howto:gromacs
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howto:gromacs [2016/04/04 09:57] kgovender |
howto:gromacs [2020/04/17 11:31] kgovender |
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| ====== Gromacs ====== | ====== Gromacs ====== | ||
| - | Execute **qgromacs_5.1.2** on login node and follow the prompts. | + | Execute **qgromacs_2018** on login node and follow the prompts. |
| This script handles PBS setup and submission. | This script handles PBS setup and submission. | ||
| Sets up the mpi environment variables allowing you to run over multiple processors and nodes. | Sets up the mpi environment variables allowing you to run over multiple processors and nodes. | ||
| Line 30: | Line 30: | ||
| Enter number of nodes on which to run job | 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** 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 total walltime (hour:minute) | ||
| | | ||
/var/www/wiki/data/pages/howto/gromacs.txt · Last modified: 2020/04/17 11:33 by kgovender
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