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howto:gromacs

Gromacs

The available Easy Scripts (cpu and gpu versions) for Gromacs are:

qgromacs_2024-1, qgromacs_2023-1, qgromacs_2022-4, qgromacs_2020-1,qgromacs_2019-4, qgromacs_2018-6, qgromacs_2018-2 and qgromacs_2018

qgromacs_2024-1_gpu, qgromacs_2023-1_gpu, qgromacs_2021-1_gpu, qgromacs_2020-1_gpu, qgromacs_2019-4_gpu and qgromacs_2018-6_gpu

Execute any of these Easy Scripts on the login node (on a lustre subdirectory) and follow the prompts. This script handles PBS setup and submission. Sets up the mpi environment variables allowing you to run over multiple processors and nodes. Examples of script execution are provided below.

Note, please first include this module load - even better if your add this line to your .bashrc:

module load chpc/easy_scripts
                  EXAMPLE1
Enter project name/shortname
CHEM0100
Enter default filename for all file options (without any extension to the file)
test
Enter number of nodes on which to run job
1
Enter total walltime (hour:minute)
2:00
Enter email address
testing@gmail.com
Generated pbs file for test
Do you wish to submit job to cluster (y/n)
y
  EXAMPLE2 [PLEASE TAKE NOTE OF EMPTY SPACES]
Enter project name/shortname
CHEM0100
Enter default filename for all file options (without any extension to the file)
test
Enter number of nodes on which to run job

Enter total walltime (hour:minute)

Enter email address
testing@gmail.com
Generated pbs file for test
Do you wish to submit job to cluster (y/n)
y

Gromacs on GPU

Please note that you need to first be added to the gpu_1 queue before you can submit jobs to the GPU cluster

Execute qgromacs_2018-2_gpu, qgromacs_2018-6_gpu, qgromacs_2019-4_gpu, qgromacs_2020-1_gpu or qgromacs_2021-1 on the login node and follow the prompts. Examples of script execution are provided below.

                  EXAMPLE1
Enter research programme name
CHEM0100
Enter default filename for all file options (without any extension to the file)
test
Enter total walltime (hour:minute)
2:00
Enter email address
testing@gmail.com
Generated pbs file for test
Do you wish to submit job to cluster (y/n)
y
 
  EXAMPLE2 [PLEASE TAKE NOTE OF EMPTY SPACES]
Enter research programme name
CHEM0100
Enter default filename for all file options (without any extension to the file)
test
Enter total walltime (hour:minute)

Enter email address
testing@gmail.com
Generated pbs file for test
Do you wish to submit job to cluster (y/n)
y
/app/dokuwiki/data/pages/howto/gromacs.txt · Last modified: 2024/03/19 17:45 by alopis