log iso-timestamp instead of seconds-since-start

Grid/Benchmark_Grid.cpp

@@ -1,7 +1,7 @@
 /*
 Copyright © 2015 Peter Boyle <paboyle@ph.ed.ac.uk>
 Copyright © 2022 Antonin Portelli <antonin.portelli@me.com>
-Copyright © 2024 Simon Buerger <simon.buerger@rwth-aachen.de>
+Copyright © 2022 Simon Buerger <simon.buerger@rwth-aachen.de>
 
 This is a fork of Benchmark_ITT.cpp from Grid
 
@@ -29,43 +29,6 @@ int NN_global;
 
 nlohmann::json json_results;
 
-// NOTE: Grid::GridClock is just a typedef to
-// `std::chrono::high_resolution_clock`, but `Grid::usecond` rounds to
-// microseconds (no idea why, probably wasnt ever relevant before), so we need
-// our own wrapper here.
-double usecond_precise()
-{
-  using namespace std::chrono;
-  auto nsecs = duration_cast<nanoseconds>(GridClock::now() - Grid::theProgramStart);
-  return nsecs.count() * 1e-3;
-}
-
-std::vector<std::string> get_mpi_hostnames()
-{
-  int world_size;
-  MPI_Comm_size(MPI_COMM_WORLD, &world_size);
-
-  char hostname[MPI_MAX_PROCESSOR_NAME];
-  int name_len = 0;
-  MPI_Get_processor_name(hostname, &name_len);
-
-  // Allocate buffer to gather all hostnames
-  std::vector<char> all_hostnames(world_size * MPI_MAX_PROCESSOR_NAME);
-
-  // Use MPI_Allgather to gather all hostnames on all ranks
-  MPI_Allgather(hostname, MPI_MAX_PROCESSOR_NAME, MPI_CHAR, all_hostnames.data(),
-                MPI_MAX_PROCESSOR_NAME, MPI_CHAR, MPI_COMM_WORLD);
-
-  // Convert the gathered hostnames back into a vector of std::string
-  std::vector<std::string> hostname_list(world_size);
-  for (int i = 0; i < world_size; ++i)
-  {
-    hostname_list[i] = std::string(&all_hostnames[i * MPI_MAX_PROCESSOR_NAME]);
-  }
-
-  return hostname_list;
-}
-
 struct time_statistics
 {
   double mean;
@@ -110,7 +73,7 @@ class Benchmark
         {local[0] * mpi[0], local[1] * mpi[1], local[2] * mpi[2], local[3] * mpi[3]});
     GridCartesian *TmpGrid = SpaceTimeGrid::makeFourDimGrid(
         latt4, GridDefaultSimd(Nd, vComplex::Nsimd()), GridDefaultMpi());
-    Grid::Coordinate shm(4, 1);
+    Grid::Coordinate shm;
     GlobalSharedMemory::GetShmDims(mpi, shm);
 
     uint64_t NP = TmpGrid->RankCount();
@@ -174,7 +137,7 @@ class Benchmark
 
     Coordinate simd_layout = GridDefaultSimd(Nd, vComplexD::Nsimd());
     Coordinate mpi_layout = GridDefaultMpi();
-    Coordinate shm_layout(Nd, 1);
+    Coordinate shm_layout;
     GlobalSharedMemory::GetShmDims(mpi_layout, shm_layout);
 
     for (int mu = 0; mu < Nd; mu++)
@@ -301,170 +264,6 @@ class Benchmark
     return;
   }
 
