On Nov 12, 2012, at 11:17 AM, Alan V. Cowles wrote:

> yeah I'm not seeing the folder 11, I have a folder 2 created july 19...
> 
> 
> (galaxy_env)-bash-4.1$ pwd
> /usr/local/galaxy/galaxy-dist/database/job_working_directory/000
> 
> 
> (galaxy_env)-bash-4.1$ ls -al
> total 12
> drwxrwxr-x 3 galaxy galaxy 4096 Nov  6 14:41 .
> drwxrwxr-x 3 galaxy galaxy 4096 Jul 19 11:51 ..
> drwxrwxr-x 2 galaxy galaxy 4096 Jul 19 12:47 2
> 
> 
> should I make 11? or is it supposed to do this automatically for the job?

A working directory will be created every time a new job runs.  You can use the 
"cleanup_job" config option to control whether this directory is removed after 
job completion.

--nate

> 
> 
> 
> On 11/12/2012 10:54 AM, Nate Coraor wrote:
>> 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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