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OMERO.web (5.2.0) fails on Yosemite

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The OMERO.server installation documentation begins here and you can find OMERO.web deployment documentation here.

OMERO.web (5.2.0) fails on Yosemite

Postby pkorir » Wed Nov 11, 2015 5:16 pm

Hi,

I'm not able to log in to OMERO.web.

I get an error "Error: Server is not responding, please contact administrator." but I can successfully log in with OMERO.insight.

I get the following error in var/log/OMEROweb.log:

Code: Select all
2015-11-11 16:55:25,424 ERROR [                      omeroweb.connector] (proc.03709) 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 because I have the following DYLD_LIBRARY_PATH:

Code: Select all
/Library/Developer/Ice-3.5.1/lib:/Library/Developer/Ice-3.5.1/lib/c++11:/Applications/IMOD/lib::/usr/local/bsoft/lib


Here is the output of my configs:

Code: Select all
Ice.Default.Host=0.0.0.0
Ice.IPv6=0
omero.db.name=omero_database
omero.db.pass=********
omero.db.user=pg_user
omero.web.application_server=wsgi
omero.web.prefix=/omero
omero.web.static_url=/omero/static


And here is my diagnostic information (it shows that OMERO.web does not start):
Code: Select all
================================================================================
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 = 3743, enabled)
Server:     DropBox                        active (pid = 3744, enabled)
Server:     FileServer                     active (pid = 3745, enabled)
Server:     Indexer-0                      active (pid = 3746, enabled)
Server:     MonitorServer                  active (pid = 3747, enabled)
Server:     OMERO.Glacier2                 active (pid = 3748, enabled)
Server:     OMERO.IceStorm                 active (pid = 3751, enabled)
Server:     PixelData-0                    active (pid = 3749, enabled)
Server:     Processor-0                    active (pid = 3750, enabled)
Server:     Tables-0                       active (pid = 3752, 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                    n/a
Log files:  DropBox.log                    n/a
Log files:  FileServer.log                 n/a
Log files:  Indexer-0.log                  n/a
Log files:  MonitorServer.log              n/a
Log files:  OMEROweb.lock                  0.0 KB       
Log files:  OMEROweb.log                   4.0 KB        errors=2    warnings=0   
Log files:  OMEROweb_brokenrequest.lock    0.0 KB       
Log files:  OMEROweb_brokenrequest.log     0.0 KB       
Log files:  Processor-0.log                n/a
Log files:  Tables-0.log                   n/a
Log files:  TestDropBox.log                n/a
Log files:  Total size                     0.00 MB

Error while parsing logs

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=(unset)             
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


Any help to get OMERO.web to work will be appreciated.

Regards,

Paul
pkorir
 
Posts: 1
Joined: Wed Nov 11, 2015 4:35 pm

Re: OMERO.web (5.2.0) fails on Yosemite

Postby atarkowska » Thu Nov 12, 2015 10:31 am

Hi Paul,

I reckon you are using custom Ice build and your openssl lib may be outdated. Please follow our Mac walk through documentation https://www.openmicroscopy.org/site/sup ... ebrew.html

Ola
atarkowska
 
Posts: 327
Joined: Mon May 18, 2009 12:44 pm


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