On Thu, Jan 29, 2015 at 4:43 PM, Joseph Brent Greer <joseph.greer@northwestern.edu> wrote:

Hi all,

We have Pulsar working in a synchronous fashion using RESTful services on our local network. Now, we’re trying to use Pulsar on a remote (SGE) cluster and we will not have the ability to mount a shared file system.

What is the best way to use Galaxy to queue jobs?

Having a shared file system is definitely the best way to go if at all possible. If you definitely cannot make that happen - than Pulsar is probably the way to go - but it has limitations - it cannot for instance leverage tool shed installed dependencies and it certainly doesn't scale as well as Galaxy itself yet. I am working on these problems and am happy to help work through the problems you encounter - but I just like to throw out the warning about Pulsar.

If Pulsar is the answer, how do we defer to the cluster’s queue and have Pulsar wait on it?

So it sounds like you have experience setting up Pulsar - you will now need to set it up one a node connected to the remote cluster and open a port for it (unless you want to setup a message queue - but I recommend the RESTful mode when possible - it seems more robust currently). Once you have Pulsar setup - you will need to configure it to talk to your SGE cluster. For that you will need to install an SGE drmaa library on the node (it may already be available). Then copy local_env.sh.sample to local_env.sh in Pulsar and setup DRMAA_LIBRARY_PATH. export DRMAA_LIBRARY_PATH=/path/to/your/libdrmaa.so and finally setup a job_managers.ini file (cp job_managers.ini.sample job_managers.ini) and change the default section to something like: [manager:_default_] type=queued_drmaa More information about configuring job managers here https://pulsar.readthedocs.org/en/latest/job_managers.html. Finally - you need to configure Galaxy to use the correct Pulsar job runner - it might look something like this - https://gist.github.com/jmchilton/ca39ef1a3241d9074121. That should be it - and then Galaxy should send jobs to the cluster as needed.

How should Pulsar notify Galaxy when multiple jobs are done running?

Galaxy will poll the remote Pulsar server to determine when the jobs are complete. If you cannot open a port for pulsar to do this polling - then you will need to setup a message queue and then configure both sides to use that - I would definitely try to bully your cluster admins into opening that port before resorting to that though.

We’ve looked through the documentation and listservs and haven’t found anything directly related.

Pulsar was previously called the LWR - so there are more conversations related to it on galaxy-dev referring to it as the LWR.

Any help or suggestions would be great.

Hopefully this helps and good luck! -John

Thanks,

Joe Greer

Proteomics Center of Excellence

Northwestern University

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