Using ROSSMANN to Run GOSET StudiesOmar 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– 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 <JobId>

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.