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gamess [2017/09/21 17:41]
jokinsey Created the Gamess page
gamess [2017/09/21 18:39]
jokinsey Added Parallel Example
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 The General Atomic and Molecular Electronic Structure System (GAMESS) is a general ab initio quantum chemistry package. It is maintained by Mark Gordon'​s research group at Iowa State University. Source code, documentation and examples are available at the [[ http://​www.msg.ameslab.gov/​index.html|GAMESS website]]. The General Atomic and Molecular Electronic Structure System (GAMESS) is a general ab initio quantum chemistry package. It is maintained by Mark Gordon'​s research group at Iowa State University. Source code, documentation and examples are available at the [[ http://​www.msg.ameslab.gov/​index.html|GAMESS website]].
 +
 +====Environment Setup====
 +
 +You will need to add these lines to your ''​$HOME/​.bashrc''​ file to load the dependencies for the Gamess module. This will load the dependencies when you login to the system, however if you can also add these lines to your scripts instead.
 +
 +<​code>​
 +module load mkl/12.1.5
 +module load intel/​12.1.5
 +module load mvapich2/​1.8
 +module load gamess
 +</​code> ​
 +
 +====Serial Example====
 +
 +Create a directory to specify where to run the examples named ''​GAMESS-JOBS''​ in your ''​$HOME''​ directory, and copy one of the example files from ''/​share/​apps/​gamess/​test/​standard''​. In this example we use file ''​exam47.inp''​.
 +
 +<​code>​
 +razor-l3:​jokinsey:​~$ mkdir GAMESS-JOBS
 +razor-l3:​jokinsey:​~$ cp /​share/​app/​gamess/​test/​standard/​exam47.inp GAMESS-JOBS/​
 +</​code>​
 +
 +Create a script named ''​gamess.pbs'',​ with your favorite text editor, in your ''​$HOME/​GAMESS-JOBS''​ directory to run our example job.
 +
 +<​code>​
 +#!/bin/bash
 +#PBS -N gamess
 +#PBS -q tiny16core
 +#PBS -j oe
 +#PBS -o gamess.$PBS_JOBID
 +#PBS -l nodes=1:​ppn=16
 +#PBS -l walltime=1:​00:​00
 +
 +cd $PBS_O_WORKDIR
 +
 +rungms exam47 01 1 16 >& exam47.log
 +</​code>​
 +
 +Notice the 3 numbers following the input file name in the last line of the script. ​ **01** stands for a version number of the GAMESS executable (this number will not change since we have a single comipled version of gamess labeled gamess.01.x). ​ The next number **1** is the number of parallel processes to run (all of the example input files provided with gamess are small and have to be executed serially). **16** is the number of cores per node (in the queue tiny16core each node has 16 cores). ​ Submit the job to the queue:
 +
 +<​code>​
 +razor-l3:​jokinsey:​~/​GAMESS-JOBS$ qsub gamess.pbs
 +</​code>​
 +
 +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