Open Microscopy Environment

Hi Folks,

TL:DR - How do I set up environment variables?

working through the OMERO install for Linux... almost there.

setup - VM hosted on VMWare, running Centos6.6, 64 bit. (this is a test install - proof of concept)

Have mostly managed to work around several version incompatibility issues "outside" the yum process, especially postgresql-9.4 and ice3.5

I'm failing at the last[1] hurdle - setting up the environment variables. How do I set up environment variables? (never done it...)

/omero admin diagnostics

================================================================================
OMERO Diagnostics 5.1.2-ice35-b45
================================================================================

Commands: java -version 1.7.0 (/usr/bin/java)
Commands: python -V 2.6.6 (/usr/bin/python)
Commands: icegridnode --version 3.5.1 (/usr/bin/icegridnode)
Commands: icegridadmin --version 3.5.1 (/usr/bin/icegridadmin)
Commands: psql --version 9.4.4 (/usr/bin/psql)

Server: icegridnode not started

Log dir: /home/omero/omero/OMERO.server-5.1.2-ice35-b45/var/log exists

Log files: Blitz-0.log 67.0 KB errors=9 warnings=0
Log files: DropBox.log 1.0 KB errors=2 warnings=1
Log files: FileServer.log 0.0 KB errors=1 warnings=0
Log files: Indexer-0.log 3.0 KB errors=1 warnings=0
Log files: MonitorServer.log 0.0 KB errors=1 warnings=0
Log files: OMEROweb.log 0.0 KB
Log files: OMEROweb_request.log 0.0 KB
Log files: PixelData-0.log 4.0 KB errors=1 warnings=0
Log files: Processor-0.log 17.0 KB errors=10 warnings=5
Log files: Tables-0.log n/a
Log files: TestDropBox.log n/a
Log files: master.err 112.0 KB errors=599 warnings=0
Log files: master.out 0.0 KB
Log files: Total size 0.21 MB


Environment:OMERO_HOME=(unset)
Environment:OMERO_NODE=(unset)
Environment:OMERO_MASTER=(unset)
Environment:OMERO_USERDIR=(unset)
Environment:OMERO_TMPDIR=(unset)
Environment:PATH=/usr/lib64/qt-3.3/bin:/usr/local/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin:/home/omero/bin
Environment:PYTHONPATH=(unset)
Environment:ICE_HOME=(unset)
Environment:LD_LIBRARY_PATH=(unset)
Environment:DYLD_LIBRARY_PATH=(unset)

Cannot list deployed applications.
OMERO data dir:'/OMERO' Exists? True Is writable? True
OMERO temp dir:'/home/omero/omero/tmp' Exists? True Is writable? True (Size: 0)

JVM settings: Blitz -Xmx1555m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions
JVM settings: Indexer -Xmx1037m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions
JVM settings: Pixeldata -Xmx1555m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions
JVM settings: Repository -Xmx1037m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions

OMERO.web status... [NOT STARTED]


[1] I say 'last' ... I mean 'latest'...

What environment variables are your trying to set? Did you try following the Linux walkthrough?
https://www.openmicroscopy.org/site/sup ... rough.html

Thanks, Simon

Hey Simon,
Thanks for that link - I'd seen it, but I was following the OMERO.server installation instructions...

https://www.openmicroscopy.org/site/sup ... ation.html

in part because redhat not debian... (I can translate, but wasn't really groking that I needed to look at both pages...)

To be clear... because it's not explicitly stated - I edit then add settings.env as an executable text file in /etc/profile.d/ and it should all just work?

bulwynkl wrote:To be clear... because it's not explicitly stated - I edit then add settings.env as an executable text file in /etc/profile.d/ and it should all just work?

Hi Paul,

The settings.env env vars are only to bootstrap the installation scripts with the your preferred installation configuration, not needed for OMERO itself. For example, the system_setup.sh script, referred to on the same (walkthrough) page, creates a Data Dir from the env var declared in settings.env file like so:

Code: Select all

mkdir -p "$OMERO_DATA_DIR"
chown omero "$OMERO_DATA_DIR"

So it's just part of the install walkthrough, and not required for a running server.

If we could have a copy of your Blitz log to help diagnose why OMERO won't start, that'd be great.

You can upload somewhere and include a link, attach to a forum post, send to the ome-users mailing list, or upload to our QA system at https://www.openmicroscopy.org/qa2/qa/upload/

All the best,

Kenny

Hey Ken,

Blitz-log-extract.txt uploaded - being just the latest start attempt.

suspect I've stuffed up the ICE install - (know I've stuffed up the python install).

On the plus side - it's a test VM so I can relatively easily start again

Hi Paul,

from the Blitz log, the main error is the Protocol family unavailable which had been reported in this forum thread:

Code: Select all

Caused by: java.net.SocketException: Protocol family unavailable
        at sun.nio.ch.Net.bind0(Native Method) ~[na:1.7.0_85]
        at sun.nio.ch.Net.bind(Net.java:463) ~[na:1.7.0_85]
        at sun.nio.ch.Net.bind(Net.java:455) ~[na:1.7.0_85]
        at sun.nio.ch.ServerSocketChannelImpl.bind(ServerSocketChannelImpl.java:223) ~[na:1.7.0_85]
        at sun.nio.ch.ServerSocketAdaptor.bind(ServerSocketAdaptor.java:74) ~[na:1.7.0_85]
        at IceInternal.Network.doBind(Network.java:245) ~[ice.jar:na]
        ... 68 common frames omitted


Have you tried the suggestion from the Server fails to start section of the troubleshooting page to set the Ice.IPv6 configuration?

Best,
Sebastien

Sebastien

thanks - problem solved....

Great, thanks for letting us know, Paul.

Best,
Sebastien