-  static void Latency(void)
-  {
-    int Nwarmup = 100;
-    int Nloop = 300;
-
-    std::cout << GridLogMessage << "Benchmarking point-to-point latency" << std::endl;
-    grid_small_sep();
-    grid_printf("from to      mean(usec)           err           max\n");
-
-    int ranks;
-    int me;
-    MPI_Comm_size(MPI_COMM_WORLD, &ranks);
-    MPI_Comm_rank(MPI_COMM_WORLD, &me);
-
-    int bytes = 8;
-    void *buf_from = acceleratorAllocDevice(bytes);
-    void *buf_to = acceleratorAllocDevice(bytes);
-    nlohmann::json json_latency;
-    for (int from = 0; from < ranks; ++from)
-      for (int to = 0; to < ranks; ++to)
-      {
-        if (from == to)
-          continue;
-
-        std::vector<double> t_time(Nloop);
-        time_statistics timestat;
-        MPI_Status status;
-
-        for (int i = -Nwarmup; i < Nloop; ++i)
-        {
-          double start = usecond_precise();
-          if (from == me)
-          {
-            auto err = MPI_Send(buf_from, bytes, MPI_CHAR, to, 0, MPI_COMM_WORLD);
-            assert(err == MPI_SUCCESS);
-          }
-          if (to == me)
-          {
-            auto err =
-                MPI_Recv(buf_to, bytes, MPI_CHAR, from, 0, MPI_COMM_WORLD, &status);
-            assert(err == MPI_SUCCESS);
-          }
-          double stop = usecond_precise();
-          if (i >= 0)
-            t_time[i] = stop - start;
-        }
-        // important: only 'from' and 'to' have meaningful timings. we use
-        // 'from's.
-        MPI_Bcast(t_time.data(), Nloop, MPI_DOUBLE, from, MPI_COMM_WORLD);
-
-        timestat.statistics(t_time);
-        grid_printf("%2d %2d %15.4f %15.3f %15.4f\n", from, to, timestat.mean,
-                    timestat.err, timestat.max);
-        nlohmann::json tmp;
-        tmp["from"] = from;
-        tmp["to"] = to;
-        tmp["time_usec"] = timestat.mean;
-        tmp["time_usec_error"] = timestat.err;
-        tmp["time_usec_min"] = timestat.min;
-        tmp["time_usec_max"] = timestat.max;
-        tmp["time_usec_full"] = t_time;
-        json_latency.push_back(tmp);
-      }
-    json_results["latency"] = json_latency;
-
-    acceleratorFreeDevice(buf_from);
-    acceleratorFreeDevice(buf_to);
-  }
-
-  static void P2P(void)
-  {
-    // IMPORTANT: The P2P benchmark uses "MPI_COMM_WORLD" communicator, which is
-    // not the quite the same as Grid.communicator. Practically speaking, the
-    // latter one contains the same MPI-ranks but in a different order. Grid
-    // does this make sure it can exploit ranks with shared memory (i.e.
-    // multiple ranks on the same node) as best as possible.
-
-    // buffer-size to benchmark. This number is the same as the largest one used
-    // in the "Comms()" benchmark. ( L=48, Ls=12, double-prec-complex,
-    // half-color-spin-vector. ). Mostly an arbitrary choice, but nice to match
-    // it here
-    size_t bytes = 127401984;
-
-    int Nwarmup = 20;
-    int Nloop = 100;
-
-    std::cout << GridLogMessage << "Benchmarking point-to-point bandwidth" << std::endl;
-    grid_small_sep();
-    grid_printf("from to      mean(usec)           err           min           "
-                "bytes    rate (GiB/s)\n");
-
-    int ranks;
-    int me;
-    MPI_Comm_size(MPI_COMM_WORLD, &ranks);
-    MPI_Comm_rank(MPI_COMM_WORLD, &me);
-
-    void *buf_from = acceleratorAllocDevice(bytes);
-    void *buf_to = acceleratorAllocDevice(bytes);
-    nlohmann::json json_p2p;
-    for (int from = 0; from < ranks; ++from)
-      for (int to = 0; to < ranks; ++to)
-      {
-        if (from == to)
-          continue;
-
-        std::vector<double> t_time(Nloop);
-        time_statistics timestat;
-        MPI_Status status;
-
-        for (int i = -Nwarmup; i < Nloop; ++i)
-        {
-          double start = usecond_precise();
-          if (from == me)
-          {
-            auto err = MPI_Send(buf_from, bytes, MPI_CHAR, to, 0, MPI_COMM_WORLD);
-            assert(err == MPI_SUCCESS);
-          }
-          if (to == me)
-          {
-            auto err =
-                MPI_Recv(buf_to, bytes, MPI_CHAR, from, 0, MPI_COMM_WORLD, &status);
-            assert(err == MPI_SUCCESS);
-          }
-          double stop = usecond_precise();
-          if (i >= 0)
-            t_time[i] = stop - start;
-        }
-        // important: only 'from' and 'to' have meaningful timings. we use
-        // 'from's.
-        MPI_Bcast(t_time.data(), Nloop, MPI_DOUBLE, from, MPI_COMM_WORLD);
-
-        timestat.statistics(t_time);
-        double rate = bytes / (timestat.mean / 1.e6) / 1024. / 1024. / 1024.;
-        double rate_err = rate * timestat.err / timestat.mean;
-        double rate_max = rate * timestat.mean / timestat.min;
-        double rate_min = rate * timestat.mean / timestat.max;
-
-        grid_printf("%2d %2d %15.4f %15.3f %15.4f %15d %15.2f\n", from, to, timestat.mean,
-                    timestat.err, timestat.min, bytes, rate);
-
-        nlohmann::json tmp;
-        tmp["from"] = from;
-        tmp["to"] = to;
-        tmp["bytes"] = bytes;
-        tmp["time_usec"] = timestat.mean;
-        tmp["time_usec_error"] = timestat.err;
-        tmp["time_usec_min"] = timestat.min;
-        tmp["time_usec_max"] = timestat.max;
-        tmp["time_usec_full"] = t_time;
-        nlohmann::json tmp_rate;
-        tmp_rate["mean"] = rate;
-        tmp_rate["error"] = rate_err;
-        tmp_rate["max"] = rate_max;
-        tmp_rate["min"] = rate_min;
-        tmp["rate_GBps"] = tmp_rate;
-
-        json_p2p.push_back(tmp);
-      }
-    json_results["p2p"] = json_p2p;
-
-    acceleratorFreeDevice(buf_from);
-    acceleratorFreeDevice(buf_to);
-  }
-
   static void Memory(void)
   {
     const int Nvec = 8;
@@ -726,6 +525,8 @@ class Benchmark
 
