MOLECULAR DYNAMICS PERFORMANCE GUIDE - COMPUTE 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. ml StdEnv/2020 gcc/9.3.0 cuda/11.4 openmpi/4.0.3 ambertools/21
    5. source $EBROOTAMBERTOOLS/amber.sh
    6. 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. DATADIR=/home/svassili/scratch/sander-quick
    5. ml StdEnv/2020 gcc/9.3.0 cuda/11.4 openmpi/4.0.3 ambertools/21
    6. source $EBROOTAMBERTOOLS/amber.sh
    7. 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