Lammps polaris

component-tests/README.md

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+# Tuning Individual Components of MOFA
+
+Evaluate each part of our workflow in isolation from the rest of the application.

component-tests/lammps-md/README.md

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+# Test LAMMPS MD
+
+Run MD simulations using LAMMPS to establish tradeoffs between run length, execution time, and measured volume change.

component-tests/lammps-md/run_test.py

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+"""Test LAMMPS by running a large number of MD simulations with different runtimes"""
+from platform import node
+import argparse
+import json
+
+from tqdm import tqdm
+from ase import Atoms
+import parsl
+from parsl.config import Config
+from parsl.app.python import PythonApp
+from parsl.executors import HighThroughputExecutor
+from parsl.providers import PBSProProvider
+from parsl.launchers import MpiExecLauncher
+
+from mofa.model import MOFRecord
+from mofa.scoring.geometry import LatticeParameterChange
+from mofa.utils.conversions import write_to_string
+
+
+def test_function(mof: MOFRecord, lammps_invocation: list[str], timesteps: int) -> tuple[float, list[Atoms]]:
+    """Run a LAMMPS simulation, report runtime and resultant traj
+
+    Args:
+        strc: MOF to use
+        lammps_invocation: Command to invoke LAMMPS
+        timesteps: Number of MD time steps
+    Returns:
+        - Runtime (s)
+        - MD trajectory
+    """
+    from mofa.simulation.lammps import LAMMPSRunner
+    from time import perf_counter
+    from pathlib import Path
+
+    run_dir = Path(f'run-{timesteps}')
+    run_dir.mkdir(exist_ok=True, parents=True)
+
+    # Run
+    lmp_runner = LAMMPSRunner(lammps_invocation, lmp_sims_root_path=str(run_dir))
+    start_time = perf_counter()
+    output = lmp_runner.run_molecular_dynamics(mof, timesteps, timesteps // 5)
+    run_time = perf_counter() - start_time
+
+    return run_time, output
+
+
+if __name__ == "__main__":
+    # Get the length of the runs, etc
+    parser = argparse.ArgumentParser()
+    parser.add_argument('--timesteps', help='Number of timesteps to run', default=1000, type=int)
+    parser.add_argument('--config', help='Which compute configuration to use', default='local')
+    args = parser.parse_args()
+
+    # Select the correct configuraion
+    if args.config == "local":
+        lammps_cmd = ['/home/lward/Software/lammps-2Aug2023/build/lmp', '-sf', 'omp']
+        config = Config(executors=[HighThroughputExecutor(max_workers=1, cpu_affinity='block')])
+    elif args.config == "polaris":
+        lammps_cmd = ('/lus/eagle/projects/ExaMol/mofa/lammps-2Aug2023/src/lmp_polaris_nvhpc_kokkos '
+                      '-k on g 1 -sf kk -pk kokkos neigh half neigh/qeq full newton on ').split()
+        config = Config(retries=1, executors=[
+            HighThroughputExecutor(
+                max_workers=4,
+                cpu_affinity='block-reverse',
+                available_accelerators=4,
+                provider=PBSProProvider(
+                    launcher=MpiExecLauncher(bind_cmd="--cpu-bind", overrides="--depth=64 --ppn 1"),
+                    account='ExaMol',
+                    queue='debug',
+                    select_options="ngpus=4",
+                    scheduler_options="#PBS -l filesystems=home:eagle",
+                    worker_init="""
+module load kokkos
+module load nvhpc/23.3
+module list
+source activate /lus/eagle/projects/ExaMol/mofa/mof-generation-at-scale/env-polaris
+
+cd $PBS_O_WORKDIR
+pwd
+which python
+hostname
+                    """,
+                    nodes_per_block=1,
+                    init_blocks=1,
+                    min_blocks=0,
+                    max_blocks=1,
+                    cpus_per_node=32,
+                    walltime="1:00:00",
+                )
+            )
+        ])
+    else:
+        raise ValueError(f'Configuration not defined: {args.config}')
+
+    # Prepare parsl
+    parsl.load(config)
+    test_app = PythonApp(test_function)
+
+    # Submit each MOF
+    futures = []
+    with open('example-mofs.json') as fp:
+        for line in fp:
+            mof = MOFRecord(**json.loads(line))
+            future = test_app(mof, lammps_cmd, args.timesteps)
+            future.mof = mof
+            futures.append(future)
+
+    # Store results
+    scorer = LatticeParameterChange()
+    for future in tqdm(futures):
+        runtime, traj = future.result()
+
+        # Get the strain
+        # TODO (wardlt): Simplify how we compute strain
+        traj_vasp = [write_to_string(t, 'vasp') for t in traj]
+        mof = future.mof
+        mof.md_trajectory['uff'] = traj_vasp
+        strain = scorer.score_mof(mof)
+
+        # Store the result
+        with open('runtimes.json', 'a') as fp:
+            print(json.dumps({
+                'host': node(),
+                'lammps_cmd': lammps_cmd,
+                'timesteps': args.timesteps,
+                'mof': mof.name,
+                'runtime': runtime,
+                'strain': strain
+            }), file=fp)

