Difference between revisions of "GROMACS"
From SciNet Users Documentation
m (→GROMACS 2016.5) |
m (→Gromacs on Mist GPU cluster) |
||
| Line 29: | Line 29: | ||
=== Gromacs on Mist GPU cluster === | === Gromacs on Mist GPU cluster === | ||
| − | See details | + | See details on Mist page: [https://docs.scinet.utoronto.ca/index.php/Mist#Gromacs Gromacs on Mist] |
Revision as of 18:58, 24 February 2020
GROMACS 2016.5
GROMACS is a versatile molecular dynamics package. A thorough treatment of GROMACS can be found on the Compute Canada page. Here is a sample Niagara run script:
#!/bin/bash
#
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=10
#SBATCH --cpus-per-task=4
#SBATCH --time=11:00:00
#SBATCH --job-name test
module load intel/2018.2
module load intelmpi/2018.2
module load gromacs/2016.5
# DIRECTORY TO RUN - $PBS_O_WORKDIR is directory job was submitted from
cd $SLURM_SUBMIT_DIR
export OMP_NUM_THREADS="${SLURM_CPUS_PER_TASK:-1}"
srun gmx_mpi mdrun -deffnm md
The above script requests 1 node and runs gromacs in a hybrid mode, in 10 groups of 4 processors.
Note that GROMACS is well-suited to use on GPUs, of which Niagara has none. As such running on CC systems which have GPUs, such as Graham and Cedar, is recommended.
Gromacs on Mist GPU cluster
See details on Mist page: Gromacs on Mist
