Using ROSSMANN to Run GOSET Studies
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Transcript of Using ROSSMANN to Run GOSET Studies
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Using ROSSMANN to Run GOSET StudiesOmar Laldin
(using materials from Jonathan Crider,
Harish Suryanarayana)Feb. 3, 2014
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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
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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\
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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
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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…
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Cluster Profile Settings• Add a new profile:– Click on +Add Import rossmann.settings
• Rename rossmann_Import rossmann_sudhoff
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Cluster Profile Settings• Update profile settings– Click on rossmann_sudhoff Edit
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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
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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
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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
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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>
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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.