Has anyone seen a similar error like this before. We are unsure if galaxy is causing the issue or it is being cuased by slurm as it seems galaxy is prematurely deleting a file.
galaxy.jobs.runners DEBUG 2017-06-14 19:36:45,719 (3261/143577) Unable to cleanup /cm/shared/apps/galaxy/prod/galaxy/database/jobs_directory/003/3261/galaxy_3261.ec: [Errno 2] No such file or directory: '/cm/shared/apps/galaxy/prod/galaxy/database/jobs_directory/003/3261/galaxy_3261.ec' galaxy.jobs.output_checker DEBUG 2017-06-14 19:36:45,725 Tool produced standard error failing job - [slurmstepd: get_exit_code task 0 died by signal
Hi Evan,
If this is something that you rarely see and your filesystem is on a network drive, you could try setting `retry_job_output_collection` to 10 in the galaxy.ini file. This will let galaxy try to collection the output files 10 times, which should help if there is some delay for the filesystem to be updated.
Best, Marius
On 14 June 2017 at 22:02, evan clark eclark28@fau.edu wrote:
Has anyone seen a similar error like this before. We are unsure if galaxy is causing the issue or it is being cuased by slurm as it seems galaxy is prematurely deleting a file.
galaxy.jobs.runners DEBUG 2017-06-14 19:36:45,719 (3261/143577) Unable to cleanup /cm/shared/apps/galaxy/prod/galaxy/database/jobs_directory/ 003/3261/galaxy_3261.ec: [Errno 2] No such file or directory: '/cm/shared/apps/galaxy/prod/galaxy/database/jobs_directory/003/3261/ galaxy_3261.ec' galaxy.jobs.output_checker DEBUG 2017-06-14 19:36:45,725 Tool produced standard error failing job - [slurmstepd: get_exit_code task 0 died by signal ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/
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That may work, but now we are getting this error.
Exception happened during processing of request from ('127.0.0.1', 43030) Traceback (most recent call last): File "/cm/shared/apps/galaxy/prod/galaxy/.venv/lib/python2.7/site-packages/paste/httpserver.py", line 1085, in process_request_in_thread self.finish_request(request, client_address) File "/cm/shared/apps/galaxy/requirements/python/lib/python2.7/SocketServer.py", line 331, in finish_request self.RequestHandlerClass(request, client_address, self) File "/cm/shared/apps/galaxy/requirements/python/lib/python2.7/SocketServer.py", line 654, in __init__ self.finish() File "/cm/shared/apps/galaxy/requirements/python/lib/python2.7/SocketServer.py", line 713, in finish self.wfile.close() File "/cm/shared/apps/galaxy/requirements/python/lib/python2.7/socket.py", line 283, in close self.flush() File "/cm/shared/apps/galaxy/requirements/python/lib/python2.7/socket.py", line 307, in flush self._sock.sendall(view[write_offset:write_offset+buffer_size]) error: [Errno 32] Broken pipe
Marius van den Beek mailto:m.vandenbeek@gmail.com June 14, 2017 4:31 PM Hi Evan,
If this is something that you rarely see and your filesystem is on a network drive, you could try setting `retry_job_output_collection` to 10 in the galaxy.ini file. This will let galaxy try to collection the output files 10 times, which should help if there is some delay for the filesystem to be updated.
Best, Marius
My understanding is that this is not an error, it's an interruption in the communication with a client. This should be harmless if it doesn't happen at a massive rate. You probably have many more of these in your logs.
On Jun 14, 2017 11:04 PM, "evan clark" eclark28@fau.edu wrote:
That may work, but now we are getting this error.
Exception happened during processing of request from ('127.0.0.1', 43030) Traceback (most recent call last): File "/cm/shared/apps/galaxy/prod/galaxy/.venv/lib/python2.7/ site-packages/paste/httpserver.py", line 1085, in process_request_in_thread self.finish_request(request, client_address) File "/cm/shared/apps/galaxy/requirements/python/lib/python2.7/SocketServer.py", line 331, in finish_request self.RequestHandlerClass(request, client_address, self) File "/cm/shared/apps/galaxy/requirements/python/lib/python2.7/SocketServer.py", line 654, in __init__ self.finish() File "/cm/shared/apps/galaxy/requirements/python/lib/python2.7/SocketServer.py", line 713, in finish self.wfile.close() File "/cm/shared/apps/galaxy/requirements/python/lib/python2.7/socket.py", line 283, in close self.flush() File "/cm/shared/apps/galaxy/requirements/python/lib/python2.7/socket.py", line 307, in flush self._sock.sendall(view[write_offset:write_offset+buffer_size]) error: [Errno 32] Broken pipe
Marius van den Beek m.vandenbeek@gmail.com June 14, 2017 4:31 PM Hi Evan,
If this is something that you rarely see and your filesystem is on a network drive, you could try setting `retry_job_output_collection` to 10 in the galaxy.ini file. This will let galaxy try to collection the output files 10 times, which should help if there is some delay for the filesystem to be updated.
Best, Marius
galaxy-dev@lists.galaxyproject.org
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evan clark -
Marius van den Beek