Advice On Disabling Sge Queue On Galaxy-Cloudman

Question: Advice On Disabling Sge Queue On Galaxy-Cloudman

6.7 years ago by

John Major • 40 wrote:

Hello All- I'd like to launch a galaxy-cloudman head node which does not accept SGE jobs, but as jobs are submitted go to compute nodes (or cause compute node to be added when auto-scale is on). Primarily, this is b/c I'd like to have the head node be a cheaper instance which can run long term, and only fire up more expensive compute nodes as they are actually needed. How would I enable this? Thanks- John

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modified 6.7 years ago by Enis Afgan • 50 • written 6.7 years ago by John Major • 40

6.7 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hi John, Since this question is about a Cloud installation, I am going to forward your question over to the galaxy-dev@bx.psu.edu mailing list so that the development community will have a better chance of seeing it and providing feedback. http://wiki.g2.bx.psu.edu/Support#Mailing_Lists Thanks! Jen Galaxy team -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/Support

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6.7 years ago by

Enis Afgan • 50

Enis Afgan • 50 wrote:

Hi John, Theoretically, this is a straightforward task but in reality CloudMan gets in the way of making it stick. Namely, if you are to manually remove the master instance from being an execution host, CloudMan will add it back in the next time a node is added or removed from the cluster, thus negating your manual modification. So, I will add this feature to CloudMan itself but I cannot commit to a date right now. It should be soon though. In the mean time, if you'd like to script this yourself via an add-hoc solution that runs periodically, below is the procedure for manually removing a node from SGE's execution host list: ubuntu@ip-10-204-170-63:~$ sudo -s root@ip-10-204-170-63:~# qhost HOSTNAME ARCH NCPU LOAD MEMTOT MEMUSE SWAPTO SWAPUS global - - - - - - - ip-10-204-170-63 lx24-amd64 1 1.11 615.2M 161.6M 0.0 0.0 # Remove the host from the list of execution hosts root@ip-10-204-170-63:~# qconf -de ip-10-204-170-63 Host object "ip-10-204-170-63" is still referenced in cluster queue "all.q". # Edit the configuration of allhosts and remove the host in question. If this is the only host in the list, replace it's name with word NONE root@ip-10-204-170-63:~# qconf -mhgrp "@allhosts" root@ip-10-204-170-63.ec2.internal modified "@allhosts" in host group list # Show configuraiton of group allhosts root@ip-10-204-170-63:~# qconf -shgrp "@allhosts" group_name @allhosts hostlist NONE # The hos is now removed from the list of execution hosts root@ip-10-204-170-63:~# qstat -f root@ip-10-204-170-63:~#

ADD COMMENT • link written 6.7 years ago by Enis Afgan • 50

6.7 years ago by

Enis Afgan • 50

Enis Afgan • 50 wrote:

Hi John, I'm glad you found an alternative solution. Late last night, I realized I had forgotten to email you yesterday as I completed implementing the feature for disabling the master from running jobs within CloudMan ( https://bitbucket.org/galaxy/cloudman/changeset/b21e967d30f9). I have not yet updated the official CloudMan (because there are some other features I'd like to add before doing so) but it is possible to get this code by pulling CloudMan's source from bitbucket, creating cm.tar.gz, and uploading it to your cluster's bucket. Let me know if you'd like to give it a shot and I can point you to a couple of scripts to make that task trivial. I also like the solution you found because it does not necessarily exclude the master from running jobs, just limits it. I'll see about adding that option as well.

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