On Nov 6, 2012, at 2:44 PM, Alan V. Cowles wrote:

> 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

Hi Alan,

You're using the "run jobs as the actual user" code?  It looks like the job's 
working directory 
(/usr/local/galaxy/galaxy-dist/database/job_working_directory/000/11) does not 
exist after the job finishes running:

> 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'

Which is why you're getting the errors about changing permissions.

--nate

> 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 <alan.cow...@duke.edu> 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
>>> 
>>> 
>>> 
>>> 
>>> 
>>> -- 
>>> http://galaxyproject.org/
>>> http://getgalaxy.org/
>>> http://usegalaxy.org/
>>> http://wiki.galaxyproject.org/
>>> 
>> 
> 
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