Sep 162016
My notes for installing Son of Grid Engine (SGE) on commodity cluster.
Page Contents
Intro
Grab from here the following RPM packages:
gridengine-8.1.9-1.el6.x86_64.rpm gridengine-debuginfo-8.1.9-1.el6.x86_64.rpm gridengine-devel-8.1.9-1.el6.noarch.rpm gridengine-drmaa4ruby-8.1.9-1.el6.noarch.rpm gridengine-execd-8.1.9-1.el6.x86_64.rpm gridengine-guiinst-8.1.9-1.el6.noarch.rpm gridengine-qmaster-8.1.9-1.el6.x86_64.rpm gridengine-qmon-8.1.9-1.el6.x86_64.rpm
(at the time of writing version 8.1.9).
For your convenience, the following one liner should fetch these for you 🙂
cd /tmp; for i in gridengine-8.1.9-1.el6.x86_64.rpm gridengine-debuginfo-8.1.9-1.el6.x86_64.rpm gridengine-devel-8.1.9-1.el6.noarch.rpm gridengine-drmaa4ruby-8.1.9-1.el6.noarch.rpm gridengine-execd-8.1.9-1.el6.x86_64.rpm gridengine-guiinst-8.1.9-1.el6.noarch.rpm gridengine-qmaster-8.1.9-1.el6.x86_64.rpm gridengine-qmon-8.1.9-1.el6.x86_64.rpm; do wget https://arc.liv.ac.uk/downloads/SGE/releases/8.1.9/$i;done
Pick one server that will be serving as a master node in your cluster, referred later as qmaster.
For smaller clusters it can happily run on small VM (say 2x vCPU, 2GB RAM) maximising your resource usage.
Install EPEL on all nodes
rpm -Uvh http://dl.fedoraproject.org/pub/epel/epel-release-latest-6.noarch.rpm
Install prerequisits on all nodes
yum install -y perl-Env.noarch perl-Exporter.noarch perl-File-BaseDir.noarch perl-Getopt-Long.noarch perl-libs perl-POSIX-strptime.x86_64 perl-XML-Simple.noarch jemalloc munge-libs hwloc lesstif csh ruby xorg-x11-fonts xterm java xorg-x11-fonts-ISO8859-1-100dpi xorg-x11-fonts-ISO8859-1-75dpi mailx
Install GridEngine packages on all nodes
cd /tmp/ yum localinstall gridengine-*
Install Qmaster
cd /opt/sge ./install_qmaster
Accepting defaults should just work, well you might want to run it under different user than r00t so:
"Please enter a valid user name >> sgeadmin"
Make sure to add GridEngine to global environment:
cp /opt/sge/default/common/settings.sh /etc/profile.d/sge.sh
NFS export SGE root to nodes in your cluster
vim /etc/exports
/opt/sge 10.10.80.0/255.255.255.0(rw,no_root_squash,sync,no_subtree_check,nohide)
and mount share on exec nodes
vim /etc/fstab
qmaster:/opt/sge /opt/sge nfs tcp,intr,noatime 0 0
Installing exec nodes
cd /opt/sge ./install_execd
Just go with the flow here. Once done you should be able to see your exec nodes:
# qhost HOSTNAME ARCH NCPU NSOC NCOR NTHR LOAD MEMTOT MEMUSE SWAPTO SWAPUS ---------------------------------------------------------------------------------------------- global - - - - - - - - - - execnode01 lx-amd64 8 2 8 8 0.12 15.6G 5.2G 20.0G 104.9M execnode02 lx-amd64 8 2 8 8 0.00 15.7G 1.3G 21.1G 0.0 execnode03 lx-amd64 8 2 8 8 0.00 15.7G 1.4G 21.1G 18.6M
That means you can start submitting jobs to your cluster, either interactive with qlogin or qrsh or batch jobs with qsub.
