NWChem 4.7 on Rachel

To run jobs, first download the template script nwScript. You can transfer files to the server using the scp command. Files can be edited on the server using emacs, pico, vi, etc.

The nwScript file contains the following…

#!/bin/csh a title line user for specifying the shell – ignore and don’t change

#PBS -l walltime=20:00:00 the total requested time (in this case 20 hours of wall time or real time)

#PBS -l nodes=1:ppn=4 the total number of nodes and processors requested (1 nodes, 4 processors). Since Rachel is really only 1 node, only

ever set nodes=1. For more processors, only change ppn=?

#PBS -j oe controls batch output – ignore and don’t change

#PBS -m ae tells server to e-mail when job completes or if it aborted due to an error

#PBS -M jjwilke@ccc.uga.edu the e-mail address notice is to be sent to

set echo controls batch output – ignore and don’t change

source /usr/local/Modules/default/init/csh

module load nwchem-4.7 loads nwchem

set base = $PBS_O_WORKDIR the folder you are currently in… you should submit jobs from the folder that has the input file

set job = input the name of your job.. probably best to just call it input.nw

set scr = $LOCAL/${job}.$PBS_JOBID controls scratch directory – probably best to ignore and not change

if ( -d $scr ) then

rm -rf $scr if an old scratch directory exists, the script removes it. This is important

endif to ensure that there is enough space in the scratch folder to run the job.

mkdir $scr

cd $scr initialize scratch directory

cp $base/$job.nw ./ moves your NWChem input file to the scratch directory

mpirun -np ${PBS_VPPN} nwchem $job.nw > $base/$job.out the command that starts the program

mpiclean

# clean up files if no longer needed

cd $SCRATCH

rm -f $scr

Warnings!!!

1. For this submit script, my input file must be named input.nw because of the line
set job = input

2. Never specify anything but 1 node. Rachel is only a single node with a gazillion processors!

3. You are allowed a maximum of 1 week wall time (real time)… but it lowers your priority considerably
if you request more.

4. Make sure you submit the PBS script from the same folder your input file is in.

To actually submit the job, you must type

qsub [scriptname]

To monitor the whole queue, use qstat commands like you do for zuul.