GROMACS-Sapelo2: Difference between revisions
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===Description=== | ===Description=== | ||
GROMACS is a package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. | GROMACS is a package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. | ||
=== Running Program === | === Running Program === | ||
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module load GROMACS/2019.4-fosscuda-2019b-PLUMED-2.5.3 | module load GROMACS/2019.4-fosscuda-2019b-PLUMED-2.5.3 | ||
</pre> | </pre> | ||
'''Version 2020''' | '''Version 2020''' | ||
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module load GROMACS/2020-foss-2019b | module load GROMACS/2020-foss-2019b | ||
</pre> | </pre> | ||
'''Version 2020.3''' | '''Version 2020.3''' | ||
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Note that this version of Gromacs works on nodes with K20Xm, K40, K80, P100, and V100 GPU cards. | Note that this version of Gromacs works on nodes with K20Xm, K40, K80, P100, and V100 GPU cards. | ||
Sample job submission script sub.sh to run v. 2021.4 and use 10 CPU cores and 1 GPU K40 card: | Sample job submission script sub.sh to run v. 2021.4 and use 10 CPU cores and 1 GPU K40 card: | ||
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Also, choose an appropriate number of cores per node (ppn), a suitable wall time (the example | Also, choose an appropriate number of cores per node (ppn), a suitable wall time (the example | ||
above specifies 4 days), and a suitable amount of memory. | above specifies 4 days), and a suitable amount of memory. | ||
Submit the job to the queue with | Submit the job to the queue with | ||
Revision as of 14:00, 19 January 2022
Category
Chemistry
Program On
Sapelo2
Version
4.5.6-gompi-2019b, 2019.4-fosscuda-2019b-PLUMED-2.5.3, 2020-fosscuda-2019b, 2020.3-fosscuda-2019b, 2021.2-fosscuda-2020b, 2021.3-fosscuda-2020b, 2021.4-fosscuda-2020b
Author / Distributor
First developed in Herman Berendsens group at Groningen University.
Current head authors and project leaders:
Erik Lindahl (Stockholm Center for Biomembrane Research, Stockholm, SE) David van der Spoel (Biomedical Centre, Uppsala, SE) Berk Hess (Max Planck Institute for Polymer Research, Mainz, DE) .
Description
GROMACS is a package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.
Running Program
Also refer to Running Jobs on Sapelo2.
For more information on Environment Modules on Sapelo2 please see the Lmod page.
Version 2019.4
This version was compiled with fosscuda-2019b. It was patched with PLUMED. It is installed in /apps/eb/GROMACS/2019.4-fosscuda-2019b-PLUMED-2.5.3. To use this version of Gromacs, please first load its module with
module load GROMACS/2019.4-fosscuda-2019b-PLUMED-2.5.3
Version 2020
This version was compiled with fosscuda-2019b. It is installed in apps/eb/GROMACS/2020-foss-2019b. To use this version of Gromacs, please first load its module with
module load GROMACS/2020-foss-2019b
Version 2020.3
This version was compiled with fosscuda-2019b. It is installed in apps/eb/GROMACS/2020.3-foss-2019b. To use this version of Gromacs, please first load its module with
module load GROMACS/2020.3-foss-2019b
Version 2021.2
This version was compiled with fosscuda-2020b. It is installed in apps/eb/GROMACS/2021.2-foss-2020b. To use this version of Gromacs, please first load its module with
module load GROMACS/2021.2-foss-2020b
Version 2021.3
This version was compiled with fosscuda-2020b. It is installed in apps/eb/GROMACS/2021.3-foss-2020b. To use this version of Gromacs, please first load its module with
module load GROMACS/2021.3-foss-2020b
Version 2021.4
This version was compiled with fosscuda-2020b. It is installed in apps/eb/GROMACS/2021.4-foss-2020b. To use this version of Gromacs, please first load its module with
module load GROMACS/2021.4-foss-2020b
Note that this version of Gromacs works on nodes with K20Xm, K40, K80, P100, and V100 GPU cards.
Sample job submission script sub.sh to run v. 2021.4 and use 10 CPU cores and 1 GPU K40 card:
#PBS -S /bin/bash #PBS -q gpu_q #PBS -N testjob #PBS -l nodes=1:ppn=10:gpus=1:K40 #PBS -l walltime=4:00:00:00 #PBS -l mem=20gb cd $PBS_O_WORKDIR module load GROMACS/2021.4-foss-2020b source $EBROOTGROMACS/bin/GMXRC gmx mdrun -nt $PBS_NP [options]
where [options] need to be replaced by the arguments you wish to use. The job name testjob should be replaced by a name that is appropriate for your job. Also, choose an appropriate number of cores per node (ppn), a suitable wall time (the example above specifies 4 days), and a suitable amount of memory.
Submit the job to the queue with
qsub sub.sh
Documentation
Please see http://www.gromacs.org/
Installation
System
64-bit Linux