Difference between revisions of "QMUL Multicore Gridengine Configuration"
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(Created page with " Create parallel environment (PE) with dynamic cores PE configuration and attach this to th equeue that will run the multicore jobs qconf -sp smp, (man sge_pe for mor info...") |
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| + | 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")}' | ||
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| + | 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 | ||
https://twiki.cern.ch/twiki/bin/view/LCG/SGE | https://twiki.cern.ch/twiki/bin/view/LCG/SGE | ||
Revision as of 15:03, 5 August 2014
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
