Merge branch 'develop' into feature/json-fix

.travis.yml

@@ -9,68 +9,6 @@ matrix:
     - os:        osx
       osx_image: xcode8.3
       compiler: clang
-    - compiler: gcc
-      dist: trusty
-      sudo: required
-      addons:
-        apt:
-          sources:
-            - ubuntu-toolchain-r-test
-          packages:
-            - g++-4.9
-            - libmpfr-dev
-            - libgmp-dev
-            - libmpc-dev
-            - libopenmpi-dev
-            - openmpi-bin
-            - binutils-dev
-      env: VERSION=-4.9
-    - compiler: gcc
-      dist: trusty
-      sudo: required
-      addons:
-        apt:
-          sources:
-            - ubuntu-toolchain-r-test
-          packages:
-            - g++-5
-            - libmpfr-dev
-            - libgmp-dev
-            - libmpc-dev
-            - libopenmpi-dev
-            - openmpi-bin
-            - binutils-dev
-      env: VERSION=-5
-    - compiler: clang
-      dist: trusty
-      addons:
-        apt:
-          sources:
-            - ubuntu-toolchain-r-test
-          packages:
-            - g++-4.8
-            - libmpfr-dev
-            - libgmp-dev
-            - libmpc-dev
-            - libopenmpi-dev
-            - openmpi-bin
-            - binutils-dev
-      env: CLANG_LINK=http://llvm.org/releases/3.8.0/clang+llvm-3.8.0-x86_64-linux-gnu-ubuntu-14.04.tar.xz
-    - compiler: clang
-      dist: trusty
-      addons:
-        apt:
-          sources:
-            - ubuntu-toolchain-r-test
-          packages:
-            - g++-4.8
-            - libmpfr-dev
-            - libgmp-dev
-            - libmpc-dev
-            - libopenmpi-dev
-            - openmpi-bin
-            - binutils-dev
-      env: CLANG_LINK=http://llvm.org/releases/3.7.0/clang+llvm-3.7.0-x86_64-linux-gnu-ubuntu-14.04.tar.xz
       
 before_install:
     - export GRIDDIR=`pwd`
@@ -106,9 +44,3 @@ script:
     - make -j4
     - ./benchmarks/Benchmark_dwf --threads 1 --debug-signals
     - make check
-    - echo make clean
-    - if [[ "$TRAVIS_OS_NAME" == "linux" ]] && [[ "$CC" == "clang" ]]; then ../configure --enable-precision=single --enable-simd=SSE4 --enable-comms=mpi-auto ; fi
-    - if [[ "$TRAVIS_OS_NAME" == "linux" ]] && [[ "$CC" == "clang" ]]; then make -j4; fi
-    - if [[ "$TRAVIS_OS_NAME" == "linux" ]] && [[ "$CC" == "clang" ]]; then mpirun.openmpi -n 2 ./benchmarks/Benchmark_dwf --threads 1 --mpi 2.1.1.1; fi
-
-

README.md

@@ -1,18 +1,4 @@
-# Grid
+# Grid [![Teamcity status](http://ci.cliath.ph.ed.ac.uk/app/rest/builds/aggregated/strob:(buildType:(affectedProject(id:Grid)),branch:name:develop)/statusIcon.svg)](http://ci.cliath.ph.ed.ac.uk/project.html?projectId=Grid&tab=projectOverview) [![Travis status](https://travis-ci.org/paboyle/Grid.svg?branch=develop)](https://travis-ci.org/paboyle/Grid)
-<table>
-<tr>
-    <td>Last stable release</td>
-    <td><a href="https://travis-ci.org/paboyle/Grid">
-    <img src="https://travis-ci.org/paboyle/Grid.svg?branch=master"></a>
-    </td>
-</tr>
-<tr>
-    <td>Development branch</td>
-    <td><a href="https://travis-ci.org/paboyle/Grid">
-    <img src="https://travis-ci.org/paboyle/Grid.svg?branch=develop"></a>
-    </td>
-</tr>
-</table>
 
 **Data parallel C++ mathematical object library.**
 
@@ -324,6 +310,13 @@ one rank per socket. If using the Intel MPI library, threads should be pinned to
 ```
 This is the default. 
 
+#### Expected Skylake Gold 6148 dual socket (single prec, single node 20+20 cores) performance using NUMA MPI mapping): 
+
+mpirun -n 2 benchmarks/Benchmark_dwf --grid 16.16.16.16 --mpi 2.1.1.1 --cacheblocking 2.2.2.2 --dslash-asm --shm 1024 --threads 18 
+
+TBA
+
+
 ### Build setup for AMD EPYC / RYZEN
 
 The AMD EPYC is a multichip module comprising 32 cores spread over four distinct chips each with 8 cores.
@@ -378,6 +371,14 @@ echo GOMP_CUP_AFFINITY $GOMP_CPU_AFFINITY
 $@
 ```
 
+Performance:
+
+#### Expected AMD EPYC 7601 dual socket (single prec, single node 32+32 cores) performance using NUMA MPI mapping): 
+
+mpirun  -np 8 ./omp_bind.sh ./Benchmark_dwf --threads 8 --mpi 2.2.2.1 --dslash-unroll --grid 16.16.16.16 --cacheblocking 4.4.4.4
+
+TBA
+
 ### Build setup for BlueGene/Q
 
 To be written...

TODO

@@ -2,18 +2,20 @@ TODO:
 ---------------
 
 Large item work list:
-1)- MultiRHS with spread out extra dim -- Go through filesystem with SciDAC I/O
 
+1)- BG/Q port and check
 2)- Christoph's local basis expansion Lanczos
-3)- BG/Q port and check
+3)- Precision conversion and sort out localConvert      <-- partial
-4)- Precision conversion and sort out localConvert      <-- partial
+
   - Consistent linear solver flop count/rate -- PARTIAL, time but no flop/s yet
-5)- Physical propagator interface
+4)- Physical propagator interface
-6)- Conserved currents
+5)- Conserved currents
-7)- Multigrid Wilson and DWF, compare to other Multigrid implementations
+6)- Multigrid Wilson and DWF, compare to other Multigrid implementations
-8)- HDCR resume
+7)- HDCR resume
 
 Recent DONE 
+
+-- MultiRHS with spread out extra dim -- Go through filesystem with SciDAC I/O.  <--- DONE
 -- Lanczos Remove DenseVector, DenseMatrix; Use Eigen instead. <-- DONE
 -- GaugeFix into central location                      <-- DONE
 -- Scidac and Ildg metadata handling                   <-- DONE

