howto:namd
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howto:namd [2016/04/12 08:45] kgovender created |
howto:namd [2024/08/12 13:28] (current) alopis |
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| Run **qnamd_2.11** in order to generate a PBS script and submit a job to the cluster. | Run **qnamd_2.11** in order to generate a PBS script and submit a job to the cluster. | ||
| Examples of the script are provided below: | Examples of the script are provided below: | ||
| + | |||
| + | **Note**, please first include this **module load** - even better if your add this line to your .bashrc, then the Easy Scripts should be visible and available: | ||
| + | |||
| + | module load chpc/ | ||
| Examples of input required for these scripts are provided below. | Examples of input required for these scripts are provided below. | ||
| Line 10: | Line 14: | ||
| Enter project name/ | Enter project name/ | ||
| CHEM0100 | CHEM0100 | ||
| - | Enter input file (with extension) | + | Enter input file (with .conf extension) |
| - | test.lj | + | test.conf |
| Enter number of nodes on which to run job | Enter number of nodes on which to run job | ||
| 1 | 1 | ||
| Line 26: | Line 30: | ||
| Enter project name/ | Enter project name/ | ||
| CHEM0100 | CHEM0100 | ||
| - | Enter input file (with extension) | + | Enter input file (with .conf extension) |
| - | test.lj | + | test.conf |
| Enter number of nodes on which to run job | Enter number of nodes on which to run job | ||
| | | ||
| Line 37: | Line 41: | ||
| Do you wish to submit job to cluster (y/n) | Do you wish to submit job to cluster (y/n) | ||
| y | y | ||
| + | | ||
| + | |||
| + | ====== NAMD 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 **qnamd_2.13_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 (with .conf extension) | ||
| + | test.conf | ||
| + | Enter total walltime (hour: | ||
| + | 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 (with .conf extension) | ||
| + | test.conf | ||
| + | Enter total walltime (hour: | ||
| + | | ||
| + | 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/attic/howto/namd.1460443517.txt.gz · Last modified: 2021/12/09 16:42 (external edit)
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