QMUL Multicore Gridengine Configuration
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Revision as of 15:06, 5 August 2014 by Daniel Traynor 06cc478329 (Talk | contribs)
Create parallel environment (PE) with dynamic cores PE configuration and attach this to the queue that will run the multicore jobs
For more info see https://twiki.cern.ch/twiki/bin/view/LCG/SGE
qconf -sp smp, (man sge_pe for more info)
pe_name smp slots 2448 user_lists NONE xuser_lists NONE start_proc_args /bin/true stop_proc_args /bin/true allocation_rule $pe_slots control_slaves FALSE job_is_first_task TRUE urgency_slots min accounting_summary FALSE
Reservations (draining nodes for multi core jobs) needs to be enabled. '-R y' flag enabling reservations is not added by 'sge_submit.sh' current workaround is running 'qalter -R y $list_of_mc_jobs' by a cron.
#!/bin/bash # reserve slots for jobs requesting 8 cores . /etc/profile.d/sge.sh /usr/bin/qstat -u \* | grep " 8 " | awk '{ system("/usr/bin/qalter " $1 " -R y")}' /usr/bin/qstat -u \* | grep " 2 " | awk '{ system("/usr/bin/qalter " $1 " -R y")}' /usr/bin/qstat -u \* | grep " 4 " | awk '{ system("/usr/bin/qalter " $1 " -R y")}'
While you are at it why not enable mpi, you then also get the mpi nagios check for free.
https://wiki.egi.eu/wiki/MAN03_MPI-Start_Installation_and_Configuration