Adding GROMACS

configs/LLNL-Magma-Penguin-icelake-OmniPath/auxiliary_software_files/packages.yaml

@@ -28,6 +28,16 @@ packages:
     - spec: [email protected]
       prefix: /usr/tce/backend/installations/linux-rhel8-x86_64/intel-19.0.4/intel-oneapi-mkl-2022.1.0-sksz67twjxftvwchnagedk36gf7plkrp
       buildable: false
+  hwloc:
+    externals:
+    - spec: [email protected]
+      prefix: /usr
+      buildable: false
+  fftw:
+    externals:
+    - spec: [email protected]
+      prefix: /usr/tce/packages/fftw/fftw-3.3.10
+      buildable: false
   mpi:
     externals:
     - spec: [email protected]

configs/LLNL-Pascal-Penguin-broadwell-P100-OmniPath/auxiliary_software_files/packages.yaml

@@ -27,18 +27,6 @@ packages:
     externals:
     - spec: [email protected]
       prefix: /usr
-  mpi:
-    buildable: false
-  mvapich2:
-    buildable: false
-    externals:
-    - spec: [email protected]%[email protected]
-      prefix: /usr/tce/packages/mvapich2/mvapich2-2.3.7-intel-classic-2021.6.0/
-  cuda:
-    buildable: false
-    externals:
-    - spec: [email protected]
-      prefix: /usr/tce/packages/cuda/cuda-11.8.0/
   curand:
     externals:
     - spec: [email protected]
@@ -49,16 +37,47 @@ packages:
     - spec: [email protected]
       prefix: /usr/tce/packages/cuda/cuda-11.8.0
     buildable: false
+  cuda:
+    externals:
+    - spec: [email protected]
+      prefix: /usr/tce/packages/cuda/cuda-11.8.0
+    buildable: false
   cublas:
     externals:
     - spec: [email protected]
       prefix: /usr/tce/packages/cuda/cuda-11.8.0
     buildable: false
+  cusolver:
+    externals:
+    - spec: [email protected]
+      prefix: /usr/tce/packages/cuda/cuda-11.8.0
+    buildable: false
   blas:
+    externals:
+    - spec: [email protected]
+      prefix: /usr/tce/packages/mkl/mkl-2022.1.0
+    buildable: false
+  fftw:
+    externals:
+    - spec: [email protected]
+      prefix: /usr/tce/packages/mkl/mkl-2022.1.0
     buildable: false
   lapack:
+    externals:
+    - spec: [email protected]
+      prefix: /usr/tce/packages/mkl/mkl-2022.1.0
     buildable: false
   intel-oneapi-mkl:
     externals:
     - spec: [email protected]
       prefix: /usr/tce/packages/mkl/mkl-2022.1.0/
+    buildable: false
+  mpi:
+    buildable: false
+  mvapich2:
+    externals:
+    - spec: [email protected]
+      prefix: /usr/tce/packages/mvapich2/mvapich2-2.3.7-gcc-11.2.1
+    - spec: [email protected]
+      prefix: /usr/tce/packages/mvapich2/mvapich2-2.3.7-intel-classic-2021.6.0/
+    buildable: false

configs/LLNL-Pascal-Penguin-broadwell-P100-OmniPath/spack.yaml

@@ -8,10 +8,14 @@ spack:
     default-compiler:
       spack_spec: gcc@=11.2.1
     default-mpi:
-      spack_spec: [email protected]
+      spack_spec: [email protected]-gcc1121
     compiler-gcc:
       spack_spec: gcc@=11.2.1
+    blas:
+      spack_spec: [email protected]
     cublas-cuda:
       spack_spec: cublas@{default_cuda_version}
     lapack:
       spack_spec: [email protected]
+    fftw:
+      spack_spec: [email protected]

configs/LLNL-Sierra-IBM-power9-V100-Infiniband/auxiliary_software_files/compilers.yaml

@@ -65,3 +65,21 @@ compilers:
     modules: []
     environment: {}
     extra_rpaths: []
+- compiler:
+    spec: [email protected]
+    paths:
+      cc: /usr/tce/packages/clang/clang-16.0.6-cuda-11.8.0-gcc-11.2.1/bin/clang
+      cxx: /usr/tce/packages/clang/clang-16.0.6-cuda-11.8.0-gcc-11.2.1/bin/clang++
+      f77: /usr/tce/packages/gcc/gcc-11.2.1/bin/gfortran
+      fc: /usr/tce/packages/gcc/gcc-11.2.1/bin/gfortran
+    flags:
+      cflags: -g -O2
+      cxxflags: -g -O2 -std=c++17
+      fflags: ''
+    operating_system: rhel7
+    target: ppc64le
+    modules: []
+    environment:
+      set:
+        GXX_PREFIX: "/usr/tce/packages/gcc/gcc-11.2.1"
+    extra_rpaths: []

configs/LLNL-Sierra-IBM-power9-V100-Infiniband/auxiliary_software_files/packages.yaml

