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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>​
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 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