gamess
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gamess [2017/09/21 18:39] jokinsey Added Parallel Example |
gamess [2017/10/11 14:47] (current) jokinsey Removed Parallel Example Until Problem is solved |
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| cd $PBS_O_WORKDIR | cd $PBS_O_WORKDIR | ||
| + | cp exam47.inp /scratch/$PBS_JOBID | ||
| + | cd /scratch/$PBS_JOBID | ||
| rungms exam47 01 1 16 >& exam47.log | rungms exam47 01 1 16 >& exam47.log | ||
| + | |||
| + | mv exam47.log $PBS_O_WORKDIR/ | ||
| </code> | </code> | ||
| - | Notice the 3 numbers following the input file name in the last line of the script. **01** stands for a version number of the GAMESS executable (this number will not change since we have a single comipled version of gamess labeled gamess.01.x). The next number **1** is the number of parallel processes to run (all of the example input files provided with gamess are small and have to be executed serially). **16** is the number of cores per node (in the queue tiny16core each node has 16 cores). Submit the job to the queue: | + | When we run this job we copy over the input file to the ''/scratch/$PBS_JOBID'' directory where we will run the computation. Then when the job finishes we move the ''exam47.log'' file back to the directory we submitted the job from. |
| + | |||
| + | Notice the 3 numbers following the input file name in the last line of the script. **01** stands for a version number of the GAMESS executable (this number will not change since we have a single comipled version of gamess labeled gamess.01.x). The next number **1** is the number of parallel processes to run (all of the example input files provided with gamess are small and have to be executed serially). **16** is the number of cores per node (in the queue tiny16core each node has 16 cores). Submit the job to the queue. | ||
| <code> | <code> | ||
| Line 46: | Line 52: | ||
| This should yield two files as output a schedule file for the job and a file ''exam47.log'', which holds the most important information. | This should yield two files as output a schedule file for the job and a file ''exam47.log'', which holds the most important information. | ||
| - | |||
| - | ====Parallel Example==== | ||
| - | |||
| - | Since all of the standard examples are small and must be executed serially we have to use a custom example that has been added to demonstrate Gamess's parallel functionality. This is a larger example located in ''/share/apps/gamess/tests/custom'', which we will add to our ''$HOME/GAMESS-JOBS'' directory to run. | ||
| - | |||
| - | <code> | ||
| - | razor-l3:jokinsey:~$ cp /share/apps/gamess/tests/custom/azobiscis-3CH2NO2-pentazole-g3mp2.inp ~/GAMESS-JOBS | ||
| - | razor-l3:jokinsey:~$ cd GAMESS-JOBS/ | ||
| - | </code> | ||
| - | |||
| - | Create a ''gamess.pbs'' to run this job or edit the one from the serial example. | ||
| - | |||
| - | <code> | ||
| - | #!/bin/bash | ||
| - | |||
| - | #PBS -N gamess | ||
| - | #PBS -q tiny16core | ||
| - | #PBS -j oe | ||
| - | #PBS -o gamess.$PBS_JOBID | ||
| - | #PBS -l nodes=3:ppn=16 | ||
| - | #PBS -l walltime=2:00:00 | ||
| - | |||
| - | cd $PBS_O_WORKDIR | ||
| - | |||
| - | rungms azobiscis-3CH2NO2-pentazole-g3mp2 01 48 16 >& azobiscis-3CH2NO2-pentazole-g3mp2.log | ||
| - | </code> | ||
| - | |||
| - | You may notice we changed the number of nodes to **3** and the time to **2** hours. The input and log files were changed to reflect the example and the number of parallel processes was changed to **48**. | ||
| - | |||
| - | Submit the job and when its done the relevant output will be in the ''azobiscis-3CH2NO2-pentazole-g3mp2.log'' file. | ||
| - | |||
| - | <code> | ||
| - | razor-l3:jokinsey:~/GAMESS-JOBS$ qsub gamess.pbs | ||
| - | </code> | ||
gamess.txt · Last modified: 2017/10/11 14:47 by jokinsey
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