Errors after Upgrade from 5.4.5 to 5.5.1

Hi,
After upgrading from 5.4.5 to 5.5.1 I can’t start omero server.

omero@omero:~$>OMERO.py/bin/omero admin start
WARNING:omero.install.jvmcfg:Failed to invoke java:
out:
err:Erreur : impossible de trouver ou charger la classe principale ome.services.util.JvmSettingsCheck

WARNING:omero.install.jvmcfg:Failed to parse Free from {}
WARNING:omero.install.jvmcfg:Failed to parse Total from {}
WARNING:omero.install.jvmcfg:Failed to invoke java:
out:
err:Erreur : impossible de trouver ou charger la classe principale ome.services.util.JvmSettingsCheck
.................
No descriptor given. Using etc/grid/default.xml
Waiting on startup. Use CTRL-C to exit
.............................
Failed to startup some components after 300 seconds
Calling "stop" on remaining components
Waiting on shutdown. Use CTRL-C to exit

omero@omero:~$>OMERO.py/bin/omero admin diagnostics

================================================================================
OMERO Diagnostics (admin) 5.5.1-ice36-b122
================================================================================
        
Commands:   java -version                  1.8.0     (/usr/bin/java)
Commands:   python -V                      2.7.5     (/usr/bin/python)
Commands:   icegridnode --version          3.6.5     (/usr/bin/icegridnode)
Commands:   icegridadmin --version         3.6.5     (/usr/bin/icegridadmin)
Commands:   psql --version                 9.6.15    (/usr/bin/psql)
Commands:   openssl version                1.0.2     (/usr/bin/openssl)

Server:     icegridnode                    not started

Log dir:    /home/omero/OMERO.py/var/log   exists
Log files:  Blitz-0.log                    n/a
Log files:  DropBox.log                    7.0 KB        errors=10   warnings=5   
Log files:  FileServer.log                 1.0 KB       
Log files:  Indexer-0.log                  n/a
Log files:  MonitorServer.log              1.0 KB       
Log files:  OMEROweb.lock                  empty
Log files:  OMEROweb.log                   2.0 KB        errors=0    warnings=7   
Log files:  Processor-0.log                234.0 KB      errors=67   warnings=134 
Log files:  Tables-0.log                   251.0 KB      errors=67   warnings=134 
Log files:  TestDropBox.log                n/a
Log files:  master.err                     4.0 KB        errors=5    warnings=10  
Log files:  master.out                     empty
Log files:  Total size                     0.50 MB

Error while parsing logs

Environment:OMERO_HOME=(unset)             
Environment:OMERO_NODE=(unset)             
Environment:OMERO_MASTER=(unset)           
Environment:OMERO_USERDIR=(unset)          
Environment:OMERO_TMPDIR=/tmp              
Environment:PATH=/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/home/omero/OMERO.server/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:'/tmp'                         Exists? True	Is writable? True   (Size: 60613)

JVM settings: Blitz-${index}                -Xmx600m -XX:MaxPermSize=256m -XX:+IgnoreUnrecognizedVMOptions
JVM settings: Indexer-${index}              -Xmx400m -XX:MaxPermSize=256m -XX:+IgnoreUnrecognizedVMOptions
JVM settings: PixelData-${index}            -Xmx600m -XX:MaxPermSize=256m -XX:+IgnoreUnrecognizedVMOptions
JVM settings: Repository-${index}           -Xmx400m -XX:MaxPermSize=256m -XX:+IgnoreUnrecognizedVMOptions

tail OMERO.py/var/log/master.err
!! 09/24/19 15:46:49.228 error: communicator not destroyed during global destruction.Erreur : impossible de trouver ou charger la classe principale ome.services.blitz.Entry
-! 09/24/19 15:58:27.365 OMERO.Glacier2: warning: unable to contact permissions verifier `BlitzVerifier@BlitzAdapters'
   Reference.cpp:1637: Ice::NoEndpointException:
   no suitable endpoint available for proxy `BlitzVerifier -t -e 1.1 @ BlitzAdapters'
-! 09/24/19 15:58:27.366 OMERO.Glacier2: warning: unable to contact session manager `BlitzManager@BlitzAdapters'
   Reference.cpp:1637: Ice::NoEndpointException:
   no suitable endpoint available for proxy `BlitzManager -t -e 1.1 @ BlitzAdapters'
Erreur : impossible de trouver ou charger la classe principale ome.services.blitz.Entry
Erreur : impossible de trouver ou charger la classe principale ome.services.blitz.Entry
!! 09/24/19 15:58:42.989 error: communicator not destroyed during global destruction.

Philippe

HI @pmailly

sorry

Are using the OMERO.py bundle to try and start the server. If this is the case, it might miss the required JARs and explain the issue you are getting. Have you tried downloading the OMERO.server package and re-running bin/omero admin start?

Sebastien

Hi Sebastien,

  I restarted the server with OMERO.server package and it ok now. I

had forgotten that with the version 5.4 I started the OMERO server
outside from OMERO.py, unlike the web server.

Sorry.

Philippe

Hi Philippe,

no worries at all. Glad to hear your server was upgraded and started without issue.

Sebastien