User Tools

Site Tools


nwchem

Differences

This shows you the differences between two versions of the page.

Link to this comparison view

Both sides previous revision Previous revision
nwchem [2017/09/14 20:46]
jokinsey Added NWChem page, along with environment setup and example job listings.
nwchem [2017/10/12 17:49]
jokinsey Fixed the location to run the job from in the PBS script
Line 73: Line 73:
 </​code>​ </​code>​
  
-In the directory contianing the benzene.nw input file, create ​an PBS script and name it nwchem.pbs.+In the directory contianing the benzene.nw input file, create ​a ''​PBS'' ​script and name it nwchem.pbs.
  
 <​code>​ <​code>​
 +#!/bin/bash
 #PBS -N nwchem #PBS -N nwchem
 #PBS -q tiny12core #PBS -q tiny12core
Line 84: Line 85:
  
 cd $PBS_O_WORKDIR cd $PBS_O_WORKDIR
 +cp benzene.* /​scratch/​$PBS_JOBID
 +cd /​scratch/​$PBS_JOBID
 +
 NP=$(wc -l < $PBS_NODEFILE) NP=$(wc -l < $PBS_NODEFILE)
  
 mpirun -np $NP -machinefile $PBS_NODEFILE nwchem benzene.nw > benzene.out mpirun -np $NP -machinefile $PBS_NODEFILE nwchem benzene.nw > benzene.out
 +mv benzene* bnz*  $PBS_O_WORKDIR
 </​code>​ </​code>​
 +
 +This ''​PBS''​ script moves the test files to the ''/​scratch/​$PBS_JOBID''​ directory where we will run the job then moves the output files back to the ''​$PBS_O_WORKDIR''​ where we submitted the job from.
  
 Then submit the job to be run in the queue ''​tiny12core''​ which we specified in the PBS file. Then submit the job to be run in the queue ''​tiny12core''​ which we specified in the PBS file.
nwchem.txt · Last modified: 2017/10/12 17:49 by jokinsey