Hey John,

So I’ve been happily using Pulsar to send all my Galaxy server jobs to our 
cluster here at UCL for several months now (I love it!). I am now exploring the 
‘run-as-real-user’ option for DRMAA submissions and have run into a problem. 
The files are correctly staged, correctly chowned, successfully submitted to 
the queue and the job runs. However, at job end (collection?) fails with the 
following error message in Pulsar:

Exception happened during processing of request from (‘*.*.*.*', 54321)
Traceback (most recent call last):
  File 
"/opt/rocks/lib/python2.6/site-packages/Paste-2.0.1-py2.6.egg/paste/httpserver.py",
 line 1072, in process_request_in_thread
    self.finish_request(request, client_address)
  File "/opt/rocks/lib/python2.6/SocketServer.py", line 322, in finish_request
    self.RequestHandlerClass(request, client_address, self)
  File "/opt/rocks/lib/python2.6/SocketServer.py", line 617, in __init__
    self.handle()
  File 
"/opt/rocks/lib/python2.6/site-packages/Paste-2.0.1-py2.6.egg/paste/httpserver.py",
 line 446, in handle
    BaseHTTPRequestHandler.handle(self)
  File "/opt/rocks/lib/python2.6/BaseHTTPServer.py", line 329, in handle
    self.handle_one_request()
  File 
"/opt/rocks/lib/python2.6/site-packages/Paste-2.0.1-py2.6.egg/paste/httpserver.py",
 line 441, in handle_one_request
    self.wsgi_execute()
  File 
"/opt/rocks/lib/python2.6/site-packages/Paste-2.0.1-py2.6.egg/paste/httpserver.py",
 line 291, in wsgi_execute
    self.wsgi_start_response)
  File "/cluster/galaxy/pulsar/pulsar/web/framework.py", line 39, in __call__
    return controller(environ, start_response, **request_args)
  File "/cluster/galaxy/pulsar/pulsar/web/framework.py", line 144, in 
controller_replacement
    result = self.__execute_request(func, args, req, environ)
  File "/cluster/galaxy/pulsar/pulsar/web/framework.py", line 124, in 
__execute_request
    result = func(**args)
  File "/cluster/galaxy/pulsar/pulsar/web/routes.py", line 82, in status
    return status_dict(manager, job_id)
  File "/cluster/galaxy/pulsar/pulsar/manager_endpoint_util.py", line 12, in 
status_dict
    job_status = manager.get_status(job_id)
  File "/cluster/galaxy/pulsar/pulsar/managers/stateful.py", line 95, in 
get_status
    proxy_status, state_change = self.__proxy_status(job_directory, job_id)
  File "/cluster/galaxy/pulsar/pulsar/managers/stateful.py", line 115, in 
__proxy_status
    proxy_status = self._proxied_manager.get_status(job_id)
  File 
"/cluster/galaxy/pulsar/pulsar/managers/queued_external_drmaa_original.py", 
line 62, in get_status
    external_status = super(ExternalDrmaaQueueManager, 
self)._get_status_external(external_id)
  File "/cluster/galaxy/pulsar/pulsar/managers/base/base_drmaa.py", line 31, in 
_get_status_external
    drmaa_state = self.drmaa_session.job_status(external_id)
  File "/cluster/galaxy/pulsar/pulsar/managers/util/drmaa/__init__.py", line 
50, in job_status
    return self.session.jobStatus(str(external_job_id))
  File "build/bdist.linux-x86_64/egg/drmaa/session.py", line 518, in jobStatus
    c(drmaa_job_ps, jobId, byref(status))
  File "build/bdist.linux-x86_64/egg/drmaa/helpers.py", line 299, in c
    return f(*(args + (error_buffer, sizeof(error_buffer))))
  File "build/bdist.linux-x86_64/egg/drmaa/errors.py", line 151, in error_check
    raise _ERRORS[code - 1](error_string)
InvalidJobException: code 18: The job specified by the 'jobid' does not exist.

