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. note you need to make sure that the PE SMP is listed first in order to make sure the multicore job is run only on one node. | |
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| − | + | https://wiki.egi.eu/wiki/MAN03_MPI-Start_Installation_and_Configuration | |
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| − | + | [[Category: Multicore]] | |
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Latest revision as of 11:25, 11 February 2016
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. note you need to make sure that the PE SMP is listed first in order to make sure the multicore job is run only on one node.
https://wiki.egi.eu/wiki/MAN03_MPI-Start_Installation_and_Configuration