Adding queues (for FSL)
In most cases it’s enough to have a default queue called all.q
This example will define new queues with different priorities (nice levels):
# change defaults for all.q
qconf -sq all.q |\
sed -e 's/bin\/csh/bin\/sh/' |\
sed -e 's/posix_compliant/unix_behavior/' |\
sed -e 's/priority 0/priority 20/' >\
/tmp/q.tmp
qconf -Mq /tmp/q.tmp
# add other queues
sed -e 's/all.q/verylong.q/' /tmp/q.tmp >\
/tmp/verylong.q
qconf -Aq /tmp/verylong.q
sed -e 's/all.q/long.q/' /tmp/q.tmp |\
sed -e 's/priority *20/priority 15/' >\
/tmp/long.q
qconf -Aq /tmp/long.q
sed -e 's/all.q/short.q/' /tmp/q.tmp |\
sed -e 's/priority *20/priority 10/' >\
/tmp/short.q
qconf -Aq /tmp/short.q
sed -e 's/all.q/veryshort.q/' /tmp/q.tmp |\
sed -e 's/priority *20/priority 5/' >\
/tmp/veryshort.q
qconf -Aq /tmp/veryshort.q
Monitoring your cluster
Use qmon GUI or the following commands:
# qstat -f
queuename qtype resv/used/tot. load_avg arch states --------------------------------------------------------------------------------- all.q@execnode01 BIP 0/0/8 0.12 lx-amd64 --------------------------------------------------------------------------------- all.q@execnode02 BIP 0/0/8 0.00 lx-amd64 --------------------------------------------------------------------------------- all.q@execnode03 BIP 0/0/8 0.00 lx-amd64 --------------------------------------------------------------------------------- long.q@execnode01 BIP 0/0/8 0.12 lx-amd64 --------------------------------------------------------------------------------- long.q@execnode02 BIP 0/0/8 0.00 lx-amd64 --------------------------------------------------------------------------------- long.q@execnode03 BIP 0/0/8 0.00 lx-amd64 --------------------------------------------------------------------------------- short.q@execnode01 BIP 0/0/8 0.12 lx-amd64 --------------------------------------------------------------------------------- short.q@execnode02 BIP 0/0/8 0.00 lx-amd64 --------------------------------------------------------------------------------- short.q@execnode03 BIP 0/0/8 0.00 lx-amd64 --------------------------------------------------------------------------------- verylong.q@execnode01 BIP 0/0/8 0.12 lx-amd64 --------------------------------------------------------------------------------- verylong.q@execnode02 BIP 0/0/8 0.00 lx-amd64 --------------------------------------------------------------------------------- verylong.q@execnode03 BIP 0/0/8 0.00 lx-amd64 --------------------------------------------------------------------------------- veryshort.q@execnode01 BIP 0/0/8 0.12 lx-amd64 --------------------------------------------------------------------------------- veryshort.q@execnode02 BIP 0/0/8 0.00 lx-amd64 --------------------------------------------------------------------------------- veryshort.q@execnode03 BIP 0/0/8 0.00 lx-amd64
# qhost -q
HOSTNAME ARCH NCPU NSOC NCOR NTHR LOAD MEMTOT MEMUSE SWAPTO SWAPUS ---------------------------------------------------------------------------------------------- global - - - - - - - - - - execnode01 lx-amd64 8 2 8 8 0.12 15.6G 5.2G 20.0G 104.9M all.q BIP 0/0/8 long.q BIP 0/0/8 short.q BIP 0/0/8 veryshort.q BIP 0/0/8 verylong.q BIP 0/0/8 execnode02 lx-amd64 8 2 8 8 0.00 15.7G 1.3G 21.1G 0.0 all.q BIP 0/0/8 long.q BIP 0/0/8 short.q BIP 0/0/8 veryshort.q BIP 0/0/8 verylong.q BIP 0/0/8 execnode03 lx-amd64 8 2 8 8 0.00 15.7G 1.4G 21.1G 18.6M all.q BIP 0/0/8 long.q BIP 0/0/8 short.q BIP 0/0/8 veryshort.q BIP 0/0/8 verylong.q BIP 0/0/8
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good share!