This use case describes how to run MARS jobs on the eNMR grid.
A gzipped tar file containing all the necessary files and an example of a job file for grid submission is provided for download. This use case provides a basis for executing any MARS job on the eNMR grid.
File: usecase_mars.tgz
Description of content:
This directory contains an example of using the MARS 1.1.3 software for automatic backbone assignment of proteins. The software and the example were kindly provided by Markus Zweckstetter.
Created by Victor Jaravine / Henry Jonker, BMRZ, May 2009
Input files:
- mars.jdl : job file for grid submission
- mars.run : executable script that will run the program
- input.tgz: gzipped tar file containing the example
Output files:
- output.tgz : output of MARS
Execution on the eNMR grid: (commands are in italics)
1) Login as an eNMR grid user:
voms-proxy-init -voms enmr.eu
2) Submit job file:
glite-wms-job-submit -o mars.jobid -a mars.jdl
3) Check status:
glite-wms-job-status -i mars.jobid
4) When finished get back output:
glite-wms-job-output -i mars.jobid --dir mars-output
Comments:
Other example files are available with the MARS program and can be executed on the eNMR GRID in exactly the same way as the above example using the mars.jdl and mars.run jobscripts. For assignment using residual dipolar couplings the software PALES has been deployed in addition on the eNMR grid.