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Using ROSSMANN to Run GOSET Studies

Using ROSSMANN to Run GOSET Studies. Omar Laldin ( using materials from Jonathan Crider, Harish Suryanarayana ) Feb. 3, 2014. Initial Setup. Get added as a user in the sudhoff queue Install SecureCRT 7.0 Install Cygwin-X XWin Server

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Using ROSSMANN to Run GOSET Studies

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  1. Using ROSSMANN to Run GOSET Studies Omar Laldin (using materials from Jonathan Crider, Harish Suryanarayana) Feb. 3, 2014

  2. Initial Setup • Get added as a user in the sudhoff queue • Install SecureCRT 7.0 • Install Cygwin-X XWinServer • Map a network drive to: \\samba.rcac.purdue.edu\username • Domain: OnePurdue User: username

  3. Initial Setup • Make a copy of matlab code and required libraries (GOSET, material toolbox, etc) to the mapped drive • Make sure all matlab path links are updated • Put a copy of the scheduler file (rossmann.settings) in the mapped drive • Placed in \\yara.ecn.purdue.edu\essl\esslgrp\Rossmann_Materials\

  4. MATLAB Graphics Mode • Run Cygwin-X  XWin server (Start Menu) • Run SecureCRTand connect to rossmann.rcac.purdue.edu using purdue credentials. • Check “Forward X11 packets” under the connection properties menu • Start interactive session on sudhoffnode for XX hours • qsub –I –q sudhoff –l nodes=1:ppn=1 –l walltime=XX:00:00 –v DISPLAY • Load and start Matlab on rossmann -bash-3.2$ module load matlab -bash-3.2$ matlab

  5. Matlab Graphics Mode • Create a new cluster profile (a cluster refers to the parallel computing cores and/or distributed computing nodes) • Navigate to Manage Cluster Profiles…

  6. Cluster Profile Settings • Add a new profile: • Click on +Add Import  rossmann.settings • Rename rossmann_Import rossmann_sudhoff

  7. Cluster Profile Settings • Update profile settings • Click on rossmann_sudhoff Edit

  8. Cluster Profile Settings • Under “Additional command line arguments for job submission” • Change –q standby -l walltime=01:00:00to –q sudhoff –l walltime=XX:00:00as desired • XX is the number of hours required from cores • Under “Resource list parameter” • Change –l nodes=1:ppn=^N^ to –l nodes= #nodes :ppn= #cores • Note: #nodes <=10, #cores <= 24 • e.g. –l nodes=1:ppn=24

  9. Running Code Graphics Mode • Close Cluster Profile Manager • Open #nodes x #cores (e.g. 24) workers: • matlabpool open rossmann_sudhoff 24 • Run the code • GAP.ev_pp=true; % parallel process • GAP.ev_npg=24; % number of workers

  10. MATLAB Batch Mode • Run SecureCRTand connect to rossmann.rcac.purdue.eduas before • Load and start MATLAB on rossmann -bash-3.2$ module load matlab -bash-3.2$ matlab –nodisplay • Turn off reporting in GOSET • GAP.rp_lvl=0; % no reporting

  11. MATLAB Batch Mode • Run your code: • job=batch(‘myscript’,’matlabpool’,24, … ’Configuration’,’rossmann_sudhoff’, … ’CaptureDiary’,true) • Check status of your job • qstat –u username • Check status of sudhoff queue • qlist • Delete job • qdel <JobId>

  12. Some Common Issues • Directly copying the code to network drive doesn’t work • Update MATLAB directory links using addpath from top-level script. • Change ‘\’ to ‘/’in all the paths (including MATLAB load command) • Change number of cores in GOSET • Do a trial run with Npop = 2 and Ngen = 2, make sure all result files are saved.

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