howto:gromacs
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howto:gromacs [2014/09/08 09:58] dane typo |
howto:gromacs [2020/04/17 11:33] (current) kgovender |
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| ====== Gromacs ====== | ====== Gromacs ====== | ||
| - | This page is out-of-date. For updated information you can look at these two pages: [[howto:bioinformatics#gromacs|sun gromacs]]; [[howto:gpu_gromacs|gpu gromacs]]. | + | Execute **qgromacs_2018**, **qgromacs_2018-2**,**qgromacs_2019-4** or **qgromacs_2020-1** on login node 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. | ||
| + | |||
| + | 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** or **qgromacs_2020-1_gpu** on 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 | ||
/var/www/wiki/data/attic/howto/gromacs.1410163129.txt.gz · Last modified: 2014/09/08 09:58 by dane
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