On Tue, Mar 11, 2014 at 11:44 AM, Peter Cock <p.j.a.c...@googlemail.com> wrote:
> Hi all,
>
> Some of our split BLAST jobs using the parallelism feature have
> been failing (apparently for a while, so this is not a recent problem
> from changes in the BLAST wrappers) as follows:
>
> <quote>
> The Galaxy framework encountered the following error while attempting
> to run the tool:
>
> Traceback (most recent call last):
>   File "/mnt/galaxy/galaxy-dist/lib/galaxy/jobs/runners/tasks.py",
> line 141, in queue_job
>     job_wrapper.finish( stdout, stderr, job_exit_code )
>   File "/mnt/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py", line
> 962, in finish
>     if ( not self.external_output_metadata.external_metadata_set_successfully(
> dataset, self.sa_session ) and
> self.app.config.retry_metadata_internally ):
>   File "/mnt/galaxy/galaxy-dist/lib/galaxy/datatypes/metadata.py",
> line 638, in external_metadata_set_successfully
>     rval, rstring = simplejson.load( open(
> metadata_files.filename_results_code ) )
>   File 
> "/mnt/galaxy/galaxy-dist/eggs/simplejson-2.1.1-py2.6-linux-x86_64-ucs4.egg/simplejson/__init__.py",
> line 328, in load
>     use_decimal=use_decimal, **kw)
>   File 
> "/mnt/galaxy/galaxy-dist/eggs/simplejson-2.1.1-py2.6-linux-x86_64-ucs4.egg/simplejson/__init__.py",
> line 384, in loads
>     return _default_decoder.decode(s)
>   File 
> "/mnt/galaxy/galaxy-dist/eggs/simplejson-2.1.1-py2.6-linux-x86_64-ucs4.egg/simplejson/decoder.py",
> line 402, in decode
>     obj, end = self.raw_decode(s, idx=_w(s, 0).end())
>   File 
> "/mnt/galaxy/galaxy-dist/eggs/simplejson-2.1.1-py2.6-linux-x86_64-ucs4.egg/simplejson/decoder.py",
> line 420, in raw_decode
>     raise JSONDecodeError("No JSON object could be decoded", s, idx)
> JSONDecodeError: No JSON object could be decoded: line 1 column 0 (char 0)
>
> Tool execution generated the following error message:
>
> Unable to finish job
> </quote>
>
> Reading the code, this is breaking after all the child jobs have
> finished, and the data has been merged, during the external
> set metadata step.
>
> This specific example was BLAST XML output, and the merge
> had produced a 4.2 GB file which ended mid record (evidently
> the output merge was not really successful).
>
> However, as a partial XML file, it would be invalid and might
> this cause problems with something in the metadata setting
> code - and explain the reported error?
>
> Peter

Clues from my log:

2014-03-11T07:11:16.635421+00:00 ppserver galaxy.jobs.splitters.multi
ERROR 2014-03-11 07:11:16,563 Error merging files#012Traceback (most
recent call last):#012  File
"/mnt/galaxy/galaxy-dist/lib/galaxy/jobs/splitters/multi.py", line
153, in do_merge#012    output_type.merge(output_files,
output_file_name, **extra_merge_args)#012  File
"/mnt/galaxy/galaxy-dist/lib/galaxy/datatypes/data.py", line 572, in
merge#012    shutil.copyfileobj(open(fsrc, 'rb'), fdst)#012  File
"/usr/lib64/python2.6/shutil.py", line 31, in copyfileobj#012
fdst.write(buf)#012IOError: [Errno 28] No space left on device

2014-03-11T07:11:25.594665+00:00 ppserver galaxy.jobs.runners.tasks
ERROR 2014-03-11 07:11:25,558 Job wrapper finish method
failed#012Traceback (most recent call last):#012  File
"/mnt/galaxy/galaxy-dist/lib/galaxy/jobs/runners/tasks.py", line 141,
in queue_job#012    job_wrapper.finish( stdout, stderr, job_exit_code
)#012  File "/mnt/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py",
line 962, in finish#012    if ( not
self.external_output_metadata.external_metadata_set_successfully(
dataset, self.sa_session ) and
self.app.config.retry_metadata_internally ):#012  File
"/mnt/galaxy/galaxy-dist/lib/galaxy/datatypes/metadata.py", line 638,
in external_metadata_set_successfully#012    rval, rstring =
simplejson.load( open( metadata_files.filename_results_code ) )#012
File 
"/mnt/galaxy/galaxy-dist/eggs/simplejson-2.1.1-py2.6-linux-x86_64-ucs4.egg/simplejson/__init__.py",
line 328, in load#012    use_decimal=use_decimal, **kw)#012  File
"/mnt/galaxy/galaxy-dist/eggs/simplejson-2.1.1-py2.6-linux-x86_64-ucs4.egg/simplejson/__init__.py",
line 384, in loads#012    return _default_decoder.decode(s)#012  File
"/mnt/galaxy/galaxy-dist/eggs/simplejson-2.1.1-py2.6-linux-x86_64-ucs4.egg/simplejson/decoder.py",
line 402, in decode#012    obj, end = self.raw_decode(s, idx=_w(s,
0).end())#012  File
"/mnt/galaxy/galaxy-dist/eggs/simplejson-2.1.1-py2.6-linux-x86_64-ucs4.egg/simplejson/decoder.py",
line 420, in raw_decode#012    raise JSONDecodeError("No JSON object
could be decoded", s, idx)#012JSONDecodeError: No JSON object could be
decoded: line 1 column 0 (char 0)

So this looks like the root cause was a full partition, but Galaxy handled
this poorly (showing a JSON error rather than disk full).

This proposed patch should give a more helpful error message from the
metadata script, which is a start:

$ hg diff lib/galaxy/datatypes/metadata.py
diff -r 26f58e05aa10 lib/galaxy/datatypes/metadata.py
--- a/lib/galaxy/datatypes/metadata.py    Mon Nov 04 14:58:55 2013 -0500
+++ b/lib/galaxy/datatypes/metadata.py    Tue Mar 11 14:12:09 2014 +0000
@@ -635,7 +635,14 @@
         metadata_files = self.get_output_filenames_by_dataset(
dataset, sa_session )
         if not metadata_files:
             return False # this file doesn't exist
-        rval, rstring = simplejson.load( open(
metadata_files.filename_results_code ) )
+        if 0 == os.path.getsize(metadata_files.filename_results_code):
+            log.debug( 'setting metadata externally failed for %s %s:
%s empty' % ( dataset.__class__.__name__, dataset.id,
metadata_files.filename_results_code ) )
+            return False
+        try:
+            rval, rstring = simplejson.load( open(
metadata_files.filename_results_code ) )
+        except Exception as e:
+            log.debug( 'setting metadata externally failed for %s %s:
%s' % ( dataset.__class__.__name__, dataset.id, e ) )
+            return False
         if not rval:
             log.debug( 'setting metadata externally failed for %s %s:
%s' % ( dataset.__class__.__name__, dataset.id, rstring ) )
         return rval


Testing this is complicated without setting up a dedicated (small)
partition though to deliberately run out of space...

Peter
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