PSA

Overview

There is no description available for this software.

Restrictions on use

Access to this software is very restricted. No-one other than users from the pb02 contributing group may be granted access. Permission to grant access must ALWAYS be sought from the Perdita Barran.

Set up procedure

We now recommend loading modulefiles within your jobscript so that you have a full record of how the job was run. See the example jobscript below for how to do this. Alternatively, you may load modulefiles on the login node and let the job inherit these settings.

Load BOTH of the following modulefiles:

module load apps/binapps/msms/2.2.6.1
module load apps/binapps/psa/2

Running the application

Please do not run PSA on the login node. Jobs should be submitted to the compute nodes via batch.

Batch job submission

Create a batch submission script (which will load the modulefile in the jobscript), for example:

#!/bin/bash --login

#$ -cwd                 # Job runs in current directory - where submitted from
#$ -pe smp.pe 6         # For most of the time the software only uses 1 core, 
                        # but java processes sometimes need resource
                        # & restricting it seems tricky hence we recommend requesting 6 cores.

### It is useful to have a specific dir for the job. 
### If you run it multiple times in the same dir it overwrites existing files.
mkdir ${JOB_ID}

### Copy the required files to the dir where all the application output will go
cp *.inp ${JOB_ID}
cp *.xyz ${JOB_ID}
cd ${JOB_ID}

### The command line for the application
### The -Xss256m setting cannot be set higher for this example input data, if it is the job produces an out of memory issue.

java -XX:ParallelGCThreads=1 -XX:ParallelCMSThreads=1 -Xmx1g -Xss256m -Dpsa.general.ncore=1 -Dpsa.shape.SESexecutable=$MSMS_HOME/msms.x86_64Linux2.2.6.1.staticgcc -Dpsa.home=$PSA_HOME -Dpsa.scratch=$PSA_SCRATCH -Dpsa.config=$PSA_HOME/config/psa.defaults.config -jar "$PSA_HOME/dist/PSA-2.0.jar" example.psa.nitrogen.inp

Submit the jobscript using:

qsub scriptname

where scriptname is the name of your jobscript.