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PyPcaZip
Overview
PyPcaZip is a package using principle component analysis to compress trajectory data. It is a re-implementation by the ExTASY project www.extasy-project.org of the PCAZIP toolkit developed and distributed by the Laughton Group at the University of Nottingham, UK, and the Orozco group at the University of Barcelona, Spain.
Version 1.5.1 is installed on the CSF.
Restrictions on use
There are no restrictions on accessing this software on the CSF.
Set up procedure
To access the software you must first load the modulefile:
module load apps/binapps/pypcazip/1.5.1
This will automatically load the Anaconda Python (v2.3.0) modulefile which provides Python 2.7.10.
Running the application
Please do not run PyPcaZip on the login node. Jobs should be submitted to the compute nodes via batch. The following executables are available:
pyPcaunzip pyPcazip pyPczclust pyPczcomp pyPczdump pyPczplot
You may run the executable on the login node with the --help flag added to see a summary for command-line flags.
Only the pyPcazip utility may be run in parallel using MPI parallelism – see below.
Serial batch job submission
Make sure you have the modulefile loaded then create a batch submission script, for example:
#!/bin/bash #$ -S /bin/bash #$ -cwd # Job will run from the current directory #$ -V # Job will inherit current environment settings ## This is a serial jobscript (1 core) so turn off MPI parallelism with --nompi pyPcazip --nompi -i INPUT -a ALBUM -t TOPOLOGY -o OUTPUT ## Other tools are serial-only no pyPcaunzip -t TOPOLOGY -c COMPRESSED -o OUTPUT
Submit the jobscript using:
qsub scriptname
where scriptname is the name of your jobscript.
Parallel batch job submission
Only the pyPcazip utility may be run in parallel.
Make sure you have the modulefile loaded then create a batch submission script, for example:
#!/bin/bash #$ -S /bin/bash #$ -cwd # Job will run from the current directory #$ -V # Job will inherit current environment settings #$ -pe smp.pe 4 # Single node parallel job (num cores can be 2 to 24) ## $NSLOTS is automatically set to the number of cores give above mpirun -n $NSLOTS pyPcazip -i INPUT -a ALBUM -t TOPOLOGY -o OUTPUT
Submit the jobscript using:
qsub scriptname
where scriptname is the name of your jobscript.
Further info
Updates
None.