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Hi Josh,<br>
<br>
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/...<br>
Then I couldn't get OMERO to start. It would print dot after dot but
not quite start.<br>
<br>
$ bin/omero admin start<br>
No descriptor given. Using etc/grid/default.xml<br>
Waiting on startup. Use CTRL-C to exit<br>
...........^CCancelled<br>
<br>
bin/omero admin diagnostics<br>
<br>
================================================================================<br>
OMERO Diagnostics 5.2.0-ice35-b12<br>
================================================================================<br>
<br>
Commands: java -version 1.8.0 (/usr/bin/java)<br>
Commands: python -V 2.7.10
(/usr/bin/python)<br>
Commands: icegridnode --version 3.5.1
(/Library/Developer/Ice-3.5/bin/icegridnode)<br>
Commands: icegridadmin --version 3.5.1
(/Library/Developer/Ice-3.5/bin/icegridadmin)<br>
Commands: psql --version 9.4.5
(/Applications/Postgres.app/Contents/Versions/9.4/bin/psql)<br>
<br>
Server: icegridnode running<br>
Server: Blitz-0 inactive (disabled)<br>
Server: DropBox inactive (disabled)<br>
Server: FileServer active (pid = 1922,
enabled)<br>
Server: Indexer-0 inactive (disabled)<br>
Server: MonitorServer active (pid = 1924,
enabled)<br>
Server: OMERO.Glacier2 active (pid = 1925,
enabled)<br>
Server: OMERO.IceStorm active (pid = 1928,
enabled)<br>
Server: PixelData-0 inactive (disabled)<br>
Server: Processor-0 activating (enabled)<br>
Server: Tables-0 activating (enabled)<br>
Server: TestDropBox inactive (enabled)<br>
<br>
Log dir: /Users/pkorir/omero/OMERO.server-5.2.0-ice35-b12/var/log
exists<br>
Log files: Blitz-0.log 23.0 KB errors=6
warnings=0 <br>
Log files: DropBox.log 1.0 KB errors=2
warnings=1 <br>
Log files: FileServer.log 0.0 KB <br>
Log files: Indexer-0.log 2.0 KB errors=1
warnings=0 <br>
Log files: MonitorServer.log 0.0 KB <br>
Log files: OMEROweb.log n/a<br>
Log files: PixelData-0.log 3.0 KB errors=1
warnings=0 <br>
Log files: Processor-0.log 0.0 KB <br>
Log files: Tables-0.log 0.0 KB <br>
Log files: TestDropBox.log n/a<br>
Log files: master.err 0.0 KB errors=0
warnings=2 <br>
Log files: master.out 0.0 KB <br>
Log files: Total size 0.03 MB<br>
<br>
<br>
Environment:OMERO_HOME=(unset) <br>
Environment:OMERO_NODE=(unset) <br>
Environment:OMERO_MASTER=(unset) <br>
Environment:OMERO_USERDIR=(unset) <br>
Environment:OMERO_TMPDIR=(unset) <br>
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
<br>
Environment:PYTHONPATH=:/Users/pkorir/omero/OMERO.server/lib/python
<br>
Environment:ICE_HOME=/Library/Developer/Ice-3.5 <br>
Environment:LD_LIBRARY_PATH=/Library/Developer/Ice-3.5/lib:/Library/Developer/Ice-3.5/lib/c++11:
<br>
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
<br>
<br>
OMERO SSL port:4064 <br>
OMERO TCP port:4063 <br>
OMERO data dir:'/OMERO' Exists? True Is
writable? True<br>
OMERO temp dir:'/Users/pkorir/omero/tmp' Exists? True Is
writable? True (Size: 0)<br>
<br>
JVM settings: Blitz-${index} -Xmx2576m
-XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions<br>
JVM settings: Indexer-${index} -Xmx1717m
-XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions<br>
JVM settings: PixelData-${index} -Xmx2576m
-XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions<br>
JVM settings: Repository-${index} -Xmx1717m
-XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions<br>
<br>
OMERO.web status... [NOT STARTED]<br>
Django version: 1.8.6<br>
<br>
<br>
The following failed to run.<br>
$ bin/omero config remove Ice.Plugin.IceSSL IceSSL:createIceSSL<br>
No JSON object could be decoded<br>
<br>
Therefore, I had to delete OMERO.server and the folder it pointed to
and copy it afresh. Thank God I wasn't using Homebrew!<br>
<br>
Hope that helps.<br>
<br>
Paul<br>
<br>
<br>
<div class="moz-cite-prefix">On 13/11/2015 08:11, Josh Moore wrote:<br>
</div>
<blockquote
cite="mid:CAD3Ea=U816cp918JHE199n-m0Sro5Pa4dy2zdchoG2h2Q0dNcQ@mail.gmail.com"
type="cite">
<pre wrap="">Hi Paul,
On Thu, Nov 12, 2015 at 5:05 PM, Paul Kibet Korir <a class="moz-txt-link-rfc2396E" href="mailto:pkorir@ebi.ac.uk"><pkorir@ebi.ac.uk></a> wrote:
</pre>
<blockquote type="cite">
<pre wrap="">Hi Aleksandra,
</pre>
</blockquote>
<pre wrap="">...
</pre>
<blockquote type="cite">
<pre wrap="">
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
</pre>
<blockquote type="cite">
<pre wrap="">'self._optSetProp(id, "Ice.Plugin.IceSSL", "IceSSL:createIceSSL")'
</pre>
</blockquote>
<pre wrap="">to read
</pre>
<blockquote type="cite">
<pre wrap="">'self._optSetProp(id, "Ice.Plugin.IceSSL",
"/Library/Developer/Ice-3.5/lib/IceSSL:createIceSSL")'
</pre>
</blockquote>
<pre wrap="">
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"
</pre>
</blockquote>
<pre wrap="">
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.
</pre>
<blockquote type="cite">
<pre wrap="">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 <a class="moz-txt-link-freetext" href="https://www.openmicroscopy.org/site/sup">https://www.openmicroscopy.org/site/sup</a> …
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 <a class="moz-txt-link-rfc2396E" href="mailto:pkorir@ebi.ac.uk"><pkorir@ebi.ac.uk></a> 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
<a class="moz-txt-link-abbreviated" href="mailto:ome-users@lists.openmicroscopy.org.uk">ome-users@lists.openmicroscopy.org.uk</a>
<a class="moz-txt-link-freetext" href="http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users">http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users</a>
The University of Dundee is a registered Scottish Charity, No: SC015096
_______________________________________________
ome-users mailing list
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<a class="moz-txt-link-freetext" href="http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users">http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users</a>
--
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
<a class="moz-txt-link-abbreviated" href="mailto:ome-users@lists.openmicroscopy.org.uk">ome-users@lists.openmicroscopy.org.uk</a>
<a class="moz-txt-link-freetext" href="http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users">http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users</a>
</pre>
</blockquote>
<pre wrap="">_______________________________________________
ome-users mailing list
<a class="moz-txt-link-abbreviated" href="mailto:ome-users@lists.openmicroscopy.org.uk">ome-users@lists.openmicroscopy.org.uk</a>
<a class="moz-txt-link-freetext" href="http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users">http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users</a>
</pre>
</blockquote>
<br>
<div class="moz-signature">-- <br>
With kind regards,<br>
<br>
<strong>Paul K Korir, PhD</strong><br>
<i>Scientific Programmer</i><br>
EMBL-EBI<br>
Main Building, A2-35,<br>
WTGC, Hinxton, Cambridge CB10 1SD<br>
P: +44 1223 49 44 22<br>
F: +44 1223 49 44 68</div>
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