Open Microscopy Environment

Hi wanted to upgrade Omero from 5.1.3 to 5.2 today, but something went wrong in the process.
First, disclaimer, this server is shared between multiple users, so it's quite likely an issue with a user having changed configuration parameters without reporting it, rather than a problem with Omero per se.
Anyway, the issue seems to be with the Ice connection.
>omero --debug=debug admin start returns

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Installing OMERO.master Windows service.
Successfully installed OMERO.master Windows service.
Starting OMERO.master Windows service.
Returning popen: ['icegridadmin', '--Ice.Config=D:\\OmeroAdmin\\etc\\internal.cf
g', '-e', 'node ping master']
Server not reachable: exception ::Ice::NoEndpointException
{
    proxy = BlitzManager -t -e 1.1 @ BlitzAdapters
}

I've tried falling back to 5.1.4, as well as creating a new database, basically everything as a new install with a different binaries directory as well. I've previously been using the pre-compiled Ice 3.5 (against Python 2.7) without any problem. Nonetheless, I've downloaded 64-bit Ice for Windows x64 with 64-bit Python 2.7, and overwritten the previous Ice install with it, but that didn't help.

Here's what >omero admin diagnostics returns:

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================================================================================
OMERO Diagnostics 5.1.4-ice35-b55
================================================================================
       
Commands:   java -version                  1.8.0     (C:\ProgramData\Oracle\Java\javapath\java.EXE)
Commands:   python -V                      2.7.10    (C:\Anaconda\python.EXE -- 2 others)
Commands:   icegridnode --version          3.5.1     (C:\Ice\Ice35\bin\icegridnode.EXE)
Commands:   icegridadmin --version         3.5.1     (C:\Ice\Ice35\bin\icegridadmin.EXE)
Commands:   psql --version                 9.4.4     (C:\Program Files\PostgreSQL\9.4\bin\psql.EXE)

Server:     icegridnode                    not started

Log dir:    D:\OmeroAdmin\var\log          exists

Log files:  Blitz-0.log                    n/a
Log files:  DropBox.log                    0.0 KB        errors=3    warnings=0   
Log files:  FileServer.log                 0.0 KB       
Log files:  Indexer-0.log                  n/a
Log files:  MonitorServer.log              0.0 KB       
Log files:  OMEROweb.log                   n/a
Log files:  Processor-0.log                3.0 KB        errors=2    warnings=1   
Log files:  Tables-0.log                   3.0 KB        errors=2    warnings=1   
Log files:  TestDropBox.log                n/a
Log files:  master.err                     0.0 KB       
Log files:  master.out                     0.0 KB       
Log files:  Total size                     0.01 MB


Environment:OMERO_HOME=D:\OmeroAdmin       
Environment:OMERO_NODE=(unset)             
Environment:OMERO_MASTER=(unset)           
Environment:OMERO_USERDIR=(unset)         
Environment:OMERO_TMPDIR=C:\TEMP           
Environment:PATH=C:\Anaconda;C:\Anaconda\Scripts;C:\Program Files\Microsoft MPI\Bin\;C:\ProgramData\Oracle\Java\javapath;C:\Windows\system32;C:\Windows;C:\Windows\System32\Wbem;C:\Windows\System32\WindowsPowerShell\v1.0\;C:\Program Files\MATLAB\R2015a\runtime\win64;C:\Program Files\MATLAB\R2015a\bin;C:\Program Files\PostgreSQL\9.4\bin;D:\OmeroAdmin\bin;C:\Program Files\MATLAB\R2014b\runtime\win64;C:\Program Files\MATLAB\R2014b\bin;C:\Program Files\MATLAB\R2012a\runtime\win64;C:\Program Files\MATLAB\R2012a\bin;C:\Program Files (x86)\Microsoft SQL Server\100\Tools\Binn\;C:\Program Files (x86)\Microsoft SQL Server\100\DTS\Binn\;C:\Ice\Ice35\bin
Environment:PYTHONPATH=C:\Ice\Ice35\python
Environment:ICE_HOME=(unset)               
Environment:LD_LIBRARY_PATH=(unset)       
Environment:DYLD_LIBRARY_PATH=C:\Ice\Ice35\lib

