Molpro

Setting up the environment

To set up the environment load the version of the software that you want to use. For example for version 2010.1.25 use:

$ module add molpro/2010.1.25

Scratch files

Molpro writes a larges amount of temporary or scratch files. By default these are written to the /tmp directory on compute nodes. The /tmp directories are usually fairly small and may fill up quickly causing jobs to fail. In this case, to avoid these failures you may need to change the location of the scratch files. You can redirect these scratch files to another directory, such as the local SSD, or an area on /nobackup using the -d argument, e.g.:

# Use locally allocated space
$ molpro -d $TMPDIR
# or if this is insufficient
$ molpro -d /nobackup/your_scratch_directory

The directory /nobackup/your_scratch_directory is a directory that you create in the /nobackup area. Read more about the /nobackup filesystem here.

Example job scripts

Serial job submission

To run jobs through the batch scheduler, you need to submit them by using the command qsub <script name>. Below is an example job script. The example script below requests 1Gb RAM per core, and a single core for 2 hours, using the current environment and running from the current working directory. It runs the molpro script called example.com.

#!/bin/bash
#$ -l h_rt=2:0:0
#$ -l h_vmem=1G
#$ -V
#$ -cwd
molpro -d $TMPDIR example.com

MPP job submission

This is the same as the serial version, but asks for 8 cores and uses the MPP mode.

#!/bin/bash
#$ -l h_rt=2:0:0
#$ -l h_vmem=1G
#$ -pe smp 8
#$ -V
#$ -cwd
molprop -n $NSLOTS -d $TMPDIR example.com

MPPX job submission

This is the same as the serial version, but asks for 8 cores and uses the MPPX mode.

#!/bin/bash
#$ -l h_rt=2:0:0
#$ -l h_vmem=1G
#$ -pe smp 8
#$ -V
#$ -cwd
molprox -t $NSLOTS -d $TMPDIR example.com