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 Map a network drive to: \\samba.rcac.purdue.edu\username \\samba.rcac.purdue.edu\username – Domain: OnePurdue User: username

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\

MATLAB Graphics Mode Run Cygwin-X  XWin server (Start Menu) Run SecureCRT and connect to rossmann.rcac.purdue.edu using purdue credentials. – Check “Forward X11 packets” under the connection properties menu Start interactive session on sudhoff node 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

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…

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

Cluster Profile Settings Update profile settings – Click on rossmann_sudhoff  Edit

Cluster Profile Settings Under “Additional command line arguments for job submission” – Change –q standby -l walltime=01:00:00 to –q sudhoff –l walltime=XX:00:00 as 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

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

MATLAB Batch Mode Run SecureCRT and connect to rossmann.rcac.purdue.edu as 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

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

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.