same error without the symlink, this time with actual syntax: 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/", line 293, in finish
File "/usr/local/galaxy/galaxy-dist/lib/galaxy/jobs/", 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/", line 679, in _change_ownership
    assert p.returncode == 0
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' - - [06/Nov/2012:14:41:07 -0400] "POST /library_common/library_item_updates HTTP/1.1" 200 - ""; "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.


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 < <>> 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.



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