Galaxy is failing due to a segfault in libdrmaa
[9116874.391434] python[5211]: segfault at 0 ip 00007fcb9fd8ae62 sp 
00007fcb9affe490 error 4 in[7fcb9fc29000+1b9000]

I first started observing this in the last few weeks. After the first event I 
pulled in this changeset

Handle invalid job ids in the drmaa runner.

but I'm still seeing the segfault.

I think this is some correlated log information from before the patch…

Error - <type 'exceptions.UnboundLocalError'>: local variable 'job' referenced 
before assignment
 line 143 in __call__
  app_iter = self.application(environ, start_response)
line 80 in __call__
  return self.application(environ, start_response)
 line 91 in __call__
  return environ, start_response )
 line 632 in __call__
  return self.application(environ, start_response)
File '/mnt/ngswork/galaxy/galaxy-dist/lib/galaxy/web/framework/', line 
160 in __call__
  body = method( trans, **kwargs )
 line 1025 in show_params
  return trans.fill_template( "show_params.mako", inherit_chain=inherit_chain, 
history=trans.get_history(), hda=hda, job=job, tool=tool, 
params_objects=params_objects )
UnboundLocalError: local variable 'job' referenced before assignment

after applying 4a95ae9
I see this DEBUG 2012-12-05 10:34:20,968 Stopping job 25519: DEBUG 2012-12-05 10:34:20,971 stopping job 25519 in drmaa 
runner DEBUG 2012-12-05 10:34:20,983 (25519/22378) User 
killed running job, but it was already dead - - [05/Dec/2012:10:34:19 -0400] "GET 
/datasets/414fa4e8d28bb2be/delete_async HTTP/1.1" 200 - 
 "Mozilla/4.0 (compatible; MSIE 8.0; Windows NT 5.1; Trident/4.0; InfoPath.2; 
.NET CLR 2.0.50727; .NET CLR 3.0.4506.2152; .NET CLR 3.5.30729)" INFO 2012-12-05 10:34:21,073 (25520) Job unable to run: one 
or more inputs deleted DEBUG 2012-12-05 10:34:22,251 Stopping job 25520: DEBUG 2012-12-05 10:34:22,253 stopping job 25520 in drmaa 

Any ideas?


Brad Langhorst<>

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