QChem2.1 on BigBen – DFT Only!!!

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

The qchemScript file contains the following…

#!/bin/csh

#PBS –V don’t know and don’t care… it’s just supposed to be there

#PBS -N alanine sets the job name to alanine (this doesn’t really affect anything… this is just what will show up when you type qstat)

#PBS -l walltime=0:05:00 sets the walltime to 5 minutes

#PBS -j oe don’t know and don’t care… it’s just supposed to be there

#PBS -l size=2 tells script to use 2 processors

#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

setenv IOBUF_SIZE 32768 commands for iobuffers… probably important because bigben is not particularly fast with disk access

setenv IOBUF_COUNT 5

setenv IOBUF_PARAMS

setenv QC /usr/local/packages/QCHEM QChem needs so many variables… why Peter Gill? Why?

setenv QCSOURCE $QC

setenv QCAUX $QC/aux

setenv QCSCRATCH $SCRATCH/qchem_$PBS_JOBID

setenv QCPLATFORM LINUX_Ix86

setenv QCPARALLEL true

source $QC/bin/qchem.setup

mkdir $QCSCRATCH makes the scratch directory

cd $PBS_O_WORKDIR move to the current working directory

pbsyod -small_pages $QC/exe/qcprog.exe input.dat $QCSCRATCH/ > output.dat runs the command – this assumes your input file is input.dat

rm -rf $QCSCRATCH remove scratch

Warnings!!!

1. For this submit script, my input file must be named input.dat because of the line
pbsyod -small_pages $QC/exe/qcprog.exe input.dat $QCSCRATCH/ > output.dat

2. Never specify anything but a multiple of 2 processors. BigBen is a bunch of 2 processor nodes – so make it an even number.

3. You are allowed a maximum of 12 hours wall time. This machine is for massive jobs (integral direct preferably) that you want done fast.
Any long optimizations should go to Rachel or one of our machines.

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]

If this doesn’t work, you may need to modify executable permission on the script. In that case, type

chmod 755 [scriptname]

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