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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