QChem 3.1 on Rachel

To run jobs, first download the template script qchem3_1Script. You can transfer files to the server using the scp command. Files can be edited on the server using vi, vi, etc.

The script 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

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

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

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

cd $base

module load qchem loads qchem

source $QC/bin/marvel.csh set qchem variables, make directories, and such

mkdir $LOCAL/qchem.$PBS_JOBID

setenv $QCSCRATCH $LOCAL/qchem.$PBS_JOBID

set in = input.dat this part assumes that your input file is input.dat and output file is output.dat

set out = output.dat CHANGE THIS IF YOU HAVE DIFFERENT NAMES!

qchem -np ${PBS_VPPN} $in $out executes qchem

mpiclean

#UNCOMMENT IF YOU DO NOT WISH TO RESTART

#rm -rf $scr/*

Warnings!!!

1. For this submit script, my input file must be named input.dat and output file must be output.dat because of the line
set in = input.dat
set out = output.dat

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

3. Only DFT is available for Parallel! If you want to do MP2, use MPQC!!!

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

5. 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.