Son of Gridengine
- 1 Introduction
- 2 Steps
- 3 Administration
After Oracle bought Sun and then shut-sourced the Sun Grid Engine, Open Grid Engine made a release based SGEv5 in 2012 which hey called GE2011. However there were no further releases. Then ARC at the University of Liverpool started releasing its "Son of Gridengine and have been maintaining updates to it at least as far March 2016.
Until September 2016, the Queue manager in the marvin cluster was GE2011 which was getting a bit old, so when the queue manager failed due to a corrupted database
Administrative host setup
All nodes must be set up as administrative hosts, despite the fact that only the master seems to be "administrative"
Getting the XML::Simple perl module
The RPMForge Extra repository are need for this. These can be installed via an RPM, and afterwards the Extra branch of the repo much be enabled as it is not enabled by default.
Note that it is best to disable this after all the RPMs have been installed
Install the Son of Gridware RPMs
Centos 7 requires the epel repo installed
And the following packages:
yum install jemalloc-3.6.0 lesstif-0.95.2 munge-libs-0.5.11 libdb4-utils-4.8.30
yum install -y gridengine-8.1.9-1.el6.x86_64.rpm gridengine-devel-8.1.9-1.el6.noarch.rpm gridengine-execd-8.1.9-1.el6.x86_64.rpm gridengine-qmaster-8.1.9-1.el6.x86_64.rpm gridengine-qmon-8.1.9-1.el6.x86_64.rpm
For a worker node this is rather excessive, but such is the nature of the binary-chek stage of the "install_exec" script that all of these are necessary.
copying the default/common directory over to the node
NOTE: Below is from Ramon, but when JW setup Phylo /opt/sge/default already existed, with the same date and file sizes as other nodes so not sure it's needed? First the default directroy must be created:
ssh nodeX 'mkdir /opt/sge/default'
And then followed by:
scp -r common node8:/opt/sge/default
chown -R sgeadmin.gridware sge
Add the following two lines to /etc/bashrc
SGE_ROOT=/opt/sge; export SGE_ROOT; PATH=/opt/sge/bin/lx-x64:$PATH
Note: on the older centos6 nodes the path is /opt/sge/bin/linux-x64, but the newer centos7 node had it as /opt/sge/bin/lx-x64.
Add the new server to the admin host
(following this: https://docs.oracle.com/cd/E19957-01/820-0697/i999062/index.html) So for phylo, run this on marvin:
qconf -ah phylo
check it's been added
should show it's been added.
Move into /opt/sge/ and run in install_execd. Follow the instructions above. For phylo everything was default.
Creating a new parallel environment
- Copy out an current parallel envioment out to a file
- edit this file as you wish
qconf -Ap <my_pe_file>
A crucial oversight is to forget that this new parallel environment needs to be inserted into the queue's configration.
Queues and hostgroups
the dohfq.sh script accepts a rootname and list of numbers. The rootname becomes @rootname hostgroup and rootname.q for the queue. Node0 is in fact marvin. 1, is node 1 etc. These are the nodes to be ncluded in the new queue.