benchmarks/Benchmark_ITT.cc

@@ -0,0 +1,797 @@
+    /*************************************************************************************
+
+    Grid physics library, www.github.com/paboyle/Grid 
+
+    Source file: ./benchmarks/Benchmark_memory_bandwidth.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;
+
+typedef WilsonFermion5D<DomainWallVec5dImplR> WilsonFermion5DR;
+typedef WilsonFermion5D<DomainWallVec5dImplF> WilsonFermion5DF;
+typedef WilsonFermion5D<DomainWallVec5dImplD> WilsonFermion5DD;
+
+
+std::vector<int> L_list;
+std::vector<int> Ls_list;
+std::vector<double> mflop_list;
+
+double mflop_ref;
+double mflop_ref_err;
+
+int NN_global;
+
+struct time_statistics{
+  double mean;
+  double err;
+  double min;
+  double max;
+
+  void statistics(std::vector<double> v){
+      double sum = std::accumulate(v.begin(), v.end(), 0.0);
+      mean = sum / v.size();
+
+      std::vector<double> diff(v.size());
+      std::transform(v.begin(), v.end(), diff.begin(), [=](double x) { return x - mean; });
+      double sq_sum = std::inner_product(diff.begin(), diff.end(), diff.begin(), 0.0);
+      err = std::sqrt(sq_sum / (v.size()*(v.size() - 1)));
+
+      auto result = std::minmax_element(v.begin(), v.end());
+      min = *result.first;
+      max = *result.second;
+}
+};
+
+void comms_header(){
+  std::cout <<GridLogMessage << " L  "<<"\t"<<" Ls  "<<"\t"
+            <<std::setw(11)<<"bytes"<<"MB/s uni (err/min/max)"<<"\t\t"<<"MB/s bidi (err/min/max)"<<std::endl;
+};
+
+Gamma::Algebra Gmu [] = {
+  Gamma::Algebra::GammaX,
+  Gamma::Algebra::GammaY,
+  Gamma::Algebra::GammaZ,
+  Gamma::Algebra::GammaT
+};
+struct controls {
+  int Opt;
+  int CommsOverlap;
+  Grid::CartesianCommunicator::CommunicatorPolicy_t CommsAsynch;
+  //  int HugePages;
+};
+
+class Benchmark {
+public:
+  static void Decomposition (void ) {
+
+    int threads = GridThread::GetThreads();
+    std::cout<<GridLogMessage << "=================================================================================="<<std::endl;
+    std::cout<<GridLogMessage << "= Grid is setup to use "<<threads<<" threads"<<std::endl;
+    std::cout<<GridLogMessage << "=================================================================================="<<std::endl;
+    std::cout<<GridLogMessage<<"Grid Default Decomposition patterns\n";
+    std::cout<<GridLogMessage<<"\tOpenMP threads : "<<GridThread::GetThreads()<<std::endl;
+    std::cout<<GridLogMessage<<"\tMPI tasks      : "<<GridCmdVectorIntToString(GridDefaultMpi())<<std::endl;
+    std::cout<<GridLogMessage<<"\tvReal          : "<<sizeof(vReal )*8    <<"bits ; " <<GridCmdVectorIntToString(GridDefaultSimd(4,vReal::Nsimd()))<<std::endl;
+    std::cout<<GridLogMessage<<"\tvRealF         : "<<sizeof(vRealF)*8    <<"bits ; " <<GridCmdVectorIntToString(GridDefaultSimd(4,vRealF::Nsimd()))<<std::endl;
+    std::cout<<GridLogMessage<<"\tvRealD         : "<<sizeof(vRealD)*8    <<"bits ; " <<GridCmdVectorIntToString(GridDefaultSimd(4,vRealD::Nsimd()))<<std::endl;
+    std::cout<<GridLogMessage<<"\tvComplex       : "<<sizeof(vComplex )*8 <<"bits ; " <<GridCmdVectorIntToString(GridDefaultSimd(4,vComplex::Nsimd()))<<std::endl;
+    std::cout<<GridLogMessage<<"\tvComplexF      : "<<sizeof(vComplexF)*8 <<"bits ; " <<GridCmdVectorIntToString(GridDefaultSimd(4,vComplexF::Nsimd()))<<std::endl;
+    std::cout<<GridLogMessage<<"\tvComplexD      : "<<sizeof(vComplexD)*8 <<"bits ; " <<GridCmdVectorIntToString(GridDefaultSimd(4,vComplexD::Nsimd()))<<std::endl;
+    std::cout<<GridLogMessage << "=================================================================================="<<std::endl;
+
+  }
+
+  static void Comms(void)
+  {
+    int Nloop=200;
+    int nmu=0;
+    int maxlat=32;
+
+    std::vector<int> simd_layout = GridDefaultSimd(Nd,vComplexD::Nsimd());
+    std::vector<int> mpi_layout  = GridDefaultMpi();
+
+    for(int mu=0;mu<Nd;mu++) if (mpi_layout[mu]>1) nmu++;
+
+    std::vector<double> t_time(Nloop);
+    time_statistics timestat;
+
+    std::cout<<GridLogMessage << "===================================================================================================="<<std::endl;
+    std::cout<<GridLogMessage << "= Benchmarking threaded STENCIL halo exchange in "<<nmu<<" dimensions"<<std::endl;
+    std::cout<<GridLogMessage << "===================================================================================================="<<std::endl;
+    comms_header();
+
+    for(int lat=4;lat<=maxlat;lat+=4){
+      for(int Ls=8;Ls<=8;Ls*=2){
+
+	std::vector<int> latt_size  ({lat*mpi_layout[0],
+	      lat*mpi_layout[1],
+	      lat*mpi_layout[2],
+	      lat*mpi_layout[3]});
+
+	GridCartesian     Grid(latt_size,simd_layout,mpi_layout);
+	RealD Nrank = Grid._Nprocessors;
+	RealD Nnode = Grid.NodeCount();
+	RealD ppn = Nrank/Nnode;
+
+	std::vector<HalfSpinColourVectorD *> xbuf(8);
+	std::vector<HalfSpinColourVectorD *> rbuf(8);
+	Grid.ShmBufferFreeAll();
+	for(int d=0;d<8;d++){
+	  xbuf[d] = (HalfSpinColourVectorD *)Grid.ShmBufferMalloc(lat*lat*lat*Ls*sizeof(HalfSpinColourVectorD));
+	  rbuf[d] = (HalfSpinColourVectorD *)Grid.ShmBufferMalloc(lat*lat*lat*Ls*sizeof(HalfSpinColourVectorD));
+	  bzero((void *)xbuf[d],lat*lat*lat*Ls*sizeof(HalfSpinColourVectorD));
+	  bzero((void *)rbuf[d],lat*lat*lat*Ls*sizeof(HalfSpinColourVectorD));
+	}
+
+	int bytes=lat*lat*lat*Ls*sizeof(HalfSpinColourVectorD);
+	int ncomm;
+	double dbytes;
+	std::vector<double> times(Nloop);
+	for(int i=0;i<Nloop;i++){
+
+	  double start=usecond();
+
+	  dbytes=0;
+	  ncomm=0;
+
+	  parallel_for(int dir=0;dir<8;dir++){
+
+	    double tbytes;
+	    int mu =dir % 4;
+
+	    if (mpi_layout[mu]>1 ) {
+	        
+	      int xmit_to_rank;
+	      int recv_from_rank;
+	      if ( dir == mu ) { 
+		int comm_proc=1;
+		Grid.ShiftedRanks(mu,comm_proc,xmit_to_rank,recv_from_rank);
+	      } else { 
+		int comm_proc = mpi_layout[mu]-1;
+		Grid.ShiftedRanks(mu,comm_proc,xmit_to_rank,recv_from_rank);
+	      }
+	      tbytes= Grid.StencilSendToRecvFrom((void *)&xbuf[dir][0], xmit_to_rank,
+						 (void *)&rbuf[dir][0], recv_from_rank,
+						 bytes,dir);
+	  
+#ifdef GRID_OMP
+#pragma omp atomic
+#endif
+	      ncomm++;
+
+#ifdef GRID_OMP
+#pragma omp atomic
+#endif
+	      dbytes+=tbytes;
+	    }
+	  }
+	  Grid.Barrier();
+	  double stop=usecond();
+	  t_time[i] = stop-start; // microseconds
+	}
+
+	timestat.statistics(t_time);
+	//	for(int i=0;i<t_time.size();i++){
+	//	  std::cout << i<<" "<<t_time[i]<<std::endl;
+	//	}
+
+	dbytes=dbytes*ppn;
+	double xbytes    = dbytes*0.5;
+	double rbytes    = dbytes*0.5;
+	double bidibytes = dbytes;
+
+	std::cout<<GridLogMessage << std::setw(4) << lat<<"\t"<<Ls<<"\t"
+		 <<std::setw(11) << bytes<< std::fixed << std::setprecision(1) << std::setw(7)
+		 <<std::right<< xbytes/timestat.mean<<"  "<< xbytes*timestat.err/(timestat.mean*timestat.mean)<< " "
+		 <<xbytes/timestat.max <<" "<< xbytes/timestat.min  
+		 << "\t\t"<<std::setw(7)<< bidibytes/timestat.mean<< "  " << bidibytes*timestat.err/(timestat.mean*timestat.mean) << " "
+		 << bidibytes/timestat.max << " " << bidibytes/timestat.min << std::endl;
+
+ 
+	
+	    }
+    }    
+
+    return;
+  }
+
+  static void Memory(void)
+  {
+    const int Nvec=8;
+    typedef Lattice< iVector< vReal,Nvec> > LatticeVec;
+    typedef iVector<vReal,Nvec> Vec;
+
+    std::vector<int> simd_layout = GridDefaultSimd(Nd,vReal::Nsimd());
+    std::vector<int> mpi_layout  = GridDefaultMpi();
+
+    std::cout<<GridLogMessage << "=================================================================================="<<std::endl;
+    std::cout<<GridLogMessage << "= Benchmarking a*x + y bandwidth"<<std::endl;
+    std::cout<<GridLogMessage << "=================================================================================="<<std::endl;
+    std::cout<<GridLogMessage << "  L  "<<"\t\t"<<"bytes"<<"\t\t\t"<<"GB/s"<<"\t\t"<<"Gflop/s"<<"\t\t seconds"<< "\t\tGB/s / node"<<std::endl;
+    std::cout<<GridLogMessage << "----------------------------------------------------------"<<std::endl;
+  
+    uint64_t NP;
+    uint64_t NN;
+
+
+  uint64_t lmax=48;
+#define NLOOP (100*lmax*lmax*lmax*lmax/lat/lat/lat/lat)
+
+    GridSerialRNG          sRNG;      sRNG.SeedFixedIntegers(std::vector<int>({45,12,81,9}));
+    for(int lat=8;lat<=lmax;lat+=4){
+
+      std::vector<int> latt_size  ({lat*mpi_layout[0],lat*mpi_layout[1],lat*mpi_layout[2],lat*mpi_layout[3]});
+      int64_t vol= latt_size[0]*latt_size[1]*latt_size[2]*latt_size[3];
+      GridCartesian     Grid(latt_size,simd_layout,mpi_layout);
+
+      NP= Grid.RankCount();
+      NN =Grid.NodeCount();
+
+      Vec rn ; random(sRNG,rn);
+
+      LatticeVec z(&Grid); z=rn;
+      LatticeVec x(&Grid); x=rn;
+      LatticeVec y(&Grid); y=rn;
+      double a=2.0;
+
+      uint64_t Nloop=NLOOP;
+
+      double start=usecond();
+      for(int i=0;i<Nloop;i++){
+	z=a*x-y;
+        x._odata[0]=z._odata[0]; // force serial dependency to prevent optimise away
+        y._odata[4]=z._odata[4];
+      }
+      double stop=usecond();
+      double time = (stop-start)/Nloop*1000;
+     
+      double flops=vol*Nvec*2;// mul,add
+      double bytes=3.0*vol*Nvec*sizeof(Real);
+      std::cout<<GridLogMessage<<std::setprecision(3) 
+	       << lat<<"\t\t"<<bytes<<"   \t\t"<<bytes/time<<"\t\t"<<flops/time<<"\t\t"<<(stop-start)/1000./1000.
+	       << "\t\t"<< bytes/time/NN <<std::endl;
+
+    }
+  };
+
+  static double DWF5(int Ls,int L)
+  {
+    RealD mass=0.1;
+    RealD M5  =1.8;
+
+    double mflops;
+    double mflops_best = 0;
+    double mflops_worst= 0;
+    std::vector<double> mflops_all;
+
+    ///////////////////////////////////////////////////////
+    // Set/Get the layout & grid size
+    ///////////////////////////////////////////////////////
+    int threads = GridThread::GetThreads();
+    std::vector<int> mpi = GridDefaultMpi(); assert(mpi.size()==4);
+    std::vector<int> local({L,L,L,L});
+
+    GridCartesian         * TmpGrid   = SpaceTimeGrid::makeFourDimGrid(std::vector<int>({64,64,64,64}), 
+								       GridDefaultSimd(Nd,vComplex::Nsimd()),GridDefaultMpi());
+    uint64_t NP = TmpGrid->RankCount();
+    uint64_t NN = TmpGrid->NodeCount();
+    NN_global=NN;
+    uint64_t SHM=NP/NN;
+
+    std::vector<int> internal;
+    if      ( SHM == 1 )   internal = std::vector<int>({1,1,1,1});
+    else if ( SHM == 2 )   internal = std::vector<int>({2,1,1,1});
+    else if ( SHM == 4 )   internal = std::vector<int>({2,2,1,1});
+    else if ( SHM == 8 )   internal = std::vector<int>({2,2,2,1});
+    else assert(0);
+
+    std::vector<int> nodes({mpi[0]/internal[0],mpi[1]/internal[1],mpi[2]/internal[2],mpi[3]/internal[3]});
+    std::vector<int> latt4({local[0]*nodes[0],local[1]*nodes[1],local[2]*nodes[2],local[3]*nodes[3]});
+
+    ///////// Welcome message ////////////
+    std::cout<<GridLogMessage << "=================================================================================="<<std::endl;
+    std::cout<<GridLogMessage << "Benchmark DWF Ls vec on "<<L<<"^4 local volume "<<std::endl;
+    std::cout<<GridLogMessage << "* Global volume  : "<<GridCmdVectorIntToString(latt4)<<std::endl;
+    std::cout<<GridLogMessage << "* Ls             : "<<Ls<<std::endl;
+    std::cout<<GridLogMessage << "* MPI ranks      : "<<GridCmdVectorIntToString(mpi)<<std::endl;
+    std::cout<<GridLogMessage << "* Intranode      : "<<GridCmdVectorIntToString(internal)<<std::endl;
+    std::cout<<GridLogMessage << "* nodes          : "<<GridCmdVectorIntToString(nodes)<<std::endl;
+    std::cout<<GridLogMessage << "* Using "<<threads<<" threads"<<std::endl;
+    std::cout<<GridLogMessage << "=================================================================================="<<std::endl;
+
+    ///////// Lattice Init ////////////
+    GridCartesian         * UGrid    = SpaceTimeGrid::makeFourDimGrid(latt4, GridDefaultSimd(Nd,vComplex::Nsimd()),GridDefaultMpi());
+    GridRedBlackCartesian * UrbGrid  = SpaceTimeGrid::makeFourDimRedBlackGrid(UGrid);
+    GridCartesian         * sUGrid   = SpaceTimeGrid::makeFourDimDWFGrid(latt4,GridDefaultMpi());
+    GridRedBlackCartesian * sUrbGrid = SpaceTimeGrid::makeFourDimRedBlackGrid(sUGrid);
+    GridCartesian         * sFGrid   = SpaceTimeGrid::makeFiveDimDWFGrid(Ls,UGrid);
+    GridRedBlackCartesian * sFrbGrid = SpaceTimeGrid::makeFiveDimDWFRedBlackGrid(Ls,UGrid);
+
+    ///////// RNG Init ////////////
+    std::vector<int> seeds4({1,2,3,4});
+    std::vector<int> seeds5({5,6,7,8});
+    GridParallelRNG          RNG4(UGrid);  RNG4.SeedFixedIntegers(seeds4);
+    GridParallelRNG          RNG5(sFGrid);  RNG5.SeedFixedIntegers(seeds5);
+    std::cout << GridLogMessage << "Initialised RNGs" << std::endl;
+
+    ///////// Source preparation ////////////
+    LatticeFermion src   (sFGrid); random(RNG5,src);
+    LatticeFermion tmp   (sFGrid);
+
+    RealD N2 = 1.0/::sqrt(norm2(src));
+    src = src*N2;
+    
+    LatticeGaugeField Umu(UGrid);  SU3::HotConfiguration(RNG4,Umu); 
+
+    WilsonFermion5DR sDw(Umu,*sFGrid,*sFrbGrid,*sUGrid,*sUrbGrid,M5);
+    LatticeFermion src_e (sFrbGrid);
+    LatticeFermion src_o (sFrbGrid);
+    LatticeFermion r_e   (sFrbGrid);
+    LatticeFermion r_o   (sFrbGrid);
+    LatticeFermion r_eo  (sFGrid);
+    LatticeFermion err   (sFGrid);
+    {
+
+      pickCheckerboard(Even,src_e,src);
+      pickCheckerboard(Odd,src_o,src);
+
+#if defined(AVX512) 
+      const int num_cases = 6;
+      std::string fmt("A/S ; A/O ; U/S ; U/O ; G/S ; G/O ");
+#else
+      const int num_cases = 4;
+      std::string fmt("U/S ; U/O ; G/S ; G/O ");
+#endif
+      controls Cases [] = {
+#ifdef AVX512
+	{ QCD::WilsonKernelsStatic::OptInlineAsm , QCD::WilsonKernelsStatic::CommsThenCompute ,CartesianCommunicator::CommunicatorPolicySequential  },
+	{ QCD::WilsonKernelsStatic::OptInlineAsm , QCD::WilsonKernelsStatic::CommsAndCompute  ,CartesianCommunicator::CommunicatorPolicySequential  },
+#endif
+	{ QCD::WilsonKernelsStatic::OptHandUnroll, QCD::WilsonKernelsStatic::CommsThenCompute ,CartesianCommunicator::CommunicatorPolicySequential  },
+	{ QCD::WilsonKernelsStatic::OptHandUnroll, QCD::WilsonKernelsStatic::CommsAndCompute  ,CartesianCommunicator::CommunicatorPolicySequential  },
+	{ QCD::WilsonKernelsStatic::OptGeneric   , QCD::WilsonKernelsStatic::CommsThenCompute ,CartesianCommunicator::CommunicatorPolicySequential  },
+	{ QCD::WilsonKernelsStatic::OptGeneric   , QCD::WilsonKernelsStatic::CommsAndCompute  ,CartesianCommunicator::CommunicatorPolicySequential  }
+      }; 
+
+      for(int c=0;c<num_cases;c++) {
+
+	QCD::WilsonKernelsStatic::Comms = Cases[c].CommsOverlap;
+	QCD::WilsonKernelsStatic::Opt   = Cases[c].Opt;
+	CartesianCommunicator::SetCommunicatorPolicy(Cases[c].CommsAsynch);
+
+	std::cout<<GridLogMessage << "=================================================================================="<<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;
+	if ( WilsonKernelsStatic::Comms == WilsonKernelsStatic::CommsAndCompute ) std::cout << GridLogMessage<< "* Using Overlapped Comms/Compute" <<std::endl;
+	if ( WilsonKernelsStatic::Comms == WilsonKernelsStatic::CommsThenCompute) std::cout << GridLogMessage<< "* Using sequential comms compute" <<std::endl;
+	if ( sizeof(Real)==4 )   std::cout << GridLogMessage<< "* SINGLE precision "<<std::endl;
+	if ( sizeof(Real)==8 )   std::cout << GridLogMessage<< "* DOUBLE precision "<<std::endl;
+	std::cout<<GridLogMessage << "=================================================================================="<<std::endl;
+
+	int nwarm = 100;
+	uint64_t ncall = 1000;
+
+	double t0=usecond();
+	sFGrid->Barrier();
+	for(int i=0;i<nwarm;i++){
+	  sDw.DhopEO(src_o,r_e,DaggerNo);
+	}
+	sFGrid->Barrier();
+	double t1=usecond();
+
+	sDw.ZeroCounters();
+	time_statistics timestat;
+	std::vector<double> t_time(ncall);
+	for(uint64_t i=0;i<ncall;i++){
+	  t0=usecond();
+	  sDw.DhopEO(src_o,r_e,DaggerNo);
+	  t1=usecond();
+	  t_time[i] = t1-t0;
+	}
+	sFGrid->Barrier();
+	
+	double volume=Ls;  for(int mu=0;mu<Nd;mu++) volume=volume*latt4[mu];
+	double flops=(1344.0*volume)/2;
+	double mf_hi, mf_lo, mf_err;
+
+	timestat.statistics(t_time);
+	mf_hi = flops/timestat.min;
+	mf_lo = flops/timestat.max;
+	mf_err= flops/timestat.min * timestat.err/timestat.mean;
+
+	mflops = flops/timestat.mean;
+	mflops_all.push_back(mflops);
+	if ( mflops_best == 0   ) mflops_best = mflops;
+	if ( mflops_worst== 0   ) mflops_worst= mflops;
+	if ( mflops>mflops_best ) mflops_best = mflops;
+	if ( mflops<mflops_worst) mflops_worst= mflops;
+
+	std::cout<<GridLogMessage << std::fixed << std::setprecision(1)<<"sDeo mflop/s =   "<< mflops << " ("<<mf_err<<") " << mf_lo<<"-"<<mf_hi <<std::endl;
+	std::cout<<GridLogMessage << std::fixed << std::setprecision(1)<<"sDeo mflop/s per rank   "<< mflops/NP<<std::endl;
+	std::cout<<GridLogMessage << std::fixed << std::setprecision(1)<<"sDeo mflop/s per node   "<< mflops/NN<<std::endl;
+
+	sDw.Report();
+
+      }
+      double robust = mflops_worst/mflops_best;;
+      std::cout<<GridLogMessage << "=================================================================================="<<std::endl;
+      std::cout<<GridLogMessage << L<<"^4 x "<<Ls<< " sDeo Best  mflop/s        =   "<< mflops_best << " ; " << mflops_best/NN<<" per node " <<std::endl;
+      std::cout<<GridLogMessage << L<<"^4 x "<<Ls<< " sDeo Worst mflop/s        =   "<< mflops_worst<< " ; " << mflops_worst/NN<<" per node " <<std::endl;
+
+      std::cout<<GridLogMessage <<std::setprecision(3)<< L<<"^4 x "<<Ls<< " Performance Robustness   =   "<< robust <<std::endl;
+      std::cout<<GridLogMessage <<fmt << std::endl;
+      std::cout<<GridLogMessage;
+
+      for(int i=0;i<mflops_all.size();i++){
+	std::cout<<mflops_all[i]/NN<<" ; " ;
+      }
+      std::cout<<std::endl;
+      std::cout<<GridLogMessage << "=================================================================================="<<std::endl;
+
+    }
+    return mflops_best;
+  }
+
+  static double DWF(int Ls,int L, double & robust)
+  {
+    RealD mass=0.1;
+    RealD M5  =1.8;
+
+    double mflops;
+    double mflops_best = 0;
+    double mflops_worst= 0;
+    std::vector<double> mflops_all;
+
+    ///////////////////////////////////////////////////////
+    // Set/Get the layout & grid size
+    ///////////////////////////////////////////////////////
+    int threads = GridThread::GetThreads();
+    std::vector<int> mpi = GridDefaultMpi(); assert(mpi.size()==4);
+    std::vector<int> local({L,L,L,L});
+
+    GridCartesian         * TmpGrid   = SpaceTimeGrid::makeFourDimGrid(std::vector<int>({64,64,64,64}), 
+								       GridDefaultSimd(Nd,vComplex::Nsimd()),GridDefaultMpi());
+    uint64_t NP = TmpGrid->RankCount();
+    uint64_t NN = TmpGrid->NodeCount();
+    NN_global=NN;
+    uint64_t SHM=NP/NN;
+
+    std::vector<int> internal;
+    if      ( SHM == 1 )   internal = std::vector<int>({1,1,1,1});
+    else if ( SHM == 2 )   internal = std::vector<int>({2,1,1,1});
+    else if ( SHM == 4 )   internal = std::vector<int>({2,2,1,1});
+    else if ( SHM == 8 )   internal = std::vector<int>({2,2,2,1});
+    else assert(0);
+
+    std::vector<int> nodes({mpi[0]/internal[0],mpi[1]/internal[1],mpi[2]/internal[2],mpi[3]/internal[3]});
+    std::vector<int> latt4({local[0]*nodes[0],local[1]*nodes[1],local[2]*nodes[2],local[3]*nodes[3]});
+
+    ///////// Welcome message ////////////
+    std::cout<<GridLogMessage << "=================================================================================="<<std::endl;
+    std::cout<<GridLogMessage << "Benchmark DWF on "<<L<<"^4 local volume "<<std::endl;
+    std::cout<<GridLogMessage << "* Global volume  : "<<GridCmdVectorIntToString(latt4)<<std::endl;
+    std::cout<<GridLogMessage << "* Ls             : "<<Ls<<std::endl;
+    std::cout<<GridLogMessage << "* MPI ranks      : "<<GridCmdVectorIntToString(mpi)<<std::endl;
+    std::cout<<GridLogMessage << "* Intranode      : "<<GridCmdVectorIntToString(internal)<<std::endl;
+    std::cout<<GridLogMessage << "* nodes          : "<<GridCmdVectorIntToString(nodes)<<std::endl;
+    std::cout<<GridLogMessage << "* Using "<<threads<<" threads"<<std::endl;
+    std::cout<<GridLogMessage << "=================================================================================="<<std::endl;
+
+
+    ///////// Lattice Init ////////////
+    GridCartesian         * UGrid   = SpaceTimeGrid::makeFourDimGrid(latt4, GridDefaultSimd(Nd,vComplex::Nsimd()),GridDefaultMpi());
+    GridRedBlackCartesian * UrbGrid = SpaceTimeGrid::makeFourDimRedBlackGrid(UGrid);
+    GridCartesian         * FGrid   = SpaceTimeGrid::makeFiveDimGrid(Ls,UGrid);
+    GridRedBlackCartesian * FrbGrid = SpaceTimeGrid::makeFiveDimRedBlackGrid(Ls,UGrid);
+
+    
+    ///////// RNG Init ////////////
+    std::vector<int> seeds4({1,2,3,4});
+    std::vector<int> seeds5({5,6,7,8});
+    GridParallelRNG          RNG4(UGrid);  RNG4.SeedFixedIntegers(seeds4);
+    GridParallelRNG          RNG5(FGrid);  RNG5.SeedFixedIntegers(seeds5);
+    std::cout << GridLogMessage << "Initialised RNGs" << std::endl;
+
+    ///////// Source preparation ////////////
+    LatticeFermion src   (FGrid); random(RNG5,src);
+    LatticeFermion ref   (FGrid);
+    LatticeFermion tmp   (FGrid);
+
+    RealD N2 = 1.0/::sqrt(norm2(src));
+    src = src*N2;
+    
+    LatticeGaugeField Umu(UGrid);  SU3::HotConfiguration(RNG4,Umu); 
+
+    DomainWallFermionR Dw(Umu,*FGrid,*FrbGrid,*UGrid,*UrbGrid,mass,M5);
+
+    ////////////////////////////////////
+    // Naive wilson implementation
+    ////////////////////////////////////
+    {
+      LatticeGaugeField Umu5d(FGrid); 
+      std::vector<LatticeColourMatrix> U(4,FGrid);
+      for(int ss=0;ss<Umu._grid->oSites();ss++){
+	for(int s=0;s<Ls;s++){
+	  Umu5d._odata[Ls*ss+s] = Umu._odata[ss];
+	}
+      }
+      ref = zero;
+      for(int mu=0;mu<Nd;mu++){
+	U[mu] = PeekIndex<LorentzIndex>(Umu5d,mu);
+      }
+      for(int mu=0;mu<Nd;mu++){
+	
+	tmp = U[mu]*Cshift(src,mu+1,1);
+	ref=ref + tmp - Gamma(Gmu[mu])*tmp;
+	
+	tmp =adj(U[mu])*src;
+	tmp =Cshift(tmp,mu+1,-1);
+	ref=ref + tmp + Gamma(Gmu[mu])*tmp;
+      }
+      ref = -0.5*ref;
+    }
+
+    LatticeFermion src_e (FrbGrid);
+    LatticeFermion src_o (FrbGrid);
+    LatticeFermion r_e   (FrbGrid);
+    LatticeFermion r_o   (FrbGrid);
+    LatticeFermion r_eo  (FGrid);
+    LatticeFermion err   (FGrid);
+    {
+
+      pickCheckerboard(Even,src_e,src);
+      pickCheckerboard(Odd,src_o,src);
+
+#if defined(AVX512) 
+      const int num_cases = 6;
+      std::string fmt("A/S ; A/O ; U/S ; U/O ; G/S ; G/O ");
+#else
+      const int num_cases = 4;
+      std::string fmt("U/S ; U/O ; G/S ; G/O ");
+#endif
+      controls Cases [] = {
+#ifdef AVX512
+	{ QCD::WilsonKernelsStatic::OptInlineAsm , QCD::WilsonKernelsStatic::CommsThenCompute ,CartesianCommunicator::CommunicatorPolicySequential  },
+	{ QCD::WilsonKernelsStatic::OptInlineAsm , QCD::WilsonKernelsStatic::CommsAndCompute  ,CartesianCommunicator::CommunicatorPolicySequential  },
+#endif
+	{ QCD::WilsonKernelsStatic::OptHandUnroll, QCD::WilsonKernelsStatic::CommsThenCompute ,CartesianCommunicator::CommunicatorPolicySequential  },
+	{ QCD::WilsonKernelsStatic::OptHandUnroll, QCD::WilsonKernelsStatic::CommsAndCompute  ,CartesianCommunicator::CommunicatorPolicySequential  },
+	{ QCD::WilsonKernelsStatic::OptGeneric   , QCD::WilsonKernelsStatic::CommsThenCompute ,CartesianCommunicator::CommunicatorPolicySequential  },
+	{ QCD::WilsonKernelsStatic::OptGeneric   , QCD::WilsonKernelsStatic::CommsAndCompute  ,CartesianCommunicator::CommunicatorPolicySequential  }
+      }; 
+
+      for(int c=0;c<num_cases;c++) {
+
+	QCD::WilsonKernelsStatic::Comms = Cases[c].CommsOverlap;
+	QCD::WilsonKernelsStatic::Opt   = Cases[c].Opt;
+	CartesianCommunicator::SetCommunicatorPolicy(Cases[c].CommsAsynch);
+
+	std::cout<<GridLogMessage << "=================================================================================="<<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;
+	if ( WilsonKernelsStatic::Comms == WilsonKernelsStatic::CommsAndCompute ) std::cout << GridLogMessage<< "* Using Overlapped Comms/Compute" <<std::endl;
+	if ( WilsonKernelsStatic::Comms == WilsonKernelsStatic::CommsThenCompute) std::cout << GridLogMessage<< "* Using sequential comms compute" <<std::endl;
+	if ( sizeof(Real)==4 )   std::cout << GridLogMessage<< "* SINGLE precision "<<std::endl;
+	if ( sizeof(Real)==8 )   std::cout << GridLogMessage<< "* DOUBLE precision "<<std::endl;
+	std::cout<<GridLogMessage << "=================================================================================="<<std::endl;
+
+	int nwarm = 200;
+	double t0=usecond();
+	FGrid->Barrier();
+	for(int i=0;i<nwarm;i++){
+	  Dw.DhopEO(src_o,r_e,DaggerNo);
+	}
+	FGrid->Barrier();
+	double t1=usecond();
+	//	uint64_t ncall = (uint64_t) 2.5*1000.0*1000.0*nwarm/(t1-t0);
+	//	if (ncall < 500) ncall = 500;
+	uint64_t ncall = 1000;
+
+	FGrid->Broadcast(0,&ncall,sizeof(ncall));
+
+	//	std::cout << GridLogMessage << " Estimate " << ncall << " calls per second"<<std::endl;
+	Dw.ZeroCounters();
+
+	time_statistics timestat;
+	std::vector<double> t_time(ncall);
+	for(uint64_t i=0;i<ncall;i++){
+	  t0=usecond();
+	  Dw.DhopEO(src_o,r_e,DaggerNo);
+	  t1=usecond();
+	  t_time[i] = t1-t0;
+	}
+	FGrid->Barrier();
+	
+	double volume=Ls;  for(int mu=0;mu<Nd;mu++) volume=volume*latt4[mu];
+	double flops=(1344.0*volume)/2;
+	double mf_hi, mf_lo, mf_err;
+
+	timestat.statistics(t_time);
+	mf_hi = flops/timestat.min;
+	mf_lo = flops/timestat.max;
+	mf_err= flops/timestat.min * timestat.err/timestat.mean;
+
+	mflops = flops/timestat.mean;
+	mflops_all.push_back(mflops);
+	if ( mflops_best == 0   ) mflops_best = mflops;
+	if ( mflops_worst== 0   ) mflops_worst= mflops;
+	if ( mflops>mflops_best ) mflops_best = mflops;
+	if ( mflops<mflops_worst) mflops_worst= mflops;
+
+	std::cout<<GridLogMessage << std::fixed << std::setprecision(1)<<"Deo mflop/s =   "<< mflops << " ("<<mf_err<<") " << mf_lo<<"-"<<mf_hi <<std::endl;
+	std::cout<<GridLogMessage << std::fixed << std::setprecision(1)<<"Deo mflop/s per rank   "<< mflops/NP<<std::endl;
+	std::cout<<GridLogMessage << std::fixed << std::setprecision(1)<<"Deo mflop/s per node   "<< mflops/NN<<std::endl;
+
+	Dw.Report();
+
+	Dw.DhopEO(src_o,r_e,DaggerNo);
+	Dw.DhopOE(src_e,r_o,DaggerNo);
+	setCheckerboard(r_eo,r_o);
+	setCheckerboard(r_eo,r_e);
+	err = r_eo-ref; 
+	std::cout<<GridLogMessage << "norm diff   "<< norm2(err)<<std::endl;
+	assert((norm2(err)<1.0e-4));
+
+      }
+      robust = mflops_worst/mflops_best;
+      std::cout<<GridLogMessage << "=================================================================================="<<std::endl;
+      std::cout<<GridLogMessage << L<<"^4 x "<<Ls<< " Deo Best  mflop/s        =   "<< mflops_best << " ; " << mflops_best/NN<<" per node " <<std::endl;
+      std::cout<<GridLogMessage << L<<"^4 x "<<Ls<< " Deo Worst mflop/s        =   "<< mflops_worst<< " ; " << mflops_worst/NN<<" per node " <<std::endl;
+      std::cout<<GridLogMessage << std::fixed<<std::setprecision(3)<< L<<"^4 x "<<Ls<< " Performance Robustness   =   "<< robust  <<std::endl;
+      std::cout<<GridLogMessage <<fmt << std::endl;
+      std::cout<<GridLogMessage ;
+
+      for(int i=0;i<mflops_all.size();i++){
+	std::cout<<mflops_all[i]/NN<<" ; " ;
+      }
+      std::cout<<std::endl;
+      std::cout<<GridLogMessage << "=================================================================================="<<std::endl;
+
+    }
+    return mflops_best;
+  }
+
+};
+
+int main (int argc, char ** argv)
+{
+  Grid_init(&argc,&argv);
+
+  CartesianCommunicator::SetCommunicatorPolicy(CartesianCommunicator::CommunicatorPolicySequential);
+#ifdef KNL
+  LebesgueOrder::Block = std::vector<int>({8,2,2,2});
+#else
+  LebesgueOrder::Block = std::vector<int>({2,2,2,2});
+#endif
+  Benchmark::Decomposition();
+
+  int do_memory=1;
+  int do_comms =1;
+  int do_su3   =0;
+  int do_wilson=1;
+  int do_dwf   =1;
+
+  if ( do_su3 ) {
+    // empty for now
+  }
+
+  int sel=2;
+  std::vector<int> L_list({8,12,16,24});
+
+  //int sel=1;
+  //  std::vector<int> L_list({8,12});
+  std::vector<double> robust_list;
+
+  std::vector<double> wilson;
+  std::vector<double> dwf4;
+  std::vector<double> dwf5;
+
+  if ( do_wilson ) {
+    int Ls=1;
+    std::cout<<GridLogMessage << "=================================================================================="<<std::endl;
+    std::cout<<GridLogMessage << " Wilson dslash 4D vectorised" <<std::endl;
+    std::cout<<GridLogMessage << "=================================================================================="<<std::endl;
+    for(int l=0;l<L_list.size();l++){
+      double robust;
+      wilson.push_back(Benchmark::DWF(1,L_list[l],robust));
+    }
+  }
+
+  int Ls=16;
+  if ( do_dwf ) {
+    std::cout<<GridLogMessage << "=================================================================================="<<std::endl;
+    std::cout<<GridLogMessage << " Domain wall dslash 4D vectorised" <<std::endl;
+    std::cout<<GridLogMessage << "=================================================================================="<<std::endl;
+    for(int l=0;l<L_list.size();l++){
+      double robust;
+      double result = Benchmark::DWF(Ls,L_list[l],robust) ;
+      dwf4.push_back(result);
+      robust_list.push_back(robust);
+    }
+  }
+
+  if ( do_dwf ) {
+    std::cout<<GridLogMessage << "=================================================================================="<<std::endl;
+    std::cout<<GridLogMessage << " Domain wall dslash 4D vectorised" <<std::endl;
+    std::cout<<GridLogMessage << "=================================================================================="<<std::endl;
+    for(int l=0;l<L_list.size();l++){
+      dwf5.push_back(Benchmark::DWF5(Ls,L_list[l]));
+    }
+
+  }
+
+  if ( do_dwf ) {
+
+  std::cout<<GridLogMessage << "=================================================================================="<<std::endl;
+  std::cout<<GridLogMessage << " Summary table Ls="<<Ls <<std::endl;
+  std::cout<<GridLogMessage << "=================================================================================="<<std::endl;
+  std::cout<<GridLogMessage << "L \t\t Wilson \t DWF4 \t DWF5 " <<std::endl;
+  for(int l=0;l<L_list.size();l++){
+    std::cout<<GridLogMessage << L_list[l] <<" \t\t "<< wilson[l]<<" \t "<<dwf4[l]<<" \t "<<dwf5[l] <<std::endl;
+  }
+  std::cout<<GridLogMessage << "=================================================================================="<<std::endl;
+  }
+
+  int NN=NN_global;
+  if ( do_memory ) {
+    std::cout<<GridLogMessage << "=================================================================================="<<std::endl;
+    std::cout<<GridLogMessage << " Memory benchmark " <<std::endl;
+    std::cout<<GridLogMessage << "=================================================================================="<<std::endl;
+    Benchmark::Memory();
+  }
+
+  if ( do_comms && (NN>1) ) {
+    std::cout<<GridLogMessage << "=================================================================================="<<std::endl;
+    std::cout<<GridLogMessage << " Communications benchmark " <<std::endl;
+    std::cout<<GridLogMessage << "=================================================================================="<<std::endl;
+    Benchmark::Comms();
+  }
+
+  if ( do_dwf ) {
+  std::cout<<GridLogMessage << "=================================================================================="<<std::endl;
+  std::cout<<GridLogMessage << " Per Node Summary table Ls="<<Ls <<std::endl;
+  std::cout<<GridLogMessage << "=================================================================================="<<std::endl;
+  std::cout<<GridLogMessage << " L \t\t Wilson\t\t DWF4  \t\t DWF5 " <<std::endl;
+  for(int l=0;l<L_list.size();l++){
+    std::cout<<GridLogMessage << L_list[l] <<" \t\t "<< wilson[l]/NN<<" \t "<<dwf4[l]/NN<<" \t "<<dwf5[l] /NN<<std::endl;
+  }
+  std::cout<<GridLogMessage << "=================================================================================="<<std::endl;
+
+  std::cout<<GridLogMessage << "=================================================================================="<<std::endl;
+  std::cout<<GridLogMessage << " Comparison point     result: "  << dwf4[sel]/NN << " Mflop/s per node"<<std::endl;
+  std::cout<<std::setprecision(3);
+  std::cout<<GridLogMessage << " Comparison point robustness: "  << robust_list[sel] <<std::endl;
+  std::cout<<GridLogMessage << "=================================================================================="<<std::endl;
+
+  }
+
+
+  Grid_finalize();
+}

