QMUL Multicore Gridengine Configuration

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

https://twiki.cern.ch/twiki/bin/view/LCG/SGE