Cannot list deployed applications.
OMERO data dir:'D:\\fk_OmeroBinaries'         Exists? True   Is writable? True
OMERO temp dir:'C:\TEMP'                      Exists? True   Is writable? True   (Size: 77)

JVM settings: Blitz                         -Xmx7200m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions
JVM settings: Indexer                       -Xmx4800m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions
JVM settings: Pixeldata                     -Xmx7200m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions
JVM settings: Repository                    -Xmx4800m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions

OMERO.web status... [NOT STARTED]


and additional debug diagnostic outputs:

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Returning popen: ['java', '-version']
Returning popen: ['python', '-V']
Returning popen: ['icegridnode', '--version']
Returning popen: ['icegridadmin', '--version']
Returning popen: ['psql', '--version']
Returning popen: ['icegridadmin', '--Ice.Config=D:\\OmeroAdmin\\etc\\internal.cf
g', '-e', 'server list']

                Stdout:

                Stderr:
icegridadmin: could not contact the default locator:
Network.cpp:2513: Ice::ConnectionRefusedException:
connection refused: The remote computer refused the network connection.


Error while parsing logs
Returning popen: ['icegridadmin', '--Ice.Config=D:\\OmeroAdmin\\etc\\internal.cf
g', '-e', 'application list']

            Stdout:

            Stderr:
icegridadmin: could not contact the default locator:
Network.cpp:2513: Ice::ConnectionRefusedException:
connection refused: The remote computer refused the network connection.

Any idea how to fix this?
Thanks!

Hi

Could you delete the OMERO.server/var directory and restart OMERO? If that fails then delete the var directory, reboot your computer, and try again?

If that still doesn't help, could you post the output of:

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omero config get --hide-password
omero admin diagnostics


(I'd like to see your diagnostics again in case something changed after the reboot).

Thanks, Simon

Deleting OMERO.server/var folding and deleting followed by restarting didn't solve the issue. Interestingly, the second time, I got a barrage of threat warnings from Symantec antivirus, related to Icegridadmin. I disactivated the antivirus, but it didn't change the result.
Here are the outcomes of

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>omero config get --hide-password

omero.data.dir=D:\\OmeroBinaries
omero.db.name=omero_database
omero.db.pass=********
omero.db.user=omero_user


and

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>omero admin diagnostics

================================================================================
OMERO Diagnostics 5.1.4-ice35-b55
================================================================================
       
Commands:   java -version                  1.8.0     (C:\ProgramData\Oracle\Java\javapath\java.EXE)
Commands:   python -V                      2.7.10    (C:\Anaconda\python.EXE -- 2 others)
Commands:   icegridnode --version          3.5.1     (C:\Ice\Ice35\bin\icegridnode.EXE)
Commands:   icegridadmin --version         3.5.1     (C:\Ice\Ice35\bin\icegridadmin.EXE)
Commands:   psql --version                 9.4.4     (C:\Program Files\PostgreSQL\9.4\bin\psql.EXE)

Server:     icegridnode                    not started

Log dir:    D:\OmeroAdmin\var\log          exists

Log files:  Blitz-0.log                    n/a
Log files:  DropBox.log                    0.0 KB        errors=3    warnings=0   
Log files:  FileServer.log                 0.0 KB       
Log files:  Indexer-0.log                  n/a
Log files:  MonitorServer.log              0.0 KB       
Log files:  OMEROweb.log                   n/a
Log files:  Processor-0.log                14.0 KB       errors=8    warnings=4   
Log files:  Tables-0.log                   15.0 KB       errors=8    warnings=4   
Log files:  TestDropBox.log                n/a
Log files:  master.err                     0.0 KB       
Log files:  master.out                     0.0 KB       
Log files:  Total size                     0.03 MB


