[ome-users] omero 5.2.1 on Ubuntu 14.04 LTS + nginx wigs - broken. Little help?

[Jake Carroll]

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