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 >>> ___________________________________________________________ >>> Please keep all replies on the list by using "reply all" >>> in your mail client. To manage your subscriptions to this >>> and other Galaxy lists, please use the interface at: >>> >>> http://lists.bx.psu.edu/ > ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
