{"id":3051,"date":"2016-06-02T13:11:21","date_gmt":"2016-06-02T13:11:21","guid":{"rendered":"http:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/?page_id=3051"},"modified":"2018-10-03T16:09:42","modified_gmt":"2018-10-03T16:09:42","slug":"pypcazip","status":"publish","type":"page","link":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/software\/applications\/pypcazip\/","title":{"rendered":"PyPcaZip"},"content":{"rendered":"

Overview<\/h2>\n

PyPcaZip<\/a> is a package using principle component analysis to compress trajectory data. It is a re-implementation by the ExTASY project www.extasy-project.org<\/a> 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.<\/p>\n

Version 1.5.1 is installed on the CSF.<\/p>\n

Restrictions on use<\/h2>\n

There are no restrictions on accessing this software on the CSF.<\/p>\n

Set up procedure<\/h2>\n

To access the software you must first load the modulefile:<\/p>\n

\r\nmodule load apps\/binapps\/pypcazip\/1.5.1\r\n<\/pre>\n
This will automatically load the Anaconda Python (v2.3.0) modulefile which provides Python 2.7.10.<\/p>\n
Running the application<\/h2>\n
Please do not run PyPcaZip on the login node. Jobs should be submitted to the compute nodes via batch. The following executables are available:<\/p>\n
\r\npyPcaunzip  pyPcazip    pyPczclust  pyPczcomp   pyPczdump   pyPczplot\r\n<\/pre>\n
You may run the executable on the login node with the --help<\/code> flag added to see a summary for command-line flags.<\/p>\n
Only the pyPcazip<\/code> utility may be run in parallel using MPI parallelism – see below.<\/p>\n
Serial batch job submission<\/h3>\n
Make sure you have the modulefile loaded then create a batch submission script, for example:<\/p>\n
\r\n#!\/bin\/bash\r\n#$ -S \/bin\/bash\r\n#$ -cwd             # Job will run from the current directory\r\n#$ -V               # Job will inherit current environment settings\r\n\r\n## This is a serial jobscript (1 core) so turn off MPI parallelism with --nompi\r\npyPcazip --nompi -i INPUT<\/em> -a ALBUM<\/em> -t TOPOLOGY<\/em> -o <\/em>OUTPUT<\/em>\r\n\r\n## Other tools are serial-only no \r\npyPcaunzip -t TOPOLOGY<\/em> -c COMPRESSED<\/em> -o <\/em>OUTPUT<\/em>\r\n<\/pre>\n
Submit the jobscript using: <\/p>\n
qsub scriptname<\/em><\/pre>\n
where scriptname<\/em> is the name of your jobscript.<\/p>\n
Parallel batch job submission<\/h3>\n
Only the pyPcazip<\/code> utility may be run in parallel.<\/p>\n
Make sure you have the modulefile loaded then create a batch submission script, for example:<\/p>\n
\r\n#!\/bin\/bash\r\n#$ -S \/bin\/bash\r\n#$ -cwd             # Job will run from the current directory\r\n#$ -V               # Job will inherit current environment settings\r\n#$ -pe smp.pe 4     # Single node parallel job (num cores can be 2 to 24)\r\n\r\n## $NSLOTS is automatically set to the number of cores give above\r\nmpirun -n $NSLOTS pyPcazip -i INPUT<\/em> -a ALBUM<\/em> -t TOPOLOGY<\/em> -o <\/em>OUTPUT<\/em>\r\n\r\n<\/pre>\n
Submit the jobscript using: <\/p>\n
qsub scriptname<\/em><\/pre>\n
where scriptname<\/em> is the name of your jobscript.<\/p>\n
Further info<\/h2>\n