         FGrid->Broadcast(0, &ncall, sizeof(ncall));
 
+        Dw.ZeroCounters();
+
         time_statistics timestat;
         std::vector<double> t_time(ncall);
         for (uint64_t i = 0; i < ncall; i++)
@@ -920,6 +721,7 @@ class Benchmark
         uint64_t ncall = 500;
 
         FGrid->Broadcast(0, &ncall, sizeof(ncall));
+        Ds.ZeroCounters();
 
         time_statistics timestat;
         std::vector<double> t_time(ncall);
@@ -987,47 +789,11 @@ int main(int argc, char **argv)
 {
   Grid_init(&argc, &argv);
 
-  int Ls = 1;
-  bool do_su4 = true;
-  bool do_memory = true;
-  bool do_comms = true;
-  bool do_flops = true;
-
-  // NOTE: these two take O((number of ranks)^2) time, which might be a lot, so they are
-  // off by default
-  bool do_latency = false;
-  bool do_p2p = false;
-
   std::string json_filename = ""; // empty indicates no json output
   for (int i = 0; i < argc; i++)
   {
-    auto arg = std::string(argv[i]);
+    if (std::string(argv[i]) == "--json-out")
-    if (arg == "--json-out")
       json_filename = argv[i + 1];
-    if (arg == "--benchmark-su4")
-      do_su4 = true;
-    if (arg == "--benchmark-memory")
-      do_memory = true;
-    if (arg == "--benchmark-comms")
-      do_comms = true;
-    if (arg == "--benchmark-flops")
-      do_flops = true;
-    if (arg == "--benchmark-latency")
-      do_latency = true;
-    if (arg == "--benchmark-p2p")
-      do_p2p = true;
-    if (arg == "--no-benchmark-su4")
-      do_su4 = false;
-    if (arg == "--no-benchmark-memory")
-      do_memory = false;
-    if (arg == "--no-benchmark-comms")
-      do_comms = false;
-    if (arg == "--no-benchmark-flops")
-      do_flops = false;
-    if (arg == "--no-benchmark-latency")
-      do_latency = false;
-    if (arg == "--no-benchmark-p2p")
-      do_p2p = false;
   }
 
