On Jan 9, 2013, at 12:18 AM, Kyle Ellrott wrote:

> I'm running a test Galaxy system on a cluster (merged galaxy-dist on Janurary 
> 4th). And I've noticed some odd behavior from the DRMAA job runner. 
> I'm running a multithread system, one web server, one job_manager, and three 
> job_handlers. DRMAA is the default job runner (the command for tophat2 is 
> drmaa://-V -l mem_total=7G -pe smp 2/), with SGE 6.2u5 being the engine 
> underneath. 
> 
> My test involves trying to run three different Tophat2 jobs. The first two 
> seem to start up (and get put on the SGE queue), but the third stays grey, 
> with the job manager listing it in state 'new' with command line 'None'. It 
> doesn't seem to leave this state. Both of the jobs that actually got onto the 
> queue die (reasons unknown, but much to early, probably some tophat/bowtie 
> problem), but one job is listed in error state with stderr as 'Job output not 
> returned from cluster', while the other job (which is no longer in the SGE 
> queue) is still listed as running. 

Hi Kyle,

It sounds like there are bunch of issues here.  Do you have any limits set as 
to the number of concurrent jobs allowed?  If not, you may need to add a bit of 
debugging information to the manager or handler code to figure out why the 
'new' job is not being dispatched for execution.

For the 'error' job, more information about output collection should be 
available from the Galaxy server log.  If you have general SGE problems this 
may not be Galaxy's fault.  You do need to make sure that the stdout/stderr 
files are able to be properly copied back to the Galaxy server upon job 
completion.

For the 'running' job, make sure you've got 'set_metadata_externally = True' in 
your Galaxy config.

--nate

> 
> Any ideas?
> 
> 
> Kyle
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