@@ -48,26 +48,45 @@ packages:
     - spec: [email protected]
       prefix: /usr/tce/packages/cuda/cuda-11.8.0
     buildable: false
-  blas:
+  cublas:
     externals:
     - spec: [email protected]
       prefix: /usr/tce/packages/cuda/cuda-10.1.243
     - spec: [email protected]
       prefix: /usr/tce/packages/cuda/cuda-11.8.0
     buildable: false
+  cusolver:
+    externals:
+    - spec: [email protected]
+      prefix: /usr/tce/packages/cuda/cuda-11.8.0
+    buildable: false
+  blas:
+    externals:
+    - spec: [email protected]
+      prefix: /usr/tcetmp/packages/blas/blas-3.6.0-gfortran-4.8.5
+    buildable: false
+  fftw:
+    externals:
+    - spec: [email protected]
+      prefix: /usr/tcetmp/packages/fftw/fftw-3.3.10-xl-2023.06.28
+    buildable: false
   lapack:
     externals:
-    - spec: lapack-xl@3.9.0
-      prefix: /usr/tcetmp/packages/lapack/lapack-3.9.0-xl-2020.03.18
+    - spec: lapack-xl@3.6.0
+      prefix: /usr/tcetmp/packages/lapack/lapack-3.6.0-gfortran-4.8.5
     buildable: false
   mpi:
     externals:
-    - spec: [email protected]cuda-11.8.0
+    - spec: [email protected]cuda11.8.0
       prefix: /usr/tce/packages/spectrum-mpi/spectrum-mpi-rolling-release-xl-2022.08.19-cuda-11.8.0
       extra_attributes:
         ldflags: "-lmpiprofilesupport -lmpi_ibm_usempi -lmpi_ibm_mpifh -lmpi_ibm"
-    - spec: [email protected]cuda-10.1.243
+    - spec: [email protected]cuda10.1.243
       prefix: /usr/tce/packages/spectrum-mpi/spectrum-mpi-rolling-release-xl-2022.08.19-cuda-10.1.243
       extra_attributes:
         ldflags: "-lmpiprofilesupport -lmpi_ibm_usempi -lmpi_ibm_mpifh -lmpi_ibm"
+    - spec: [email protected]
+      prefix: /usr/tce/packages/spectrum-mpi/spectrum-mpi-rolling-release-clang-16.0.6-cuda-11.8.0-gcc-11.2.1
+      extra_attributes:
+        ldflags: "-lmpiprofilesupport -lmpi_ibm_usempi -lmpi_ibm_mpifh -lmpi_ibm"
     buildable: false

configs/LLNL-Sierra-IBM-power9-V100-Infiniband/spack.yaml

@@ -6,12 +6,16 @@
 spack:
   packages:
     default-compiler:
-      spack_spec: xl@16.1.1-2022.08.19-cuda{default_cuda_version}
+      spack_spec: clang@16.0.6-cuda{default_cuda_version}
     default-mpi:
-      spack_spec: [email protected]
+      spack_spec: [email protected]-clang16.0.6-cuda{default_cuda_version}
     compiler-gcc:
       spack_spec: [email protected]
+    blas:
+      spack_spec: [email protected]
     cublas-cuda:
-      spack_spec: cublas@{default_cuda_version} 
+      spack_spec: cublas@{default_cuda_version}
     lapack:
-      spack_spec: [email protected]
+      spack_spec: [email protected]
+    fftw:
+      spack_spec: [email protected]

configs/LLNL-Sierra-IBM-power9-V100-Infiniband/variables.yaml

@@ -9,7 +9,7 @@ variables:
   mpi_command: '/usr/tcetmp/bin/lrun -n {n_ranks} -T {processes_per_node} {gtl_flag}'
   batch_submit: 'bsub -q pdebug {execute_experiment}'
   batch_nodes: '#BSUB -nnodes {n_nodes}'
-  batch_ranks: '#BSUB -nnodes {n_nodes}'
+  batch_ranks: ''
   batch_timeout: '#BSUB -W {batch_time}'
   default_cuda_version: '11.8.0'
   cuda_arch: '70'

configs/LLNL-Tioga-HPECray-zen3-MI250X-Slingshot/auxiliary_software_files/packages.yaml