   CartesianCommunicator::SetCommunicatorPolicy(
@@ -1039,6 +805,12 @@ int main(int argc, char **argv)
 #endif
   Benchmark::Decomposition();
 
+  int do_su4 = 1;
+  int do_memory = 1;
+  int do_comms = 1;
+  int do_flops = 1;
+  int Ls = 1;
+
   int sel = 4;
   std::vector<int> L_list({8, 12, 16, 24, 32});
   int selm1 = sel - 1;
@@ -1071,22 +843,6 @@ int main(int argc, char **argv)
     Benchmark::Comms();
   }
 
-  if (do_latency)
-  {
-    grid_big_sep();
-    std::cout << GridLogMessage << " Latency benchmark " << std::endl;
-    grid_big_sep();
-    Benchmark::Latency();
-  }
-
-  if (do_p2p)
-  {
-    grid_big_sep();
-    std::cout << GridLogMessage << " Point-To-Point benchmark " << std::endl;
-    grid_big_sep();
-    Benchmark::P2P();
-  }
-
   if (do_flops)
   {
     Ls = 1;
@@ -1146,8 +902,6 @@ int main(int argc, char **argv)
     json_results["flops"] = tmp_flops;
   }
 
-  json_results["hostnames"] = get_mpi_hostnames();
-
   if (!json_filename.empty())
   {
     std::cout << GridLogMessage << "writing benchmark results to " << json_filename

Grid/systems/tursa/spack-bootstrap.sh

@@ -4,13 +4,7 @@ set -euo pipefail
 
 gcc_spec='gcc@9.4.0'
 cuda_spec='cuda@11.4.0'
-
+hdf5_spec='hdf5@1.10.7'
-# hdf5 and fftw depend on OpenMPI, which we install manually. To make sure this
-# dependency is picked by spack, we specify the compiler here explicitly. For
-# most other packages we dont really care about the compiler (i.e. system
-# compiler versus ${gcc_spec})
-hdf5_spec="hdf5@1.10.7+cxx+threadsafe%${gcc_spec}"
-fftw_spec="fftw%${gcc_spec}"
 
 if (( $# != 1 )); then
     echo "usage: $(basename "$0") <env dir>" 1>&2
@@ -24,7 +18,7 @@ cd "${cwd}"
 
 # General configuration ########################################################
 # build with 128 tasks
-echo 'config:
+echo 'config:                                  
   build_jobs: 128
   build_stage:
     - $spack/var/spack/stage
@@ -44,23 +38,26 @@ rm external.yaml
 
 # Base compilers ###############################################################
 # configure system base
-
-spack env create base
-spack env activate base
 spack compiler find --scope site
 
-# install GCC, CUDA
+# install GCC, CUDA & LLVM
-spack add ${gcc_spec} ${cuda_spec}
+spack install ${gcc_spec} ${cuda_spec} llvm
-spack concretize
+
-spack env depfile -o Makefile.tmp
+spack load llvm
-make -j128 -f Makefile.tmp
 spack compiler find --scope site
+spack unload llvm
+
+spack load ${gcc_spec}
+spack compiler find --scope site
+spack unload ${gcc_spec}
 
 # Manual compilation of OpenMPI & UCX ##########################################
 # set build directories
 mkdir -p "${dir}"/build
 cd "${dir}"/build
 
+spack load ${gcc_spec} ${cuda_spec}
+
 cuda_path=$(spack find --format "{prefix}" cuda)
 gdrcopy_path=/mnt/lustre/tursafs1/apps/gdrcopy/2.3.1
 
@@ -127,8 +124,8 @@ mkdir build_gpu; cd build_gpu
              --with-cuda="${cuda_path}" --disable-getpwuid        \
              --with-verbs --with-slurm --enable-mpi-fortran=all   \
              --with-pmix=internal --with-libevent=internal
-make -j 128
+make -j 128 
-make install
+make install 
 cd ..
 
