Added: worker nodes are now submit hosts as well:
https://bitbucket.org/galaxy/cloudman/changeset/b4c66783b42fb559b35b689363b34826d00ced34
This will be generally available with the next release of CloudMan is made
(however, there is no immediate plans for doing so as quite a bit of other
details need to ironed out before the code is stable).
On Sat, Sep 15, 2012 at 4:36 AM, greg margeem...@gmail.com wrote:
Hey all,
Here's the one-liner I came up with for my users to run until this is
changed in Galaxy:
$ qconf -sconfl | xargs -l sudo -E -u sgeadmin
/opt/sge/bin/lx24-amd64/qconf -as
(in case anyone is interested)
-Greg
On Fri, Sep 14, 2012 at 2:27 PM, greg margeem...@gmail.com wrote:
Spoke too soon!
$ sudo -E -u sgeadmin /opt/sge/bin/lx24-amd64/qconf -as
ip-10-29-213-80.ec2.internal
worked fine. -E tells sudo to use the users environment.
-Greg
On Fri, Sep 14, 2012 at 2:24 PM, greg margeem...@gmail.com wrote:
Ok, here's what I tried:
$ sudo -u sgeadmin qconf -as ip-10-29-213-80.ec2.internal
sudo: qconf: command not found
So then I tried:
$ which qconf
/opt/sge/bin/lx24-amd64/qconf
$ sudo -u sgeadmin /opt/sge/bin/lx24-amd64/qconf -as
ip-10-29-213-80.ec2.internal
critical error: Please set the environment variable SGE_ROOT.
So then I tried:
$ echo $SGE_ROOT
/opt/sge
$ sudo -u sgeadmin export SGE_ROOT=/opt/sge
sudo: export: command not found
Any ideas? I don't have the greatest understanding of the export
command.
Thanks again,
Greg
On Fri, Sep 14, 2012 at 8:23 AM, greg margeem...@gmail.com wrote:
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
On Thu, Sep 13, 2012 at 5:00 PM, James Taylor ja...@jamestaylor.org
wrote:
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
On Thu, Sep 13, 2012 at 4:17 PM, greg margeem...@gmail.com 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
On Thu, Sep 13, 2012 at 3:59 PM, greg margeem...@gmail.com 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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