Benchmark benchRIB

Now that we installed GROMACS we are going to run a set of benchmarks and agregate the results.

benchRIB

C5n

cat > run-gromacs-c5n.sbatch << EOF
#!/bin/bash
#SBATCH --job-name=benchRIB-gromacs-2021.1
#SBATCH --exclusive
#SBATCH --output=%x_%j.out

spack env activate aws
spack load gromacs@2021.1 arch=linux-amzn2-skylake_avx512
time mpirun -n 18 gmx_mpi mdrun -ntomp 4 -s /fsx/input/gromacs/benchRIB.tpr -resethway
EOF
sbatch -p c5n run-gromacs-c5n.sbatch

C5a

cat > run-gromacs-c5a.sbatch << EOF
#!/bin/bash
#SBATCH --job-name=benchRIB-gromacs-2021.1
#SBATCH --exclusive
#SBATCH --output=%x_%j.out

spack env activate aws
spack load gromacs@2021.1 arch=linux-amzn2-zen
time mpirun -n 48 gmx_mpi mdrun -ntomp 2 -s /fsx/input/gromacs/benchRIB.tpr -resethway
EOF
sbatch -p c5a run-gromacs-c5a.sbatch

benchMEM

C5n

cat > run-gromacs-c5n.sbatch << EOF
#!/bin/bash
#SBATCH --job-name=benchMEM-gromacs-2021.1
#SBATCH --exclusive
#SBATCH --output=%x_%j.out

spack env activate aws
spack load gromacs@2021.1 arch=linux-amzn2-skylake_avx512
time mpirun -n 18 gmx_mpi mdrun -ntomp 4 -s /fsx/input/gromacs/benchMEM.tpr -resethway
EOF
sbatch -p c5n run-gromacs-c5n.sbatch

C5a

cat > run-gromacs-c5a.sbatch << EOF
#!/bin/bash
#SBATCH --job-name=benchMEM-gromacs-2021.1
#SBATCH --exclusive
#SBATCH --output=%x_%j.out

spack env activate aws
spack load gromacs@2021.1 arch=linux-amzn2-zen
time mpirun -n 48 gmx_mpi mdrun -ntomp 2 -s /fsx/input/gromacs/benchMEM.tpr -resethway
EOF
sbatch -p c5a run-gromacs-c5a.sbatch