benchmarks/Benchmark_comms.cc

@@ -68,7 +68,7 @@ int main (int argc, char ** argv)
 
   int Nloop=100;
   int nmu=0;
-  int maxlat=24;
+  int maxlat=32;
   for(int mu=0;mu<Nd;mu++) if (mpi_layout[mu]>1) nmu++;
 
   std::cout << GridLogMessage << "Number of iterations to average: "<< Nloop << std::endl;
@@ -80,7 +80,7 @@ int main (int argc, char ** argv)
   std::cout<<GridLogMessage << "===================================================================================================="<<std::endl;
   header();
   for(int lat=4;lat<=maxlat;lat+=4){
-    for(int Ls=8;Ls<=32;Ls*=2){
+    for(int Ls=8;Ls<=8;Ls*=2){
 
       std::vector<int> latt_size  ({lat*mpi_layout[0],
       				    lat*mpi_layout[1],
@@ -92,11 +92,16 @@ int main (int argc, char ** argv)
       RealD Nnode = Grid.NodeCount();
       RealD ppn = Nrank/Nnode;
 
-      std::vector<std::vector<HalfSpinColourVectorD> > xbuf(8,std::vector<HalfSpinColourVectorD>(lat*lat*lat*Ls));
+      std::vector<Vector<HalfSpinColourVectorD> > xbuf(8);	
-      std::vector<std::vector<HalfSpinColourVectorD> > rbuf(8,std::vector<HalfSpinColourVectorD>(lat*lat*lat*Ls));
+      std::vector<Vector<HalfSpinColourVectorD> > rbuf(8);
 
       int ncomm;
       int bytes=lat*lat*lat*Ls*sizeof(HalfSpinColourVectorD);
+      for(int mu=0;mu<8;mu++){
+	xbuf[mu].resize(lat*lat*lat*Ls);
+	rbuf[mu].resize(lat*lat*lat*Ls);
+	//	std::cout << " buffers " << std::hex << (uint64_t)&xbuf[mu][0] <<" " << (uint64_t)&rbuf[mu][0] <<std::endl;
+      }
 
       for(int i=0;i<Nloop;i++){
       double start=usecond();
@@ -112,7 +117,6 @@ int main (int argc, char ** argv)
 	    int comm_proc=1;
 	    int xmit_to_rank;
 	    int recv_from_rank;
-	    
 	    Grid.ShiftedRanks(mu,comm_proc,xmit_to_rank,recv_from_rank);
 	    Grid.SendToRecvFromBegin(requests,
 				   (void *)&xbuf[mu][0],
@@ -163,7 +167,7 @@ int main (int argc, char ** argv)
   header();
 
   for(int lat=4;lat<=maxlat;lat+=4){
-    for(int Ls=8;Ls<=32;Ls*=2){
+    for(int Ls=8;Ls<=8;Ls*=2){
 
       std::vector<int> latt_size  ({lat,lat,lat,lat});
 
@@ -172,9 +176,14 @@ int main (int argc, char ** argv)
       RealD Nnode = Grid.NodeCount();
       RealD ppn = Nrank/Nnode;
 
-      std::vector<std::vector<HalfSpinColourVectorD> > xbuf(8,std::vector<HalfSpinColourVectorD>(lat*lat*lat*Ls));
+      std::vector<Vector<HalfSpinColourVectorD> > xbuf(8);
-      std::vector<std::vector<HalfSpinColourVectorD> > rbuf(8,std::vector<HalfSpinColourVectorD>(lat*lat*lat*Ls));
+      std::vector<Vector<HalfSpinColourVectorD> > rbuf(8);
 
+      for(int mu=0;mu<8;mu++){
+	xbuf[mu].resize(lat*lat*lat*Ls);
+	rbuf[mu].resize(lat*lat*lat*Ls);
+	//	std::cout << " buffers " << std::hex << (uint64_t)&xbuf[mu][0] <<" " << (uint64_t)&rbuf[mu][0] <<std::endl;
+      }
 
       int ncomm;
       int bytes=lat*lat*lat*Ls*sizeof(HalfSpinColourVectorD);
@@ -249,7 +258,7 @@ int main (int argc, char ** argv)
   header();
 
   for(int lat=4;lat<=maxlat;lat+=4){
-    for(int Ls=8;Ls<=32;Ls*=2){
+    for(int Ls=8;Ls<=8;Ls*=2){
 
       std::vector<int> latt_size  ({lat*mpi_layout[0],
       				    lat*mpi_layout[1],
@@ -299,7 +308,7 @@ int main (int argc, char ** argv)
 					      xmit_to_rank,
 					      (void *)&rbuf[mu][0],
 					      recv_from_rank,
-					      bytes);
+					      bytes,mu);
 	
 	    comm_proc = mpi_layout[mu]-1;
 	  
@@ -310,11 +319,11 @@ int main (int argc, char ** argv)
 					      xmit_to_rank,
 					      (void *)&rbuf[mu+4][0],
 					      recv_from_rank,
-					      bytes);
+					      bytes,mu+4);
 	  
 	  }
 	}
-	Grid.StencilSendToRecvFromComplete(requests);
+	Grid.StencilSendToRecvFromComplete(requests,0);
 	Grid.Barrier();
 	double stop=usecond();
 	t_time[i] = stop-start; // microseconds
@@ -346,7 +355,7 @@ int main (int argc, char ** argv)
   header();
 
   for(int lat=4;lat<=maxlat;lat+=4){
-    for(int Ls=8;Ls<=32;Ls*=2){
+    for(int Ls=8;Ls<=8;Ls*=2){
 
       std::vector<int> latt_size  ({lat*mpi_layout[0],
       				    lat*mpi_layout[1],
@@ -393,8 +402,8 @@ int main (int argc, char ** argv)
 					      xmit_to_rank,
 					      (void *)&rbuf[mu][0],
 					      recv_from_rank,
-					      bytes);
+					      bytes,mu);
-	    Grid.StencilSendToRecvFromComplete(requests);
+	    Grid.StencilSendToRecvFromComplete(requests,mu);
 	    requests.resize(0);
 
 	    comm_proc = mpi_layout[mu]-1;
@@ -406,8 +415,8 @@ int main (int argc, char ** argv)
 					      xmit_to_rank,
 					      (void *)&rbuf[mu+4][0],
 					      recv_from_rank,
-					      bytes);
+					      bytes,mu+4);
-	    Grid.StencilSendToRecvFromComplete(requests);
+	    Grid.StencilSendToRecvFromComplete(requests,mu+4);
 	    requests.resize(0);
 	  
 	  }
@@ -436,5 +445,97 @@ int main (int argc, char ** argv)
     }
   }    
 
+
+
+  std::cout<<GridLogMessage << "===================================================================================================="<<std::endl;
+  std::cout<<GridLogMessage << "= Benchmarking threaded STENCIL halo exchange in "<<nmu<<" dimensions"<<std::endl;
+  std::cout<<GridLogMessage << "===================================================================================================="<<std::endl;
+  header();
+
+  for(int lat=4;lat<=maxlat;lat+=4){
+    for(int Ls=8;Ls<=8;Ls*=2){
+
+      std::vector<int> latt_size  ({lat*mpi_layout[0],
+      				    lat*mpi_layout[1],
+      				    lat*mpi_layout[2],
+      				    lat*mpi_layout[3]});
+
+      GridCartesian     Grid(latt_size,simd_layout,mpi_layout);
+      RealD Nrank = Grid._Nprocessors;
+      RealD Nnode = Grid.NodeCount();
+      RealD ppn = Nrank/Nnode;
+
+      std::vector<HalfSpinColourVectorD *> xbuf(8);
+      std::vector<HalfSpinColourVectorD *> rbuf(8);
+      Grid.ShmBufferFreeAll();
+      for(int d=0;d<8;d++){
+	xbuf[d] = (HalfSpinColourVectorD *)Grid.ShmBufferMalloc(lat*lat*lat*Ls*sizeof(HalfSpinColourVectorD));
+	rbuf[d] = (HalfSpinColourVectorD *)Grid.ShmBufferMalloc(lat*lat*lat*Ls*sizeof(HalfSpinColourVectorD));
+	bzero((void *)xbuf[d],lat*lat*lat*Ls*sizeof(HalfSpinColourVectorD));
+	bzero((void *)rbuf[d],lat*lat*lat*Ls*sizeof(HalfSpinColourVectorD));
+      }
+
+      int ncomm;
+      int bytes=lat*lat*lat*Ls*sizeof(HalfSpinColourVectorD);
+      double dbytes;
+      for(int i=0;i<Nloop;i++){
+	double start=usecond();
+
+	std::vector<CartesianCommunicator::CommsRequest_t> requests;
+	dbytes=0;
+	ncomm=0;
+
+	parallel_for(int dir=0;dir<8;dir++){
+
+	  double tbytes;
+	  int mu =dir % 4;
+
+	  if (mpi_layout[mu]>1 ) {
+	  
+	    ncomm++;
+	    int xmit_to_rank;
+	    int recv_from_rank;
+	    if ( dir == mu ) { 
+	      int comm_proc=1;
+	      Grid.ShiftedRanks(mu,comm_proc,xmit_to_rank,recv_from_rank);
+	    } else { 
+	      int comm_proc = mpi_layout[mu]-1;
+	      Grid.ShiftedRanks(mu,comm_proc,xmit_to_rank,recv_from_rank);
+	    }
+
+	    tbytes= Grid.StencilSendToRecvFrom((void *)&xbuf[dir][0], xmit_to_rank,
+					       (void *)&rbuf[dir][0], recv_from_rank, bytes,dir);
+
+#pragma omp atomic
+	    dbytes+=tbytes;
+	  }
+	}
+	Grid.Barrier();
+	double stop=usecond();
+	t_time[i] = stop-start; // microseconds
+      }
+
+      timestat.statistics(t_time);
+
+      dbytes=dbytes*ppn;
+      double xbytes    = dbytes*0.5;
+      double rbytes    = dbytes*0.5;
+      double bidibytes = dbytes;
+
+
+      std::cout<<GridLogMessage << std::setw(4) << lat<<"\t"<<Ls<<"\t"
+               <<std::setw(11) << bytes<< std::fixed << std::setprecision(1) << std::setw(7)
+               <<std::right<< xbytes/timestat.mean<<"  "<< xbytes*timestat.err/(timestat.mean*timestat.mean)<< " "
+               <<xbytes/timestat.max <<" "<< xbytes/timestat.min  
+               << "\t\t"<<std::setw(7)<< bidibytes/timestat.mean<< "  " << bidibytes*timestat.err/(timestat.mean*timestat.mean) << " "
+               << bidibytes/timestat.max << " " << bidibytes/timestat.min << std::endl;
+ 
+    }
+  }    
+
+  std::cout<<GridLogMessage << "===================================================================================================="<<std::endl;
+  std::cout<<GridLogMessage << "= All done; Bye Bye"<<std::endl;
+  std::cout<<GridLogMessage << "===================================================================================================="<<std::endl;
+
   Grid_finalize();
 }

benchmarks/Benchmark_dwf.cc

@@ -503,9 +503,9 @@ int main (int argc, char ** argv)
   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_e)<1.0e-4);
-  //assert(norm2(src_o)<1.0e-4);
+  assert(norm2(src_o)<1.0e-4);
-
   Grid_finalize();
+  exit(0);
 }
 

configure.ac

@@ -13,6 +13,10 @@ m4_ifdef([AM_SILENT_RULES], [AM_SILENT_RULES([yes])])
 ################ Get git info
 #AC_REVISION([m4_esyscmd_s([./scripts/configure.commit])])
 
+################ Set flags
+# do not move!
+CXXFLAGS="-O3 $CXXFLAGS"
+
 ############### Checks for programs
 AC_PROG_CXX
 AC_PROG_RANLIB
@@ -27,7 +31,6 @@ AX_GXX_VERSION
 AC_DEFINE_UNQUOTED([GXX_VERSION],["$GXX_VERSION"],
       [version of g++ that will compile the code])
 
-CXXFLAGS="-O3 $CXXFLAGS"
 
 
 ############### Checks for typedefs, structures, and compiler characteristics
@@ -55,6 +58,10 @@ AC_CHECK_HEADERS(numaif.h)
 AC_CHECK_DECLS([ntohll],[], [], [[#include <arpa/inet.h>]])
 AC_CHECK_DECLS([be64toh],[], [], [[#include <arpa/inet.h>]])
 
+############## Standard libraries
+AC_CHECK_LIB([m],[cos])
+AC_CHECK_LIB([stdc++],[abort])
+
 ############### GMP and MPFR
 AC_ARG_WITH([gmp],
     [AS_HELP_STRING([--with-gmp=prefix],
@@ -324,8 +331,41 @@ case ${ac_PRECISION} in
      double)
        AC_DEFINE([GRID_DEFAULT_PRECISION_DOUBLE],[1],[GRID_DEFAULT_PRECISION is DOUBLE] )
      ;;
+     *)
+     AC_MSG_ERROR([${ac_PRECISION} unsupported --enable-precision option]);
+     ;;
 esac
 
+######################  Shared memory allocation technique under MPI3
+AC_ARG_ENABLE([shm],[AC_HELP_STRING([--enable-shm=shmget|shmopen|hugetlbfs],
+              [Select SHM allocation technique])],[ac_SHM=${enable_shm}],[ac_SHM=shmopen])
+
+case ${ac_SHM} in
+
+     shmget)
+     AC_DEFINE([GRID_MPI3_SHMGET],[1],[GRID_MPI3_SHMGET] )
+     ;;
+
+     shmopen)
+     AC_DEFINE([GRID_MPI3_SHMOPEN],[1],[GRID_MPI3_SHMOPEN] )
+     ;;
+
+     hugetlbfs)
+     AC_DEFINE([GRID_MPI3_SHMMMAP],[1],[GRID_MPI3_SHMMMAP] )
+     ;;
+
+     *)
+     AC_MSG_ERROR([${ac_SHM} unsupported --enable-shm option]);
+     ;;
+esac
+
+######################  Shared base path for SHMMMAP
+AC_ARG_ENABLE([shmpath],[AC_HELP_STRING([--enable-shmpath=path],
+              [Select SHM mmap base path for hugetlbfs])],
+	      [ac_SHMPATH=${enable_shmpath}],
+	      [ac_SHMPATH=/var/lib/hugetlbfs/pagesize-2MB/])
+AC_DEFINE_UNQUOTED([GRID_SHM_PATH],["$ac_SHMPATH"],[Path to a hugetlbfs filesystem for MMAPing])
+
 ############### communication type selection
 AC_ARG_ENABLE([comms],[AC_HELP_STRING([--enable-comms=none|mpi|mpi-auto|mpi3|mpi3-auto|shmem],
               [Select communications])],[ac_COMMS=${enable_comms}],[ac_COMMS=none])
@@ -335,14 +375,14 @@ case ${ac_COMMS} in
         AC_DEFINE([GRID_COMMS_NONE],[1],[GRID_COMMS_NONE] )
         comms_type='none'
      ;;
-     mpi3l*)
-       AC_DEFINE([GRID_COMMS_MPI3L],[1],[GRID_COMMS_MPI3L] )
-       comms_type='mpi3l'
-     ;;
      mpi3*)
         AC_DEFINE([GRID_COMMS_MPI3],[1],[GRID_COMMS_MPI3] )
         comms_type='mpi3'
      ;;
+     mpit)
+        AC_DEFINE([GRID_COMMS_MPIT],[1],[GRID_COMMS_MPIT] )
+        comms_type='mpit'
+     ;;
      mpi*)
         AC_DEFINE([GRID_COMMS_MPI],[1],[GRID_COMMS_MPI] )
         comms_type='mpi'
@@ -370,7 +410,7 @@ esac
 AM_CONDITIONAL(BUILD_COMMS_SHMEM, [ test "${comms_type}X" == "shmemX" ])
 AM_CONDITIONAL(BUILD_COMMS_MPI,   [ test "${comms_type}X" == "mpiX" ])
 AM_CONDITIONAL(BUILD_COMMS_MPI3,  [ test "${comms_type}X" == "mpi3X" ] )
-AM_CONDITIONAL(BUILD_COMMS_MPI3L, [ test "${comms_type}X" == "mpi3lX" ] )
+AM_CONDITIONAL(BUILD_COMMS_MPIT,  [ test "${comms_type}X" == "mpitX" ] )
 AM_CONDITIONAL(BUILD_COMMS_NONE,  [ test "${comms_type}X" == "noneX" ])
 
 ############### RNG selection
@@ -475,6 +515,8 @@ compiler version            : ${ax_cv_gxx_version}
 SIMD                        : ${ac_SIMD}${SIMD_GEN_WIDTH_MSG}
 Threading                   : ${ac_openmp}
 Communications type         : ${comms_type}
+Shared memory allocator     : ${ac_SHM}
+Shared memory mmap path     : ${ac_SHMPATH}
 Default precision           : ${ac_PRECISION}
 Software FP16 conversion    : ${ac_SFW_FP16}
 RNG choice                  : ${ac_RNG}

lib/Makefile.am

@@ -10,8 +10,8 @@ if BUILD_COMMS_MPI3
   extra_sources+=communicator/Communicator_base.cc
 endif
 
-if BUILD_COMMS_MPI3L
+if BUILD_COMMS_MPIT
-  extra_sources+=communicator/Communicator_mpi3_leader.cc
+  extra_sources+=communicator/Communicator_mpit.cc
   extra_sources+=communicator/Communicator_base.cc
 endif
 

lib/algorithms/iterative/BlockConjugateGradient.h

@@ -87,15 +87,22 @@ void ThinQRfact (Eigen::MatrixXcd &m_rr,
   ////////////////////////////////////////////////////////////////////////////////////////////////////
   sliceInnerProductMatrix(m_rr,R,R,Orthog);
 
-  ////////////////////////////////////////////////////////////////////////////////////////////////////
+  // Force manifest hermitian to avoid rounding related
-  // Cholesky from Eigen
+  m_rr = 0.5*(m_rr+m_rr.adjoint());
-  // There exists a ldlt that is documented as more stable
-  ////////////////////////////////////////////////////////////////////////////////////////////////////
-  Eigen::MatrixXcd L    = m_rr.llt().matrixL(); 
 
+#if 0
+  std::cout << " Calling Cholesky  ldlt on m_rr "  << m_rr <<std::endl;
+  Eigen::MatrixXcd L_ldlt = m_rr.ldlt().matrixL(); 
+  std::cout << " Called Cholesky  ldlt on m_rr "  << L_ldlt <<std::endl;
+  auto  D_ldlt = m_rr.ldlt().vectorD(); 
+  std::cout << " Called Cholesky  ldlt on m_rr "  << D_ldlt <<std::endl;
+#endif
+
+  //  std::cout << " Calling Cholesky  llt on m_rr "  <<std::endl;
+  Eigen::MatrixXcd L    = m_rr.llt().matrixL(); 
+  //  std::cout << " Called Cholesky  llt on m_rr "  << L <<std::endl;
   C    = L.adjoint();
   Cinv = C.inverse();
-
   ////////////////////////////////////////////////////////////////////////////////////////////////////
   // Q = R C^{-1}
   //
@@ -103,7 +110,6 @@ void ThinQRfact (Eigen::MatrixXcd &m_rr,
   //
   // NB maddMatrix conventions are Right multiplication X[j] a[j,i] already
   ////////////////////////////////////////////////////////////////////////////////////////////////////
-  // FIXME:: make a sliceMulMatrix to avoid zero vector
   sliceMulMatrix(Q,Cinv,R,Orthog);
 }
 ////////////////////////////////////////////////////////////////////////////////////////////////////
@@ -199,7 +205,12 @@ void BlockCGrQsolve(LinearOperatorBase<Field> &Linop, const Field &B, Field &X)
 
