Difference between revisions of "GROMACS"

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(Created page with "===GROMACS v2.12=== [http://www.gromacs.org GROMACS] is a versatile molecular dynamics package. A thorough treatment of GROMACS can be found on the [https://docs.computecana...")
 
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===GROMACS v2.12===
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===GROMACS 2018.6===
  
[http://www.gromacs.org GROMACS] is a versatile molecular dynamics package.  A thorough treatment of GROMACS can be found on the [https://docs.computecanada.ca/wiki/GROMACS Compute Canada page].  Here is a sample Niagara run script:
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[http://www.gromacs.org GROMACS] is a versatile molecular dynamics package.  A thorough treatment of GROMACS can be found on the [https://docs.alliancecan.ca/wiki/GROMACS {{Alliance}} page].  Here is a sample Niagara run script:
  
 
<source lang="bash">
 
<source lang="bash">
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#SBATCH --job-name test
 
#SBATCH --job-name test
  
module load intel/2018.2
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module load intel/2019u3
module load intelmpi/2018.2
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module load intelmpi/2019u3
module load gromacs/2016.5
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module load gromacs/2018.6
  
# DIRECTORY TO RUN - $PBS_O_WORKDIR is directory job was submitted from
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# DIRECTORY TO RUN - $SLURM_SUBMIT_DIR is directory job was submitted from
 
cd $SLURM_SUBMIT_DIR
 
cd $SLURM_SUBMIT_DIR
  
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The above script requests 1 node and runs gromacs in a hybrid mode, in 10 groups of 4 processors.
 
The above script requests 1 node and runs gromacs in a hybrid mode, in 10 groups of 4 processors.
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Note that GROMACS is well-suited to use on GPUs, of which Niagara has none.  Running on [[Mist]] is recommended.  Alternatively, running on {{Alliance}} systems which have GPUs, such as [https://docs.computecanada.ca/wiki/Graham Graham] and [https://docs.computecanada.ca/wiki/Cedar Cedar], is also an option.
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=== Gromacs on Mist GPU cluster ===
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See details on Mist page: [https://docs.scinet.utoronto.ca/index.php/Mist#Gromacs Gromacs on Mist]

Latest revision as of 14:25, 25 May 2022

GROMACS 2018.6

GROMACS is a versatile molecular dynamics package. A thorough treatment of GROMACS can be found on the Alliance (formerly 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/2019u3
module load intelmpi/2019u3
module load gromacs/2018.6

# DIRECTORY TO RUN - $SLURM_SUBMIT_DIR 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. Running on Mist is recommended. Alternatively, running on Alliance (formerly Compute Canada) systems which have GPUs, such as Graham and Cedar, is also an option.

Gromacs on Mist GPU cluster

See details on Mist page: Gromacs on Mist