Open Microscopy Environment

Hello all,

My lab has been trying to install Omero 4.1.1 on a machine running RHEL 5. The specific issue we are having is with Ice. We have tried to install Ice 3.3.1 and everything seems to install just fine; there are no errors when we make or install. However, our installation of Python cannot find Ice, and so when we try to run the command:

bin/omero config set omero.db.name 'myDatabase'

We get an error that says Python cannot find the module Ice. Our installation of python is 2.6.5 and is located at /usr/local/Python-2.6.5. Our installation of Ice is at /usr/share/Ice-3.3.1. We have tried adding the location of Ice to the Python path variable, but that doesn't solve the problem either. Your thoughts would be greatly appreciated. Thanks.

Definitly IcePy is not in your PYTHONPATH

Your paths could be set by:

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export PATH=/Library/Ice/3.3/bin:$PATH
export PYTHONPATH=/Library/Ice/3.3/python:$PYTHONPATH

Could you please show us your environment variables, like: PATH, LD_LIBRARY_PATH, PYTHONPATH, etc.

Also could you please run python console and try to import Ice, like below:

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mac:~ ola$ python
Python 2.4.6 (#1, Apr 23 2009, 15:08:46)
[GCC 4.0.1 (Apple Inc. build 5488)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import Ice
>>>

Thanks for the reply.

These are the environment variables:

PYTHONPATH = /usr/local/Python-2.6.5

PATH = /usr/java/jdk1.5.0_16/bin:/usr/local/apache-ant-1.7.1/bin:
/usr/local/gmod/apollo/bin:
/usr/kerberos/bin:
/usr/local/bin:/bin:/usr/bin:/home/sflygare/bin

LD_LIBRARY_PATH = blank

The Python folder for Ice on my machine is located at:

/opt/Ice-3.3.1/python

So I used the python console and did the following:

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Python 2.6.5 (r265:79063, Jul  2 2010, 14:31:13)
[GCC 4.1.2 20071124 (Red Hat 4.1.2-42)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import sys
>>> sys.path.append('/opt/Ice-3.3.1/python')
>>> import Ice


And the following is happening:

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Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "Ice.py", line 19, in <module>
    import IcePy
ImportError: libIce.so.33: cannot open shared object file: No such file or directory


Inside the folder /opt/Ice-3.3.1/python I have the following files:

IcePy.so

IcePy.so.33

IcePy.so.3.3.1

Honestly, we are at a loss as to what is happening here. Thanks.

First off: if you've compiled your own Python and/or installed Python from an RPM that is not part of the RHEL 5 default install you will have to compile IcePy against that Python version yourself; the IcePy RPMs will be of little use to you.

I assume this is what you've attempted to do? Or have you moved/changed something from /usr/share/Ice-3.3.1? Is this Ice installation from source?

You will have to set both PYTHONPATH and LD_LIBRARY_PATH depending on the answers to the above.

its now working. thanks for your help