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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