@@ -193,6 +193,13 @@ packages:
       prefix: /opt/cray/pe/libsci/23.05.1.4/gnu/10.3/x86_64/
   lapack:
     buildable: false
+  hypre:
+    variants: amdgpu_target=gfx90a
+  hwloc:
+    externals:
+    - spec: [email protected]
+      prefix: /usr
+      buildable: false
   mpi:
     buildable: false
   cray-mpich:

experiments/gromacs/cuda/execute_experiment.tpl

@@ -0,0 +1,16 @@
+#!/bin/bash
+
+## Copyright 2023 Lawrence Livermore National Security, LLC and other
+## Benchpark Project Developers. See the top-level COPYRIGHT file for details.
+##
+## SPDX-License-Identifier: Apache-2.0
+
+{batch_nodes}
+{batch_ranks}
+{batch_timeout}
+
+cd {experiment_run_dir}
+
+{experiment_setup}
+
+{command}

experiments/gromacs/cuda/ramble.yaml

@@ -0,0 +1,61 @@
+# Copyright 2023 Lawrence Livermore National Security, LLC and other
+# Benchpark Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: Apache-2.0
+
+ramble:
+  config:
+    deprecated: true
+    spack_flags:
+      install: '--add --keep-stage'
+      concretize: '-U -f'
+
+  applications:
+    gromacs:
+      workloads:
+        water_gmx50_adac:
+          env_vars:
+            set:
+              OMP_PROC_BIND: close
+              OMP_PLACES: threads
+              OMP_NUM_THREADS: '{omp_num_threads}'
+          variables:
+            experiment_setup: ''
+            n_ranks: '{processes_per_node} * {n_nodes}'
+            processes_per_node: '2'
+            n_nodes: '4'
+            omp_num_threads: '10'
+            target: 'gpu'
+          experiments:
+            gromacs_water_gmx50_adac_size{size}_dlb{dlb}_pin{pin}_target{target}_maxh{maxh}_nsteps{nsteps}_nstlist{nstlist}_npme{npme}:
+              variables:
+                dlb: 'no'
+                pin: 'off'
+                nb: '{target}'
+                pme: 'auto'
+                bonded: 'cpu'
+                update: '{target}'
+                maxh: '0.05'
+                nsteps: '1000'
+                nstlist: '200'
+                npme: '1'
+                size: '1536'
+
+  spack:
+    concretized: true
+    packages:
+      gromacs:
+        spack_spec: [email protected] +mpi+openmp+cuda~hwloc~double cuda_arch=={cuda_arch}
+        compiler: default-compiler
+      cuda:
+        spack_spec: cuda@{default_cuda_version}+allow-unsupported-compilers
+        compiler: default-compiler
+    environments:
+      gromacs:
+        packages:
+        - cuda
+        - blas
+        - lapack
+        - default-mpi
+        - fftw
+        - gromacs

experiments/gromacs/openmp/execute_experiment.tpl

@@ -0,0 +1,18 @@
+#!/bin/bash
+
+## Copyright 2023 Lawrence Livermore National Security, LLC and other
+## Benchpark Project Developers. See the top-level COPYRIGHT file for details.
+##
+## SPDX-License-Identifier: Apache-2.0
+
+{batch_nodes}
+{batch_ranks}
+{batch_timeout}
+
+cd {experiment_run_dir}
+
+{spack_setup}
+
+{experiment_setup}
+
+{command}

experiments/gromacs/openmp/ramble.yaml

@@ -0,0 +1,59 @@
+# Copyright 2023 Lawrence Livermore National Security, LLC and other
+# Benchpark Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: Apache-2.0
+
+ramble:
+  config:
+    deprecated: true
+    spack_flags:
+      install: '--add --keep-stage'
+      concretize: '-U -f'
+
+  applications:
+    gromacs:
+      workloads:
+        water_gmx50_adac:
+          env_vars:
+            set:
+              OMP_PROC_BIND: close
+              OMP_PLACES: threads
+              OMP_NUM_THREADS: '{omp_num_threads}'
+          variables:
+            experiment_setup: ''
+            n_ranks: '{processes_per_node} * {n_nodes}'
+            processes_per_node: '4'
+            n_nodes: '2'
+            omp_num_threads: '16'
+            target: 'cpu'
+          experiments:
+            gromacs_water_gmx50_adac_size{size}_dlb{dlb}_pin{pin}_target{target}_maxh{maxh}_nsteps{nsteps}_nstlist{nstlist}_npme{npme}:
+              variables:
+                dlb: 'no'
+                pin: 'off'
+                nb: '{target}'
+                pme: 'auto'
+                bonded: '{target}'
+                update: '{target}'
+                maxh: '0.05'
+                nsteps: '1000'
+                nstlist: '200'
+                npme: '0'
+                size: '1536'
+
+  spack:
+    concretized: true
+    packages:
+      fftw:
+        spack_spec: [email protected] +mpi+openmp
+        compiler: default-compiler
+      gromacs:
+        spack_spec: gromacs@main +mpi+openmp~hwloc
+        compiler: default-compiler
+    environments:
+      gromacs:
+        packages:
+        - lapack
+        - default-mpi
+        - fftw
+        - gromacs

repo/cusolver/package.py

@@ -0,0 +1,11 @@
+# Copyright 2023 Lawrence Livermore National Security, LLC and other
+# Benchpark Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: Apache-2.0
+
+from spack.package import *
+
+
+class Cusolver(Package):
+
+    provides("lapack")