[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 08:11:21 GMT 2015
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 As I already pointed to you on our forum, your openssl lib may be outdated.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
>
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> ome-users mailing list
> ome-users at lists.openmicroscopy.org.uk
> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>
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