[ome-users] Omero web update problem
Olivier Miquel
olivier.miquel at mri.cnrs.fr
Tue Nov 7 11:00:51 GMT 2017
Hi Jean-Marie,
We just managed to find the cause.
The gunicorn command was not found for the omero system user.
We just installed it via the debian packaging system for the whole
system and now OMERO.web starts and seems to runs fine.
Basically :
aptitude install gunicorn
Thanks for the reply.
O.
On 07/11/2017 11:33, Jean-Marie Burel (Staff) wrote:
> Hi Olivier
>
> Sorry to hear that OMERO.web does not start
>
> Will it be possible to paste us your configuration for
> OMERO.server/web and nginx?
> See https://docs.openmicroscopy.org/omero/5.4.0/sysadmins/cli/config.html
>
> Cheers
>
> Jmarie
>
> From: ome-users <ome-users-bounces at lists.openmicroscopy.org.uk
> <mailto:ome-users-bounces at lists.openmicroscopy.org.uk>> on behalf of
> Olivier Miquel <olivier.miquel at mri.cnrs.fr
> <mailto:olivier.miquel at mri.cnrs.fr>>
> Reply-To: OME User Support List <ome-users at lists.openmicroscopy.org.uk
> <mailto:ome-users at lists.openmicroscopy.org.uk>>
> Date: Monday, 6 November 2017 at 16:00
> To: "ome-users at lists.openmicroscopy.org.uk
> <mailto:ome-users at lists.openmicroscopy.org.uk>"
> <ome-users at lists.openmicroscopy.org.uk
> <mailto:ome-users at lists.openmicroscopy.org.uk>>
> Subject: [ome-users] Omero web update problem
>
> Hi,
>
> We are trying to migrate our omero 5.2.2 server in the newer 5.4.0
> version.
>
> The upgrade of the OMERO.server part went fine so far ( from 5.2.2 to
> 5.3.5 then 5.3.5 to 5.4.0).
> It starts and i can connect using the newer Insight client.
>
> However OMERO.web won't start, even after i disabled all the web apps.
>
> I want to follow this procedure ( server + omero web on same machine )
> :
> https://docs.openmicroscopy.org/omero/5.4.0/sysadmins/unix/install-web/walkthrough/omeroweb-install-with-server-debian-ice3.6.html
>
> If someone could give me a clue where to search, it would be nice.
>
> When i try to start OMERO.web it i got this error:
> # sudo -u omero OMERO.server/bin/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/apps/OMERO/OMERO.server/lib/python/omeroweb/static', 606 unmodified, 2 post-processed.
> Clearing expired sessions. This may take some time... [OK]
> Starting OMERO.web... Traceback (most recent call last):
> File "OMERO.server/bin/omero", line 125, in <module>
> rv = omero.cli.argv()
> File "/home/omero/apps/OMERO/OMERO.server/lib/python/omero/cli.py", line 1613, in argv
> cli.invoke(args[1:])
> File "/home/omero/apps/OMERO/OMERO.server/lib/python/omero/cli.py", line 1088, in invoke
> stop = self.onecmd(line, previous_args)
> File "/home/omero/apps/OMERO/OMERO.server/lib/python/omero/cli.py", line 1165, in onecmd
> self.execute(line, previous_args)
> File "/home/omero/apps/OMERO/OMERO.server/lib/python/omero/cli.py", line 1247, in execute
> args.func(args)
> File "/home/omero/apps/OMERO/OMERO.server/lib/python/omero/install/windows_warning.py", line 26, in wrapper
> return func(self, *args, **kwargs)
> File "/home/omero/apps/OMERO/OMERO.server/lib/python/omero/plugins/web.py", line 81, in wrapper
> return func(self, *args, **kwargs)
> File "/home/omero/apps/OMERO/OMERO.server/lib/python/omero/plugins/web.py", line 601, in start
> rv = self.ctx.popen(args=runserver, cwd=location) # popen
> File "/home/omero/apps/OMERO/OMERO.server/lib/python/omero/cli.py", line 1338, in popen