 # openmpi cpu build
@@ -144,62 +141,60 @@ make -j 128
 make install
 cd "${dir}"
 
-ucx_spec_gpu="ucx@1.12.0.GPU%${gcc_spec}"
-ucx_spec_cpu="ucx@1.12.0.CPU%${gcc_spec}"
-openmpi_spec_gpu="openmpi@4.1.1.GPU%${gcc_spec}"
-openmpi_spec_cpu="openmpi@4.1.1.CPU%${gcc_spec}"
-
 # Add externals to spack
 echo "packages:
   ucx:
     externals:
-    - spec: \"${ucx_spec_gpu}\"
+    - spec: \"ucx@1.12.0.GPU%gcc@9.4.0\"
       prefix: ${dir}/prefix/ucx_gpu
-    - spec: \"${ucx_spec_cpu}\"
+    - spec: \"ucx@1.12.0.CPU%gcc@9.4.0\"
       prefix: ${dir}/prefix/ucx_cpu
     buildable: False
   openmpi:
     externals:
-    - spec: \"${openmpi_spec_gpu}\"
+    - spec: \"openmpi@4.1.1.GPU%gcc@9.4.0\"
       prefix: ${dir}/prefix/ompi_gpu
-    - spec: \"${openmpi_spec_cpu}\"
+    - spec: \"openmpi@4.1.1.CPU%gcc@9.4.0\"
       prefix: ${dir}/prefix/ompi_cpu
     buildable: False" > spack.yaml
 
 spack config --scope site add -f spack.yaml
 rm spack.yaml
-spack env deactivate
+spack install ucx@1.12.0.GPU%gcc@9.4.0 openmpi@4.1.1.GPU%gcc@9.4.0
+spack install ucx@1.12.0.CPU%gcc@9.4.0 openmpi@4.1.1.CPU%gcc@9.4.0
 
 cd "${cwd}"
 
 # environments #################################################################
 dev_tools=("autoconf" "automake" "libtool" "jq" "git")
+ompi_gpu_hash=$(spack find --format "{hash}" openmpi@4.1.1.GPU)
+ompi_cpu_hash=$(spack find --format "{hash}" openmpi@4.1.1.CPU)
 
 spack env create grid-gpu
 spack env activate grid-gpu
-spack compiler find --scope site
+spack add ${gcc_spec} ${cuda_spec} "${dev_tools[@]}" 
-spack add ${gcc_spec} ${cuda_spec} ${ucx_spec_gpu} ${openmpi_spec_gpu}
+spack add ucx@1.12.0.GPU%gcc@9.4.0 openmpi@4.1.1.GPU%gcc@9.4.0
-spack add ${hdf5_spec} ${fftw_spec}
+spack add ${hdf5_spec}+cxx+threadsafe ^/"${ompi_gpu_hash}"
-spack add openssl gmp mpfr c-lime "${dev_tools[@]}"
+spack add fftw ^/"${ompi_gpu_hash}"
-spack concretize
+spack add openssl gmp mpfr c-lime
-spack env depfile -o Makefile.tmp
+spack install
-make -j128 -f Makefile.tmp
 spack env deactivate
 
 spack env create grid-cpu
 spack env activate grid-cpu
-spack compiler find --scope site
+spack add llvm "${dev_tools[@]}" 
-spack add ${gcc_spec} ${ucx_spec_cpu} ${openmpi_spec_cpu}
+spack add ucx@1.12.0.CPU%gcc@9.4.0 openmpi@4.1.1.CPU%gcc@9.4.0
-spack add ${hdf5_spec} ${fftw_spec}
+spack add ${hdf5_spec}+cxx+threadsafe ^/"${ompi_cpu_hash}"
-spack add openssl gmp mpfr c-lime "${dev_tools[@]}"
+spack add fftw ^/"${ompi_cpu_hash}"
-spack concretize
+spack add openssl gmp mpfr c-lime
-spack env depfile -o Makefile.tmp
+spack install
-make -j128 -f Makefile.tmp
 spack env deactivate
 
+spack install jq git
+
 # Final setup ##################################################################
 spack clean
-#spack gc -y  # "spack gc" tends to get hung up for unknown reasons
+spack gc -y
 
 # add more environment variables in module loading
 spack config --scope site add 'modules:prefix_inspections:lib:[LD_LIBRARY_PATH,LIBRARY_PATH]'