Environment:OMERO_HOME=D:\OmeroAdmin       
Environment:OMERO_NODE=(unset)             
Environment:OMERO_MASTER=(unset)           
Environment:OMERO_USERDIR=(unset)         
Environment:OMERO_TMPDIR=C:\TEMP           
Environment:PATH=C:\Anaconda;C:\Anaconda\Scripts;C:\Program Files\Microsoft MPI\Bin\;C:\ProgramData\Oracle\Java\javapath;C:\Windows\system32;C:\Windows;C:\Windows\System32\Wbem;C:\Windows\System32\WindowsPowerShell\v1.0\;C:\Program Files\MATLAB\R2015a\runtime\win64;C:\Program Files\MATLAB\R2015a\bin;C:\Program Files\PostgreSQL\9.4\bin;D:\OmeroAdmin\bin;C:\Program Files\MATLAB\R2014b\runtime\win64;C:\Program Files\MATLAB\R2014b\bin;C:\Program Files\MATLAB\R2012a\runtime\win64;C:\Program Files\MATLAB\R2012a\bin;C:\Program Files (x86)\Microsoft SQL Server\100\Tools\Binn\;C:\Program Files (x86)\Microsoft SQL Server\100\DTS\Binn\;C:\Ice\Ice35\bin;C:\Users\Vincent.GeekLU\AppData\Roaming\Dashlane\3.2.6.89099\bin\Firefox_Extension\{442718d9-475e-452a-b3e1-fb1ee16b8e9f}\components;C:\Users\Vincent.GeekLU\AppData\Roaming\Dashlane\3.5.2.94798\bin\Firefox_Extension\{442718d9-475e-452a-b3e1-fb1ee16b8e9f}\components;C:\Users\Vincent.GeekLU\AppData\Local\Box\Box Edit\
Environment:PYTHONPATH=C:\Ice\Ice35\python
Environment:ICE_HOME=(unset)               
Environment:LD_LIBRARY_PATH=(unset)       
Environment:DYLD_LIBRARY_PATH=C:\Ice\Ice35\lib

Cannot list deployed applications.
OMERO data dir:'D:\\OmeroBinaries'            Exists? True   Is writable? True
OMERO temp dir:'C:\TEMP'                      Exists? True   Is writable? True   (Size: 77)

JVM settings: Blitz                         -Xmx7200m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions
JVM settings: Indexer                       -Xmx4800m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions
JVM settings: Pixeldata                     -Xmx7200m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions
JVM settings: Repository                    -Xmx4800m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions

OMERO.web status... [NOT STARTED]


I just want to pitch in how I solved this problem. I have built an installer program which goes through all the necessary steps and prerequisites to get the Omero server working.

I also went from Omero 5.1.4 to 5.2 and I experienced the same error message. My problem apparently was that I did a complete 32bit installation previously, with the ZeroC Ice 3.4.2.msi installer, and using Python 2.6. This all worked perfectly well.

When I upgraded, I decided to also upgrade Python to 2.7, but still a 32bit installation. I then also chose to download the 32 bit binaries compiled against python 2.7 32bit of Ice 3.5.1 which are available for download on the openmicroscopy website. This seemed to work well on half the PC's I ran my installer on, but on the other half I got the mentioned error. All PC's were actually clean Windows 8 64 bit systems, so that was indeed strange.

The problem seems to have been that because all systems were 64 bit, the downloadable 32 bit Ice3.5.1 binaries did not work on all systems. After I did a complete re-install of all components for 64 bit, including Python 2.7 64 bit, the Ice3.5.1 python2.7 64 bit binaries, etc. etc. did I finally manage to get everything working again on all PC's.

Just to be clear: so now as far as you know the only thing on the system that has changed is the Ice distribution that you're using? Previously you were using Python from anaconda as well? Any thoughts on what might else have changed?

Could you possibly take a look at the Event Viewer and see if there are any application error messages?

All the best,
~Josh.

Thank you both for your feedback. The issue is now solved.
Josh, basically, as far as I was aware nothing had changed. I had "re-installed" Ice 64 bit just to make sure this wasn't the source of the problem, but I used the same version as before, and it didn't fix anything.
Inspired by kverbist's comments above, I checked whether all components were 64 bit. Low and behold, Java 8 had recently been updated, using a 32 bit distribution. I upgraded that to 64 bit, then, for good measure, also re-installed 64 bit versions of Python dependencies and re-configured Omero. Now everything works!
So, apparently, the issue was due to Java.

Thanks for letting us know. If you have any clues whether from the logs or the Event Viewer which would point to the 32/64-bit, don't hesitate to pass them along. Otherwise, this will just have to go on the checklist of things to double check.

All the best!
~Josh.

Good to hear I was of some help!