[ome-users] omero 5.2.1 on Ubuntu 14.04 LTS + nginx wigs - broken. Little help?
Aleksandra Tarkowska (Staff)
A.Tarkowska at dundee.ac.uk
Sat Dec 19 06:23:34 GMT 2015
Hi Jake
I understand you are upgrading from 5.1?
Did you stop 'bin/omero web stop' before upgrade?
Could you show the output of 'ps aux | grep django.pid'
And 'bin/omero web status'
If there are still old fastcgi processes running you have to kill them by hand.
Ola
> On 18 Dec 2015, at 23:39, Jake Carroll <jake.carroll at uq.edu.au> wrote:
>
> Hi all.
>
> Well, it is near the holiday season and I thought I would give my users a nice gift, of an OMERO upgrade. It went fairly smoothly to begin with, but, noting that fastCGI was out and wsgi was in, I followed the instructions. The OMERO server comes up fine, and the insight clients are interacting with it fabulously, but the omeroweb client *is not*. We’re cooked.
>
> Diagnostics:
>
> omero at omero-prod-gen2:/var/log$ omero admin diagnostics
>
>
> ================================================================================
> OMERO Diagnostics 5.2.1-ice35-b15
> ================================================================================
>
> Commands: java -version 1.7.0 (/usr/bin/java)
> Commands: python -V 2.7.6 (/usr/bin/python)
> Commands: icegridnode --version 3.5.1 (/usr/bin/icegridnode)
> Commands: icegridadmin --version 3.5.1 (/usr/bin/icegridadmin)
> Commands: psql --version 9.3.10 (/usr/bin/psql)
>
>
> Server: icegridnode running
> Server: Blitz-0 active (pid = 13490, enabled)
> Server: DropBox active (pid = 13513, enabled)
> Server: FileServer active (pid = 13522, enabled)
> Server: Indexer-0 active (pid = 13523, enabled)
> Server: MonitorServer active (pid = 13524, enabled)
> Server: OMERO.Glacier2 active (pid = 13526, enabled)
> Server: OMERO.IceStorm active (pid = 13540, enabled)
> Server: PixelData-0 active (pid = 13544, enabled)
> Server: Processor-0 active (pid = 13560, enabled)
> Server: Tables-0 active (pid = 13553, enabled)
> Server: TestDropBox inactive (enabled)
>
>
> Log dir: /home/omero/OMERO.server/var/log exists
> Log files: Blitz-0.log 3.0 MB errors=76 warnings=257
> Log files: DropBox.log 5.0 KB errors=2 warnings=2
> Log files: FileServer.log 0.0 KB
> Log files: Indexer-0.log 63.0 KB errors=0 warnings=348
> Log files: MonitorServer.log 2.0 KB
> Log files: OMEROweb.lock 0.0 KB
> Log files: OMEROweb.log 3.0 KB errors=0 warnings=14
> Log files: OMEROweb_brokenrequest.lock 0.0 KB
> Log files: OMEROweb_brokenrequest.log 0.0 KB
> Log files: PixelData-0.log 64.0 KB errors=0 warnings=348
> Log files: Processor-0.log 260.0 KB errors=76 warnings=18
> Log files: Tables-0.log 19.0 KB errors=8 warnings=5
> Log files: TestDropBox.log n/a
> Log files: master.err 4.0 KB errors=0 warnings=5
> Log files: master.out 0.0 KB
> Log files: Total size 4.15 MB
>
>
> Environment:OMERO_HOME=(unset)
> Environment:OMERO_NODE=(unset)
> Environment:OMERO_MASTER=(unset)
> Environment:OMERO_USERDIR=(unset)
> Environment:OMERO_TMPDIR=(unset)
> Environment:PATH=/home/omero/OMERO.server/bin:/usr/local/bin:/usr/bin:/bin:/usr/local/games:/usr/games
> Environment:PYTHONPATH=/usr/CellProfiler:/usr/lib/python2.7/dist-packages:
> Environment:ICE_HOME=/usr/share/Ice-3.5.1
> Environment:LD_LIBRARY_PATH=/usr/lib/jvm/java-7-openjdk-amd64/jre/lib/amd64/server:/usr/lib/jvm/java-7-openjdk-amd64:/usr/lib/jvm/java-7-openjdk-amd64/include
> Environment:DYLD_LIBRARY_PATH=(unset)
>
>
> OMERO SSL port:4064
> OMERO TCP port:4063
> OMERO data dir:'/omero.store.ceph' Exists? True Is writable? True
> OMERO temp dir:'/home/omero/omero/tmp' Exists? True Is writable? True (Size: 24229)
>
>
> JVM settings: Blitz-${index} -Xmx7200m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions
> JVM settings: Indexer-${index} -Xmx4800m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions
> JVM settings: PixelData-${index} -Xmx7200m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions
> JVM settings: Repository-${index} -Xmx4800m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions
>
>
> OMERO.web status... [RUNNING] (PID 14434)
> Django version: 1.8.7
>
>
> So, when I start up the omero web components:
>
> omero at omero-prod-gen2:/var/log$ omero web start
> Post-processed 'omeroweb.viewer.min.css' as 'omeroweb.viewer.min.css'
> Post-processed 'omeroweb.viewer.min.js' as 'omeroweb.viewer.min.js'
>
>
> 0 static files copied to '/home/omero/OMERO.server/lib/python/omeroweb/static', 728 unmodified, 2 post-processed.
> Clearing expired sessions. This may take some time... [OK]
> Starting OMERO.web... [OK]
>
>
> Looks pretty good!
>
> So lets try to get to the front page.
>
> 502 Bad Gateway________________________________________
> nginx/1.4.6 (Ubuntu)
>
>
> So, that’s a fail.
>
> Let’s look at the error logs for nginx:
>
> 015/12/19 09:31:57 [error] 1960#0: *99 upstream prematurely closed connection while reading response header from upstream, client: xxx.xxx.xxx.xxx, server: omero-prod-gen2, request: "GET / HTTP/1.1", upstream: "fastcgi://0.0.0.0:4080", host: “xxx.xxx.xxx.xxx”
>
> Many many times. I noticed it is still making reference to fastcgi:// which isn’t present at all in my nginx config. Seems odd?
>
> Hoping I can still give my users a nice seasonal upgrade!
>
> Thank you, community.
>
> -jc
>
>
>
>
>
>
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