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October 14, 2005Guassian Performance Workshop at Jackson State University The Mississippi Center for Supercomputing Research Gaussian Performance Workshop At Jackson State University
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October 14, 2005Guassian Performance Workshop at Jackson State University Topics Estimating Parallel Efficiency with qstat –f Emails to Researchers Parallel Efficiency Example New g03sub
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October 14, 2005Guassian Performance Workshop at Jackson State University qstat –f Redwood Example qstat -f 7508 | grep resources resources_used.cpupercent = 601 resources_used.cput = 96:32:39 resources_used.mem = 421584kb resources_used.ncpus = 2 resources_used.vmem = 846304kb resources_used.walltime = 53:15:14 96 / 53 = …. Speedup = 1.81 1.81 / 2 = … Efficiency = 90.5%
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October 14, 2005Guassian Performance Workshop at Jackson State University qstat –f Sweetgum Example sweetgum> qstat -f 466 | grep resources resources_used.cpupercent = 98 resources_used.cput = 133:48:31 resources_used.mem = 360320kb resources_used.ncpus = 4 resources_used.vmem = 1082416kb resources_used.walltime = 136:04:22 133 / 136 = …. Speedup = 0.98 0.98 / 4 = … Efficiency = 24.5%
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October 14, 2005Guassian Performance Workshop at Jackson State University Emails to Researchers http://www.mcsr.olemiss.edu/admin/pbsjobs/pbsjobs.php -Job id 466 -Job id 7508
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October 14, 2005Guassian Performance Workshop at Jackson State University Mimosa Parallel Efficiency - Can’t use resources_used.cput - Can’t trust resources_used.cpupercent - Run same job on 1, 2, 4 nodes & compare wallclock times - qstat –f | grep exec_host - rsh to nodes and execute “top”
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October 14, 2005Guassian Performance Workshop at Jackson State University Mimosa Example - Gaussian job took 8 days on 8 nodes - Same job took 11 days on 4 nodes - Same job took 13 days on 1 node - 8 node speedup: 1.5x - 8 node parallel efficiency: 19% - 4 node speedup: 1.3x - 4 node parallel efficiency: 64%
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October 14, 2005Guassian Performance Workshop at Jackson State University Mimosa Example - User saved 5 days by running on 1 node - If user had only 8 nodes… - And had 8 similar jobs to run… - If he runs them as 1 node jobs… - He can finish all 8 in 13 days. - If he runs then as 8 node jobs… - It will take 64 days to finish them all.
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October 14, 2005Guassian Performance Workshop at Jackson State University newg03sub - Validates input file memory with PBS - Validates input file %nprocl and %nprocs with PBS - Adds prefix to job name based on calculation type - Names scratch file directories based on jobid - Takes additional input parameter: max disk/scratch file - Example: -/ptmp/jghale/benchmarking/sweetgum/h artree-fock/medium/first/400mb/2proc
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