[ome-users] Omero web update problem
Andrea Falconi
andrea.falconi at gmail.com
Tue Nov 7 11:07:17 GMT 2017
Hi Jean-Marie,
On another note, perhaps it might be worth mentioning in the docs that on
Debian you should install Gunicorn as a Debian package. This page
*
https://docs.openmicroscopy.org/omero/5.4.0/sysadmins/unix/install-web/web-deployment.html
mentions Omero.Web can be deployed with Nginx and Gunicorn, but then the
Debian 9 installation walkthrough page
*
https://docs.openmicroscopy.org/omero/5.4.0/sysadmins/unix/install-web/walkthrough/omeroweb-install-with-server-debian-ice3.6.html
only says to install Nginx. If we may suggest a small improvement, that
would be to change these two lines
Install NGINX:
apt-get -y install nginx
into:
Install NGINX and Gunicorn:
apt-get -y install nginx gunicorn
Regards
/a
On 7 November 2017 at 12:00, Olivier Miquel <olivier.miquel at mri.cnrs.fr>
wrote:
> 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> on behalf
> of Olivier Miquel <olivier.miquel at mri.cnrs.fr>
> Reply-To: OME User Support List <ome-users at lists.openmicroscopy.org.uk>
> Date: Monday, 6 November 2017 at 16:00
> To: "ome-users at lists.openmicroscopy.org.uk" <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
>
> _______________________________________________
> ome-users mailing listome-users at lists.openmicroscopy.org.ukhttp://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>
>
>
> --
> Olivier Miquel
> Administrateur Système et Réseau
> Plate-forme technologique MRI
> Tel : 06.50.19.27.43Mail:olivier.miquel at mri.cnrs.fr
>
>
> _______________________________________________
> ome-users mailing list
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>
>
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