[ome-users] OMERO.web (5.2.0) login on Yosemite fails with "Error: Server is not responding, please contact administrator."
Paul Kibet Korir
pkorir at ebi.ac.uk
Thu Nov 12 16:05:45 GMT 2015
Hi Aleksandra,
Thank you very much for your reply.
I would like to avoid using Homebrew because it requires system changes
(e.g. changing permissions in /usr/local) that I'm not happy with. As
you might have seen, I've asked another question about using 'bin/omero
admin rewrite'. I've manually edited entries with IceSSL:createIceSSL as
mentioned in detail below based on instructions from the ZeroC website
(check out
https://doc.zeroc.com/display/Ice35/Using+the+OS+X+Binary+Distribution#UsingtheOSXBinaryDistribution-OverviewoftheOSXbinarydistribution).
I had installed Ice-3.5.1 from the binary from
https://zeroc.com/downloads/ice/3.5/, which installs to
/Library/Developer/Ice-3.5.1 on my Mac.
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"
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 outdated.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
> <https://www.openmicroscopy.org/site/support/omero5.2/sysadmins/unix/server-install-homebrew.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
>> <mailto: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 <http://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
>> <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
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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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