envs/README.md

@@ -1 +1,24 @@
 Environment files for different resources
+
+## Building LAMMPS on Polaris
+
+Follow the instructions [from ALCF for building LAMMPS with Kokkos](https://github.com/argonne-lcf/GettingStarted/tree/master/Applications/Polaris/LAMMPS)
+
+```bash
+#! /bin/bash
+
+# Make the build environment
+module use /soft/modulefiles
+module load cudatoolkit-standalone/11.8.0
+module load kokkos
+module list
+
+# Build
+cd src
+cd MAKE/MACHINES/
+wget -c https://github.com/argonne-lcf/GettingStarted/raw/master/Applications/Polaris/LAMMPS/Makefile.polaris_nvhpc_kokkos
+cd ../..
+pwd
+#make yes-most
+make polaris_nvhpc_kokkos -j 16
+```

mofa/simulation/disable_mps_polaris.sh

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+#!/bin/bash -l
+
+echo quit | nvidia-cuda-mps-control

mofa/simulation/enable_mps_polaris.sh

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+#!/bin/bash -l
+
+export CUDA_MPS_PIPE_DIRECTORY=/tmp/nvidia-mps
+export CUDA_MPS_LOG_DIRECTORY=/tmp/nvidia-log
+CUDA_VISIBLE_DEVICES=0,1,2,3 nvidia-cuda-mps-control -d
+echo "start_server -uid $( id -u )" | nvidia-cuda-mps-control

