Open Microscopy Environment

Hi,

I have followed the procedure https://docs.openmicroscopy.org/omero/5 ... ebrew.html till "Binary repository" and then followed https://docs.openmicroscopy.org/omero/5 ... yment.html to setup a lightweight server. I am using a pre-build server (OMERO.server-5.4.0-ice36-b74) downloaded from omero site on my Mac OS 10.11.6. When I run "omero admin start" it gives me popup asking for "Python to accept incoming network connections", which I allow but the command fails:

Code: Select all

(omero) NCATS-2003754-M:~ sajidmo$ omero admin start
No descriptor given. Using etc/grid/default.xml
Waiting on startup. Use CTRL-C to exit
.N............................
Failed to startup some components after 300 seconds
Calling "stop" on remaining components
Waiting on shutdown. Use CTRL-C to exit

Below is the profile file containing the environment variables:

Code: Select all

JAVA_HOME=/Library/Java/JavaVirtualMachines/jdk-9.0.1.jdk/Contents/Home
ANT_HOME=/Users/sajidmo/Downloads/apache-ant-1.10.1
export ANT_HOME
export JAVA_HOME
export PATH=${PATH}:${ANT_HOME}/bin
export LANG=en_US.UTF-8
export LANGUAGE=en_US:en
alias startVmOmero="source ~/Virtual/omero/bin/activate"
# Pre-built server…
export OMERO_SERVER=/Users/sajidmo/downloads/OMERO.server-5.4.0-ice36-b74
export PATH=${PATH}:${OMERO_SERVER}/bin
alias startPg='pg_ctl -D /opt/homebrew/var/postgres -l /opt/homebrew/var/postgres/server.log -w start'
alias stopPg='pg_ctl -D /opt/homebrew/var/postgres -l /opt/homebrew/var/postgres/server.log -w stop'
export PYTHONPATH=$PYTHONPATH:/Users/sajidmo/projects/omero-iviewer/plugin

Any ideas how to fix this problem? Is there any log I could check to help point out the problem? Thanks

Hi,

We've a troubleshooting page at https://docs.openmicroscopy.org/omero/5 ... oting.html which may help

Minimally, there are a few logs which would be useful to share with us here to allow us to see what's going on.

• Output of bin/omero admin diagnostics
• Output of bin/omero config get --hide-password (Blank out any passwords)
• OMERO.server logs: ${OMERO_SERVER}/var/log

Cheers,

Kenny

Thanks Kenny. I will look at the troubleshooting page but here are the logs that you requested. Please let me know if you find anything. Thanks

Output of omero admin diagnostics

Code: Select all

(omero) NCATS-2003754-M:omero sajidmo$ omero admin diagnostics

================================================================================
OMERO Diagnostics (admin) 5.4.0-ice36-b74
================================================================================
       
Commands:   java -version                  9.0.1     (/usr/bin/java)
Commands:   python -V                      2.7.10    (/Users/sajidmo/Virtual/omero/bin/python -- 2 others)
Commands:   icegridnode --version          3.6.4     (/opt/homebrew/bin/icegridnode)
Commands:   icegridadmin --version         3.6.4     (/opt/homebrew/bin/icegridadmin)
Commands:   psql --version                 10.1      (/opt/homebrew/bin/psql)

Server:     icegridnode                    not started

Log dir:    /Users/sajidmo/downloads/OMERO.server-5.4.0-ice36-b74/var/log exists
Log files:  Blitz-0.log                    1.0 MB        errors=30   warnings=35 
Log files:  DropBox.log                    16.0 KB       errors=19   warnings=10 
Log files:  FileServer.log                 3.0 KB       
Log files:  Indexer-0.log                  493.0 KB      errors=36   warnings=81 
Log files:  MonitorServer.log              4.0 KB        errors=1    warnings=0   
Log files:  OMEROweb.lock                  0.0 KB       
Log files:  OMEROweb.log                   370.0 KB      errors=16   warnings=25 
Log files:  PixelData-0.log                493.0 KB      errors=36   warnings=81 
Log files:  Processor-0.log                259.0 KB      errors=54   warnings=108
Log files:  Tables-0.log                   n/a
Log files:  TestDropBox.log                n/a
Log files:  master.err                     13.0 KB       errors=10   warnings=18 
Log files:  master.out                     0.0 KB       
Log files:  Total size                     3.09 MB


Environment:OMERO_HOME=(unset)             
Environment:OMERO_NODE=(unset)             
Environment:OMERO_MASTER=(unset)           
Environment:OMERO_USERDIR=(unset)         
Environment:OMERO_TMPDIR=(unset)           
Environment:PATH=/Users/sajidmo/Virtual/omero/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/homebrew/bin:/usr/local/munki:/Users/sajidmo/Downloads/apache-ant-1.10.1/bin:/Users/sajidmo/downloads/OMERO.server-5.4.0-ice36-b74/bin
Environment:PYTHONPATH=:/Users/sajidmo/projects/omero-iviewer/plugin
Environment:ICE_HOME=(unset)               
Environment:LD_LIBRARY_PATH=(unset)       
Environment:DYLD_LIBRARY_PATH=(unset)     

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

JVM settings: Blitz-${index}                -Xmx5153m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions
JVM settings: Indexer-${index}              -Xmx3435m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions
JVM settings: PixelData-${index}            -Xmx5153m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions
JVM settings: Repository-${index}           -Xmx3435m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions
(omero) NCATS-2003754-M:omero sajidmo$

Output of omero config get --hide-password

Code: Select all

(omero) NCATS-2003754-M:omero sajidmo$ omero config get --hide-password
omero.data.dir=/Users/sajidmo/omero
omero.db.name=omero_database
omero.db.pass=********
omero.db.user=db_user
omero.web.application_server=development
omero.web.apps=["omero_iviewer"]
omero.web.debug=True
(omero) NCATS-2003754-M:omero sajidmo$

${OMERO_SERVER}/var/log logs are attached.

Hey Kenny,

I found out that I was still using the python provided by OS. I updated the PATH variable to point to homebrew version and it fixed the problem. I will let you know if I run into any other problem. Thanks

Regards,