[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
Fri Nov 13 11:12:42 GMT 2015
Hi Josh,
That didn't go quite as well as I wanted... In short, it didn't work. I
then had a hard time trying to remove that config because it seems to
have copied it to all the other applications' (Blitz, DropBox, ...)
configs in var/master/...
Then I couldn't get OMERO to start. It would print dot after dot but not
quite start.
$ bin/omero admin start
No descriptor given. Using etc/grid/default.xml
Waiting on startup. Use CTRL-C to exit
...........^CCancelled
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 inactive (disabled)
Server: DropBox inactive (disabled)
Server: FileServer active (pid = 1922, enabled)
Server: Indexer-0 inactive (disabled)
Server: MonitorServer active (pid = 1924, enabled)
Server: OMERO.Glacier2 active (pid = 1925, enabled)
Server: OMERO.IceStorm active (pid = 1928, enabled)
Server: PixelData-0 inactive (disabled)
Server: Processor-0 activating (enabled)
Server: Tables-0 activating (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 23.0 KB errors=6
warnings=0
Log files: DropBox.log 1.0 KB errors=2
warnings=1
Log files: FileServer.log 0.0 KB
Log files: Indexer-0.log 2.0 KB errors=1
warnings=0
Log files: MonitorServer.log 0.0 KB
Log files: OMEROweb.log n/a
Log files: PixelData-0.log 3.0 KB errors=1
warnings=0
Log files: Processor-0.log 0.0 KB
Log files: Tables-0.log 0.0 KB
Log files: TestDropBox.log n/a
Log files: master.err 0.0 KB errors=0
warnings=2
Log files: master.out 0.0 KB
Log files: Total size 0.03 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/lib:/Library/Developer/Ice-3.5/lib/c++11:
Environment:DYLD_LIBRARY_PATH=/Library/Developer/Ice-3.5/lib:/Library/Developer/Ice-3.5/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
The following failed to run.
$ bin/omero config remove Ice.Plugin.IceSSL IceSSL:createIceSSL
No JSON object could be decoded
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
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
>>
>> _______________________________________________
>> ome-users mailing list
>> ome-users at lists.openmicroscopy.org.uk
>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>>
>>
>> --
>> 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
>>
> _______________________________________________
> ome-users mailing list
> ome-users at lists.openmicroscopy.org.uk
> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
--
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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