mofa/simulation/lammps-polaris-compile.bash

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+module purge
+
+export PATH=/soft/buildtools/cmake/cmake-3.23.2/cmake-3.23.2-linux-x86_64/bin:/opt/anaconda3x/bin:/opt/clmgr/sbin:/opt/clmgr/bin:/opt/sgi/sbin:/opt/sgi/bin:/usr/local/bin:/usr/bin:/bin:/opt/c3/bin:/dbhome/db2cat/sqllib/bin:/dbhome/db2cat/sqllib/adm:/dbhome/db2cat/sqllib/misc:/dbhome/db2cat/sqllib/gskit/bin:/usr/lib/mit/bin:/usr/lib/mit/sbin:/opt/pbs/bin:/sbin:/opt/cray/pe/bin
+export LD_LIBRARY_PATH=/dbhome/db2cat/sqllib/lib64:/dbhome/db2cat/sqllib/lib64/gskit:/dbhome/db2cat/sqllib/lib32
+export LIBRARY_PATH=/dbhome/db2cat/sqllib/lib64:/dbhome/db2cat/sqllib/lib64/gskit:/dbhome/db2cat/sqllib/lib32
+export MANPATH=/usr/share/lmod/lmod/share/man:/usr/local/man:/usr/share/man:/opt/c3/man:/opt/pbs/share/man:/opt/clmgr/man:/opt/sgi/share/man:/opt/clmgr/share/man:/opt/clmgr/lib/cm-cli/man
+export CPATH=
+
+export PATH=/opt/nvidia/hpc_sdk/Linux_x86_64/23.3/comm_libs/12.0/nvshmem/bin:$PATH
+export PATH=/opt/nvidia/hpc_sdk/Linux_x86_64/23.3/comm_libs/12.0/nccl/bin:$PATH
+export PATH=/opt/nvidia/hpc_sdk/Linux_x86_64/23.3/comm_libs/openmpi4/openmpi-4.0.5/bin:$PATH
+export PATH=/opt/nvidia/hpc_sdk/Linux_x86_64/23.3/compilers/extras/qd/bin:$PATH
+export PATH=/opt/nvidia/hpc_sdk/Linux_x86_64/23.3/compilers/bin:$PATH
+export PATH=/opt/nvidia/hpc_sdk/Linux_x86_64/23.3/compilers/extras/qd/bin:$PATH
+export PATH=/opt/nvidia/hpc_sdk/Linux_x86_64/23.3/compilers/share/llvm/bin:$PATH
+export PATH=/opt/nvidia/hpc_sdk/Linux_x86_64/23.3/cuda/12.0/bin:$PATH
+
+export LIBRARY_PATH=/opt/nvidia/hpc_sdk/Linux_x86_64/23.3/comm_libs/12.0/nvshmem/lib:$LIBRARY_PATH
+export LIBRARY_PATH=/opt/nvidia/hpc_sdk/Linux_x86_64/23.3/comm_libs/12.0/nccl/lib:$LIBRARY_PATH
+export LIBRARY_PATH=/opt/nvidia/hpc_sdk/Linux_x86_64/23.3/comm_libs/openmpi4/openmpi-4.0.5/lib:$LIBRARY_PATH
+export LIBRARY_PATH=/opt/nvidia/hpc_sdk/Linux_x86_64/23.3/math_libs/lib64:$LIBRARY_PATH
+export LIBRARY_PATH=/opt/nvidia/hpc_sdk/Linux_x86_64/23.3/compilers/lib:$LIBRARY_PATH
+export LIBRARY_PATH=/opt/nvidia/hpc_sdk/Linux_x86_64/23.3/compilers/extras/qd/lib:$LIBRARY_PATH
+export LIBRARY_PATH=/opt/nvidia/hpc_sdk/Linux_x86_64/23.3/cuda/12.0/extras/CUPTI/lib64:$LIBRARY_PATH
+export LIBRARY_PATH=/opt/nvidia/hpc_sdk/Linux_x86_64/23.3/cuda/12.0/lib64:$LIBRARY_PATH
+export LIBRARY_PATH=/opt/nvidia/hpc_sdk/Linux_x86_64/23.3/math_libs/lib64:$LIBRARY_PATH
+export LIBRARY_PATH=/opt/nvidia/hpc_sdk/Linux_x86_64/23.3/math_libs/lib64/stubs:$LIBRARY_PATH
+
+export LD_LIBRARY_PATH=/opt/nvidia/hpc_sdk/Linux_x86_64/23.3/comm_libs/12.0/nvshmem/lib:$LD_LIBRARY_PATH
+export LD_LIBRARY_PATH=/opt/nvidia/hpc_sdk/Linux_x86_64/23.3/comm_libs/12.0/nccl/lib:$LD_LIBRARY_PATH
