[ome-users] Omero web update problem
Jean-Marie Burel (Staff)
j.burel at dundee.ac.uk
Tue Nov 7 11:37:12 GMT 2017
Hi Andrea and Olivier
Thanks for the detailed information and the suggestion for the documentation
We will clarify the documentation
I am glad that you have everything working
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 Andrea Falconi <andrea.falconi at gmail.com<mailto:andrea.falconi at gmail.com>>
Reply-To: OME User Support List <ome-users at lists.openmicroscopy.org.uk<mailto:ome-users at lists.openmicroscopy.org.uk>>
Date: Tuesday, 7 November 2017 at 12:32
To: OME User Support List <ome-users at lists.openmicroscopy.org.uk<mailto:ome-users at lists.openmicroscopy.org.uk>>
Subject: Re: [ome-users] Omero web update problem
Hi Jean-Marie,
Yes, Gunicorn does get installed through `pip` but then it isn't available in the user's path as Olivier pointed out earlier. The problem is that `lib/python/.../web.py` expects `gunicorn` to be in the path. In our case, this line gets hit:
https://github.com/openmicroscopy/openmicroscopy/blob/develop/components/tools/OmeroPy/src/omero/plugins/web.py#L601
which builds this command:
gunicorn -D -p '/home/omero/apps/OMERO/OMERO.server-5.4.0-ice36-b74/var/django.pid' --bind 127.0.0.1:4080<http://127.0.0.1:4080> --workers 11 --threads 1 --timeout 60 --max-requests 500 omeroweb.wsgi:application
Hope this helps.
Regards
/a
On 7 November 2017 at 12:03, Jean-Marie Burel (Staff) <j.burel at dundee.ac.uk<mailto:j.burel at dundee.ac.uk>> wrote:
Hi oliver
Glad that you managed to sort it out
Gunicorn should have been installed during the following step
pip install -r OMERO.server/share/web/requirements-py27.txt
Was it not the case?
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: Tuesday, 7 November 2017 at 12:00
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: Re: [ome-users] Omero web update problem
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
_______________________________________________
ome-users mailing list
ome-users at lists.openmicroscopy.org.uk<mailto:ome-users at lists.openmicroscopy.org.uk>http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
--
Olivier Miquel
Administrateur Système et Réseau
Plate-forme technologique MRI
Tel : 06.50.19.27.43
Mail:olivier.miquel at mri.cnrs.fr<mailto:Mail:olivier.miquel at mri.cnrs.fr>
The University of Dundee is a registered Scottish Charity, No: SC015096
_______________________________________________
ome-users mailing list
ome-users at lists.openmicroscopy.org.uk<mailto:ome-users at lists.openmicroscopy.org.uk>
http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
The University of Dundee is a registered Scottish Charity, No: SC015096
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.openmicroscopy.org.uk/pipermail/ome-users/attachments/20171107/4870d8f5/attachment.html>
More information about the ome-users
mailing list