> stdout=stdout, stderr=stderr)
> File "/usr/lib/python2.7/subprocess.py", line 390, in __init__
> errread, errwrite)
> File "/usr/lib/python2.7/subprocess.py", line 1024, in _execute_child
> raise child_exception
> *OSError: [Errno 2] No such file or directory*
>
> ------------
>
> OUTPUT of omero diagnostics :
> ================================================================================
> OMERO Diagnostics (admin) 5.4.0-ice36-b74
> ================================================================================
>
> Commands: java -version 1.8.0 (/usr/bin/java)
> Commands: python -V 2.7.13 (/usr/bin/python)
> Commands: icegridnode --version 3.6.3 (/usr/bin/icegridnode)
> Commands: icegridadmin --version 3.6.3 (/usr/bin/icegridadmin)
> Commands: psql --version 9.6.4 (/usr/bin/psql)
>
> Server: icegridnode running
> Server: Blitz-0 active (pid = 19312, enabled)
> Server: DropBox active (pid = 21514, enabled)
> Server: FileServer active (pid = 21518, enabled)
> Server: Indexer-0 active (pid = 19339, enabled)
> Server: MonitorServer active (pid = 21517, enabled)
> Server: OMERO.Glacier2 active (pid = 19343, enabled)
> Server: OMERO.IceStorm active (pid = 19345, enabled)
> Server: PixelData-0 active (pid = 19347, enabled)
> Server: Processor-0 active (pid = 21521, enabled)
> Server: Tables-0 active (pid = 21515, enabled)
> Server: TestDropBox inactive (enabled)
>
> Log dir: /home/omero/apps/OMERO/OMERO.server-5.4.0-ice36-b74/var/log exists
> Log files: Blitz-0.log 2.0 MB errors=18 warnings=5
> Log files: DropBox.log 7.0 KB errors=0 warnings=2
> Log files: FileServer.log 0.0 KB
> Log files: Indexer-0.log 9.0 KB
> Log files: MonitorServer.log 4.0 KB
> Log files: OMEROweb.lock 0.0 KB
> Log files: OMEROweb.log 1.0 KB errors=0 warnings=6
> Log files: PixelData-0.log 10.0 KB
> Log files: Processor-0.log 141.0 KB errors=0 warnings=17
> Log files: Tables-0.log 5.0 KB errors=0 warnings=1
> Log files: TestDropBox.log n/a
> Log files: master.err 4.0 KB errors=2 warnings=2
> Log files: master.out 0.0 KB
> Log files: Total size 2.42 MB
>
>
> Environment:OMERO_HOME=(unset)
> Environment:OMERO_NODE=(unset)
> Environment:OMERO_MASTER=(unset)
> Environment:OMERO_USERDIR=(unset)
> Environment:OMERO_TMPDIR=(unset)
> Environment:PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
> Environment:PYTHONPATH=(unset)
> Environment:ICE_HOME=(unset)
> Environment:LD_LIBRARY_PATH=(unset)
> Environment:DYLD_LIBRARY_PATH=(unset)
>
> OMERO SSL port:4064
> OMERO TCP port:4063
> OMERO data dir:'/home/omero/apps/OMERO/OMERO.data' Exists? True Is writable? True
> OMERO temp dir:'/home/omero/omero/tmp' Exists? True Is writable? True (Size: 0)
>
> JVM settings: Blitz-${index} -Xmx13516m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions
> JVM settings: Indexer-${index} -Xmx3686m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions
> JVM settings: PixelData-${index} -Xmx3686m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions
> JVM settings: Repository-${index} -Xmx3686m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions
>
>
>
>
>
>
>
>
>
> The University of Dundee is a registered Scottish Charity, No: SC015096
>
>
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--
Olivier Miquel
Administrateur Système et Réseau
Plate-forme technologique MRI
Tel : 06.50.19.27.43
Mail:olivier.miquel at mri.cnrs.fr
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