So I finally figured it out (thanks to the help from the IRC folks, bag and
natefoo).

I incorrectly had my job_conf.xml setup where no job runners were set. All
is working now.


--
Adam Brenner
Computer Science, Undergraduate Student
Donald Bren School of Information and Computer Sciences

Research Computing Support
Office of Information Technology
http://www.oit.uci.edu/rcs/

University of California, Irvine
www.ics.uci.edu/~aebrenne/
aebre...@uci.edu


On Sun, Apr 14, 2013 at 1:54 PM, Adam Brenner <aebre...@uci.edu> wrote:

> Anyone have any ideas? Still have not sorted this out....
>
>
> --
> Adam Brenner
> Computer Science, Undergraduate Student
> Donald Bren School of Information and Computer Sciences
>
> Research Computing Support
> Office of Information Technology
> http://www.oit.uci.edu/rcs/
>
> University of California, Irvine
> www.ics.uci.edu/~aebrenne/
> aebre...@uci.edu
>
>
> On Thu, Apr 11, 2013 at 2:24 PM, Adam Brenner <aebre...@uci.edu> wrote:
>
>> FYI: Here are the entries in paster.log. If you notice no job_handlers
>> are being sent. I performed tests on both nginx reverse proxy and direct
>> localhost:8080 (limited to our private network on campus)
>>
>> 128.200.34.227 - - [11/Apr/2013:13:24:40 -0700] "GET
>> /tool_runner?tool_id=upload1 HTTP/1.0" 200 - "
>> http://ghtf-hpc.oit.uci.edu/root/tool_menu"; "Mozilla/5.0 (Macintosh;
>> Intel Mac OS X 10_8_3) AppleWebKit/536.28.10 (KHTML, like Gecko)
>> Version/6.0.3 Safari/536.28.10"
>> galaxy.tools.actions.upload_common INFO 2013-04-11 13:24:44,173 tool
>> upload1 created job id 8
>> 128.200.34.227 - - [11/Apr/2013:13:24:43 -0700] "POST /tool_runner/index
>> HTTP/1.0" 200 - "http://ghtf-hpc.oit.uci.edu/tool_runner?tool_id=upload1";
>> "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_8_3) AppleWebKit/536.28.10
>> (KHTML, like Gecko) Version/6.0.3 Safari/536.28.10"
>> 128.200.34.227 - - [11/Apr/2013:13:24:44 -0700] "GET /history HTTP/1.0"
>> 200 - "http://ghtf-hpc.oit.uci.edu/tool_runner/index"; "Mozilla/5.0
>> (Macintosh; Intel Mac OS X 10_8_3) AppleWebKit/536.28.10 (KHTML, like
>> Gecko) Version/6.0.3 Safari/536.28.10"
>> 128.200.34.227 - - [11/Apr/2013:13:24:44 -0700] "GET
>> /api/histories/56959efe847bb360 HTTP/1.0" 200 - "
>> http://ghtf-hpc.oit.uci.edu/history"; "Mozilla/5.0 (Macintosh; Intel Mac
>> OS X 10_8_3) AppleWebKit/536.28.10 (KHTML, like Gecko) Version/6.0.3
>> Safari/536.28.10"
>>
>>
>> --
>> Adam Brenner
>> Computer Science, Undergraduate Student
>> Donald Bren School of Information and Computer Sciences
>>
>> Research Computing Support
>> Office of Information Technology
>> http://www.oit.uci.edu/rcs/
>>
>> University of California, Irvine
>> www.ics.uci.edu/~aebrenne/
>> aebre...@uci.edu
>>
>>
>> On Thu, Apr 11, 2013 at 12:39 PM, Adam Brenner <aebre...@uci.edu> wrote:
>>
>>> Howdy Galaxy Admins,
>>>
>>> I am installing Galaxy on our HPC cluster and running into a strange
>>> issue that I can no longer debug further. I am running the latest galaxy
>>> build as of Tuesday April 9th.
>>>     hg clone https://bitbucket.org/galaxy/galaxy-dist/
>>>     hg update stable
>>>
>>> When a user tries to upload a file via the web interface, nginx reverse
>>> proxy setup as described here
>>> http://wiki.galaxyproject.org/Admin/Config/Performance/nginx%20Proxy,
>>> the upload stays in a state of "Job is waiting to run."
>>>
>>> The job stays like this for both FTP uploads, and uploads via browser.
>>> The dataset is a 319 bytes (both FTP and upload via browser)
>>>
>>> My universe_wsgi.ini variables are like so:
>>>      .. under [app:main] ....
>>>      new_file_path = /som/galaxy/tmp
>>>      file_path = /som/galaxy/datasets/files
>>>      track_jobs_in_database = True
>>>      job_manager = manager
>>>      job_handlers = handler0,handler1
>>>      ... before [app:main] in [server:main] ....
>>>
>>>      [server:main]
>>>      use = egg:Paste#http
>>>      port = 8080
>>>      host = 127.0.0.1
>>>      use_threadpool = true
>>>      threadpool_workers = 5
>>>
>>>      [server:manager]
>>>      use = egg:Paste#http
>>>      port = 8079
>>>      host = 127.0.0.1
>>>      use_threadpool = true
>>>      threadpool_workers = 5
>>>
>>>      [server:handler0]
>>>      use = egg:Paste#http
>>>      port = 8090
>>>      host = 127.0.0.1
>>>      use_threadpool = true
>>>      threadpool_workers = 5
>>>
>>>      [server:handler1]
>>>      use = egg:Paste#http
>>>      port = 8091
>>>      host = 127.0.0.1
>>>      use_threadpool = true
>>>      threadpool_workers = 5
>>>
>>>
>>> Galaxy, for now, is running under the root user and is installed in
>>> /data/apps/galaxy (NFS mount) and the tmp files are stored on a GlusterFS
>>> system under /som/galaxy/.
>>>
>>> I have tried removing the extra job managers and handlers so I just have
>>> server:main and this still continues to happen. The paster.log files (with
>>> DEBUG = True) does not show any errors from python or issues writing to
>>> file. All POST and GET responses are recorded and nothing else.
>>>
>>> What I find strange is that if I look in new_file_path I do see my
>>> dataset as
>>>     upload_file_data_Zx_1rK
>>> and cat'ing the file shows the correct contents. The items listed in
>>> my file_path (the dataset_*.dat) files are empty/blank..but are created.
>>>
>>> Any ideas as to why its failing? Is it nginx? I only have it redirect
>>> 8080, and none of the other job managers / handlers...is that an issue? Do
>>> you think its permissions on the my file_path or new_file_path directories?
>>>
>>> A very stumped Adam.....
>>>
>>> --
>>> Adam Brenner
>>> Computer Science, Undergraduate Student
>>> Donald Bren School of Information and Computer Sciences
>>>
>>> Research Computing Support
>>> Office of Information Technology
>>> http://www.oit.uci.edu/rcs/
>>>
>>> University of California, Irvine
>>> www.ics.uci.edu/~aebrenne/
>>> aebre...@uci.edu
>>>
>>
>>
>
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