same error without the symlink, this time with actual syntax:
galaxy.jobs ERROR 2012-11-06 14:41:06,596 (11) Failed to change
ownership of
/usr/local/galaxy/galaxy-dist/database/job_working_directory/000/11, failing
Traceback (most recent call last):
File "/usr/local/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py",
line 293, in finish
self.reclaim_ownership()
File "/usr/local/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py",
line 693, in reclaim_ownership
self._change_ownership( self.galaxy_system_pwent[0], str(
self.galaxy_system_pwent[3] ) )
File "/usr/local/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py",
line 679, in _change_ownership
assert p.returncode == 0
AssertionError
galaxy.objectstore CRITICAL 2012-11-06 14:41:08,863
/usr/local/galaxy/galaxy-dist/database/job_working_directory/000/11
delete error [Errno 2] No such file or directory:
'/usr/local/galaxy/galaxy-dist/database/job_working_directory/000/11'
152.3.172.61 - - [06/Nov/2012:14:41:07 -0400] "POST
/library_common/library_item_updates HTTP/1.1" 200 -
"http://galaxy.igsp.duke.edu:8080/library_common/browse_library?status=done&show_deleted=False&cntrller=library_admin&message=Added+7+datasets+to+the+library+__sq__Omics__sq__+%28each+is+selected%29.++Click+the+Go+button+at+the+bottom+of+this+page+to+edit+the+permissions+on+these+datasets+if+necessary.&id=5969b1f7201f12ae&created_ldda_ids=1462%2C1463%2C1464%2C1465%2C1466%2C1467%2C1468";
"Mozilla/5.0 (X11; Linux x86_64; rv:16.0) Gecko/20100101 Firefox/16.0"
On 11/06/2012 02:20 PM, Alan V. Cowles wrote:
I tossed the symlink and mounted the san:/vol/galaxy_sata/data/galaxy
to /usr/local/galaxy, though we use symlinks daily for practically all
of our softwares and programs practically invisibly, but I am happy to
try anything to get it going.
AC
On 11/06/2012 02:12 PM, Dave Clements wrote:
Hi Alan,
I'm CC'ing the Galaxy-Dev list on my response to your question.
I talked with Jen Jackson on this. Her suggestion is that the
symlink is most likely the problem somehow - this time. When in
doubt, getting rid of these good place to start. So recommended
starting solution to try - use full paths for everything. Also
probably keep all on same partition for the best performance, but
that would be hard to defend (there was some debate about this recently).
Many thanks to Jen for her (as always) careful consideration.
Dave C.
On Mon, Nov 5, 2012 at 7:15 AM, Alan V. Cowles <[email protected]
<mailto:[email protected]>> wrote:
Hey Dave,
Thanks for getting back in touch with me.
We are running our galaxy instance on a vm... with Centos (RHEL)
6.2, 2 vcpus, and 2gb vram, with a remote postgresql prod server
as our database instance.
Our first issue was trying to get it so we could load sequence
and larger files directly from an nfs mounted directory on the
server, without uploading via the web (php vs large files
problem.) We accomplished this via the data libraries interface
but it's still not very user intuitive.
Our first demo user attempted to upload 3 large files and
actually filled up the / partition on the server as galaxy was
installed at /usr/local.
After scrapping and rebuilding that, we now have a several
hundred GB nfs partition, mounted and /usr/local/galaxy is a
symlink to a folder on this volume.
The issue we are currently seeing is during an upload, or even
just linking files it runs for a while before erroring out and
saying there is no information on the error. The file seems to be
there and taking up the correct amount of disk space but galaxy
has a red bar.
The galaxy server instance is running back grounded in a screen
so we can always switch over and look at the output it shows to
standard out as errors happen, and it seems that it has trouble
changing permissions on the files in the nfs directory, even
though, root squash is disabled, and the entire directory is 777
at the top level and everything underneath is owned galaxy:galaxy.
AC
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