+export LD_LIBRARY_PATH=/opt/nvidia/hpc_sdk/Linux_x86_64/23.3/comm_libs/openmpi4/openmpi-4.0.5/lib:$LD_LIBRARY_PATH
+export LD_LIBRARY_PATH=/opt/nvidia/hpc_sdk/Linux_x86_64/23.3/math_libs/lib64:$LD_LIBRARY_PATH
+export LD_LIBRARY_PATH=/opt/nvidia/hpc_sdk/Linux_x86_64/23.3/compilers/lib:$LD_LIBRARY_PATH
+export LD_LIBRARY_PATH=/opt/nvidia/hpc_sdk/Linux_x86_64/23.3/compilers/extras/qd/lib:$LD_LIBRARY_PATH
+export LD_LIBRARY_PATH=/opt/nvidia/hpc_sdk/Linux_x86_64/23.3/cuda/12.0/extras/CUPTI/lib64:$LD_LIBRARY_PATH
+export LD_LIBRARY_PATH=/opt/nvidia/hpc_sdk/Linux_x86_64/23.3/cuda/12.0/lib64:$LD_LIBRARY_PATH
+export LD_LIBRARY_PATH=/opt/nvidia/hpc_sdk/Linux_x86_64/23.3/math_libs/lib64:$LD_LIBRARY_PATH
+export LD_LIBRARY_PATH=/opt/nvidia/hpc_sdk/Linux_x86_64/23.3/math_libs/lib64/stubs:$LD_LIBRARY_PATH
+
+export CPATH=/opt/nvidia/hpc_sdk/Linux_x86_64/23.3/comm_libs/12.0/nvshmem/include:$CPATH
+export CPATH=/opt/nvidia/hpc_sdk/Linux_x86_64/23.3/comm_libs/12.0/nccl/include:$CPATH
+export CPATH=/opt/nvidia/hpc_sdk/Linux_x86_64/23.3/comm_libs/openmpi4/openmpi-4.0.5/include:$CPATH
+export CPATH=/opt/nvidia/hpc_sdk/Linux_x86_64/23.3/compilers/extras/qd/include/qd:$CPATH
+export CPATH=/opt/nvidia/hpc_sdk/Linux_x86_64/23.3/compilers/include:$CPATH
+export CPATH=/opt/nvidia/hpc_sdk/Linux_x86_64/23.3/cuda/12.0/include:$CPATH
+export CPATH=/opt/nvidia/hpc_sdk/Linux_x86_64/23.3/math_libs/include:$CPATH
+
+export OPAL_PREFIX=/opt/nvidia/hpc_sdk/Linux_x86_64/23.3/comm_libs/openmpi4/openmpi-4.0.5
+export MANPATH=/opt/nvidia/hpc_sdk/Linux_x86_64/23.3/compilers/man:$MANPATH
+
+
+cd /grand/projects/RAPINS/xiaoliyan/lmp20230802stb/build-gpu-nvhpc
+cmake ../cmake -DCMAKE_BUILD_TYPE=release \
+-DCMAKE_C_COMPILER=nvc++ \
+-DCMAKE_CXX_COMPILER=nvc++ \
+-DCMAKE_FORTRAN_COMPILER=nvfortran \
+-DCMAKE_CXX_STANDARD=17 \
+-DLAMMPS_MEMALIGN=64 \
+-DLAMMPS_SIZES=bigbig \
+-DPKG_MISC=on \
+-DPKG_ML-SNAP=on \
+-DPKG_MOFFF=on \
+-DFFT=KISS \
+-DPKG_QEQ=on \
+-DPKG_REAXFF=on \
+-DPKG_PTM=on \
+-DPKG_RIGID=on \
+-DPKG_MOLECULE=on \
+-DPKG_EXTRA-MOLECULE=on \
+-DPKG_EXTRA-FIX=on \
+-DPKG_KSPACE=on \
+-DPKG_MANYBODY=on \
+-DPKG_GRANULAR=on \
+-DPKG_GPU=on \
+-DGPU_API=cuda \
+-DGPU_PREC=double \
+-DGPU_ARCH=sm_80 \
+-DGPU_DEBUG=yes \
+-DCUDA_MPS_SUPPORT=yes \
+-DBUILD_OMP=yes \
+-DBUILD_MPI=yes \
+-DCUDA_NVCC_FLAGS="-std=c++17 -Xcompiler -fopenmp --allow-unsupported-compiler" \
+-DCMAKE_CXX_FLAGS="-std=c++17 -DCUDA_PROXY -fopenmp -g -O3 -mp" \
+-DCMAKE_C_FLAGS="-std=c++17 -DCUDA_PROXY -fopenmp -g -O3 -mp" \
+-DCMAKE_FORTRAN_FLAGS="-std=c++17 -DCUDA_PROXY -fopenmp -g -O3 -mp"
+
+make -j 16
+
+#LMPEXE=/grand/projects/RAPINS/xiaoliyan/lmp20230802stb/build-gpu-nvhpc/lmp

