num++;
 	  }
 	  converged++;
-	  std::cout<<GridLogMessage << " converged on eval " << converged << " of " << Nk << std::endl;
+	  std::cout << " converged on eval " << converged << " of " << Nk << std::endl;
 	} else {
 	  break;
 	}
       }
 #endif
-      std::cout<<GridLogMessage << "Got " << converged << " so far " <<std::endl;	
+      std::cout << "Got " << converged << " so far " <<std::endl;	
     }
 
     ///Check
@@ -1105,9 +1008,7 @@ PARALLEL_FOR_LOOP
 
       DenseVector<RealD> goodval(this->get);
 
-#ifndef USE_LAPACK
       EigenSort(evals,evecs);
-#endif
 
       int NM = Nm;
 

lib/algorithms/iterative/Matrix.h

@@ -36,7 +36,7 @@ Author: Peter Boyle <paboyle@ph.ed.ac.uk>
 #include <iomanip>
 #include <complex>
 #include <typeinfo>
-#include <Grid/Grid.h>
+#include <Grid.h>
 
 
 /** Sign function **/

lib/algorithms/iterative/SchurRedBlack.h

@@ -141,85 +141,5 @@ namespace Grid {
     }     
   };
 
-  ///////////////////////////////////////////////////////////////////////////////////////////////////////
-  // Take a matrix and form a Red Black solver calling a Herm solver
-  // Use of RB info prevents making SchurRedBlackSolve conform to standard interface
-  ///////////////////////////////////////////////////////////////////////////////////////////////////////
-  template<class Field> class SchurRedBlackDiagTwoSolve {
-  private:
-    OperatorFunction<Field> & _HermitianRBSolver;
-    int CBfactorise;
-  public:
-
-    /////////////////////////////////////////////////////
-    // Wrap the usual normal equations Schur trick
-    /////////////////////////////////////////////////////
-  SchurRedBlackDiagTwoSolve(OperatorFunction<Field> &HermitianRBSolver)  :
-     _HermitianRBSolver(HermitianRBSolver) 
-    { 
-      CBfactorise=0;
-    };
-
-    template<class Matrix>
-      void operator() (Matrix & _Matrix,const Field &in, Field &out){
-
-      // FIXME CGdiagonalMee not implemented virtual function
-      // FIXME use CBfactorise to control schur decomp
-      GridBase *grid = _Matrix.RedBlackGrid();
-      GridBase *fgrid= _Matrix.Grid();
-
-      SchurDiagTwoOperator<Matrix,Field> _HermOpEO(_Matrix);
- 
-      Field src_e(grid);
-      Field src_o(grid);
-      Field sol_e(grid);
-      Field sol_o(grid);
-      Field   tmp(grid);
-      Field  Mtmp(grid);
-      Field resid(fgrid);
-
-      pickCheckerboard(Even,src_e,in);
-      pickCheckerboard(Odd ,src_o,in);
-      pickCheckerboard(Even,sol_e,out);
-      pickCheckerboard(Odd ,sol_o,out);
-    
-      /////////////////////////////////////////////////////
-      // src_o = Mdag * (source_o - Moe MeeInv source_e)
-      /////////////////////////////////////////////////////
-      _Matrix.MooeeInv(src_e,tmp);     assert(  tmp.checkerboard ==Even);
-      _Matrix.Meooe   (tmp,Mtmp);      assert( Mtmp.checkerboard ==Odd);     
-      tmp=src_o-Mtmp;                  assert(  tmp.checkerboard ==Odd);     
-
-      // get the right MpcDag
-      _HermOpEO.MpcDag(tmp,src_o);     assert(src_o.checkerboard ==Odd);       
-
-      //////////////////////////////////////////////////////////////
-      // Call the red-black solver
-      //////////////////////////////////////////////////////////////
-      std::cout<<GridLogMessage << "SchurRedBlack solver calling the MpcDagMp solver" <<std::endl;
-//      _HermitianRBSolver(_HermOpEO,src_o,sol_o);  assert(sol_o.checkerboard==Odd);
-      _HermitianRBSolver(_HermOpEO,src_o,tmp);  assert(tmp.checkerboard==Odd);
-      _Matrix.MooeeInv(tmp,sol_o);        assert(  sol_o.checkerboard   ==Odd);
-
-      ///////////////////////////////////////////////////
-      // sol_e = M_ee^-1 * ( src_e - Meo sol_o )...
-      ///////////////////////////////////////////////////
-      _Matrix.Meooe(sol_o,tmp);        assert(  tmp.checkerboard   ==Even);
-      src_e = src_e-tmp;               assert(  src_e.checkerboard ==Even);
-      _Matrix.MooeeInv(src_e,sol_e);   assert(  sol_e.checkerboard ==Even);
-     
-      setCheckerboard(out,sol_e); assert(  sol_e.checkerboard ==Even);
-      setCheckerboard(out,sol_o); assert(  sol_o.checkerboard ==Odd );
-
-      // Verify the unprec residual
-      _Matrix.M(out,resid); 
-      resid = resid-in;
-      RealD ns = norm2(in);
-      RealD nr = norm2(resid);
-
-      std::cout<<GridLogMessage << "SchurRedBlackDiagTwo solver true unprec resid "<< std::sqrt(nr/ns) <<" nr "<< nr <<" ns "<<ns << std::endl;
-    }     
-  };
-
 }
 #endif