   Linop.HermOp(X, AD);
   tmp = B - AD;  
+  //std::cout << GridLogMessage << " initial tmp " << norm2(tmp)<< std::endl;
   ThinQRfact (m_rr, m_C, m_Cinv, Q, tmp);
+  //std::cout << GridLogMessage << " initial Q " << norm2(Q)<< std::endl;
+  //std::cout << GridLogMessage << " m_rr " << m_rr<<std::endl;
+  //std::cout << GridLogMessage << " m_C " << m_C<<std::endl;
+  //std::cout << GridLogMessage << " m_Cinv " << m_Cinv<<std::endl;
   D=Q;
 
   std::cout << GridLogMessage<<"BlockCGrQ computed initial residual and QR fact " <<std::endl;
@@ -221,12 +232,14 @@ void BlockCGrQsolve(LinearOperatorBase<Field> &Linop, const Field &B, Field &X)
     MatrixTimer.Start();
     Linop.HermOp(D, Z);      
     MatrixTimer.Stop();
+    //std::cout << GridLogMessage << " norm2 Z " <<norm2(Z)<<std::endl;
 
     //4. M  = [D^dag Z]^{-1}
     sliceInnerTimer.Start();
     sliceInnerProductMatrix(m_DZ,D,Z,Orthog);
     sliceInnerTimer.Stop();
     m_M       = m_DZ.inverse();
+    //std::cout << GridLogMessage << " m_DZ " <<m_DZ<<std::endl;
     
     //5. X  = X + D MC
     m_tmp     = m_M * m_C;

lib/allocator/AlignedAllocator.cc

@@ -1,7 +1,5 @@
-
-
-
 #include <Grid/GridCore.h>
+#include <fcntl.h>
 
 namespace Grid {
 
@@ -11,7 +9,7 @@ int PointerCache::victim;
 
 void *PointerCache::Insert(void *ptr,size_t bytes) {
 
-  if (bytes < 4096 ) return NULL;
+  if (bytes < 4096 ) return ptr;
 
 #ifdef GRID_OMP
   assert(omp_in_parallel()==0);
@@ -63,4 +61,37 @@ void *PointerCache::Lookup(size_t bytes) {
   return NULL;
 }
 
+
+void check_huge_pages(void *Buf,uint64_t BYTES)
+{
+#ifdef __linux__
+  int fd = open("/proc/self/pagemap", O_RDONLY);
+  assert(fd >= 0);
+  const int page_size = 4096;
+  uint64_t virt_pfn = (uint64_t)Buf / page_size;
+  off_t offset = sizeof(uint64_t) * virt_pfn;
+  uint64_t npages = (BYTES + page_size-1) / page_size;
+  uint64_t pagedata[npages];
+  uint64_t ret = lseek(fd, offset, SEEK_SET);
+  assert(ret == offset);
+  ret = ::read(fd, pagedata, sizeof(uint64_t)*npages);
+  assert(ret == sizeof(uint64_t) * npages);
+  int nhugepages = npages / 512;
+  int n4ktotal, nnothuge;
+  n4ktotal = 0;
+  nnothuge = 0;
+  for (int i = 0; i < nhugepages; ++i) {
+    uint64_t baseaddr = (pagedata[i*512] & 0x7fffffffffffffULL) * page_size;
+    for (int j = 0; j < 512; ++j) {
+      uint64_t pageaddr = (pagedata[i*512+j] & 0x7fffffffffffffULL) * page_size;
+      ++n4ktotal;
+      if (pageaddr != baseaddr + j * page_size)
+	++nnothuge;
+      }
+  }
+  int rank = CartesianCommunicator::RankWorld();
+  printf("rank %d Allocated %d 4k pages, %d not in huge pages\n", rank, n4ktotal, nnothuge);
+#endif
+}
+
 }

lib/allocator/AlignedAllocator.h

@@ -64,6 +64,8 @@ namespace Grid {
 
   };
 
+  void check_huge_pages(void *Buf,uint64_t BYTES);
+
 ////////////////////////////////////////////////////////////////////
 // A lattice of something, but assume the something is SIMDized.
 ////////////////////////////////////////////////////////////////////
@@ -92,12 +94,20 @@ public:
     size_type bytes = __n*sizeof(_Tp);
 
     _Tp *ptr = (_Tp *) PointerCache::Lookup(bytes);
+    //    if ( ptr != NULL ) 
+    //      std::cout << "alignedAllocator "<<__n << " cache hit "<< std::hex << ptr <<std::dec <<std::endl;
 
+    //////////////////
+    // Hack 2MB align; could make option probably doesn't need configurability
+    //////////////////
+//define GRID_ALLOC_ALIGN (128)
+#define GRID_ALLOC_ALIGN (2*1024*1024)
 #ifdef HAVE_MM_MALLOC_H
-    if ( ptr == (_Tp *) NULL ) ptr = (_Tp *) _mm_malloc(bytes,128);
+    if ( ptr == (_Tp *) NULL ) ptr = (_Tp *) _mm_malloc(bytes,GRID_ALLOC_ALIGN);
 #else
-    if ( ptr == (_Tp *) NULL ) ptr = (_Tp *) memalign(128,bytes);
+    if ( ptr == (_Tp *) NULL ) ptr = (_Tp *) memalign(GRID_ALLOC_ALIGN,bytes);
 #endif
+    //    std::cout << "alignedAllocator " << std::hex << ptr <<std::dec <<std::endl;
     // First touch optimise in threaded loop
     uint8_t *cp = (uint8_t *)ptr;
 #ifdef GRID_OMP
@@ -111,6 +121,7 @@ public:
 
   void deallocate(pointer __p, size_type __n) { 
     size_type bytes = __n * sizeof(_Tp);
+
     pointer __freeme = (pointer)PointerCache::Insert((void *)__p,bytes);
 
 #ifdef HAVE_MM_MALLOC_H
@@ -189,17 +200,19 @@ public:
   pointer allocate(size_type __n, const void* _p= 0) 
   {
 #ifdef HAVE_MM_MALLOC_H
-    _Tp * ptr = (_Tp *) _mm_malloc(__n*sizeof(_Tp),128);
+    _Tp * ptr = (_Tp *) _mm_malloc(__n*sizeof(_Tp),GRID_ALLOC_ALIGN);
 #else
-    _Tp * ptr = (_Tp *) memalign(128,__n*sizeof(_Tp));
+    _Tp * ptr = (_Tp *) memalign(GRID_ALLOC_ALIGN,__n*sizeof(_Tp));
 #endif
     size_type bytes = __n*sizeof(_Tp);
     uint8_t *cp = (uint8_t *)ptr;
+    if ( ptr ) { 
     // One touch per 4k page, static OMP loop to catch same loop order
 #pragma omp parallel for schedule(static)
       for(size_type n=0;n<bytes;n+=4096){
 	cp[n]=0;
       }
+    }
     return ptr;
   }
   void deallocate(pointer __p, size_type) { 

lib/cartesian/Cartesian_base.h

@@ -185,17 +185,18 @@ public:
     ////////////////////////////////////////////////////////////////
 
     void show_decomposition(){
-      std::cout << GridLogMessage << "Full Dimensions    : " << _fdimensions << std::endl;
+      std::cout << GridLogMessage << "\tFull Dimensions    : " << _fdimensions << std::endl;
-      std::cout << GridLogMessage << "Global Dimensions  : " << _gdimensions << std::endl;
+      std::cout << GridLogMessage << "\tSIMD layout        : " << _simd_layout << std::endl;
-      std::cout << GridLogMessage << "Local Dimensions   : " << _ldimensions << std::endl;
+      std::cout << GridLogMessage << "\tGlobal Dimensions  : " << _gdimensions << std::endl;
-      std::cout << GridLogMessage << "Reduced Dimensions : " << _rdimensions << std::endl;
+      std::cout << GridLogMessage << "\tLocal Dimensions   : " << _ldimensions << std::endl;
-      std::cout << GridLogMessage << "Outer strides      : " << _ostride << std::endl;
+      std::cout << GridLogMessage << "\tReduced Dimensions : " << _rdimensions << std::endl;
-      std::cout << GridLogMessage << "Inner strides      : " << _istride << std::endl;
+      std::cout << GridLogMessage << "\tOuter strides      : " << _ostride << std::endl;
-      std::cout << GridLogMessage << "iSites             : " << _isites << std::endl;
+      std::cout << GridLogMessage << "\tInner strides      : " << _istride << std::endl;
-      std::cout << GridLogMessage << "oSites             : " << _osites << std::endl;
+      std::cout << GridLogMessage << "\tiSites             : " << _isites << std::endl;
-      std::cout << GridLogMessage << "lSites             : " << lSites() << std::endl;        
+      std::cout << GridLogMessage << "\toSites             : " << _osites << std::endl;
-      std::cout << GridLogMessage << "gSites             : " << gSites() << std::endl;
+      std::cout << GridLogMessage << "\tlSites             : " << lSites() << std::endl;        
-      std::cout << GridLogMessage << "Nd                 : " << _ndimension << std::endl;             
+      std::cout << GridLogMessage << "\tgSites             : " << gSites() << std::endl;
+      std::cout << GridLogMessage << "\tNd                 : " << _ndimension << std::endl;             
     } 
 
     ////////////////////////////////////////////////////////////////

lib/cartesian/Cartesian_full.h

@@ -63,8 +63,7 @@ public:
     }
     GridCartesian(const std::vector<int> &dimensions,
                   const std::vector<int> &simd_layout,
-		  const std::vector<int> &processor_grid
+                  const std::vector<int> &processor_grid) : GridBase(processor_grid)
-		  ) : GridBase(processor_grid)
     {
       ///////////////////////
       // Grid information
@@ -84,28 +83,34 @@ public:
 
       _fsites = _gsites = _osites = _isites = 1;
 
-        for(int d=0;d<_ndimension;d++){
+      for (int d = 0; d < _ndimension; d++)
+      {
         _fdimensions[d] = dimensions[d];   // Global dimensions
         _gdimensions[d] = _fdimensions[d]; // Global dimensions
         _simd_layout[d] = simd_layout[d];
         _fsites = _fsites * _fdimensions[d];
         _gsites = _gsites * _gdimensions[d];
 
-	  //FIXME check for exact division
-
         // Use a reduced simd grid
         _ldimensions[d] = _gdimensions[d] / _processors[d]; //local dimensions
+        assert(_ldimensions[d] * _processors[d] == _gdimensions[d]);
+
         _rdimensions[d] = _ldimensions[d] / _simd_layout[d]; //overdecomposition
+        assert(_rdimensions[d] * _simd_layout[d] == _ldimensions[d]);
+
         _lstart[d] = _processor_coor[d] * _ldimensions[d];
         _lend[d] = _processor_coor[d] * _ldimensions[d] + _ldimensions[d] - 1;
         _osites *= _rdimensions[d];
         _isites *= _simd_layout[d];
 
         // Addressing support
-	  if ( d==0 ) {
+        if (d == 0)
+        {
           _ostride[d] = 1;
           _istride[d] = 1;
-	  } else {
+        }
+        else
+        {
           _ostride[d] = _ostride[d - 1] * _rdimensions[d - 1];
           _istride[d] = _istride[d - 1] * _simd_layout[d - 1];
         }
@@ -120,19 +125,18 @@ public:
 
       int block = 1;
       int nblock = 1;
-        for(int d=0;d<_ndimension;d++) nblock*=_rdimensions[d];
+      for (int d = 0; d < _ndimension; d++)
+        nblock *= _rdimensions[d];
 
-        for(int d=0;d<_ndimension;d++){
+      for (int d = 0; d < _ndimension; d++)
+      {
         nblock /= _rdimensions[d];
         _slice_block[d] = block;
         _slice_stride[d] = _ostride[d] * _rdimensions[d];
         _slice_nblock[d] = nblock;
         block = block * _rdimensions[d];
       }
-
     };
 };
-
-
 }
 #endif

lib/cartesian/Cartesian_red_black.h

@@ -161,28 +161,35 @@ public:
 
       _checker_dim_mask = checker_dim_mask;
 
-      for(int d=0;d<_ndimension;d++){
+      for (int d = 0; d < _ndimension; d++)
+      {
         _fdimensions[d] = dimensions[d];
         _gdimensions[d] = _fdimensions[d];
         _fsites = _fsites * _fdimensions[d];
         _gsites = _gsites * _gdimensions[d];
 
-	if (d==_checker_dim) {
+        if (d == _checker_dim)
+        {
+          assert((_gdimensions[d] & 0x1) == 0);
           _gdimensions[d] = _gdimensions[d] / 2; // Remove a checkerboard
         }
         _ldimensions[d] = _gdimensions[d] / _processors[d];
+        assert(_ldimensions[d] * _processors[d] == _gdimensions[d]);
         _lstart[d] = _processor_coor[d] * _ldimensions[d];
         _lend[d] = _processor_coor[d] * _ldimensions[d] + _ldimensions[d] - 1;
 
         // Use a reduced simd grid
         _simd_layout[d] = simd_layout[d];
-	_rdimensions[d]= _ldimensions[d]/_simd_layout[d];
+        _rdimensions[d] = _ldimensions[d] / _simd_layout[d]; // this is not checking if this is integer
+        assert(_rdimensions[d] * _simd_layout[d] == _ldimensions[d]);
         assert(_rdimensions[d] > 0);
 
         // all elements of a simd vector must have same checkerboard.
         // If Ls vectorised, this must still be the case; e.g. dwf rb5d
-	if ( _simd_layout[d]>1 ) {
+        if (_simd_layout[d] > 1)
-	  if ( checker_dim_mask[d] ) { 
+        {
+          if (checker_dim_mask[d])
+          {
             assert((_rdimensions[d] & 0x1) == 0);
           }
         }
@@ -191,15 +198,16 @@ public:
         _isites *= _simd_layout[d];
 
         // Addressing support
-	if ( d==0 ) {
+        if (d == 0)
+        {
           _ostride[d] = 1;
           _istride[d] = 1;
-	} else {
+        }
+        else
+        {
           _ostride[d] = _ostride[d - 1] * _rdimensions[d - 1];
           _istride[d] = _istride[d - 1] * _simd_layout[d - 1];
         }
-
-
       }
 
       ////////////////////////////////////////////////////////////////////////////////////////////
@@ -211,9 +219,11 @@ public:
 
       int block = 1;
       int nblock = 1;
-      for(int d=0;d<_ndimension;d++) nblock*=_rdimensions[d];
+      for (int d = 0; d < _ndimension; d++)
+        nblock *= _rdimensions[d];
 
-      for(int d=0;d<_ndimension;d++){
+      for (int d = 0; d < _ndimension; d++)
+      {
         nblock /= _rdimensions[d];
         _slice_block[d] = block;
         _slice_stride[d] = _ostride[d] * _rdimensions[d];
@@ -225,23 +235,29 @@ public:
       // Create a checkerboard lookup table
       ////////////////////////////////////////////////
       int rvol = 1;
-      for(int d=0;d<_ndimension;d++){
+      for (int d = 0; d < _ndimension; d++)
+      {
         rvol = rvol * _rdimensions[d];
       }
       _checker_board.resize(rvol);
-      for(int osite=0;osite<_osites;osite++){
+      for (int osite = 0; osite < _osites; osite++)
+      {
         _checker_board[osite] = CheckerBoardFromOindex(osite);
       }
-      
     };
+
   protected:
     virtual int oIndex(std::vector<int> &coor)
     {
       int idx = 0;
-      for(int d=0;d<_ndimension;d++) {
+      for (int d = 0; d < _ndimension; d++)
-	if( d==_checker_dim ) {
+      {
+        if (d == _checker_dim)
+        {
           idx += _ostride[d] * ((coor[d] / 2) % _rdimensions[d]);
-	} else {
+        }
+        else
+        {
           idx += _ostride[d] * (coor[d] % _rdimensions[d]);
         }
       }
@@ -251,16 +267,19 @@ protected:
     virtual int iIndex(std::vector<int> &lcoor)
     {
       int idx = 0;
-        for(int d=0;d<_ndimension;d++) {
+      for (int d = 0; d < _ndimension; d++)
-	  if( d==_checker_dim ) {
+      {
+        if (d == _checker_dim)
+        {
           idx += _istride[d] * (lcoor[d] / (2 * _rdimensions[d]));
-	  } else { 
+        }
+        else
+        {
           idx += _istride[d] * (lcoor[d] / _rdimensions[d]);
         }
       }
       return idx;
     }
 };
-
 }
 #endif

lib/communicator/Communicator_base.cc

@@ -26,6 +26,10 @@ Author: Peter Boyle <paboyle@ph.ed.ac.uk>
     *************************************************************************************/
     /*  END LEGAL */
 #include <Grid/GridCore.h>
+#include <fcntl.h>
+#include <unistd.h>
+#include <limits.h>
+#include <sys/mman.h>
 
 namespace Grid {
 
@@ -33,8 +37,11 @@ namespace Grid {
 // Info that is setup once and indept of cartesian layout
 ///////////////////////////////////////////////////////////////
 void *              CartesianCommunicator::ShmCommBuf;
-uint64_t            CartesianCommunicator::MAX_MPI_SHM_BYTES   = 128*1024*1024; 
+uint64_t            CartesianCommunicator::MAX_MPI_SHM_BYTES   = 1024LL*1024LL*1024LL; 
-CartesianCommunicator::CommunicatorPolicy_t  CartesianCommunicator::CommunicatorPolicy= CartesianCommunicator::CommunicatorPolicyConcurrent;
+CartesianCommunicator::CommunicatorPolicy_t  
+CartesianCommunicator::CommunicatorPolicy= CartesianCommunicator::CommunicatorPolicyConcurrent;
+int CartesianCommunicator::nCommThreads = -1;
+int CartesianCommunicator::Hugepages = 0;
 
 /////////////////////////////////
 // Alloc, free shmem region
@@ -89,25 +96,43 @@ void CartesianCommunicator::GlobalSumVector(ComplexD *c,int N)
   GlobalSumVector((double *)c,2*N);
 }
 
-#if !defined( GRID_COMMS_MPI3) && !defined (GRID_COMMS_MPI3L)
+#if !defined( GRID_COMMS_MPI3) 
 
 int                      CartesianCommunicator::NodeCount(void)    { return ProcessorCount();};
 int                      CartesianCommunicator::RankCount(void)    { return ProcessorCount();};
-
+#endif
+#if !defined( GRID_COMMS_MPI3) && !defined (GRID_COMMS_MPIT)
+double CartesianCommunicator::StencilSendToRecvFrom( void *xmit,
+						     int xmit_to_rank,
+						     void *recv,
+						     int recv_from_rank,
+						     int bytes, int dir)
+{
+  std::vector<CommsRequest_t> list;
+  // Discard the "dir"
+  SendToRecvFromBegin   (list,xmit,xmit_to_rank,recv,recv_from_rank,bytes);
+  SendToRecvFromComplete(list);
+  return 2.0*bytes;
+}
 double CartesianCommunicator::StencilSendToRecvFromBegin(std::vector<CommsRequest_t> &list,
 							 void *xmit,
 							 int xmit_to_rank,
 							 void *recv,
 							 int recv_from_rank,
-						       int bytes)
+							 int bytes, int dir)
 {
+  // Discard the "dir"
   SendToRecvFromBegin(list,xmit,xmit_to_rank,recv,recv_from_rank,bytes);
   return 2.0*bytes;
 }
-void CartesianCommunicator::StencilSendToRecvFromComplete(std::vector<CommsRequest_t> &waitall)
+void CartesianCommunicator::StencilSendToRecvFromComplete(std::vector<CommsRequest_t> &waitall,int dir)
 {
   SendToRecvFromComplete(waitall);
 }
+#endif
+
+#if !defined( GRID_COMMS_MPI3) 
+
 void CartesianCommunicator::StencilBarrier(void){};
 
 commVector<uint8_t> CartesianCommunicator::ShmBufStorageVector;
@@ -121,8 +146,25 @@ void *CartesianCommunicator::ShmBufferTranslate(int rank,void * local_p) {
   return NULL;
 }
 void CartesianCommunicator::ShmInitGeneric(void){
+#if 1
+
+  int mmap_flag = MAP_SHARED | MAP_ANONYMOUS;
+#ifdef MAP_HUGETLB
+  if ( Hugepages ) mmap_flag |= MAP_HUGETLB;
+#endif
+  ShmCommBuf =(void *) mmap(NULL, MAX_MPI_SHM_BYTES, PROT_READ | PROT_WRITE, mmap_flag, -1, 0); 
+  if (ShmCommBuf == (void *)MAP_FAILED) {
+    perror("mmap failed ");
+    exit(EXIT_FAILURE);  
+  }
+#ifdef MADV_HUGEPAGE
+  if (!Hugepages ) madvise(ShmCommBuf,MAX_MPI_SHM_BYTES,MADV_HUGEPAGE);
+#endif
+#else 
   ShmBufStorageVector.resize(MAX_MPI_SHM_BYTES);
   ShmCommBuf=(void *)&ShmBufStorageVector[0];
+#endif
+  bzero(ShmCommBuf,MAX_MPI_SHM_BYTES);
 }
 
 #endif

lib/communicator/Communicator_base.h

@@ -38,7 +38,7 @@ Author: Peter Boyle <paboyle@ph.ed.ac.uk>
 #ifdef GRID_COMMS_MPI3
 #include <mpi.h>
 #endif
-#ifdef GRID_COMMS_MPI3L
+#ifdef GRID_COMMS_MPIT
 #include <mpi.h>
 #endif
 #ifdef GRID_COMMS_SHMEM
@@ -50,12 +50,24 @@ namespace Grid {
 class CartesianCommunicator {
   public:    
 
-  // 65536 ranks per node adequate for now
+
+  ////////////////////////////////////////////
+  // Isend/Irecv/Wait, or Sendrecv blocking
+  ////////////////////////////////////////////
+  enum CommunicatorPolicy_t { CommunicatorPolicyConcurrent, CommunicatorPolicySequential };
+  static CommunicatorPolicy_t CommunicatorPolicy;
+  static void SetCommunicatorPolicy(CommunicatorPolicy_t policy ) { CommunicatorPolicy = policy; }
+
+  ///////////////////////////////////////////
+  // Up to 65536 ranks per node adequate for now
   // 128MB shared memory for comms enought for 48^4 local vol comms
   // Give external control (command line override?) of this
-
+  ///////////////////////////////////////////
   static const int MAXLOG2RANKSPERNODE = 16;            
   static uint64_t  MAX_MPI_SHM_BYTES;
+  static int       nCommThreads;
+  // use explicit huge pages
+  static int       Hugepages;
 