mofa/simulation/lammps-polaris-mps.pbs

@@ -0,0 +1,103 @@
+#!/bin/bash -l
+#PBS -l select=1:system=polaris
+#PBS -l place=scatter
+#PBS -l walltime=01:00:00
+#PBS -l filesystems=home:grand:eagle
+#PBS -q debug-scaling
+#PBS -A RAPINS
+#PBS -N test-mps-lmp
+#PBS -M xyan11@anl.gov
+#PBS -m abe
+#PBS -k doe
+#PBS -j oe
+
+lscpu
+free -h
+ulimit -s unlimited
+echo Working directory is $PBS_O_WORKDIR
+cd $PBS_O_WORKDIR
+echo Jobid: $PBS_JOBID
+echo Running on host `hostname`
+echo Running on nodes `cat $PBS_NODEFILE`
+
+export PATH=/soft/buildtools/cmake/cmake-3.23.2/cmake-3.23.2-linux-x86_64/bin:/opt/anaconda3x/bin:/opt/clmgr/sbin:/opt/clmgr/bin:/opt/sgi/sbin:/opt/sgi/bin:/usr/local/bin:/usr/bin:/bin:/opt/c3/bin:/usr/lib/mit/bin:/usr/lib/mit/sbin:/opt/pbs/bin:/sbin:/opt/cray/pe/bin
+export LD_LIBRARY_PATH=
+export LIBRARY_PATH=
+export MANPATH=/usr/share/lmod/lmod/share/man:/usr/local/man:/usr/share/man:/opt/c3/man:/opt/pbs/share/man:/opt/clmgr/man:/opt/sgi/share/man:/opt/clmgr/share/man:/opt/clmgr/lib/cm-cli/man
+export OPAL_PREFIX=
+export CPATH=
+
+export PATH=/opt/nvidia/hpc_sdk/Linux_x86_64/23.3/comm_libs/12.0/nvshmem/bin:$PATH
+export PATH=/opt/nvidia/hpc_sdk/Linux_x86_64/23.3/comm_libs/12.0/nccl/bin:$PATH
+export PATH=/opt/nvidia/hpc_sdk/Linux_x86_64/23.3/comm_libs/openmpi4/openmpi-4.0.5/bin:$PATH
+export PATH=/opt/nvidia/hpc_sdk/Linux_x86_64/23.3/compilers/extras/qd/bin:$PATH
+export PATH=/opt/nvidia/hpc_sdk/Linux_x86_64/23.3/compilers/bin:$PATH
+export PATH=/opt/nvidia/hpc_sdk/Linux_x86_64/23.3/compilers/extras/qd/bin:$PATH
+export PATH=/opt/nvidia/hpc_sdk/Linux_x86_64/23.3/compilers/share/llvm/bin:$PATH
+export PATH=/opt/nvidia/hpc_sdk/Linux_x86_64/23.3/cuda/12.0/bin:$PATH
+
+export LIBRARY_PATH=/opt/nvidia/hpc_sdk/Linux_x86_64/23.3/comm_libs/12.0/nvshmem/lib:$LIBRARY_PATH
+export LIBRARY_PATH=/opt/nvidia/hpc_sdk/Linux_x86_64/23.3/comm_libs/12.0/nccl/lib:$LIBRARY_PATH
+export LIBRARY_PATH=/opt/nvidia/hpc_sdk/Linux_x86_64/23.3/comm_libs/openmpi4/openmpi-4.0.5/lib:$LIBRARY_PATH
+export LIBRARY_PATH=/opt/nvidia/hpc_sdk/Linux_x86_64/23.3/math_libs/lib64:$LIBRARY_PATH
+export LIBRARY_PATH=/opt/nvidia/hpc_sdk/Linux_x86_64/23.3/compilers/lib:$LIBRARY_PATH
+export LIBRARY_PATH=/opt/nvidia/hpc_sdk/Linux_x86_64/23.3/compilers/extras/qd/lib:$LIBRARY_PATH
+export LIBRARY_PATH=/opt/nvidia/hpc_sdk/Linux_x86_64/23.3/cuda/12.0/extras/CUPTI/lib64:$LIBRARY_PATH
+export LIBRARY_PATH=/opt/nvidia/hpc_sdk/Linux_x86_64/23.3/cuda/12.0/lib64:$LIBRARY_PATH
+export LIBRARY_PATH=/opt/nvidia/hpc_sdk/Linux_x86_64/23.3/math_libs/lib64:$LIBRARY_PATH
+export LIBRARY_PATH=/opt/nvidia/hpc_sdk/Linux_x86_64/23.3/math_libs/lib64/stubs:$LIBRARY_PATH