With this corresponding error from my Galaxy server:

galaxy.tools.actions INFO 2016-10-13 18:47:51,851 Handled output (279.421 ms)
galaxy.tools.actions INFO 2016-10-13 18:47:52,093 Verified access to datasets 
(5.271 ms)
galaxy.tools.execute DEBUG 2016-10-13 18:47:52,118 Tool 
[toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/1.1.4] created job 
[25008<http://toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/1.1.4]%20created%20job%20[25008>]
 (560.404 ms)
galaxy.jobs DEBUG 2016-10-13 18:47:52,579 (25008) Working directory for job is: 
/Users/galaxy/galaxy-dist/database/job_working_directory/025/25008
galaxy.jobs.handler DEBUG 2016-10-13 18:47:52,591 (25008) Dispatching to pulsar 
runner
galaxy.jobs DEBUG 2016-10-13 18:47:52,677 (25008) Persisting job destination 
(destination id: hpc_low)
galaxy.jobs.runners DEBUG 2016-10-13 18:47:52,681 Job [25008] queued (90.231 ms)
galaxy.jobs.handler INFO 2016-10-13 18:47:52,699 (25008) Job dispatched
galaxy.tools.deps DEBUG 2016-10-13 18:47:53,138 Building dependency shell 
command for dependency 'samtools'
galaxy.jobs.runners.pulsar INFO 2016-10-13 18:47:53,233 Pulsar job submitted 
with job_id 25008
galaxy.jobs DEBUG 2016-10-13 18:47:53,257 (25008) Persisting job destination 
(destination id: hpc_low)
galaxy.datatypes.metadata DEBUG 2016-10-13 18:51:03,922 Cleaning up external 
metadata files
galaxy.jobs.runners.pulsar ERROR 2016-10-13 18:51:03,945 failure finishing job 
25008
Traceback (most recent call last):
  File "/Users/galaxy/galaxy-dist/lib/galaxy/jobs/runners/pulsar.py", line 386, 
in finish_job
    run_results = client.full_status()
  File "/Users/galaxy/galaxy-dist/lib/pulsar/client/client.py", line 132, in 
full_status
    return self.raw_check_complete()
  File "/Users/galaxy/galaxy-dist/lib/pulsar/client/decorators.py", line 28, in 
replacement
    return func(*args, **kwargs)
  File "/Users/galaxy/galaxy-dist/lib/pulsar/client/decorators.py", line 13, in 
replacement
    response = func(*args, **kwargs)
  File "/Users/galaxy/galaxy-dist/lib/pulsar/client/client.py", line 146, in 
raw_check_complete
    check_complete_response = self._raw_execute("status", {"job_id": 
self.job_id})
  File "/Users/galaxy/galaxy-dist/lib/pulsar/client/client.py", line 215, in 
_raw_execute
    return self.job_manager_interface.execute(command, args, data, input_path, 
output_path)
  File "/Users/galaxy/galaxy-dist/lib/pulsar/client/interface.py", line 96, in 
execute
    response = self.transport.execute(url, method=method, data=data, 
input_path=input_path, output_path=output_path)
  File "/Users/galaxy/galaxy-dist/lib/pulsar/client/transport/standard.py", 
line 34, in execute
    response = self._url_open(request, data)
  File "/Users/galaxy/galaxy-dist/lib/pulsar/client/transport/standard.py", 
line 20, in _url_open
    return urlopen(request, data)
  File 
"/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/urllib2.py",
 line 154, in urlopen
    return opener.open(url, data, timeout)
  File 
"/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/urllib2.py",
 line 437, in open
    response = meth(req, response)
  File 
"/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/urllib2.py",
 line 550, in http_response
    'http', request, response, code, msg, hdrs)
  File 
"/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/urllib2.py",
 line 475, in error
    return self._call_chain(*args)
  File 
"/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/urllib2.py",
 line 409, in _call_chain
    result = func(*args)
  File 
"/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/urllib2.py",
 line 558, in http_error_default
    raise HTTPError(req.get_full_url(), code, msg, hdrs, fp)
HTTPError: HTTP Error 500: Internal Server Error



I am running 15.10 and Python 2.7.10 on my iMac for the server and the cluster 
submission node is running Pulsar 0.5.0 and Python 2.7.12

For these tests I run Pulsar in an interactive window so I have not set the 
sudoers file up, but rather enter sudo password when requested by Pulsar (at 
the first step of chowning the staging directory). Also have rewrites set up in 
Galaxy’s pulsar_actions.yml and I am using remote_scp for the file transfers 
rather than http - although I have also tried switching back to http (as I 
noticed caching, which I am also testing, does not work with scp transfers) but 
get an identical set of error messages.

As I say, I have no troubles using a regular queued_drmaa manager in pulsar. 
Any ideas what the problem may be?

Cheers,
Rich





Richard J Poole PhD
Wellcome Trust Fellow
Department of Cell and Developmental Biology
University College London
518 Rockefeller
21 University Street, London WC1E 6DE
Office (518 Rockefeller): +44 20 7679 6577 (int. 46577)
Lab (529 Rockefeller): +44 20 7679 6133 (int. 46133)
https://www.ucl.ac.uk/cdb/academics/poole

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