   // Communicator should know nothing of the physics grid, only processor grid.
   int              _Nprocessors;     // How many in all
@@ -64,14 +76,18 @@ class CartesianCommunicator {
   std::vector<int> _processor_coor;  // linear processor coordinate
   unsigned long _ndimension;
 
-#if defined (GRID_COMMS_MPI) || defined (GRID_COMMS_MPI3) || defined (GRID_COMMS_MPI3L)
+#if defined (GRID_COMMS_MPI) || defined (GRID_COMMS_MPI3) || defined (GRID_COMMS_MPIT)
   static MPI_Comm communicator_world;
+
   MPI_Comm              communicator;
+  std::vector<MPI_Comm> communicator_halo;
+
   typedef MPI_Request CommsRequest_t;
 #else 
   typedef int CommsRequest_t;
 #endif
 
+
   ////////////////////////////////////////////////////////////////////
   // Helper functionality for SHM Windows common to all other impls
   ////////////////////////////////////////////////////////////////////
@@ -117,10 +133,6 @@ class CartesianCommunicator {
   /////////////////////////////////
   static void * ShmCommBuf;
 
-  // Isend/Irecv/Wait, or Sendrecv blocking
-  enum CommunicatorPolicy_t { CommunicatorPolicyConcurrent, CommunicatorPolicySequential };
-  static CommunicatorPolicy_t CommunicatorPolicy;
-  static void SetCommunicatorPolicy(CommunicatorPolicy_t policy ) { CommunicatorPolicy = policy; }
   
   size_t heap_top;
   size_t heap_bytes;
@@ -211,14 +223,21 @@ class CartesianCommunicator {
   
   void SendToRecvFromComplete(std::vector<CommsRequest_t> &waitall);
 
+  double StencilSendToRecvFrom(void *xmit,
+			       int xmit_to_rank,
+			       void *recv,
+			       int recv_from_rank,
+			       int bytes,int dir);
+
   double StencilSendToRecvFromBegin(std::vector<CommsRequest_t> &list,
 				    void *xmit,
 				    int xmit_to_rank,
 				    void *recv,
 				    int recv_from_rank,
-				  int bytes);
+				    int bytes,int dir);
   
-  void StencilSendToRecvFromComplete(std::vector<CommsRequest_t> &waitall);
+  
+  void StencilSendToRecvFromComplete(std::vector<CommsRequest_t> &waitall,int i);
   void StencilBarrier(void);
 
   ////////////////////////////////////////////////////////////

lib/communicator/Communicator_mpi3.cc

@@ -41,9 +41,7 @@ Author: Peter Boyle <paboyle@ph.ed.ac.uk>
 #ifdef HAVE_NUMAIF_H
 #include <numaif.h>
 #endif
-#ifndef SHM_HUGETLB
+
-#define SHM_HUGETLB 04000
-#endif
 
 namespace Grid {
 
@@ -200,7 +198,46 @@ void CartesianCommunicator::Init(int *argc, char ***argv) {
   ShmCommBuf = 0;
   ShmCommBufs.resize(ShmSize);
 
-#if 1
+  ////////////////////////////////////////////////////////////////////////////////////////////
+  // Hugetlbf and others map filesystems as mappable huge pages
+  ////////////////////////////////////////////////////////////////////////////////////////////
+#ifdef GRID_MPI3_SHMMMAP
+  char shm_name [NAME_MAX];
+  for(int r=0;r<ShmSize;r++){
+    
+    size_t size = CartesianCommunicator::MAX_MPI_SHM_BYTES;
+    sprintf(shm_name,GRID_SHM_PATH "/Grid_mpi3_shm_%d_%d",GroupRank,r);
+    //sprintf(shm_name,"/var/lib/hugetlbfs/group/wheel/pagesize-2MB/" "Grid_mpi3_shm_%d_%d",GroupRank,r);
+    //    printf("Opening file %s \n",shm_name);
+    int fd=open(shm_name,O_RDWR|O_CREAT,0666);
+    if ( fd == -1) { 
+      printf("open %s failed\n",shm_name);
+      perror("open hugetlbfs");
+      exit(0);
+    }
+    int mmap_flag = MAP_SHARED ;
+#ifdef MAP_POPULATE    
+    mmap_flag|=MAP_POPULATE;
+#endif
+#ifdef MAP_HUGETLB
+    if ( Hugepages ) mmap_flag |= MAP_HUGETLB;
+#endif
+    void *ptr = (void *) mmap(NULL, MAX_MPI_SHM_BYTES, PROT_READ | PROT_WRITE, mmap_flag,fd, 0); 
+    if ( ptr == (void *)MAP_FAILED ) {    
+      printf("mmap %s failed\n",shm_name);
+      perror("failed mmap");      assert(0);    
+    }
+    assert(((uint64_t)ptr&0x3F)==0);
+    ShmCommBufs[r] =ptr;
+    
+  }
+#endif
+  ////////////////////////////////////////////////////////////////////////////////////////////
+  // POSIX SHMOPEN ; as far as I know Linux does not allow EXPLICIT HugePages with this case
+  // tmpfs (Larry Meadows says) does not support explicit huge page, and this is used for 
+  // the posix shm virtual file system
+  ////////////////////////////////////////////////////////////////////////////////////////////
+#ifdef GRID_MPI3_SHMOPEN
   char shm_name [NAME_MAX];
   if ( ShmRank == 0 ) {
     for(int r=0;r<ShmSize;r++){
@@ -214,12 +251,21 @@ void CartesianCommunicator::Init(int *argc, char ***argv) {
       if ( fd < 0 ) {	perror("failed shm_open");	assert(0);      }
       ftruncate(fd, size);
       
-      void * ptr =  mmap(NULL,size, PROT_READ | PROT_WRITE, MAP_SHARED, fd, 0);
+      int mmap_flag = MAP_SHARED;
-      if ( ptr == MAP_FAILED ) {       perror("failed mmap");      assert(0);    }
+#ifdef MAP_POPULATE 
+      mmap_flag |= MAP_POPULATE;
+#endif
+#ifdef MAP_HUGETLB
+      if (Hugepages) mmap_flag |= MAP_HUGETLB;
+#endif
+      void * ptr =  mmap(NULL,size, PROT_READ | PROT_WRITE, mmap_flag, fd, 0);
+
+      if ( ptr == (void * )MAP_FAILED ) {       perror("failed mmap");      assert(0);    }
       assert(((uint64_t)ptr&0x3F)==0);
 
-      // Try to force numa domain on the shm segment if we have numaif.h
+// Experiments; Experiments; Try to force numa domain on the shm segment if we have numaif.h
-#ifdef HAVE_NUMAIF_H
+#if 0
+//#ifdef HAVE_NUMAIF_H
 	int status;
 	int flags=MPOL_MF_MOVE;
 #ifdef KNL
@@ -258,23 +304,34 @@ void CartesianCommunicator::Init(int *argc, char ***argv) {
       ShmCommBufs[r] =ptr;
     }
   }
-
+#endif
-#else
+  ////////////////////////////////////////////////////////////////////////////////////////////
+  // SHMGET SHMAT and SHM_HUGETLB flag
+  ////////////////////////////////////////////////////////////////////////////////////////////
+#ifdef GRID_MPI3_SHMGET
   std::vector<int> shmids(ShmSize);
 
   if ( ShmRank == 0 ) {
     for(int r=0;r<ShmSize;r++){
       size_t size = CartesianCommunicator::MAX_MPI_SHM_BYTES;
-      key_t key   = 0x4545 + r;
+      key_t key   = IPC_PRIVATE;
-      if ((shmids[r]= shmget(key,size, SHM_HUGETLB | IPC_CREAT | SHM_R | SHM_W)) < 0) {
+      int flags = IPC_CREAT | SHM_R | SHM_W;
+#ifdef SHM_HUGETLB
+      if (Hugepages) flags|=SHM_HUGETLB;
+#endif
+      if ((shmids[r]= shmget(key,size, flags)) ==-1) {
 	int errsv = errno;
 	printf("Errno %d\n",errsv);
+	printf("key   %d\n",key);
+	printf("size  %lld\n",size);
+	printf("flags %d\n",flags);
 	perror("shmget");
 	exit(1);
-      }
+      } else { 
 	printf("shmid: 0x%x\n", shmids[r]);
       }
     }
+  }
   MPI_Barrier(ShmComm);
   MPI_Bcast(&shmids[0],ShmSize*sizeof(int),MPI_BYTE,0,ShmComm);
   MPI_Barrier(ShmComm);
@@ -397,8 +454,14 @@ CartesianCommunicator::CartesianCommunicator(const std::vector<int> &processors)
 { 
   int ierr;
   communicator=communicator_world;
+
   _ndimension = processors.size();
 
+  communicator_halo.resize (2*_ndimension);
+  for(int i=0;i<_ndimension*2;i++){
+    MPI_Comm_dup(communicator,&communicator_halo[i]);
+  }
+
   ////////////////////////////////////////////////////////////////
   // Assert power of two shm_size.
   ////////////////////////////////////////////////////////////////
@@ -621,13 +684,27 @@ void CartesianCommunicator::SendToRecvFromBegin(std::vector<CommsRequest_t> &lis
   }
 }
 
+double CartesianCommunicator::StencilSendToRecvFrom( void *xmit,
+						     int dest,
+						     void *recv,
+						     int from,
+						     int bytes,int dir)
+{
+  std::vector<CommsRequest_t> list;
+  double offbytes = StencilSendToRecvFromBegin(list,xmit,dest,recv,from,bytes,dir);
+  StencilSendToRecvFromComplete(list,dir);
+  return offbytes;
+}
+
 double CartesianCommunicator::StencilSendToRecvFromBegin(std::vector<CommsRequest_t> &list,
 							 void *xmit,
 							 int dest,
 							 void *recv,
 							 int from,
-						       int bytes)
+							 int bytes,int dir)
 {
+  assert(dir < communicator_halo.size());
+
   MPI_Request xrq;
   MPI_Request rrq;
 
@@ -646,26 +723,26 @@ double CartesianCommunicator::StencilSendToRecvFromBegin(std::vector<CommsReques
   gfrom = MPI_UNDEFINED;
 #endif
   if ( gfrom ==MPI_UNDEFINED) {
-    ierr=MPI_Irecv(recv, bytes, MPI_CHAR,from,from,communicator,&rrq);
+    ierr=MPI_Irecv(recv, bytes, MPI_CHAR,from,from,communicator_halo[dir],&rrq);
     assert(ierr==0);
     list.push_back(rrq);
     off_node_bytes+=bytes;
   }
 
   if ( gdest == MPI_UNDEFINED ) {
-    ierr =MPI_Isend(xmit, bytes, MPI_CHAR,dest,_processor,communicator,&xrq);
+    ierr =MPI_Isend(xmit, bytes, MPI_CHAR,dest,_processor,communicator_halo[dir],&xrq);
     assert(ierr==0);
     list.push_back(xrq);
     off_node_bytes+=bytes;
   }
 
   if ( CommunicatorPolicy == CommunicatorPolicySequential ) { 
-    this->StencilSendToRecvFromComplete(list);
+    this->StencilSendToRecvFromComplete(list,dir);
   }
 
   return off_node_bytes;
 }
-void CartesianCommunicator::StencilSendToRecvFromComplete(std::vector<CommsRequest_t> &waitall)
+void CartesianCommunicator::StencilSendToRecvFromComplete(std::vector<CommsRequest_t> &waitall,int dir)
 {
   SendToRecvFromComplete(waitall);
 }

lib/communicator/Communicator_mpit.cc

@@ -0,0 +1,286 @@
+    /*************************************************************************************
+
+    Grid physics library, www.github.com/paboyle/Grid 
+
+    Source file: ./lib/communicator/Communicator_mpi.cc
+
+    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 */
+#include <Grid/GridCore.h>
+#include <Grid/GridQCDcore.h>
+#include <Grid/qcd/action/ActionCore.h>
+#include <mpi.h>
+
+namespace Grid {
+
+
+///////////////////////////////////////////////////////////////////////////////////////////////////
+// Info that is setup once and indept of cartesian layout
+///////////////////////////////////////////////////////////////////////////////////////////////////
+MPI_Comm CartesianCommunicator::communicator_world;
+
+// Should error check all MPI calls.
+void CartesianCommunicator::Init(int *argc, char ***argv) {
+  int flag;
+  int provided;
+  MPI_Initialized(&flag); // needed to coexist with other libs apparently
+  if ( !flag ) {
+    MPI_Init_thread(argc,argv,MPI_THREAD_MULTIPLE,&provided);
+    if ( provided != MPI_THREAD_MULTIPLE ) {
+      QCD::WilsonKernelsStatic::Comms = QCD::WilsonKernelsStatic::CommsThenCompute;
+    }
+  }
+  MPI_Comm_dup (MPI_COMM_WORLD,&communicator_world);
+  ShmInitGeneric();
+}
+
+CartesianCommunicator::CartesianCommunicator(const std::vector<int> &processors)
+{
+  _ndimension = processors.size();
+  std::vector<int> periodic(_ndimension,1);
+
+  _Nprocessors=1;
+  _processors = processors;
+  _processor_coor.resize(_ndimension);
+  
+  MPI_Cart_create(communicator_world, _ndimension,&_processors[0],&periodic[0],1,&communicator);
+  MPI_Comm_rank(communicator,&_processor);
+  MPI_Cart_coords(communicator,_processor,_ndimension,&_processor_coor[0]);
+
+  for(int i=0;i<_ndimension;i++){
+    _Nprocessors*=_processors[i];
+  }
+
+  communicator_halo.resize (2*_ndimension);
+  for(int i=0;i<_ndimension*2;i++){
+    MPI_Comm_dup(communicator,&communicator_halo[i]);
+  }
+  
+  int Size; 
+  MPI_Comm_size(communicator,&Size);
+  
+  assert(Size==_Nprocessors);
+}
+void CartesianCommunicator::GlobalSum(uint32_t &u){
+  int ierr=MPI_Allreduce(MPI_IN_PLACE,&u,1,MPI_UINT32_T,MPI_SUM,communicator);
+  assert(ierr==0);
+}
+void CartesianCommunicator::GlobalSum(uint64_t &u){
+  int ierr=MPI_Allreduce(MPI_IN_PLACE,&u,1,MPI_UINT64_T,MPI_SUM,communicator);
+  assert(ierr==0);
+}
+void CartesianCommunicator::GlobalXOR(uint32_t &u){
+  int ierr=MPI_Allreduce(MPI_IN_PLACE,&u,1,MPI_UINT32_T,MPI_BXOR,communicator);
+  assert(ierr==0);
+}
+void CartesianCommunicator::GlobalXOR(uint64_t &u){
+  int ierr=MPI_Allreduce(MPI_IN_PLACE,&u,1,MPI_UINT64_T,MPI_BXOR,communicator);
+  assert(ierr==0);
+}
+void CartesianCommunicator::GlobalSum(float &f){
+  int ierr=MPI_Allreduce(MPI_IN_PLACE,&f,1,MPI_FLOAT,MPI_SUM,communicator);
+  assert(ierr==0);
+}
+void CartesianCommunicator::GlobalSumVector(float *f,int N)
+{
+  int ierr=MPI_Allreduce(MPI_IN_PLACE,f,N,MPI_FLOAT,MPI_SUM,communicator);
+  assert(ierr==0);
+}
+void CartesianCommunicator::GlobalSum(double &d)
+{
+  int ierr = MPI_Allreduce(MPI_IN_PLACE,&d,1,MPI_DOUBLE,MPI_SUM,communicator);
+  assert(ierr==0);
+}
+void CartesianCommunicator::GlobalSumVector(double *d,int N)
+{
+  int ierr = MPI_Allreduce(MPI_IN_PLACE,d,N,MPI_DOUBLE,MPI_SUM,communicator);
+  assert(ierr==0);
+}
+void CartesianCommunicator::ShiftedRanks(int dim,int shift,int &source,int &dest)
+{
+  int ierr=MPI_Cart_shift(communicator,dim,shift,&source,&dest);
+  assert(ierr==0);
+}
+int CartesianCommunicator::RankFromProcessorCoor(std::vector<int> &coor)
+{
+  int rank;
+  int ierr=MPI_Cart_rank  (communicator, &coor[0], &rank);
+  assert(ierr==0);
+  return rank;
+}
+void  CartesianCommunicator::ProcessorCoorFromRank(int rank, std::vector<int> &coor)
+{
+  coor.resize(_ndimension);
+  int ierr=MPI_Cart_coords  (communicator, rank, _ndimension,&coor[0]);
+  assert(ierr==0);
+}
+
+// Basic Halo comms primitive
+void CartesianCommunicator::SendToRecvFrom(void *xmit,
+					   int dest,
+					   void *recv,
+					   int from,
+					   int bytes)
+{
+  std::vector<CommsRequest_t> reqs(0);
+  SendToRecvFromBegin(reqs,xmit,dest,recv,from,bytes);
+  SendToRecvFromComplete(reqs);
+}
+
+void CartesianCommunicator::SendRecvPacket(void *xmit,
+					   void *recv,
+					   int sender,
+					   int receiver,
+					   int bytes)
+{
+  MPI_Status stat;
+  assert(sender != receiver);
+  int tag = sender;
+  if ( _processor == sender ) {
+    MPI_Send(xmit, bytes, MPI_CHAR,receiver,tag,communicator);
+  }
+  if ( _processor == receiver ) { 
+    MPI_Recv(recv, bytes, MPI_CHAR,sender,tag,communicator,&stat);
+  }
+}
+
+// Basic Halo comms primitive
+void CartesianCommunicator::SendToRecvFromBegin(std::vector<CommsRequest_t> &list,
+						void *xmit,
+						int dest,
+						void *recv,
+						int from,
+						int bytes)
+{
+  int myrank = _processor;
+  int ierr;
+  if ( CommunicatorPolicy == CommunicatorPolicyConcurrent ) { 
+    MPI_Request xrq;
+    MPI_Request rrq;
+
+    ierr =MPI_Irecv(recv, bytes, MPI_CHAR,from,from,communicator,&rrq);
+    ierr|=MPI_Isend(xmit, bytes, MPI_CHAR,dest,_processor,communicator,&xrq);
+    
+    assert(ierr==0);
+    list.push_back(xrq);
+    list.push_back(rrq);
+  } else { 
+    // Give the CPU to MPI immediately; can use threads to overlap optionally
+    ierr=MPI_Sendrecv(xmit,bytes,MPI_CHAR,dest,myrank,
+		      recv,bytes,MPI_CHAR,from, from,
+		      communicator,MPI_STATUS_IGNORE);
+    assert(ierr==0);
+  }
+}
+void CartesianCommunicator::SendToRecvFromComplete(std::vector<CommsRequest_t> &list)
+{
+  if ( CommunicatorPolicy == CommunicatorPolicyConcurrent ) { 
+    int nreq=list.size();
+    std::vector<MPI_Status> status(nreq);
+    int ierr = MPI_Waitall(nreq,&list[0],&status[0]);
+    assert(ierr==0);
+  }
+}
+
+void CartesianCommunicator::Barrier(void)
+{
+  int ierr = MPI_Barrier(communicator);
+  assert(ierr==0);
+}
+
+void CartesianCommunicator::Broadcast(int root,void* data, int bytes)
+{
+  int ierr=MPI_Bcast(data,
+		     bytes,
+		     MPI_BYTE,
+		     root,
+		     communicator);
+  assert(ierr==0);
+}
+  ///////////////////////////////////////////////////////
+  // Should only be used prior to Grid Init finished.
+  // Check for this?
+  ///////////////////////////////////////////////////////
+int CartesianCommunicator::RankWorld(void){ 
+  int r; 
+  MPI_Comm_rank(communicator_world,&r);
+  return r;
+}
+void CartesianCommunicator::BroadcastWorld(int root,void* data, int bytes)
+{
+  int ierr= MPI_Bcast(data,
+		      bytes,
+		      MPI_BYTE,
+		      root,
+		      communicator_world);
+  assert(ierr==0);
+}
+
+double CartesianCommunicator::StencilSendToRecvFromBegin(std::vector<CommsRequest_t> &list,
+							 void *xmit,
+							 int xmit_to_rank,
+							 void *recv,
+							 int recv_from_rank,
+							 int bytes,int dir)
+{
+  int myrank = _processor;
+  int ierr;
+  assert(dir < communicator_halo.size());
+  
+  //  std::cout << " sending on communicator "<<dir<<" " <<communicator_halo[dir]<<std::endl;
+  // Give the CPU to MPI immediately; can use threads to overlap optionally
+  MPI_Request req[2];
+  MPI_Irecv(recv,bytes,MPI_CHAR,recv_from_rank,recv_from_rank, communicator_halo[dir],&req[1]);
+  MPI_Isend(xmit,bytes,MPI_CHAR,xmit_to_rank  ,myrank        , communicator_halo[dir],&req[0]);
+
+  list.push_back(req[0]);
+  list.push_back(req[1]);
+  return 2.0*bytes;
+}
+void CartesianCommunicator::StencilSendToRecvFromComplete(std::vector<CommsRequest_t> &waitall,int dir)
+{ 
+  int nreq=waitall.size();
+  MPI_Waitall(nreq, &waitall[0], MPI_STATUSES_IGNORE);
+};
+double CartesianCommunicator::StencilSendToRecvFrom(void *xmit,
+						    int xmit_to_rank,
+						    void *recv,
+						    int recv_from_rank,
+						    int bytes,int dir)
+{
+  int myrank = _processor;
+  int ierr;
+  assert(dir < communicator_halo.size());
+  
+  //  std::cout << " sending on communicator "<<dir<<" " <<communicator_halo[dir]<<std::endl;
+  // Give the CPU to MPI immediately; can use threads to overlap optionally
+  MPI_Request req[2];
+  MPI_Irecv(recv,bytes,MPI_CHAR,recv_from_rank,recv_from_rank, communicator_halo[dir],&req[1]);
+  MPI_Isend(xmit,bytes,MPI_CHAR,xmit_to_rank  ,myrank        , communicator_halo[dir],&req[0]);
+  MPI_Waitall(2, req, MPI_STATUSES_IGNORE);
+  return 2.0*bytes;
+}
+
+
+
+}
+

lib/cshift/Cshift.h

@@ -42,7 +42,7 @@ Author: Peter Boyle <paboyle@ph.ed.ac.uk>
 #include <Grid/cshift/Cshift_mpi.h>
 #endif 
 
