[ome-users] OMERO.web (5.2.0) login on Yosemite fails with "Error: Server is not responding, please contact administrator."
Josh Moore
josh at glencoesoftware.com
Fri Nov 13 16:47:25 GMT 2015
On Fri, Nov 13, 2015 at 12:12 PM, Paul Kibet Korir <pkorir at ebi.ac.uk> wrote:
> Hi Josh,
Hi Paul,
> That didn't go quite as well as I wanted... In short, it didn't work.
Sorry about that. But thanks for trying.
> The following failed to run.
> $ bin/omero config remove Ice.Plugin.IceSSL IceSSL:createIceSSL
> No JSON object could be decoded
Sorry for the confusion. "remove" is only for use with "append". The
correct command here to rollback (which I should have included) would
be:
$ bin/omero config set Ice.Plugin.IceSSL
> Therefore, I had to delete OMERO.server and the folder it pointed to and
> copy it afresh. Thank God I wasn't using Homebrew!
>
> Hope that helps.
> Paul
Regards,
~Josh.
> On 13/11/2015 08:11, Josh Moore wrote:
>
> Hi Paul,
>
> On Thu, Nov 12, 2015 at 5:05 PM, Paul Kibet Korir <pkorir at ebi.ac.uk> wrote:
>
> Hi Aleksandra,
>
> ...
>
> My current solution has been to include the path to the IceSSL library in
> two files (from ~/omero/OMERO.server):
>
> lib/python/omero/clients.py
> I've edited the line
>
> 'self._optSetProp(id, "Ice.Plugin.IceSSL", "IceSSL:createIceSSL")'
>
> to read
>
> 'self._optSetProp(id, "Ice.Plugin.IceSSL",
> "/Library/Developer/Ice-3.5/lib/IceSSL:createIceSSL")'
>
> and in
>
> etc/templates/grid/tempates.xml
> I've changed all instances (there were three) of "IceSSL:createIceSSL" to
> "/Library/Developer/Ice-3.5/lib/IceSSL:createIceSSL"
>
> Thanks for finding & sharing the fix! Would you mind trying one thing for
> us?
> Could you change these 2 files back to their original values and then run:
>
> bin/omero config set Ice.Plugin.IceSSL
> /Library/Developer/Ice-3.5/lib/IceSSL:createIceSSL
> bin/omero admin restart
>
> If that works, we'll document it as one of the standard properties
> that may need alteration.
> If not, we'll need to look into making it one...
>
> Thanks again.
> ~Josh.
>
>
> Thereafter, I restarted my Mac and OMERO.server.
>
> With kind regards,
>
> Paul
>
>
>
>
> On 12/11/2015 13:11, Aleksandra Tarkowska (Staff) wrote:
>
> Hi Paul
>
> As I already pointed to you on our forum, your openssl lib may be outdated.
> Please follow our Mac walk through documentation and install python and
> Romero dependences using brew https://www.openmicroscopy.org/site/sup …
> brew.html.
>
> You can check which version you are using, for example:
>
> $ otool -L /Library/Developer/Ice-3.5.1/lib/libIceSSL.35.dylib
>
> We are about to update our Mac OS X documentation and remove part that use
> build in python as this is invalid.
>
> I hope it will help.
>
> Ola
>
> On 12 Nov 2015, at 12:22, Paul Kibet Korir <pkorir at ebi.ac.uk> wrote:
>
> Hi OMERO-Users,
>
> I'd be really grateful to receive any assistance on getting OMERO.web for
> OMERO 5.2 to work on Yosemite. When I try to log in I get "Error: Server is
> not responding, please contact administrator." I can log in using
> OMERO.insight.
>
> The following error appears in var/log/OMEROweb.log:
>
> 2015-11-12 12:05:04,699 ERROR [ omeroweb.connector]
> (proc.00202) create_guest_connection:190 Cannot create a guest connection.
