MOLECULAR DYNAMICS PERFORMANCE GUIDE - Digital Research Alliance of CANADA

SOFTWARE DETAILS

ID=25, SANDER.QUICK.cuda.MPI

  • Module/Version: ambertools/21
  • Toolchain/Version: gofbc/2020.1.403.114
  • CPU instruction set: avx2
  • Example job submission script:
    1. #!/bin/bash

    2. #SBATCH --ntasks=4 --cpus-per-task=1  --gpus-per-task=1

    3. #SBATCH --mem-per-cpu=4000 --time=1:00:00

    4. 

    5. ml StdEnv/2020 gcc/9.3.0 cuda/11.4 openmpi/4.0.3 ambertools/21 

    6. source $EBROOTAMBERTOOLS/amber.sh 

    7. 

    8. srun sander.quick.cuda.MPI -O -i input.in -p complex.prmtop -c coor.rst
  • Benchmark submission script:
    1. #!/bin/bash

    2. #SBATCH --ntasks=2 --cpus-per-task=1 --gpus-per-task=1

    3. #SBATCH --mem-per-cpu=4000  --time=1:00:00

    4. 

    5. DATADIR=/home/svassili/scratch/sander-quick

    6. 

    7. ml StdEnv/2020 gcc/9.3.0 cuda/11.4 openmpi/4.0.3 ambertools/21 

    8. source $EBROOTAMBERTOOLS/amber.sh 

    9. 

    10. srun sander.quick.cuda.MPI -O -i $DATADIR/B3LYP.in -p $DATADIR/complex_solv_PNP.prmtop -c $DATADIR/mini-QMMM_4.rst -ref $DATADIR/mini-QMMM_4.rst