[ome-users] OMERO.web (5.2.0) login on Yosemite fails with "Error: Server is not responding, please contact administrator."

Aleksandra Tarkowska (Staff) A.Tarkowska at dundee.ac.uk
Thu Nov 12 13:11:17 GMT 2015


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As I already pointed to you on our forum, your openssl lib may be outdated.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
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