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? :/
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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