> Traceback (most recent call last):
> File
> "/Users/pkorir/omero/OMERO.server-5.2.0-ice35-b12/lib/python/omeroweb/connector.py",
> line 184, in create_guest_connection
> connection = self.create_gateway(useragent, guest, guest, None)
> File
> "/Users/pkorir/omero/OMERO.server-5.2.0-ice35-b12/lib/python/omeroweb/connector.py",
> line 149, in create_gateway
> useragent=useragent, anonymous=self.is_public, userip=userip)
> File
> "/Users/pkorir/omero/OMERO.server-5.2.0-ice35-b12/lib/python/omero/__init__.py",
> line 62, in client_wrapper
> return omero.gateway.BlitzGateway(*args, **kwargs)
> File
> "/Users/pkorir/omero/OMERO.server-5.2.0-ice35-b12/lib/python/omeroweb/webclient/webclient_gateway.py",
> line 130, in __init__
> super(OmeroWebGateway, self).__init__(*args, **kwargs)
> File
> "/Users/pkorir/omero/OMERO.server-5.2.0-ice35-b12/lib/python/omero/gateway/__init__.py",
> line 1479, in __init__
> self._resetOmeroClient()
> File
> "/Users/pkorir/omero/OMERO.server-5.2.0-ice35-b12/lib/python/omero/gateway/__init__.py",
> line 1921, in _resetOmeroClient
> args=['--Ice.Config='+','.join(self.ice_config)])
> File
> "/Users/pkorir/omero/OMERO.server-5.2.0-ice35-b12/lib/python/omero/__init__.py",
> line 67, in client
> return omero.clients.BaseClient(*args, **kwargs)
> File
> "/Users/pkorir/omero/OMERO.server-5.2.0-ice35-b12/lib/python/omero/clients.py",
> line 140, in __init__
> self._initData(id)
> File
> "/Users/pkorir/omero/OMERO.server-5.2.0-ice35-b12/lib/python/omero/clients.py",
> line 255, in _initData
> self.__ic = Ice.initialize(id)
> File "/Library/Python/2.7/site-packages/Ice.py", line 647, in initialize
> communicator = IcePy.Communicator(args, data)
> PluginInitializationException: exception
> ::Ice::PluginInitializationException
> {
> reason = unable to load entry point `IceSSL:createIceSSL':
> dlopen(libIceSSL.35.dylib, 10): image not found; dlopen(libIceSSL.35.so,
> 10): image not found; dlopen(libIceSSL.35.bundle, 10): image not found
> }
>
> I'm surprised by this given that I have the following environment variables:
> $ echo $LD_LIBRARY_PATH
> /Library/Developer/Ice-3.5.1/lib:/Library/Developer/Ice-3.5.1/lib/c++11:
>
> $ echo $DYLD_LIBRARY_PATH
> /Library/Developer/Ice-3.5.1/lib:/Library/Developer/Ice-3.5.1/lib/c++11:/Applications/IMOD/lib::/usr/local/bsoft/lib
>
> The above first entry of the above paths contain IceSSL.35.dyld. I've added
> the c++11 libraries just in case.
>
> Here is the output of bin/omero admin diagnostics:
> ================================================================================
> OMERO Diagnostics 5.2.0-ice35-b12
> ================================================================================
>
> Commands: java -version 1.8.0 (/usr/bin/java)
> Commands: python -V 2.7.10 (/usr/bin/python)
> Commands: icegridnode --version 3.5.1
> (/Library/Developer/Ice-3.5/bin/icegridnode)
> Commands: icegridadmin --version 3.5.1
> (/Library/Developer/Ice-3.5/bin/icegridadmin)
> Commands: psql --version 9.4.5
> (/Applications/Postgres.app/Contents/Versions/9.4/bin/psql)
>
> Server: icegridnode running
> Server: Blitz-0 active (pid = 4860, enabled)
> Server: DropBox active (pid = 4861, enabled)
> Server: FileServer active (pid = 4862, enabled)
> Server: Indexer-0 active (pid = 4863, enabled)
> Server: MonitorServer active (pid = 4864, enabled)
> Server: OMERO.Glacier2 active (pid = 4865, enabled)
> Server: OMERO.IceStorm active (pid = 4866, enabled)
> Server: PixelData-0 active (pid = 4867, enabled)
> Server: Processor-0 active (pid = 4868, enabled)
