howto:gromacs
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howto:gromacs [2018/09/10 11:34] kgovender |
howto:gromacs [2020/04/17 11:33] (current) kgovender |
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| ====== Gromacs ====== | ====== Gromacs ====== | ||
| - | Execute **qgromacs_5.1.2** on login node and follow the prompts. | + | 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. | 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 40: | Line 40: | ||
| ====== Gromacs on GPU ====== | ====== Gromacs on GPU ====== | ||
| - | Execute **qgromacs_2018-2_gpu** on login node and follow the prompts. | + | ** //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. | Examples of script execution are provided below. | ||
| EXAMPLE1 | EXAMPLE1 | ||
| - | Enter project name/shortname | + | Enter research programme name |
| CHEM0100 | CHEM0100 | ||
| Enter default filename for all file options (without any extension to the file) | Enter default filename for all file options (without any extension to the file) | ||
| Line 58: | Line 60: | ||
| EXAMPLE2 [PLEASE TAKE NOTE OF EMPTY SPACES] | EXAMPLE2 [PLEASE TAKE NOTE OF EMPTY SPACES] | ||
| - | Enter project name/shortname | + | Enter research programme name |
| CHEM0100 | CHEM0100 | ||
| Enter default filename for all file options (without any extension to the file) | Enter default filename for all file options (without any extension to the file) | ||
/var/www/wiki/data/attic/howto/gromacs.1536572074.txt.gz · Last modified: 2018/09/10 11:34 by kgovender
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