Galaxy Cloudman - Nodes Can'T Make Their Own Qsub Calls?

Question: Galaxy Cloudman - Nodes Can'T Make Their Own Qsub Calls?

6.2 years ago by

mailing list • 840 wrote:

Hi guys, I created a new Galaxy instance web launcher (https://biocloudcentral.herokuapp.com/launch) and then I ssh'd into the master node. I'm trying to run a Perl script that makes several qsub calls to other perl scripts. Now the catch is that one of those perl scripts makes its own qsub calls. And I'm getting this error when it tries to do that: Unable to run job: denied: host "ip-10-29-176-111.ec2.internal" is no submit host. Somehow this works fine on other clusters I've run this code on. Any idea what could be going on? Do I need to make all of the nodes "submit hosts"? Thanks a bunch! -Greg

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modified 6.2 years ago • written 6.2 years ago by mailing list • 840

6.2 years ago by

mailing list • 840

mailing list • 840 wrote:

As a follow up I found a command that should add the new nodes as submit hosts and I tried to run it but I got this error: $ qconf -as ip-10-28-164-178.ec2.internal denied: "ubuntu" must be manager for this operation What does it mean by manager? How would I run this command? I guess my preference is for Cloudman to do this automatically though so I'll be distributing this program to 3rd party users using the built-in cloudman sharing. I can't rightly ask users to be running qconf. Thanks again, Greg

ADD COMMENT • link written 6.2 years ago by mailing list • 840

You probably need to sudo to sgeadmin (cloudman guys correct me if you have this setup differently). I don't see any reason not to make worker nodes submit hosts by default in a future cloudman release. -- jt

ADD REPLY • link written 6.2 years ago by James Taylor ♦ 470

Thanks James. I'll give that a try. That would be excellent if you could make work nodes submit hosts by default in a future release. How would I get that on the plans? Submit a ticket somewhere? I guess in the meantime I could write a python script that runs qconf -sconfl to list all the hosts and for any that aren't listed when running qconf -ss, it would run qconf -as hostname on them. -Greg