+
+export LD_LIBRARY_PATH=/opt/nvidia/hpc_sdk/Linux_x86_64/23.3/comm_libs/12.0/nvshmem/lib:$LD_LIBRARY_PATH
+export LD_LIBRARY_PATH=/opt/nvidia/hpc_sdk/Linux_x86_64/23.3/comm_libs/12.0/nccl/lib:$LD_LIBRARY_PATH
+export LD_LIBRARY_PATH=/opt/nvidia/hpc_sdk/Linux_x86_64/23.3/comm_libs/openmpi4/openmpi-4.0.5/lib:$LD_LIBRARY_PATH
+export LD_LIBRARY_PATH=/opt/nvidia/hpc_sdk/Linux_x86_64/23.3/math_libs/lib64:$LD_LIBRARY_PATH
+export LD_LIBRARY_PATH=/opt/nvidia/hpc_sdk/Linux_x86_64/23.3/compilers/lib:$LD_LIBRARY_PATH
+export LD_LIBRARY_PATH=/opt/nvidia/hpc_sdk/Linux_x86_64/23.3/compilers/extras/qd/lib:$LD_LIBRARY_PATH
+export LD_LIBRARY_PATH=/opt/nvidia/hpc_sdk/Linux_x86_64/23.3/cuda/12.0/extras/CUPTI/lib64:$LD_LIBRARY_PATH
+export LD_LIBRARY_PATH=/opt/nvidia/hpc_sdk/Linux_x86_64/23.3/cuda/12.0/lib64:$LD_LIBRARY_PATH
+export LD_LIBRARY_PATH=/opt/nvidia/hpc_sdk/Linux_x86_64/23.3/math_libs/lib64:$LD_LIBRARY_PATH
+export LD_LIBRARY_PATH=/opt/nvidia/hpc_sdk/Linux_x86_64/23.3/math_libs/lib64/stubs:$LD_LIBRARY_PATH
+
+export CPATH=/opt/nvidia/hpc_sdk/Linux_x86_64/23.3/comm_libs/12.0/nvshmem/include:$CPATH
+export CPATH=/opt/nvidia/hpc_sdk/Linux_x86_64/23.3/comm_libs/12.0/nccl/include:$CPATH
+export CPATH=/opt/nvidia/hpc_sdk/Linux_x86_64/23.3/comm_libs/openmpi4/openmpi-4.0.5/include:$CPATH
+export CPATH=/opt/nvidia/hpc_sdk/Linux_x86_64/23.3/compilers/extras/qd/include/qd:$CPATH
+export CPATH=/opt/nvidia/hpc_sdk/Linux_x86_64/23.3/compilers/include:$CPATH
+export CPATH=/opt/nvidia/hpc_sdk/Linux_x86_64/23.3/cuda/12.0/include:$CPATH
+export CPATH=/opt/nvidia/hpc_sdk/Linux_x86_64/23.3/math_libs/include:$CPATH
+
+export OPAL_PREFIX=/opt/nvidia/hpc_sdk/Linux_x86_64/23.3/comm_libs/openmpi4/openmpi-4.0.5
+export MANPATH=/opt/nvidia/hpc_sdk/Linux_x86_64/23.3/compilers/man:$MANPATH
+
+module list
+
+export NGPUS=1
+export OMP_NUM_THREADS=1
+export OMP_PROC_BIND=spread
+export OMP_PLACES=threads
+export CUDA_VISIBLE_DEVICES=0
+export MPICH_GPU_SUPPORT_ENABLED=1
+export MPIARG="mpiexec -np 1 -npernode 1"
+export EXE="/grand/projects/RAPINS/xiaoliyan/lmp20230802stb/build-gpu-nvhpc/lmp"
+export EXE_ARG="-sf gpu -pk gpu ${NGPUS} -in in.lmp"
+
+# Enable MPS on each node allocated to job
+${MPIARG} ${PBS_O_WORKDIR}/enable_mps_polaris.sh &
+
+# record start time
+start=`date +%s`
+
+# workload
+cd ${PBS_O_WORKDIR}/inst1
+${MPIARG} ${EXE} ${EXE_ARG} &
+cd ${PBS_O_WORKDIR}/inst2
+${MPIARG} ${EXE} ${EXE_ARG} &
+
+wait
+
+# record end time
+end=`date +%s`
+echo Total MPS jobs running time was `expr $end - $start` seconds.
+
+# Disable MPS on each node allocated to job
+${MPIARG} ${PBS_O_WORKDIR}/disable_mps_polaris.sh