-#ifdef GRID_COMMS_MPI3L
+#ifdef GRID_COMMS_MPIT
 #include <Grid/cshift/Cshift_mpi.h>
 #endif 
 

lib/lattice/Lattice_reduction.h

@@ -369,6 +369,7 @@ static void sliceMaddVector(Lattice<vobj> &R,std::vector<RealD> &a,const Lattice
   }
 };
 
+/*
 inline GridBase         *makeSubSliceGrid(const GridBase *BlockSolverGrid,int Orthog)
 {
   int NN    = BlockSolverGrid->_ndimension;
@@ -387,6 +388,7 @@ inline GridBase         *makeSubSliceGrid(const GridBase *BlockSolverGrid,int Or
   }
   return (GridBase *)new GridCartesian(latt_phys,simd_phys,mpi_phys); 
 }
+*/
 
 template<class vobj>
 static void sliceMaddMatrix (Lattice<vobj> &R,Eigen::MatrixXcd &aa,const Lattice<vobj> &X,const Lattice<vobj> &Y,int Orthog,RealD scale=1.0) 
@@ -398,14 +400,15 @@ static void sliceMaddMatrix (Lattice<vobj> &R,Eigen::MatrixXcd &aa,const Lattice
   int Nblock = X._grid->GlobalDimensions()[Orthog];
 
   GridBase *FullGrid  = X._grid;
-  GridBase *SliceGrid = makeSubSliceGrid(FullGrid,Orthog);
+  //  GridBase *SliceGrid = makeSubSliceGrid(FullGrid,Orthog);
 
-  Lattice<vobj> Xslice(SliceGrid);
+  //  Lattice<vobj> Xslice(SliceGrid);
-  Lattice<vobj> Rslice(SliceGrid);
+  //  Lattice<vobj> Rslice(SliceGrid);
 
   assert( FullGrid->_simd_layout[Orthog]==1);
   int nh =  FullGrid->_ndimension;
-  int nl = SliceGrid->_ndimension;
+  //  int nl = SliceGrid->_ndimension;
+  int nl = nh-1;
 
   //FIXME package in a convenient iterator
   //Should loop over a plane orthogonal to direction "Orthog"
@@ -448,14 +451,14 @@ static void sliceMulMatrix (Lattice<vobj> &R,Eigen::MatrixXcd &aa,const Lattice<
   int Nblock = X._grid->GlobalDimensions()[Orthog];
 
   GridBase *FullGrid  = X._grid;
-  GridBase *SliceGrid = makeSubSliceGrid(FullGrid,Orthog);
+  //  GridBase *SliceGrid = makeSubSliceGrid(FullGrid,Orthog);
-
+  //  Lattice<vobj> Xslice(SliceGrid);
-  Lattice<vobj> Xslice(SliceGrid);
+  //  Lattice<vobj> Rslice(SliceGrid);
-  Lattice<vobj> Rslice(SliceGrid);
 
   assert( FullGrid->_simd_layout[Orthog]==1);
   int nh =  FullGrid->_ndimension;
-  int nl = SliceGrid->_ndimension;
+  //  int nl = SliceGrid->_ndimension;
+  int nl=1;
 
   //FIXME package in a convenient iterator
   //Should loop over a plane orthogonal to direction "Orthog"
@@ -498,18 +501,19 @@ static void sliceInnerProductMatrix(  Eigen::MatrixXcd &mat, const Lattice<vobj>
   typedef typename vobj::vector_type vector_type;
   
   GridBase *FullGrid  = lhs._grid;
-  GridBase *SliceGrid = makeSubSliceGrid(FullGrid,Orthog);
+  //  GridBase *SliceGrid = makeSubSliceGrid(FullGrid,Orthog);
   
   int Nblock = FullGrid->GlobalDimensions()[Orthog];
   
-  Lattice<vobj> Lslice(SliceGrid);
+  //  Lattice<vobj> Lslice(SliceGrid);
-  Lattice<vobj> Rslice(SliceGrid);
+  //  Lattice<vobj> Rslice(SliceGrid);
   
   mat = Eigen::MatrixXcd::Zero(Nblock,Nblock);
 
   assert( FullGrid->_simd_layout[Orthog]==1);
   int nh =  FullGrid->_ndimension;
-  int nl = SliceGrid->_ndimension;
+  //  int nl = SliceGrid->_ndimension;
+  int nl = nh-1;
 
   //FIXME package in a convenient iterator
   //Should loop over a plane orthogonal to direction "Orthog"
@@ -550,6 +554,14 @@ static void sliceInnerProductMatrix(  Eigen::MatrixXcd &mat, const Lattice<vobj>
       mat += mat_thread;
     }  
   }
+
+  for(int i=0;i<Nblock;i++){
+  for(int j=0;j<Nblock;j++){
+    ComplexD sum = mat(i,j);
+    FullGrid->GlobalSum(sum);
+    mat(i,j)=sum;
+  }}
+
   return;
 }
 

lib/log/Log.cc

@@ -95,7 +95,7 @@ void GridLogConfigure(std::vector<std::string> &logstreams) {
 ////////////////////////////////////////////////////////////
 void Grid_quiesce_nodes(void) {
   int me = 0;
-#if defined(GRID_COMMS_MPI) || defined(GRID_COMMS_MPI3) || defined(GRID_COMMS_MPI3L)
+#if defined(GRID_COMMS_MPI) || defined(GRID_COMMS_MPI3) || defined(GRID_COMMS_MPIT)
   MPI_Comm_rank(MPI_COMM_WORLD, &me);
 #endif
 #ifdef GRID_COMMS_SHMEM

lib/parallelIO/BinaryIO.h

@@ -29,7 +29,7 @@
 #ifndef GRID_BINARY_IO_H
 #define GRID_BINARY_IO_H
 
-#if defined(GRID_COMMS_MPI) || defined(GRID_COMMS_MPI3) 
+#if defined(GRID_COMMS_MPI) || defined(GRID_COMMS_MPI3) || defined(GRID_COMMS_MPIT) 
 #define USE_MPI_IO
 #else
 #undef  USE_MPI_IO
@@ -99,13 +99,14 @@ class BinaryIO {
     NerscChecksum(grid,scalardata,nersc_csum);
   }
 
-  template<class fobj> static inline void NerscChecksum(GridBase *grid,std::vector<fobj> &fbuf,uint32_t &nersc_csum)
+  template <class fobj>
+  static inline void NerscChecksum(GridBase *grid, std::vector<fobj> &fbuf, uint32_t &nersc_csum)
   {
     const uint64_t size32 = sizeof(fobj) / sizeof(uint32_t);
 
-
     uint64_t lsites = grid->lSites();
-    if (fbuf.size()==1) {
+    if (fbuf.size() == 1)
+    {
       lsites = 1;
     }
 
@@ -114,9 +115,11 @@ class BinaryIO {
       uint32_t nersc_csum_thr = 0;
 
       #pragma omp for
-      for(uint64_t local_site=0;local_site<lsites;local_site++){
+      for (uint64_t local_site = 0; local_site < lsites; local_site++)
+      {
         uint32_t *site_buf = (uint32_t *)&fbuf[local_site];
-	for(uint64_t j=0;j<size32;j++){
+        for (uint64_t j = 0; j < size32; j++)
+        {
           nersc_csum_thr = nersc_csum_thr + site_buf[j];
         }
       }
@@ -127,6 +130,7 @@ class BinaryIO {
       }
     }
   }
+
   template<class fobj> static inline void ScidacChecksum(GridBase *grid,std::vector<fobj> &fbuf,uint32_t &scidac_csuma,uint32_t &scidac_csumb)
   {
     const uint64_t size32 = sizeof(fobj)/sizeof(uint32_t);
@@ -367,12 +371,16 @@ class BinaryIO {
                   << iodata.size() * sizeof(fobj) << " bytes" << std::endl;
         std::ifstream fin;
         fin.open(file, std::ios::binary | std::ios::in);
-	if ( control & BINARYIO_MASTER_APPEND )  {
+        if (control & BINARYIO_MASTER_APPEND)
+        {
           fin.seekg(-sizeof(fobj), fin.end);
-	} else { 
+        }
+        else
+        {
           fin.seekg(offset + myrank * lsites * sizeof(fobj));
         }
-	fin.read((char *)&iodata[0],iodata.size()*sizeof(fobj));assert( fin.fail()==0);
+        fin.read((char *)&iodata[0], iodata.size() * sizeof(fobj));
+        assert(fin.fail() == 0);
         fin.close();
       }
       timer.Stop();
@@ -406,9 +414,29 @@ class BinaryIO {
       if ( (control & BINARYIO_LEXICOGRAPHIC) && (nrank > 1) ) {
 #ifdef USE_MPI_IO
         std::cout << GridLogMessage << "MPI write I/O " << file << std::endl;
-	ierr=MPI_File_open(grid->communicator,(char *) file.c_str(), MPI_MODE_RDWR|MPI_MODE_CREATE,MPI_INFO_NULL, &fh); assert(ierr==0);
+        ierr = MPI_File_open(grid->communicator, (char *)file.c_str(), MPI_MODE_RDWR | MPI_MODE_CREATE, MPI_INFO_NULL, &fh);
-	ierr=MPI_File_set_view(fh, disp, mpiObject, fileArray, "native", MPI_INFO_NULL);                        assert(ierr==0);
+        std::cout << GridLogMessage << "Checking for errors" << std::endl;
-	ierr=MPI_File_write_all(fh, &iodata[0], 1, localArray, &status);                                        assert(ierr==0);
+        if (ierr != MPI_SUCCESS)
+        {
+          char error_string[BUFSIZ];
+          int length_of_error_string, error_class;
+
+          MPI_Error_class(ierr, &error_class);
+          MPI_Error_string(error_class, error_string, &length_of_error_string);
+          fprintf(stderr, "%3d: %s\n", myrank, error_string);
+          MPI_Error_string(ierr, error_string, &length_of_error_string);
+          fprintf(stderr, "%3d: %s\n", myrank, error_string);
+          MPI_Abort(MPI_COMM_WORLD, 1); //assert(ierr == 0);
+        }
+
+        std::cout << GridLogDebug << "MPI read I/O set view " << file << std::endl;
+        ierr = MPI_File_set_view(fh, disp, mpiObject, fileArray, "native", MPI_INFO_NULL);
+        assert(ierr == 0);
+
+        std::cout << GridLogDebug << "MPI read I/O write all " << file << std::endl;
+        ierr = MPI_File_write_all(fh, &iodata[0], 1, localArray, &status);
+        assert(ierr == 0);
+
         MPI_File_close(&fh);
         MPI_Type_free(&fileArray);
         MPI_Type_free(&localArray);
@@ -416,15 +444,43 @@ class BinaryIO {
 	assert(0);
 #endif
       } else { 
-	std::ofstream fout; fout.open(file,std::ios::binary|std::ios::out|std::ios::in);
+        
+	std::ofstream fout; 
+  fout.exceptions ( std::fstream::failbit | std::fstream::badbit );
+  try {
+    fout.open(file,std::ios::binary|std::ios::out|std::ios::in);
+  } catch (const std::fstream::failure& exc) {
+    std::cout << GridLogError << "Error in opening the file " << file << " for output" <<std::endl;
+    std::cout << GridLogError << "Exception description: " << exc.what() << std::endl;
+    std::cout << GridLogError << "Probable cause: wrong path, inaccessible location "<< std::endl;
+    #ifdef USE_MPI_IO
+    MPI_Abort(MPI_COMM_WORLD,1);
+    #else
+    exit(1);
+    #endif
+  }
 	std::cout << GridLogMessage<< "C++ write I/O "<< file<<" : "
 		        << iodata.size()*sizeof(fobj)<<" bytes"<<std::endl;
+	
   if ( control & BINARYIO_MASTER_APPEND )  {
 	  fout.seekp(0,fout.end);
 	} else {
 	  fout.seekp(offset+myrank*lsites*sizeof(fobj));
 	}
-	fout.write((char *)&iodata[0],iodata.size()*sizeof(fobj));assert( fout.fail()==0);
+  
+  try {
+  	fout.write((char *)&iodata[0],iodata.size()*sizeof(fobj));//assert( fout.fail()==0);
+  }
+  catch (const std::fstream::failure& exc) {
+    std::cout << "Exception in writing file " << file << std::endl;
+    std::cout << GridLogError << "Exception description: "<< exc.what() << std::endl;
+    #ifdef USE_MPI_IO
+    MPI_Abort(MPI_COMM_WORLD,1);
+    #else
+    exit(1);
+    #endif
+  }
+
 	fout.close();
   }
   timer.Stop();
@@ -442,12 +498,15 @@ class BinaryIO {
     //////////////////////////////////////////////////////////////////////////////
     // Safety check
     //////////////////////////////////////////////////////////////////////////////
+    // if the data size is 1 we do not want to sum over the MPI ranks
+    if (iodata.size() != 1){
       grid->Barrier();
       grid->GlobalSum(nersc_csum);
       grid->GlobalXOR(scidac_csuma);
       grid->GlobalXOR(scidac_csumb);
       grid->Barrier();
     }
+  }
 
   /////////////////////////////////////////////////////////////////////////////
   // Read a Lattice of object
@@ -546,9 +605,9 @@ class BinaryIO {
     int gsites = grid->gSites();
     int lsites = grid->lSites();
 
-    uint32_t nersc_csum_tmp;
+    uint32_t nersc_csum_tmp   = 0;
-    uint32_t scidac_csuma_tmp;
+    uint32_t scidac_csuma_tmp = 0;
-    uint32_t scidac_csumb_tmp;
+    uint32_t scidac_csumb_tmp = 0;
 
     GridStopWatch timer;
 

lib/qcd/action/fermion/CayleyFermion5D.cc

@@ -414,7 +414,7 @@ void CayleyFermion5D<Impl>::SetCoefficientsInternal(RealD zolo_hi,std::vector<Co
   for(int i=0; i < Ls; i++){
     as[i] = 1.0;
     omega[i] = gamma[i]*zolo_hi; //NB reciprocal relative to Chroma NEF code
-    //    assert(fabs(omega[i])>0.0);
+    assert(omega[i]!=Coeff_t(0.0));
     bs[i] = 0.5*(bpc/omega[i] + bmc);
     cs[i] = 0.5*(bpc/omega[i] - bmc);
   }
@@ -429,7 +429,7 @@ void CayleyFermion5D<Impl>::SetCoefficientsInternal(RealD zolo_hi,std::vector<Co
   
   for(int i=0;i<Ls;i++){
     bee[i]=as[i]*(bs[i]*(4.0-this->M5) +1.0);     
-    //    assert(fabs(bee[i])>0.0);
+    assert(bee[i]!=Coeff_t(0.0));
     cee[i]=as[i]*(1.0-cs[i]*(4.0-this->M5));
     beo[i]=as[i]*bs[i];
     ceo[i]=-as[i]*cs[i];
@@ -456,10 +456,16 @@ void CayleyFermion5D<Impl>::SetCoefficientsInternal(RealD zolo_hi,std::vector<Co
     
     if ( i < Ls-1 ) {
 
+      assert(bee[i]!=Coeff_t(0.0));
+      assert(bee[0]!=Coeff_t(0.0));
+      
       lee[i] =-cee[i+1]/bee[i]; // sub-diag entry on the ith column
       
       leem[i]=mass*cee[Ls-1]/bee[0];
-      for(int j=0;j<i;j++)  leem[i]*= aee[j]/bee[j+1];
+      for(int j=0;j<i;j++) {
+	assert(bee[j+1]!=Coeff_t(0.0));
+	leem[i]*= aee[j]/bee[j+1];
+      }
       
       uee[i] =-aee[i]/bee[i];   // up-diag entry on the ith row
       
@@ -478,7 +484,7 @@ void CayleyFermion5D<Impl>::SetCoefficientsInternal(RealD zolo_hi,std::vector<Co
   { 
     Coeff_t delta_d=mass*cee[Ls-1];
     for(int j=0;j<Ls-1;j++) {
-      //      assert(fabs(bee[j])>0.0);
+      assert(bee[j] != Coeff_t(0.0));
       delta_d *= cee[j]/bee[j];
     }
     dee[Ls-1] += delta_d;

lib/qcd/action/fermion/ImprovedStaggeredFermion5D.cc

@@ -230,8 +230,15 @@ void ImprovedStaggeredFermion5D<Impl>::DhopInternal(StencilImpl & st, LebesgueOr
 {
   Compressor compressor;
   int LLs = in._grid->_rdimensions[0];
-  st.HaloExchange(in,compressor);
 
+
+
+  DhopTotalTime -= usecond();
+  DhopCommTime -= usecond();
+  st.HaloExchange(in,compressor);
+  DhopCommTime += usecond();
+  
+  DhopComputeTime -= usecond();
   // Dhop takes the 4d grid from U, and makes a 5d index for fermion
   if (dag == DaggerYes) {
     parallel_for (int ss = 0; ss < U._grid->oSites(); ss++) {
@@ -244,12 +251,15 @@ void ImprovedStaggeredFermion5D<Impl>::DhopInternal(StencilImpl & st, LebesgueOr
 	Kernels::DhopSite(st,lo,U,UUU,st.CommBuf(),LLs,sU,in,out);
     }
   }
+  DhopComputeTime += usecond();
+  DhopTotalTime   += usecond();
 }
 
 
 template<class Impl>
 void ImprovedStaggeredFermion5D<Impl>::DhopOE(const FermionField &in, FermionField &out,int dag)
 {
+  DhopCalls+=1;
   conformable(in._grid,FermionRedBlackGrid());    // verifies half grid
   conformable(in._grid,out._grid); // drops the cb check
 
@@ -261,6 +271,7 @@ void ImprovedStaggeredFermion5D<Impl>::DhopOE(const FermionField &in, FermionFie
 template<class Impl>
 void ImprovedStaggeredFermion5D<Impl>::DhopEO(const FermionField &in, FermionField &out,int dag)
 {
+  DhopCalls+=1;
   conformable(in._grid,FermionRedBlackGrid());    // verifies half grid
   conformable(in._grid,out._grid); // drops the cb check
 
@@ -272,6 +283,7 @@ void ImprovedStaggeredFermion5D<Impl>::DhopEO(const FermionField &in, FermionFie
 template<class Impl>
 void ImprovedStaggeredFermion5D<Impl>::Dhop(const FermionField &in, FermionField &out,int dag)
 {
+  DhopCalls+=2;
   conformable(in._grid,FermionGrid()); // verifies full grid
   conformable(in._grid,out._grid);
 
@@ -280,6 +292,54 @@ void ImprovedStaggeredFermion5D<Impl>::Dhop(const FermionField &in, FermionField
   DhopInternal(Stencil,Lebesgue,Umu,UUUmu,in,out,dag);
 }
 
+template<class Impl>
+void ImprovedStaggeredFermion5D<Impl>::Report(void) 
+{
+  std::vector<int> latt = GridDefaultLatt();          
+  RealD volume = Ls;  for(int mu=0;mu<Nd;mu++) volume=volume*latt[mu];
+  RealD NP = _FourDimGrid->_Nprocessors;
+  RealD NN = _FourDimGrid->NodeCount();
+
+  std::cout << GridLogMessage << "#### Dhop calls report " << std::endl;
+
+  std::cout << GridLogMessage << "ImprovedStaggeredFermion5D Number of DhopEO Calls   : " 
+	    << DhopCalls   << std::endl;
+  std::cout << GridLogMessage << "ImprovedStaggeredFermion5D TotalTime   /Calls       : " 
+	    << DhopTotalTime   / DhopCalls << " us" << std::endl;
+  std::cout << GridLogMessage << "ImprovedStaggeredFermion5D CommTime    /Calls       : " 
+	    << DhopCommTime    / DhopCalls << " us" << std::endl;
+  std::cout << GridLogMessage << "ImprovedStaggeredFermion5D ComputeTime/Calls        : " 
+	    << DhopComputeTime / DhopCalls << " us" << std::endl;
+
+  // Average the compute time
+  _FourDimGrid->GlobalSum(DhopComputeTime);
+  DhopComputeTime/=NP;
+
+  RealD mflops = 1154*volume*DhopCalls/DhopComputeTime/2; // 2 for red black counting
+  std::cout << GridLogMessage << "Average mflops/s per call                : " << mflops << std::endl;
+  std::cout << GridLogMessage << "Average mflops/s per call per rank       : " << mflops/NP << std::endl;
+  std::cout << GridLogMessage << "Average mflops/s per call per node       : " << mflops/NN << std::endl;
+  
+  RealD Fullmflops = 1154*volume*DhopCalls/(DhopTotalTime)/2; // 2 for red black counting
+  std::cout << GridLogMessage << "Average mflops/s per call (full)         : " << Fullmflops << std::endl;
+  std::cout << GridLogMessage << "Average mflops/s per call per rank (full): " << Fullmflops/NP << std::endl;
+  std::cout << GridLogMessage << "Average mflops/s per call per node (full): " << Fullmflops/NN << std::endl;
+
+  std::cout << GridLogMessage << "ImprovedStaggeredFermion5D Stencil"    <<std::endl;  Stencil.Report();
+  std::cout << GridLogMessage << "ImprovedStaggeredFermion5D StencilEven"<<std::endl;  StencilEven.Report();
+  std::cout << GridLogMessage << "ImprovedStaggeredFermion5D StencilOdd" <<std::endl;  StencilOdd.Report();
+}
+template<class Impl>
+void ImprovedStaggeredFermion5D<Impl>::ZeroCounters(void) 
+{
+  DhopCalls       = 0;
+  DhopTotalTime    = 0;
+  DhopCommTime    = 0;
+  DhopComputeTime = 0;
+  Stencil.ZeroCounters();
+  StencilEven.ZeroCounters();
+  StencilOdd.ZeroCounters();
+}
 
 /////////////////////////////////////////////////////////////////////////
 // Implement the general interface. Here we use SAME mass on all slices

lib/qcd/action/fermion/ImprovedStaggeredFermion5D.h

@@ -55,6 +55,16 @@ namespace QCD {
       FermionField _tmp;
       FermionField &tmp(void) { return _tmp; }
 
