Open Microscopy Environment

Hello all,

I've follow the installation instruction for Unix [1] and Snow Leopard [2] as I'm installing on my Mac, which is Snow Leopard 10.6.4. All the prerequisites seem to installed correctly, however when doing:

bin/omero admin start

I get the following "Ice::PluginInitializationException" error below. Any help or pointer would be greatly appreciated.

bnguyen@zero:~/omero % bin/omero admin start
No descriptor given. Using etc/grid/default.xml
icegridnode: failure occurred in daemon:
service caught unhandled Ice exception:
PluginManagerI.cpp:357: Ice::PluginInitializationException:
plug-in initialization failed: unable to load entry point `IceGridFreezeDB:createFreezeDB': dlopen(libIceGridFreezeDB.34.dylib, 10): image not found

bnguyen@zero:~/omero % bin/omero admin diagnostics

================================================================================
OMERO Diagnostics Beta-4.1.1-r5927-b91
================================================================================

Commands: java -version 1.6.0 (/usr/bin/java)
Commands: python -V 2.6.5 (/opt/local/bin/python -- 2 others)
Commands: icegridnode --version 3.4.1 (/opt/local/bin/icegridnode)
Commands: icegridadmin --version 3.4.1 (/opt/local/bin/icegridadmin)
Commands: psql --version 8.4.4 (/opt/local/lib/postgresql84/bin/psql)

Server: icegridnode not started

Log dir: /Users/bnguyen/omero/var/log exists

Log files: Blitz-0.log n/a
Log files: DropBox.log n/a
Log files: FSServer.log n/a
Log files: Indexer-0.log n/a
Log files: OMEROweb.log n/a
Log files: Processor-0.log n/a
Log files: Tables-0.log n/a
Log files: TestDropBox.log n/a
Log files: master.err 0.0 KB
Log files: master.out 0.0 KB
Log files: Total size 0.00 MB

bnguyen@zero:~/omero % cat var/log/master.err
!! 07/07/10 10:48:31.830 icegridnode: error: service caught unhandled Ice exception:
PluginManagerI.cpp:357: Ice::PluginInitializationException:
plug-in initialization failed: unable to load entry point `IceGridFreezeDB:createFreezeDB': dlopen(libIceGridFreezeDB.34.dylib, 10): image not found
!! 07/07/10 10:48:51.342 icegridnode: error: service caught unhandled Ice exception:
PluginManagerI.cpp:357: Ice::PluginInitializationException:
plug-in initialization failed: unable to load entry point `IceGridFreezeDB:createFreezeDB': dlopen(libIceGridFreezeDB.34.dylib, 10): image not found


[1] http://www.openmicroscopy.org/site/supp ... stallation
[2] http://www.openmicroscopy.org/site/supp ... g-macports

The initialization exception says that your DYLD_LIBRARY_PATH property isn't properly set. Since you are using Ice installed via macports under /opt/local/bin you'll almost certainly need to have /opt/local/lib first on DYLD_LIBRARY_PATH. What does

Code: Select all

echo $DYLD_LIBRARY_PATH


show?

However you've installed Ice 3.4 which we currently don't support. Unfortunately, the Ice version on MacPorts has been upgraded from 3.3 to 3.4 since the 10.6 MacPorts walk-through was written. You'll need to downgrade.

Sorry for the inconvenience.
~Josh

Thanks for catching that I would never would been able to figure that out. Unlucky for me, I've try googling but unable to find a way to use "port" to install an older version of "ice-python26." Do you have any suggestion?


thanks,
-bn

Unfortunately, Macports doesn't make it easy to downgrade. The official instructions for downgrading are on MacPorts trac: InstallingOlderPorts. But I had issues getting them to work.

Based on an older method outlined on http://journal.bitshaker.com/articles/2007/10/20/install-old-versions-of-ports-using-macports/, I'd suggest running:

Code: Select all

mkdir -p dports
cd dports
SOURCE="file:///`pwd`"
CONF="/opt/local/etc/macports/sources.conf"
grep "$SOURCE" $CONF || {
    echo "Must add $SOURCE to /opt/local/etc/macports/sources.conf before the official source"
    sudo vi $CONF
}

svn co --revision 61958 http://svn.macports.org/repository/macports/trunk/dports/devel/ice-cpp/ devel/ice-cpp/
svn co --revision 61958 http://svn.macports.org/repository/macports/trunk/dports/devel/ice-python26/ devel/ice-py/
portindex

sudo port install ice-cpp @3.3.1
sudo port install ice-python26 @3.3.1


In my case, sources.conf looks like this:

Code: Select all

file:////tmp/dports
rsync://rsync.macports.org/release/ports/ [default]


Alternatively, you may want to follow the following instructions for getting Ice 3.3.1 running on 10.6:

http://www.zeroc.com/forums/help-center/4553-ice-binary-distribution-os-x-10-6-a.html

Regards,
~Josh.

Thanks for the guides. I've follow the manually downloading from SVN path and one of the Library failed to compiled for that version of Ice. I'm giving up on trying to install on my Snowleopard for now.

I've successfully run and test OMERO on an Ubuntu 10.04 box and is very happy with it. The Dropbox feature is wonderful. On another note, I'm unable to successfully install on Centos 5.4 with (Python 2.4 - default) as something screwed up the password where one is unable to login no mater what.

I like to point out there's a small typo on the doc for running with mod_python [1], there's a missing trailing ' immediately before ] + sys.path"

Corrected version:


<Location "/">
SetHandler python-program
PythonHandler django.core.handlers.modpython
SetEnv DJANGO_SETTINGS_MODULE omeroweb.settings
PythonDebug On
PythonPath "['/home/omero/omero_dist/lib/python', '/home/omero/omero_dist/var/lib', '/home/omero/omero_dist/lib/python/omeroweb]' + sys.path"


</Location>


[1] http://www.openmicroscopy.org.uk/site/s ... nstall_web

Thanks for that, documentation is fixed.