Thanks a lot Chris, actually we found another place where we found rpms
for PBS Pro:
http://apps.man.poznan.pl/trac/pbs-drmaa
And it works now! :D
Have a great weekend,
L-A
Le 17/02/2012 17:07, Fields, Christopher J a écrit :
If they used a package install, I think the DRMAA libs for torque are normally
separate. For instance:
http://pkgs.org/download/torque-drmaa
If going from source, you can enable DRMAA compilation with --enable-drmaa; I
don't recall if that is on by default (I don't think it is).
chris
On Feb 17, 2012, at 3:49 AM, Louise-Amélie Schmitt wrote:
You don't need a full PBS server on that machine, just the client libraries and
configuration. i.e. if you can run 'qstat' from machine A and have it return
the queue on machine B, that should be all you need.
We asked the IT guys they did just that :) now qsub works fine from machine A!
But I still have a problem:
They have no libdrmaa.so anywhere! What should I do? If I understood correctly
it's part of the Fedstage DRMAA service provider, will it be enough installing
it on our Galaxy server?
Torque's syntax allows you to specify the server name right in the runner URL,
but pbs_python links against libtorque, which is part of the torque client,
which must be installed somewhere on the local system.
Ok, thanks a lot!
Best,
L-A
Best,
L-A
Le 30/01/2012 18:20, Nate Coraor a écrit :
On Jan 30, 2012, at 12:07 PM, Louise-Amélie Schmitt wrote:
Hi Nate,
Thanks for the leads!
But setting DRMAA_LIBRARY_PATH means I'm in trouble since the libraries are on
machine B which is maintained by our IT dept. I cannot access them from machine
A.
Is it a desperate situation? Will it work if I have a copy of those libs
somewhere? :/
Hi L-A,
The Galaxy server will need to be a submission host, so I believe it will have
to have PBS Pro installed. If it has this, then the FedStage DRMAA library
should be installable on the same host. It may be possible copy the libraries,
although I don't know whether you'd be able to configure the server address
without access to the directories in which the library will look for its
configuration.
--nate
Best,
L-A
Le 30/01/2012 17:18, Nate Coraor a écrit :
On Jan 30, 2012, at 7:37 AM, Louise-Amélie Schmitt wrote:
Hi Nate,
Thanks for the info!
I'm trying to understand how the URL for DRMAA works but I don't understand how
we can set it so it uses a different machine.
Our Galaxy runner runs on machine A and the cluster is on machine B, where do I
put B in the URL?
In the wiki there is this example:
drmaa://[native_options]/
I'm a bit confused, I would have expected something like:
drmaa://[machine]/[native_options]/
like for TORQUE. Did I miss something?
Hi L-A,
Hrm, I've only used it with SGE, which uses an environment variable to define
the cell location, and LSF, which I don't remember, but I assume it used the
default. I think if you configure the PBS Pro client on the submission host
and point DRMAA_LIBRARY_PATH at the correct libdrmaa, it will use your client
configuration. There are other PBS Pro users on the list who can hopefully
chime in with more details.
--nate
Best,
L-A
Le 19/01/2012 19:43, Nate Coraor a écrit :
On Jan 16, 2012, at 5:22 AM, Louise-Amélie Schmitt wrote:
Hello,
We want to move Galaxy's jobs from our small TORQUE local install to a big
cluster running PBS Pro.
In the universe_wsgi.ini, I changed the cluster address as follows:
default_cluster_job_runner = pbs:///
to:
default_cluster_job_runner = pbs://sub-master/clng_new/
where sub-master is the name of the machine and clng_new is the queue.
However, I get an error when trying to run any job:
galaxy.jobs.runners.pbs ERROR 2012-01-16 11:10:00,894 Connection to PBS server
for submit failed: 111: Could not find a text for this error, uhhh
This corresponds to the qsub error 111 (Cannot connect to specified server
host) which is, for some reason, caught by pbs_python as an error of its own
(111 not corresponding to any pbs_python error code, hence the
face-plant-message).
Our guess is that we might need to re-scramble the pbs_python egg with PBS
pro's libraries, is that correct?
If it's the case, what do we have to set as LIBTORQUE_DIR?
Hi L-A,
pbs_python is only designed for TORQUE, I don't think it is compatible with the
PBS Pro API. For that, you need to use the drmaa runner, which uses the
FedStage libdrmaa for PBS Pro.
--nate
Thanks,
L-A
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