galaxy crashes trying to load pbs-python, possibly related to visualization

Question: galaxy crashes trying to load pbs-python, possibly related to visualization

3.6 years ago by

wrf • 0

Germany

wrf • 0 wrote:

Hello,

Our Galaxy instance has not been able to restart since this morning. Looking at the logs, the only thing that has changed lately was when I had attempted to configure a new visualization. Then, restarting Galaxy with run.sh hit this error (including a few previous lines):

galaxy.tools.imp_exp DEBUG 2015-04-22 13:46:11,164 Loaded history import tool: __IMPORT_HISTORY__
galaxy.web.base.pluginframework INFO 2015-04-22 13:46:11,165 VisualizationsRegistry, loaded plugin: charts
galaxy.visualization.registry INFO 2015-04-22 13:46:11,166 <galaxy.visualization.registry.VisualizationsConfigParser object at 0x7f8238d7ec50>, plugin disabled: Circster. Skipping...
galaxy.web.base.pluginframework INFO 2015-04-22 13:46:11,167 VisualizationsRegistry, loaded plugin: graphview
galaxy.web.base.pluginframework INFO 2015-04-22 13:46:11,167 VisualizationsRegistry, loaded plugin: phyloviz
galaxy.web.base.pluginframework INFO 2015-04-22 13:46:11,168 VisualizationsRegistry, loaded plugin: scatterplot
galaxy.visualization.registry INFO 2015-04-22 13:46:11,169 <galaxy.visualization.registry.VisualizationsConfigParser object at 0x7f8238d7ec50>, plugin disabled: Sweepster. Skipping...
galaxy.web.base.pluginframework INFO 2015-04-22 13:46:11,170 VisualizationsRegistry, loaded plugin: trackster
galaxy.jobs.manager DEBUG 2015-04-22 13:46:11,170 Starting job handler
galaxy.jobs INFO 2015-04-22 13:46:11,170 Handler 'main' will load all configured runner plugins
galaxy.jobs.runners.state_handler_factory DEBUG 2015-04-22 13:46:11,171 Loaded 'failure' state handler from module galaxy.jobs.runners.state_handlers.resubmit
galaxy.jobs.runners DEBUG 2015-04-22 13:46:11,171 Starting 4 LocalRunner workers
galaxy.jobs DEBUG 2015-04-22 13:46:11,171 Loaded job runner 'galaxy.jobs.runners.local:LocalJobRunner' as 'local'
Traceback (most recent call last):
  File "/var/project/galaxy-dist/lib/galaxy/webapps/galaxy/buildapp.py", line 44, in app_factory
    app = UniverseApplication( global_conf = global_conf, **kwargs )
  File "/var/project/galaxy-dist/lib/galaxy/app.py", line 136, in __init__
    self.job_manager = manager.JobManager( self )
  File "/var/project/galaxy-dist/lib/galaxy/jobs/manager.py", line 23, in __init__
    self.job_handler = handler.JobHandler( app )
  File "/var/project/galaxy-dist/lib/galaxy/jobs/handler.py", line 32, in __init__
    self.dispatcher = DefaultJobDispatcher( app )
  File "/var/project/galaxy-dist/lib/galaxy/jobs/handler.py", line 715, in __init__
    self.job_runners = self.app.job_config.get_job_runner_plugins( self.app.config.server_name )
  File "/var/project/galaxy-dist/lib/galaxy/jobs/__init__.py", line 586, in get_job_runner_plugins
    module = __import__( module_name )
  File "/var/project/galaxy-dist/lib/galaxy/jobs/runners/pbs.py", line 32, in <module>
    raise Exception( egg_message % str( e ) )
Exception:

The 'pbs' runner depends on 'pbs_python' which is not installed or not
configured properly.  Galaxy's "scramble" system should make this installation
simple, please follow the instructions found at:

    http://wiki.galaxyproject.org/Admin/Config/Performance/Cluster

Additional errors may follow:
['pbs_python']

At the moment I cannot use the web server, so I cannot configure anything there. Is there some way to disable the visualization temporarily (like some flag to change to FALSE somewhere)? Does anyone know what might cause this problem, if it is not the visualization?

Many thanks!

error crash galaxy pbs • 1.6k views

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modified 3.6 years ago by carlfeberhard ♦ 390 • written 3.6 years ago by wrf • 0

3.6 years ago by

Nate Coraor ♦ 3.2k

United States

Nate Coraor ♦ 3.2k wrote:

Galaxy loads job plugins based on what's configured in the job configuration file, by default config/job_conf.xml, although this can be changed by setting job_config_file in galaxy.ini. I'd suggest checking to make sure that you did not inadvertently enable the PBSJobRunner.

ADD COMMENT • link written 3.6 years ago by Nate Coraor ♦ 3.2k

That was indeed the problem. Thanks!

ADD REPLY • link written 3.6 years ago by wrf • 0

3.6 years ago by

carlfeberhard ♦ 390

United States

carlfeberhard ♦ 390 wrote:

Hi, wrf

Reading the Traceback it looks like the problem has more to do with your copy of pbs_python and not the visualization. The last lines of a traceback will generally give you the file and line number within that file where the error occurred. From there you can use it to trace back the steps that (possibly) caused the error.

The help provided in the error message mentions the wiki location for more information on how to build an configure your job runners and, more specifically for your case, pbs_python: https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster#PBS

From what I can tell you or your admin may need to re-compile pbs_python.

If you are still concerned that it is the visualization registry: you can edit your config/galaxy.ini file, uncomment the 'visualization_plugins_directory' line, and set it to None: visualization_plugins_directory = None. This will disable *all* visualizations from loading and being shown as options in the history.

ADD COMMENT • link written 3.6 years ago by carlfeberhard ♦ 390

we are using SLURM on a gentoo system, so I'm not sure that PBS was ever configured in the first place as it is incompatible with SLURM. What would I disable to stop it from trying to load PBS?

ADD REPLY • link written 3.6 years ago by wrf • 0

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