I came up with a fix for User killed running job, but error encountered removing from DRM queue: 'DRMAAJobRunner' object has no attribute 'job_user_uid' and pushed it. -----Original Message----- From: Chorny, Ilya Sent: Friday, November 04, 2011 10:24 AM To: Chorny, Ilya; Nate Coraor (nate@bx.psu.edu) Cc: galaxy-dev@lists.bx.psu.edu Subject: RE: [galaxy-dev] Looks like actual user breaks splitting I am also getting the following error in the log file which makes no sense because the directory is empty. I will try to track it down. Thoughts? Ilya Traceback (most recent call last): File "/home/galaxy/ichorny/galaxy-central/lib/galaxy/jobs/__init__.py", line 732, in cleanup shutil.rmtree( self.working_directory ) File "/usr/lib64/python2.6/shutil.py", line 225, in rmtree onerror(os.rmdir, path, sys.exc_info()) File "/usr/lib64/python2.6/shutil.py", line 223, in rmtree os.rmdir(path) OSError: [Errno 39] Directory not empty: './database/job_working_directory/451' -----Original Message----- From: galaxy-dev-bounces@lists.bx.psu.edu [mailto:galaxy-dev-bounces@lists.bx.psu.edu] On Behalf Of Chorny, Ilya Sent: Friday, November 04, 2011 9:07 AM To: Duddy, John; Nate Coraor (nate@bx.psu.edu) Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Looks like actual user breaks splitting Nate, I get the following error when I try to kill a job. User killed running job, but error encountered removing from DRM queue: 'DRMAAJobRunner' object has no attribute 'job_user_uid'. Ilya -----Original Message----- From: galaxy-dev-bounces@lists.bx.psu.edu [mailto:galaxy-dev-bounces@lists.bx.psu.edu] On Behalf Of Duddy, John Sent: Thursday, November 03, 2011 3:55 PM To: Nate Coraor (nate@bx.psu.edu) Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Looks like actual user breaks splitting I just came to that conclusion myself. If you need me to do anything, let me know - but it sounds like you have a handle on it. Muchas gracias. John Duddy Sr. Staff Software Engineer Illumina, Inc. 9885 Towne Centre Drive San Diego, CA 92121 Tel: 858-736-3584 E-mail: jduddy@illumina.com -----Original Message----- From: Nate Coraor (nate@bx.psu.edu) [mailto:nate@bx.psu.edu] Sent: Thursday, November 03, 2011 3:53 PM To: Duddy, John Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Looks like actual user breaks splitting Nate Coraor (nate@bx.psu.edu) wrote:
Duddy, John wrote:
I'm not following you - it's been 6 months since I wrote that code ;-}
I know the feeling!
IT looks to me like a DatasetPath() object is always placed in that array, and with one exception near then, it looks like the change I made generates those objects the same way.
It's creating a dict in self.output_dataset_paths, and that dict looks like this when outputs_to_working_directory = False:
{ output_param_name : [ HDA, DatasetPath ], ... }
And this when True:
{ output_param_name : [ Dataset, DatasetPath ], ... }
Do you have a stack trace for the merge problem I can look at?
If you put this in do_merge()'s except block:
log.exception( stdout )
You'll get:
Traceback (most recent call last): File "/space/nate/galaxy-central-ichorny/lib/galaxy/jobs/splitters/multi.py", line 128, in do_merge output_type = outputs[output][0].datatype AttributeError: 'Dataset' object has no attribute 'datatype'
I could just change both methods to put an HDA in the list inside the dict there, but I haven't looked much into what output_dataset_paths is used for, so I wasn't sure what that might break.
Sorta answered it myself, it looks like you created this precisely for do_merge(), so changing it to contain the HDA fixes the problem (and shouldn't break anything else). --nate
Thanks, --nate
John Duddy Sr. Staff Software Engineer Illumina, Inc. 9885 Towne Centre Drive San Diego, CA 92121 Tel: 858-736-3584 E-mail: jduddy@illumina.com
-----Original Message----- From: Nate Coraor (nate@bx.psu.edu) [mailto:nate@bx.psu.edu] Sent: Thursday, November 03, 2011 2:22 PM To: Duddy, John Cc: Chorny, Ilya; galaxy-dev@lists.bx.psu.edu Subject: Re: Looks like actual user breaks splitting
Hi John,
It looks like the first issue is related to the change from get_output_fnames() -> compute_outputs(). When outputs_to_working_directory = False (default) this method stores/returns a HistoryDatasetAssociation, but when True, stores/returns a Dataset (the original method's behavior). Thus, accessing the object's .datatype attribute in the splitter's do_merge() fails.
Thanks, --nate
Duddy, John wrote:
I'll submit a pull request shortly...
John Duddy Sr. Staff Software Engineer Illumina, Inc. 9885 Towne Centre Drive San Diego, CA 92121 Tel: 858-736-3584 E-mail: jduddy@illumina.com
-----Original Message----- From: Nate Coraor (nate@bx.psu.edu) [mailto:nate@bx.psu.edu] Sent: Wednesday, November 02, 2011 12:24 PM To: Duddy, John Cc: Chorny, Ilya; galaxy-dev@lists.bx.psu.edu Subject: Re: Looks like actual user breaks splitting
John, Ilya,
I get further with sequence type inputs but it looks like JobWrapper.get_output_datasets_and_fnames() is not returning the right thing when outputs_to_working_directory = True
BTW, the base Data.split() method is broken after the updates to Sequence.split() since it wasn't updated to expect HistoryDatasetAssociations rather than filenames. Could you take a look at that when you get a chance?
--nate
Duddy, John wrote:
The datatype you are using does not define a split method. Are you working with our in-progress gz type or fastqillumina?
John Duddy Sr. Staff Software Engineer Illumina, Inc. 9885 Towne Centre Drive San Diego, CA 92121 Tel: 858-736-3584 E-mail: jduddy@illumina.com<mailto:jduddy@illumina.com>
From: Chorny, Ilya Sent: Wednesday, November 02, 2011 11:50 AM To: Duddy, John Cc: Nate Coraor (nate@bx.psu.edu); galaxy-dev@lists.bx.psu.edu Subject: Looks like actual user breaks splitting
Hey John,
Any thoughts?
Ilya
Traceback (most recent call last): File "/home/galaxy/ichorny/galaxy-central/lib/galaxy/jobs/runners/tasks.py", line 73, in run_job tasks = splitter.do_split(job_wrapper) File "/home/galaxy/ichorny/galaxy-central/lib/galaxy/jobs/splitters/multi.py", line 73, in do_split input_type.split(input_datasets, get_new_working_directory_name, parallel_settings) File "/home/galaxy/ichorny/galaxy-central/lib/galaxy/datatypes/data.py", line 473, in split raise Exception("Text file splitting does not support multiple files") Exception: Text file splitting does not support multiple files
Ilya Chorny Ph.D. Bioinformatics Scientist I Illumina, Inc. 9885 Towne Centre Drive San Diego, CA 92121 Work: 858.202.4582 Email: ichorny@illumina.com<mailto:ichorny@illumina.com> Website: www.illumina.com<http://www.illumina.com>
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