> Server: Tables-0 active (pid = 4869, enabled)
> Server: TestDropBox inactive (enabled)
>
> Log dir: /Users/pkorir/omero/OMERO.server-5.2.0-ice35-b12/var/log exists
> Log files: Blitz-0.log 2.0 MB errors=64
> warnings=0
> Log files: DropBox.log 8.0 KB errors=0
> warnings=3
> Log files: FileServer.log 1.0 KB
> Log files: Indexer-0.log 10.0 KB
> Log files: MonitorServer.log 4.0 KB
> Log files: OMEROweb.lock 0.0 KB
> Log files: OMEROweb.log 48.0 KB errors=22
> warnings=4
> Log files: OMEROweb_brokenrequest.lock 0.0 KB
> Log files: OMEROweb_brokenrequest.log 0.0 KB
> Log files: PixelData-0.log 12.0 KB
> Log files: Processor-0.log 228.0 KB errors=64
> warnings=3
> Log files: Tables-0.log 6.0 KB errors=0
> warnings=3
> Log files: TestDropBox.log n/a
> Log files: master.err 0.0 KB errors=0
> warnings=1
> Log files: master.out 0.0 KB
> Log files: Total size 2.89 MB
>
>
> Environment:OMERO_HOME=(unset)
> Environment:OMERO_NODE=(unset)
> Environment:OMERO_MASTER=(unset)
> Environment:OMERO_USERDIR=(unset)
> Environment:OMERO_TMPDIR=(unset)
> Environment:PATH=/Library/Developer/Ice-3.5/bin:/Applications/IMOD/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/usr/local/bsoft/bin:/Applications/Postgres.app/Contents/Versions/9.4/bin:/Users/pkorir/Code
> Environment:PYTHONPATH=:/Users/pkorir/omero/OMERO.server/lib/python
> Environment:ICE_HOME=/Library/Developer/Ice-3.5
> Environment:LD_LIBRARY_PATH=/Library/Developer/Ice-3.5.1/lib:/Library/Developer/Ice-3.5.1/lib/c++11:
> Environment:DYLD_LIBRARY_PATH=/Library/Developer/Ice-3.5.1/lib:/Library/Developer/Ice-3.5.1/lib/c++11:/Applications/IMOD/lib::/usr/local/bsoft/lib
>
> OMERO SSL port:4064
> OMERO TCP port:4063
> OMERO data dir:'/OMERO' Exists? True Is writable?
> True
> OMERO temp dir:'/Users/pkorir/omero/tmp' Exists? True Is writable?
> True (Size: 0)
>
> JVM settings: Blitz-${index} -Xmx2576m -XX:MaxPermSize=1g
> -XX:+IgnoreUnrecognizedVMOptions
> JVM settings: Indexer-${index} -Xmx1717m -XX:MaxPermSize=1g
> -XX:+IgnoreUnrecognizedVMOptions
> JVM settings: PixelData-${index} -Xmx2576m -XX:MaxPermSize=1g
> -XX:+IgnoreUnrecognizedVMOptions
> JVM settings: Repository-${index} -Xmx1717m -XX:MaxPermSize=1g
> -XX:+IgnoreUnrecognizedVMOptions
>
> OMERO.web status... [NOT STARTED]
> Django version: 1.8.6
>
> As you can see OMERO.web status is [NOT STARTED].
>
> Any pointers will be gratefully received.
>
> --
> With kind regards,
>
> Paul K Korir, PhD
> Scientific Programmer
> EMBL-EBI
> Main Building, A2-35,
> WTGC, Hinxton, Cambridge CB10 1SD
> P: +44 1223 49 44 22
> F: +44 1223 49 44 68
> _______________________________________________
> ome-users mailing list
> 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
>
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>
>
> --
> With kind regards,
>
> Paul K Korir, PhD
> Scientific Programmer
> EMBL-EBI
> Main Building, A2-35,
> WTGC, Hinxton, Cambridge CB10 1SD
> P: +44 1223 49 44 22
> F: +44 1223 49 44 68
>
> _______________________________________________
> ome-users mailing list
> ome-users at lists.openmicroscopy.org.uk
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>
>
> --
> With kind regards,
>
> Paul K Korir, PhD
> Scientific Programmer
> EMBL-EBI
> Main Building, A2-35,
> WTGC, Hinxton, Cambridge CB10 1SD
> P: +44 1223 49 44 22
> F: +44 1223 49 44 68
>
> _______________________________________________
> ome-users mailing list
> ome-users at lists.openmicroscopy.org.uk
> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
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