[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


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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<mailto:Mail:olivier.miquel at mri.cnrs.fr>

The University of Dundee is a registered Scottish Charity, No: SC015096

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