+      ////////////////////////////////////////
+      // Performance monitoring
+      ////////////////////////////////////////
+      void Report(void);
+      void ZeroCounters(void);
+      double DhopTotalTime;
+      double DhopCalls;
+      double DhopCommTime;
+      double DhopComputeTime;
+
       ///////////////////////////////////////////////////////////////
       // Implement the abstract base
       ///////////////////////////////////////////////////////////////

lib/qcd/action/fermion/WilsonCompressor.h

@@ -238,7 +238,33 @@ template<typename HCS,typename HS,typename S> using WilsonCompressor = WilsonCom
 template<class vobj,class cobj>
 class WilsonStencil : public CartesianStencil<vobj,cobj> {
 public:
-
+  double timer0;
+  double timer1;
+  double timer2;
+  double timer3;
+  double timer4;
+  double timer5;
+  double timer6;
+  uint64_t callsi;
+  void ZeroCountersi(void)
+  {
+    timer0=0;
+    timer1=0;
+    timer2=0;
+    timer3=0;
+    timer4=0;
+    timer5=0;
+    timer6=0;
+    callsi=0;
+  }
+  void Reporti(int calls)
+  {
+    if ( timer0 ) std::cout << GridLogMessage << " timer0 (HaloGatherOpt) " <<timer0/calls <<std::endl;
+    if ( timer1 ) std::cout << GridLogMessage << " timer1 (Communicate)   " <<timer1/calls <<std::endl;
+    if ( timer2 ) std::cout << GridLogMessage << " timer2 (CommsMerge )   " <<timer2/calls <<std::endl;
+    if ( timer3 ) std::cout << GridLogMessage << " timer3 (commsMergeShm) " <<timer3/calls <<std::endl;
+    if ( timer4 ) std::cout << GridLogMessage << " timer4 " <<timer4 <<std::endl;
+  }
   typedef CartesianCommunicator::CommsRequest_t CommsRequest_t;
 
   std::vector<int> same_node;
@@ -252,6 +278,7 @@ public:
     : CartesianStencil<vobj,cobj> (grid,npoints,checkerboard,directions,distances) ,
     same_node(npoints)
   { 
+    ZeroCountersi();
     surface_list.resize(0);
   };
 
@@ -261,7 +288,6 @@ public:
     // Here we know the distance is 1 for WilsonStencil
     for(int point=0;point<this->_npoints;point++){
       same_node[point] = this->SameNode(point);
-      //      std::cout << " dir " <<point<<" same_node " <<same_node[point]<<std::endl;
     }
     
     for(int site = 0 ;site< vol4;site++){
@@ -282,17 +308,28 @@ public:
   {
     std::vector<std::vector<CommsRequest_t> > reqs;
     this->HaloExchangeOptGather(source,compress);
-    this->CommunicateBegin(reqs);
+    double t1=usecond();
-    this->CommunicateComplete(reqs);
+    // Asynchronous MPI calls multidirectional, Isend etc...
+    //    this->CommunicateBegin(reqs);
+    //    this->CommunicateComplete(reqs);
+    // Non-overlapped directions within a thread. Asynchronous calls except MPI3, threaded up to comm threads ways.
+    this->Communicate();
+    double t2=usecond(); timer1 += t2-t1;
     this->CommsMerge(compress);
+    double t3=usecond(); timer2 += t3-t2;
     this->CommsMergeSHM(compress);
+    double t4=usecond(); timer3 += t4-t3;
   }
   
   template <class compressor>
   void HaloExchangeOptGather(const Lattice<vobj> &source,compressor &compress) 
   {
     this->Prepare();
+    double t0=usecond();
     this->HaloGatherOpt(source,compress);
+    double t1=usecond();
+    timer0 += t1-t0;
+    callsi++;
   }
 
   template <class compressor>
@@ -304,7 +341,9 @@ public:
     typedef typename compressor::SiteHalfSpinor     SiteHalfSpinor;
     typedef typename compressor::SiteHalfCommSpinor SiteHalfCommSpinor;
 
+    this->mpi3synctime_g-=usecond();
     this->_grid->StencilBarrier();
+    this->mpi3synctime_g+=usecond();
 
     assert(source._grid==this->_grid);
     this->halogtime-=usecond();
@@ -323,7 +362,6 @@ public:
     int dag = compress.dag;
     int face_idx=0;
     if ( dag ) { 
-      //	std::cout << " Optimised Dagger compress " <<std::endl;
       assert(same_node[Xp]==this->HaloGatherDir(source,XpCompress,Xp,face_idx));
       assert(same_node[Yp]==this->HaloGatherDir(source,YpCompress,Yp,face_idx));
       assert(same_node[Zp]==this->HaloGatherDir(source,ZpCompress,Zp,face_idx));

lib/qcd/action/fermion/WilsonFermion5D.cc

@@ -123,22 +123,24 @@ WilsonFermion5D<Impl>::WilsonFermion5D(GaugeField &_Umu,
   int vol4;
   vol4=FourDimGrid.oSites();
   Stencil.BuildSurfaceList(LLs,vol4);
+
   vol4=FourDimRedBlackGrid.oSites();
   StencilEven.BuildSurfaceList(LLs,vol4);
    StencilOdd.BuildSurfaceList(LLs,vol4);
 
-  std::cout << GridLogMessage << " SurfaceLists "<< Stencil.surface_list.size()
+   //  std::cout << GridLogMessage << " SurfaceLists "<< Stencil.surface_list.size()
-                       <<" " << StencilEven.surface_list.size()<<std::endl;
+   //                       <<" " << StencilEven.surface_list.size()<<std::endl;
 
 }
      
 template<class Impl>
 void WilsonFermion5D<Impl>::Report(void)
 {
-    std::vector<int> latt = GridDefaultLatt();          
-    RealD volume = Ls;  for(int mu=0;mu<Nd;mu++) volume=volume*latt[mu];
   RealD NP     = _FourDimGrid->_Nprocessors;
   RealD NN     = _FourDimGrid->NodeCount();
+  RealD volume = Ls;  
+  std::vector<int> latt = _FourDimGrid->GlobalDimensions();
+  for(int mu=0;mu<Nd;mu++) volume=volume*latt[mu];
 
   if ( DhopCalls > 0 ) {
     std::cout << GridLogMessage << "#### Dhop calls report " << std::endl;
@@ -184,6 +186,11 @@ void WilsonFermion5D<Impl>::Report(void)
     std::cout << GridLogMessage << "WilsonFermion5D StencilEven"<<std::endl;  StencilEven.Report();
     std::cout << GridLogMessage << "WilsonFermion5D StencilOdd" <<std::endl;  StencilOdd.Report();
   }
+  if ( DhopCalls > 0){
+    std::cout << GridLogMessage << "WilsonFermion5D Stencil     Reporti()"    <<std::endl;  Stencil.Reporti(DhopCalls);
+    std::cout << GridLogMessage << "WilsonFermion5D StencilEven Reporti()"<<std::endl;  StencilEven.Reporti(DhopCalls);
+    std::cout << GridLogMessage << "WilsonFermion5D StencilOdd  Reporti()" <<std::endl;  StencilOdd.Reporti(DhopCalls);
+  }
 }
 
 template<class Impl>
@@ -203,6 +210,9 @@ void WilsonFermion5D<Impl>::ZeroCounters(void) {
   Stencil.ZeroCounters();
   StencilEven.ZeroCounters();
   StencilOdd.ZeroCounters();
+  Stencil.ZeroCountersi();
+  StencilEven.ZeroCountersi();
+  StencilOdd.ZeroCountersi();
 }
 
 
@@ -379,7 +389,6 @@ void WilsonFermion5D<Impl>::DhopInternalOverlappedComms(StencilImpl & st, Lebesg
 {
 #ifdef GRID_OMP
   //  assert((dag==DaggerNo) ||(dag==DaggerYes));
-  typedef CartesianCommunicator::CommsRequest_t CommsRequest_t;
 
   Compressor compressor(dag);
 
@@ -388,46 +397,70 @@ void WilsonFermion5D<Impl>::DhopInternalOverlappedComms(StencilImpl & st, Lebesg
 
   DhopFaceTime-=usecond();
   st.HaloExchangeOptGather(in,compressor);
-  DhopFaceTime+=usecond();
+  st.CommsMergeSHM(compressor);// Could do this inside parallel region overlapped with comms
-  std::vector<std::vector<CommsRequest_t> > reqs;
-
-  // Rely on async comms; start comms before merge of local data
-  DhopCommTime-=usecond();
-  st.CommunicateBegin(reqs);
-
-  DhopFaceTime-=usecond();
-  st.CommsMergeSHM(compressor);
   DhopFaceTime+=usecond();
 
-  // Perhaps use omp task and region
+  double ctime=0;
-#pragma omp parallel 
+  double ptime=0;
+
+  //////////////////////////////////////////////////////////////////////////////////////////////////////
+  // Ugly explicit thread mapping introduced for OPA reasons.
+  //////////////////////////////////////////////////////////////////////////////////////////////////////
+#pragma omp parallel reduction(max:ctime) reduction(max:ptime)
   { 
+    int tid = omp_get_thread_num();
     int nthreads = omp_get_num_threads();
-    int me = omp_get_thread_num();
+    int ncomms = CartesianCommunicator::nCommThreads;
-    int myoff, mywork;
+    if (ncomms == -1) ncomms = 1;
-
+    assert(nthreads > ncomms);
-    GridThread::GetWork(len,me-1,mywork,myoff,nthreads-1);
+    if (tid >= ncomms) {
-    int sF = LLs * myoff;
+      double start = usecond();
-
+      nthreads -= ncomms;
-    if ( me == 0 ) {
+      int ttid = tid - ncomms;
-      st.CommunicateComplete(reqs);
+      int n = U._grid->oSites();
-      DhopCommTime+=usecond();
+      int chunk = n / nthreads;
+      int rem = n % nthreads;
+      int myblock, myn;
+      if (ttid < rem) {
+	myblock = ttid * chunk + ttid;
+	myn = chunk+1;
       } else {
-      // Interior links in stencil
+	myblock = ttid*chunk + rem;
-      if ( me==1 ) DhopComputeTime-=usecond();
+	myn = chunk;
-      if (dag == DaggerYes) Kernels::DhopSiteDag(st,lo,U,st.CommBuf(),sF,myoff,LLs,mywork,in,out,1,0);
+      }
-      else      	    Kernels::DhopSite(st,lo,U,st.CommBuf(),sF,myoff,LLs,mywork,in,out,1,0);
+      
-      if ( me==1 ) DhopComputeTime+=usecond();
+      // do the compute
+      if (dag == DaggerYes) {
+	for (int ss = myblock; ss < myblock+myn; ++ss) {
+	  int sU = ss;
+	  int sF = LLs * sU;
+	  Kernels::DhopSiteDag(st,lo,U,st.CommBuf(),sF,sU,LLs,1,in,out,1,0);
+	}
+      } else {
+	for (int ss = myblock; ss < myblock+myn; ++ss) {
+	  int sU = ss;
+	  int sF = LLs * sU;
+	  Kernels::DhopSite(st,lo,U,st.CommBuf(),sF,sU,LLs,1,in,out,1,0);
 	}
       }
+	ptime = usecond() - start;
+    }
+    {
+      double start = usecond();
+      st.CommunicateThreaded();
+      ctime = usecond() - start;
+    }
+  }
+  DhopCommTime += ctime;
+  DhopComputeTime+=ptime;
+
+  // First to enter, last to leave timing
+  st.CollateThreads();
 
   DhopFaceTime-=usecond();
   st.CommsMerge(compressor);
   DhopFaceTime+=usecond();
 
-  // Load imbalance alert. Should use dynamic schedule OMP for loop
-  // Perhaps create a list of only those sites with face work, and 
-  // load balance process the list.
   DhopComputeTime2-=usecond();
   if (dag == DaggerYes) {
     int sz=st.surface_list.size();
@@ -448,11 +481,9 @@ void WilsonFermion5D<Impl>::DhopInternalOverlappedComms(StencilImpl & st, Lebesg
 #else 
   assert(0);
 #endif
-
 }
 
 
-
 template<class Impl>
 void WilsonFermion5D<Impl>::DhopInternalSerialComms(StencilImpl & st, LebesgueOrder &lo,
 					 DoubledGaugeField & U,

lib/qcd/hmc/HMCResourceManager.h

@@ -165,7 +165,7 @@ class HMCResourceManager {
   // Grids
   //////////////////////////////////////////////////////////////
 
-  void AddGrid(std::string s, GridModule& M) {
+  void AddGrid(const std::string s, GridModule& M) {
     // Check for name clashes
     auto search = Grids.find(s);
     if (search != Grids.end()) {
@@ -174,14 +174,24 @@ class HMCResourceManager {
       exit(1);
     }
     Grids[s] = std::move(M);
+    std::cout << GridLogMessage << "::::::::::::::::::::::::::::::::::::::::" <<std::endl;
+    std::cout << GridLogMessage << "HMCResourceManager:" << std::endl;
+    std::cout << GridLogMessage << "Created grid set with name '" << s << "' and decomposition for the full cartesian " << std::endl;
+    Grids[s].show_full_decomposition();
+    std::cout << GridLogMessage << "::::::::::::::::::::::::::::::::::::::::" <<std::endl;
   }
 
   // Add a named grid set, 4d shortcut
-  void AddFourDimGrid(std::string s) {
+  void AddFourDimGrid(const std::string s) {
     GridFourDimModule<vComplex> Mod;
     AddGrid(s, Mod);
   }
 
+  // Add a named grid set, 4d shortcut + tweak simd lanes
+  void AddFourDimGrid(const std::string s, const std::vector<int> simd_decomposition) {
+    GridFourDimModule<vComplex> Mod(simd_decomposition);
+    AddGrid(s, Mod);
+  }
 
 
   GridCartesian* GetCartesian(std::string s = "") {

lib/qcd/hmc/HMC_GridModules.h

@@ -43,10 +43,11 @@ public:
   std::string, lattice,
   std::string, mpi);
 
-  std::vector<int> getLattice(){return strToVec<int>(lattice);}
+  std::vector<int> getLattice() const {return strToVec<int>(lattice);}
-  std::vector<int> getMpi()    {return strToVec<int>(mpi);}
+  std::vector<int> getMpi()     const {return strToVec<int>(mpi);}
 
-  void check(){
+
+  void check() const {
     if (getLattice().size() != getMpi().size() ) {
       std::cout << GridLogError
                 << "Error in GridModuleParameters: lattice and mpi dimensions "
@@ -84,6 +85,8 @@ class GridModule {
 
   void set_full(GridCartesian* grid) { grid_.reset(grid); }
   void set_rb(GridRedBlackCartesian* rbgrid) { rbgrid_.reset(rbgrid); }
+  void show_full_decomposition(){ grid_->show_decomposition(); }
+  void show_rb_decomposition(){ rbgrid_->show_decomposition(); }
 
  protected:
   std::unique_ptr<GridCartesian> grid_;
@@ -96,27 +99,68 @@ class GridModule {
 ////////////////////////////////////
 // Note: the space time grid should be out of the QCD namespace
 template <class vector_type>
-class GridFourDimModule : public GridModule {
+class GridFourDimModule : public GridModule
+{
 public:
-  GridFourDimModule() {
+  GridFourDimModule()
+  {
     using namespace QCD;
     set_full(SpaceTimeGrid::makeFourDimGrid(
-        GridDefaultLatt(), GridDefaultSimd(4, vector_type::Nsimd()),
+        GridDefaultLatt(), 
+        GridDefaultSimd(4, vector_type::Nsimd()),
         GridDefaultMpi()));
     set_rb(SpaceTimeGrid::makeFourDimRedBlackGrid(grid_.get()));
   }
 
-  GridFourDimModule(GridModuleParameters Params) {
+  GridFourDimModule(const std::vector<int> tweak_simd)
+  {
+    using namespace QCD;
+    if (tweak_simd.size() != 4)
+    {
+      std::cout << GridLogError
+                << "Error in GridFourDimModule: SIMD size different from 4" 
+                << std::endl;
+      exit(1);
+    }
+
+    // Checks that the product agrees with the expectation
+    int simd_sum = 1;
+    for (auto &n : tweak_simd)
+      simd_sum *= n;
+    std::cout << GridLogDebug << "TweakSIMD: " << tweak_simd << "  Sum: " << simd_sum << std::endl;
+
+    if (simd_sum == vector_type::Nsimd())
+    {
+      set_full(SpaceTimeGrid::makeFourDimGrid(
+          GridDefaultLatt(), 
+          tweak_simd, 
+          GridDefaultMpi()));
+      set_rb(SpaceTimeGrid::makeFourDimRedBlackGrid(grid_.get()));
+    }
+    else
+    {
+      std::cout << GridLogError 
+                << "Error in GridFourDimModule: SIMD lanes must sum to " 
+                << vector_type::Nsimd() 
+                << std::endl;
+    }
+  }
+
+  GridFourDimModule(const GridModuleParameters Params)
+  {
     using namespace QCD;
-    Params.check();
     std::vector<int> lattice_v = Params.getLattice();
     std::vector<int> mpi_v = Params.getMpi();
-    if (lattice_v.size() == 4) {
+    if (lattice_v.size() == 4)
+    {
       set_full(SpaceTimeGrid::makeFourDimGrid(
-          lattice_v, GridDefaultSimd(4, vector_type::Nsimd()),
+          lattice_v, 
+          GridDefaultSimd(4, vector_type::Nsimd()),
           mpi_v));
       set_rb(SpaceTimeGrid::makeFourDimRedBlackGrid(grid_.get()));
-    } else {
+    }
+    else
+    {
       std::cout << GridLogError
                 << "Error in GridFourDimModule: lattice dimension different from 4"
                 << std::endl;

lib/qcd/modules/ObservableModules.h

@@ -84,8 +84,6 @@ class PlaquetteMod: public ObservableModule<PlaquetteLogger<Impl>, NoParameters>
   typedef ObservableModule<PlaquetteLogger<Impl>, NoParameters> ObsBase;
   using ObsBase::ObsBase; // for constructors
 
-
-
   // acquire resource
   virtual void initialize(){
     this->ObservablePtr.reset(new PlaquetteLogger<Impl>());
@@ -94,23 +92,22 @@ class PlaquetteMod: public ObservableModule<PlaquetteLogger<Impl>, NoParameters>
   PlaquetteMod(): ObsBase(NoParameters()){}
 };
 
+
 template < class Impl >
-class TopologicalChargeMod: public ObservableModule<TopologicalCharge<Impl>, NoParameters>{
+class TopologicalChargeMod: public ObservableModule<TopologicalCharge<Impl>, TopologyObsParameters>{
-  typedef ObservableModule<TopologicalCharge<Impl>, NoParameters> ObsBase;
+  typedef ObservableModule<TopologicalCharge<Impl>, TopologyObsParameters> ObsBase;
   using ObsBase::ObsBase; // for constructors
 
-
-
   // acquire resource
   virtual void initialize(){
-    this->ObservablePtr.reset(new TopologicalCharge<Impl>());
+    this->ObservablePtr.reset(new TopologicalCharge<Impl>(this->Par_));
   }
   public:
-  TopologicalChargeMod(): ObsBase(NoParameters()){}
+  TopologicalChargeMod(TopologyObsParameters Par): ObsBase(Par){}
+  TopologicalChargeMod(): ObsBase(){}
 };
 
 
-
 }// QCD temporarily here
 
 

lib/qcd/observables/topological_charge.h

@@ -33,9 +33,45 @@ directory
 namespace Grid {
 namespace QCD {
 
+struct TopologySmearingParameters : Serializable {
+    GRID_SERIALIZABLE_CLASS_MEMBERS(TopologySmearingParameters,
+    int, steps,
+    float, step_size,
+    int, meas_interval,
+    float, maxTau);
+
+    TopologySmearingParameters(int s = 0, float ss = 0.0f, int mi = 0, float mT = 0.0f):
+        steps(s), step_size(ss), meas_interval(mi), maxTau(mT){}
+
+    template < class ReaderClass >
+    TopologySmearingParameters(Reader<ReaderClass>& Reader){
+        read(Reader, "Smearing", *this);  
+    }  
+};
+
+
+
+struct TopologyObsParameters : Serializable {
+    GRID_SERIALIZABLE_CLASS_MEMBERS(TopologyObsParameters,
+      int, interval,
+      bool, do_smearing,
+      TopologySmearingParameters, Smearing);  
+
+    TopologyObsParameters(int interval = 1, bool smearing = false):
+        interval(interval), Smearing(smearing){}
+
+    template <class ReaderClass >
+      TopologyObsParameters(Reader<ReaderClass>& Reader){
+        read(Reader, "TopologyMeasurement", *this);
+  }
+};
+
+
 // this is only defined for a gauge theory
 template <class Impl>
 class TopologicalCharge : public HmcObservable<typename Impl::Field> {
+    TopologyObsParameters Pars;
+
  public:
     // here forces the Impl to be of gauge fields
     // if not the compiler will complain
@@ -44,21 +80,40 @@ class TopologicalCharge : public HmcObservable<typename Impl::Field> {
     // necessary for HmcObservable compatibility
     typedef typename Impl::Field Field;
 
+    TopologicalCharge(int interval = 1, bool do_smearing = false):
+        Pars(interval, do_smearing){}
+    
+    TopologicalCharge(TopologyObsParameters P):Pars(P){
+        std::cout << GridLogDebug << "Creating TopologicalCharge " << std::endl;
+    }
+
     void TrajectoryComplete(int traj,
                             Field &U,
                             GridSerialRNG &sRNG,
                             GridParallelRNG &pRNG) {
 
-    Real q = WilsonLoops<Impl>::TopologicalCharge(U);
+    if (traj%Pars.interval == 0){
-
+        // Smearing
+        Field Usmear = U;
         int def_prec = std::cout.precision();
         
+        if (Pars.do_smearing){
+            // using wilson flow by default here
+            WilsonFlow<PeriodicGimplR> WF(Pars.Smearing.steps, Pars.Smearing.step_size, Pars.Smearing.meas_interval);
+            WF.smear_adaptive(Usmear, U, Pars.Smearing.maxTau);
+            Real T0   = WF.energyDensityPlaquette(Usmear);
+            std::cout << GridLogMessage << std::setprecision(std::numeric_limits<Real>::digits10 + 1)
+                      << "T0                : [ " << traj << " ] "<< T0 << std::endl;
+        }
+
+        Real q    = WilsonLoops<Impl>::TopologicalCharge(Usmear);
         std::cout << GridLogMessage
             << std::setprecision(std::numeric_limits<Real>::digits10 + 1)
             << "Topological Charge: [ " << traj << " ] "<< q << std::endl;
 
         std::cout.precision(def_prec);
         }
+    }
 
 };
 }

lib/qcd/utils/GaugeFix.h

@@ -26,8 +26,10 @@ Author: Peter Boyle <paboyle@ph.ed.ac.uk>
     /*  END LEGAL */
 //#include <Grid/Grid.h>
 
-using namespace Grid;
+#ifndef GRID_QCD_GAUGE_FIX_H
-using namespace Grid::QCD;
+#define GRID_QCD_GAUGE_FIX_H
+namespace Grid {
+namespace QCD {
 
 template <class Gimpl> 
 class FourierAcceleratedGaugeFixer  : public Gimpl {
@@ -186,3 +188,6 @@ class FourierAcceleratedGaugeFixer  : public Gimpl {
   }  
 };
 
+}
+}
+#endif

lib/simd/Grid_neon.h

@@ -82,11 +82,11 @@ namespace Optimization {
       double tmp[2]={a,b};
       return vld1q_f64(tmp);
     }
-    //Real double // N:tbc
+    //Real double
     inline float64x2_t operator()(double a){
       return vdupq_n_f64(a);
     }
-    //Integer // N:tbc
+    //Integer
     inline uint32x4_t operator()(Integer a){
       return vdupq_n_u32(a);
     }
@@ -124,33 +124,32 @@ namespace Optimization {
   // Nils: Vset untested; not used currently in Grid at all;
   // git commit 4a8c4ccfba1d05159348d21a9698028ea847e77b
   struct Vset{
-    // Complex float // N:ok
+    // Complex float
     inline float32x4_t operator()(Grid::ComplexF *a){
       float tmp[4]={a[1].imag(),a[1].real(),a[0].imag(),a[0].real()};
       return vld1q_f32(tmp);
     }
-    // Complex double // N:ok
+    // Complex double
     inline float64x2_t operator()(Grid::ComplexD *a){
       double tmp[2]={a[0].imag(),a[0].real()};
       return vld1q_f64(tmp);
     }
-    // Real float // N:ok
+    // Real float
     inline float32x4_t operator()(float *a){
       float tmp[4]={a[3],a[2],a[1],a[0]};
       return vld1q_f32(tmp);
     }
-    // Real double // N:ok
+    // Real double
     inline float64x2_t operator()(double *a){
       double tmp[2]={a[1],a[0]};
       return vld1q_f64(tmp);
     }
-    // Integer // N:ok
+    // Integer
     inline uint32x4_t operator()(Integer *a){
       return vld1q_dup_u32(a);
     }
   };
 
-  // N:leaving as is
   template <typename Out_type, typename In_type>
   struct Reduce{
     //Need templated class to overload output type
@@ -421,11 +420,6 @@ namespace Optimization {
       }
     }
 
-// working, but no restriction on n
-//    template<int n> static inline float32x4_t tRotate(float32x4_t in){ return vextq_f32(in,in,n); };
-//    template<int n> static inline float64x2_t tRotate(float64x2_t in){ return vextq_f64(in,in,n); };
-
-// restriction on n
     template<int n> static inline float32x4_t tRotate(float32x4_t in){ return vextq_f32(in,in,n%4); };
     template<int n> static inline float64x2_t tRotate(float64x2_t in){ return vextq_f64(in,in,n%2); };
 
@@ -547,7 +541,7 @@ namespace Optimization {
 
 
   //Complex double Reduce
-  template<> // N:by Boyle
+  template<>
   inline Grid::ComplexD Reduce<Grid::ComplexD, float64x2_t>::operator()(float64x2_t in){
     u128d conv; conv.v = in;
     return Grid::ComplexD(conv.f[0],conv.f[1]);
@@ -562,9 +556,7 @@ namespace Optimization {
   //Integer Reduce
   template<>
   inline Integer Reduce<Integer, uint32x4_t>::operator()(uint32x4_t in){
-    // FIXME unimplemented
+    return vaddvq_u32(in);
-    printf("Reduce : Missing integer implementation -> FIX\n");
-    assert(0);
   }
 }
 
@@ -604,3 +596,4 @@ namespace Optimization {
   typedef Optimization::TimesI      TimesISIMD;
 
 }
+

lib/stencil/Stencil.h

@@ -176,6 +176,9 @@ class CartesianStencil { // Stencil runs along coordinate axes only; NO diagonal
   // Timing info; ugly; possibly temporary
   /////////////////////////////////////////
   double commtime;
+  double mpi3synctime;
+  double mpi3synctime_g;
+  double shmmergetime;
   double gathertime;
   double gathermtime;
   double halogtime;
@@ -185,6 +188,10 @@ class CartesianStencil { // Stencil runs along coordinate axes only; NO diagonal
   double splicetime;
   double nosplicetime;
   double calls;
+  std::vector<double> comm_bytes_thr;
+  std::vector<double> comm_time_thr;
+  std::vector<double> comm_enter_thr;
+  std::vector<double> comm_leave_thr;
 
   ////////////////////////////////////////
   // Stencil query
@@ -248,6 +255,57 @@ class CartesianStencil { // Stencil runs along coordinate axes only; NO diagonal
   //////////////////////////////////////////
   // Comms packet queue for asynch thread
   //////////////////////////////////////////
+  void CommunicateThreaded()
+  {
+#ifdef GRID_OMP
+    // must be called in parallel region
+    int mythread = omp_get_thread_num();
+    int nthreads = CartesianCommunicator::nCommThreads;
+#else
+    int mythread = 0;
+    int nthreads = 1;
+#endif
+    if (nthreads == -1) nthreads = 1;
+    if (mythread < nthreads) {
+      comm_enter_thr[mythread] = usecond();
+      for (int i = mythread; i < Packets.size(); i += nthreads) {
+	uint64_t bytes = _grid->StencilSendToRecvFrom(Packets[i].send_buf,
+						      Packets[i].to_rank,
+						      Packets[i].recv_buf,
+						      Packets[i].from_rank,
+						      Packets[i].bytes,i);
+	comm_bytes_thr[mythread] += bytes;
+      }
+      comm_leave_thr[mythread]= usecond();
+      comm_time_thr[mythread] += comm_leave_thr[mythread] - comm_enter_thr[mythread];
+    }
+  }
+  
+  void CollateThreads(void)
+  {
+    int nthreads = CartesianCommunicator::nCommThreads;
+    double first=0.0;
+    double last =0.0;
+
+    for(int t=0;t<nthreads;t++) {
+
+      double t0 = comm_enter_thr[t];
+      double t1 = comm_leave_thr[t];
+      comms_bytes+=comm_bytes_thr[t];
+
+      comm_enter_thr[t] = 0.0;
+      comm_leave_thr[t] = 0.0;
+      comm_time_thr[t]   = 0.0;
+      comm_bytes_thr[t]=0;
+
+      if ( first == 0.0 ) first = t0;                   // first is t0
+      if ( (t0 > 0.0) && ( t0 < first ) ) first = t0;   // min time seen
+
+      if ( t1 > last ) last = t1;                       // max time seen
+      
+    }
+    commtime+= last-first;
+  }
   void CommunicateBegin(std::vector<std::vector<CommsRequest_t> > &reqs)
   {
     reqs.resize(Packets.size());
@@ -258,25 +316,59 @@ class CartesianStencil { // Stencil runs along coordinate axes only; NO diagonal
 						     Packets[i].to_rank,
 						     Packets[i].recv_buf,
 						     Packets[i].from_rank,
-					  Packets[i].bytes);
+						     Packets[i].bytes,i);
     }
   }
 
   void CommunicateComplete(std::vector<std::vector<CommsRequest_t> > &reqs)
   {
     for(int i=0;i<Packets.size();i++){
-      _grid->StencilSendToRecvFromComplete(reqs[i]);
+      _grid->StencilSendToRecvFromComplete(reqs[i],i);
     }
     commtime+=usecond();
   }
+  void Communicate(void)
+  {
+#ifdef GRID_OMP
+#pragma omp parallel 
+    {
+      // must be called in parallel region
+      int mythread  = omp_get_thread_num();
+      int maxthreads= omp_get_max_threads();
+      int nthreads = CartesianCommunicator::nCommThreads;
+      assert(nthreads <= maxthreads);
+
+      if (nthreads == -1) nthreads = 1;
+#else
+      int mythread = 0;
+      int nthreads = 1;
+#endif
+      if (mythread < nthreads) {
+	for (int i = mythread; i < Packets.size(); i += nthreads) {
+	  double start = usecond();
+	  comm_bytes_thr[mythread] += _grid->StencilSendToRecvFrom(Packets[i].send_buf,
+								   Packets[i].to_rank,
+								   Packets[i].recv_buf,
+								   Packets[i].from_rank,
+								   Packets[i].bytes,i);
+	  comm_time_thr[mythread] += usecond() - start;
+	}
+      }
+#ifdef GRID_OMP
+    }
+#endif
+  }
   
   template<class compressor> void HaloExchange(const Lattice<vobj> &source,compressor &compress) 
   {
     std::vector<std::vector<CommsRequest_t> > reqs;
     Prepare();
     HaloGather(source,compress);
-    CommunicateBegin(reqs);
+    // Concurrent
-    CommunicateComplete(reqs);
+    //CommunicateBegin(reqs);
+    //CommunicateComplete(reqs);
+    // Sequential, possibly threaded
+    Communicate();
     CommsMergeSHM(compress); 
     CommsMerge(compress); 
   }
@@ -337,7 +429,9 @@ class CartesianStencil { // Stencil runs along coordinate axes only; NO diagonal
   template<class compressor>
   void HaloGather(const Lattice<vobj> &source,compressor &compress)
   {
+    mpi3synctime_g-=usecond();
     _grid->StencilBarrier();// Synch shared memory on a single nodes
+    mpi3synctime_g+=usecond();
 
     // conformable(source._grid,_grid);
     assert(source._grid==_grid);
@@ -397,8 +491,12 @@ class CartesianStencil { // Stencil runs along coordinate axes only; NO diagonal
     CommsMerge(decompress,Mergers,Decompressions); 
   }
   template<class decompressor>  void CommsMergeSHM(decompressor decompress) {
+    mpi3synctime-=usecond();    
     _grid->StencilBarrier();// Synch shared memory on a single nodes
+    mpi3synctime+=usecond();    
+    shmmergetime-=usecond();    
     CommsMerge(decompress,MergersSHM,DecompressionsSHM);
+    shmmergetime+=usecond();    
   }
 
   template<class decompressor>
@@ -442,7 +540,12 @@ class CartesianStencil { // Stencil runs along coordinate axes only; NO diagonal
 		  int checkerboard,
 		  const std::vector<int> &directions,
 		  const std::vector<int> &distances) 
-   :   _permute_type(npoints), _comm_buf_size(npoints)
+   : _permute_type(npoints), 
+    _comm_buf_size(npoints),
+    comm_bytes_thr(npoints), 
+    comm_enter_thr(npoints),
+    comm_leave_thr(npoints), 
+       comm_time_thr(npoints)
   {
     face_table_computed=0;
     _npoints = npoints;
@@ -996,6 +1099,15 @@ class CartesianStencil { // Stencil runs along coordinate axes only; NO diagonal
   void ZeroCounters(void) {
     gathertime = 0.;
     commtime = 0.;
+    mpi3synctime=0.;
+    mpi3synctime_g=0.;
+    shmmergetime=0.;
+    for(int i=0;i<_npoints;i++){
+      comm_time_thr[i]=0;
+      comm_bytes_thr[i]=0;
+      comm_enter_thr[i]=0;
+      comm_leave_thr[i]=0;
+    }
     halogtime = 0.;
     mergetime = 0.;
     decompresstime = 0.;
@@ -1011,6 +1123,18 @@ class CartesianStencil { // Stencil runs along coordinate axes only; NO diagonal
 #define PRINTIT(A) AVERAGE(A); std::cout << GridLogMessage << " Stencil " << #A << " "<< A/calls<<std::endl;
     RealD NP = _grid->_Nprocessors;
     RealD NN = _grid->NodeCount();
+    double t = 0;
+    // if comm_time_thr is set they were all done in parallel so take the max
+    // but add up the bytes
+    int threaded = 0 ;
+    for (int i = 0; i < 8; ++i) {
+      if ( comm_time_thr[i]>0.0 ) {
+	threaded = 1;
+	comms_bytes += comm_bytes_thr[i];
+	if (t < comm_time_thr[i]) t = comm_time_thr[i];
+      }
+    }
+    if (threaded) commtime += t;
     
     _grid->GlobalSum(commtime);    commtime/=NP;
     if ( calls > 0. ) {
@@ -1026,6 +1150,9 @@ class CartesianStencil { // Stencil runs along coordinate axes only; NO diagonal
 	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;
       }
+      PRINTIT(mpi3synctime);
+      PRINTIT(mpi3synctime_g);
+      PRINTIT(shmmergetime);
       PRINTIT(splicetime);
       PRINTIT(nosplicetime);
     }

lib/tensors/Tensor_arith_mul.h

@@ -98,7 +98,9 @@ template<class rtype,class vtype,class mtype,int N>
 strong_inline void mult(iVector<rtype,N> * __restrict__ ret,
                  const iVector<vtype,N> * __restrict__ rhs,
                  const iScalar<mtype> * __restrict__ lhs){
-    mult(ret,lhs,rhs);
+    for(int c1=0;c1<N;c1++){
+        mult(&ret->_internal[c1],&rhs->_internal[c1],&lhs->_internal);
+    }                 
 }
     
 

lib/util/Init.cc

@@ -219,9 +219,15 @@ void Grid_init(int *argc,char ***argv)
     int MB;
     arg= GridCmdOptionPayload(*argv,*argv+*argc,"--shm");
     GridCmdOptionInt(arg,MB);
-    CartesianCommunicator::MAX_MPI_SHM_BYTES = MB*1024*1024;
+    uint64_t MB64 = MB;
+    CartesianCommunicator::MAX_MPI_SHM_BYTES = MB64*1024LL*1024LL;
   }
 
+  if( GridCmdOptionExists(*argv,*argv+*argc,"--shm-hugepages") ){
+    CartesianCommunicator::Hugepages = 1;
+  }
+
+
   if( GridCmdOptionExists(*argv,*argv+*argc,"--debug-signals") ){
     Grid_debug_handler_init();
   }
@@ -304,6 +310,7 @@ void Grid_init(int *argc,char ***argv)
     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<<"  --shm-hugepages : use explicit huge pages in mmap call "<<std::endl;    
     std::cout<<GridLogMessage<<std::endl;
     std::cout<<GridLogMessage<<"Verbose and debug:"<<std::endl;
     std::cout<<GridLogMessage<<std::endl;
@@ -356,10 +363,15 @@ void Grid_init(int *argc,char ***argv)
   if( GridCmdOptionExists(*argv,*argv+*argc,"--comms-sequential") ){
     CartesianCommunicator::SetCommunicatorPolicy(CartesianCommunicator::CommunicatorPolicySequential);
   }
+
   if( GridCmdOptionExists(*argv,*argv+*argc,"--lebesgue") ){
     LebesgueOrder::UseLebesgueOrder=1;
   }
-
+  CartesianCommunicator::nCommThreads = -1;
+  if( GridCmdOptionExists(*argv,*argv+*argc,"--comms-threads") ){
+    arg= GridCmdOptionPayload(*argv,*argv+*argc,"--comms-threads");
+    GridCmdOptionInt(arg,CartesianCommunicator::nCommThreads);
+  }
   if( GridCmdOptionExists(*argv,*argv+*argc,"--cacheblocking") ){
     arg= GridCmdOptionPayload(*argv,*argv+*argc,"--cacheblocking");
     GridCmdOptionIntVector(arg,LebesgueOrder::Block);
@@ -374,10 +386,13 @@ void Grid_init(int *argc,char ***argv)
 		  Grid_default_latt,
 		  Grid_default_mpi);
 
-  std::cout << GridLogDebug << "Requesting "<< CartesianCommunicator::MAX_MPI_SHM_BYTES <<" byte stencil comms buffers "<<std::endl;
+  std::cout << GridLogMessage << "Requesting "<< CartesianCommunicator::MAX_MPI_SHM_BYTES <<" byte stencil comms buffers "<<std::endl;
+  if ( CartesianCommunicator::Hugepages) {
+    std::cout << GridLogMessage << "Mapped stencil comms buffers as MAP_HUGETLB "<<std::endl;
+  }
 
   if( GridCmdOptionExists(*argv,*argv+*argc,"--decomposition") ){
-    std::cout<<GridLogMessage<<"Grid Decomposition\n";
+    std::cout<<GridLogMessage<<"Grid Default Decomposition patterns\n";
     std::cout<<GridLogMessage<<"\tOpenMP threads : "<<GridThread::GetThreads()<<std::endl;
     std::cout<<GridLogMessage<<"\tMPI tasks      : "<<GridCmdVectorIntToString(GridDefaultMpi())<<std::endl;
     std::cout<<GridLogMessage<<"\tvRealF         : "<<sizeof(vRealF)*8    <<"bits ; " <<GridCmdVectorIntToString(GridDefaultSimd(4,vRealF::Nsimd()))<<std::endl;
@@ -393,7 +408,7 @@ void Grid_init(int *argc,char ***argv)
 
 void Grid_finalize(void)
 {
-#if defined (GRID_COMMS_MPI) || defined (GRID_COMMS_MPI3)
+#if defined (GRID_COMMS_MPI) || defined (GRID_COMMS_MPI3) || defined (GRID_COMMS_MPIT)
   MPI_Finalize();
   Grid_unquiesce_nodes();
 #endif

tests/core/Test_fft_gfix.cc

@@ -28,6 +28,9 @@ Author: Peter Boyle <paboyle@ph.ed.ac.uk>
     /*  END LEGAL */
 #include <Grid/Grid.h>
 
+using namespace Grid;
+using namespace Grid::QCD;
+
 int main (int argc, char ** argv)
 {
   std::vector<int> seeds({1,2,3,4});
@@ -82,6 +85,7 @@ int main (int argc, char ** argv)
 
   Uorg = Uorg - Umu;
   std::cout << " Norm Difference "<< norm2(Uorg) << std::endl;
+  std::cout << " Norm "<< norm2(Umu) << std::endl;
 
 
   std::cout<< "*****************************************************************" <<std::endl;

tests/hmc/Test_hmc_EOMobiusRatio.cc

@@ -40,12 +40,6 @@ namespace Grid{
 				    double, StoppingCondition,
 				    int, MaxCGIterations,
 				    bool, ApplySmearing);
-
-    //template <class ReaderClass >
-    //FermionParameters(Reader<ReaderClass>& Reader){
-    //  read(Reader, "Mobius", *this);
-    //}
-
   };
 
   
@@ -113,9 +107,17 @@ int main(int argc, char **argv) {
   bool ApplySmearing = MyParams.Mobius.ApplySmearing;
   
   
+  // Use this if you want to tweak the default decomposition
+  // commented out as very architecture speficic
+  
+  //std::vector<int> simd_lanes({2,2,1,1});
+
+  // Grid from the command line arguments --grid and --mpi
+  // drop the simd_lanes argument to fall back to the default decomposition for the SIMD lanes
+  
+  //TheHMC.Resources.AddFourDimGrid("gauge", simd_lanes); // tweak the SIMD lanes
+  TheHMC.Resources.AddFourDimGrid("gauge"); // use default simd lanes decomposition
   
-  // Grid from the command line
-  TheHMC.Resources.AddFourDimGrid("gauge");
   // Possibile to create the module by hand 
   // hardcoding parameters or using a Reader
 

tests/hmc/Test_hmc_WilsonGauge.cc

@@ -66,7 +66,14 @@ int main(int argc, char **argv) {
   typedef PlaquetteMod<HMCWrapper::ImplPolicy> PlaqObs;
   typedef TopologicalChargeMod<HMCWrapper::ImplPolicy> QObs;
   TheHMC.Resources.AddObservable<PlaqObs>();
-  TheHMC.Resources.AddObservable<QObs>();
+  TopologyObsParameters TopParams;
+  TopParams.interval = 5;
+  TopParams.do_smearing = true;
+  TopParams.Smearing.steps = 200;
+  TopParams.Smearing.step_size = 0.01;
+  TopParams.Smearing.meas_interval = 50;
+  TopParams.Smearing.maxTau = 2.0; 
+  TheHMC.Resources.AddObservable<QObs>(TopParams);
   //////////////////////////////////////////////
 
   /////////////////////////////////////////////////////////////

tests/solver/Test_staggered_block_cg_unprec.cc

@@ -99,21 +99,27 @@ int main (int argc, char ** argv)
   std::cout << GridLogMessage << " Calling 5d CG for "<<Ls <<" right hand sides" <<std::endl;
   std::cout << GridLogMessage << "************************************************************************ "<<std::endl;
   result=zero;
+  Ds.ZeroCounters();
   CG(HermOp,src,result);
+  Ds.Report();
   std::cout << GridLogMessage << "************************************************************************ "<<std::endl;
 
   std::cout << GridLogMessage << "************************************************************************ "<<std::endl;
   std::cout << GridLogMessage << " Calling multiRHS CG for "<<Ls <<" right hand sides" <<std::endl;
   std::cout << GridLogMessage << "************************************************************************ "<<std::endl;
   result=zero;
+  Ds.ZeroCounters();
   mCG(HermOp,src,result);
+  Ds.Report();
   std::cout << GridLogMessage << "************************************************************************ "<<std::endl;
 
   std::cout << GridLogMessage << "************************************************************************ "<<std::endl;
   std::cout << GridLogMessage << " Calling Block CG for "<<Ls <<" right hand sides" <<std::endl;
   std::cout << GridLogMessage << "************************************************************************ "<<std::endl;
   result=zero;
+  Ds.ZeroCounters();
   BCGrQ(HermOp,src,result);
+  Ds.Report();
   std::cout << GridLogMessage << "************************************************************************ "<<std::endl;