Open Microscopy Environment

Need some advice/help to get around the initial configuration of OMERO.server 5.4.3.

I downloaded the OMERO.server zip file: https://downloads.openmicroscopy.org/om ... 36-b77.zip. Following the installation steps from the website, all the needed prerequisite software was downloaded and installed. When I came to start configuration (setting the data directory) of the OMERO.server, I ran into this error:

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[omero@compute-0-6 ~]$ OMERO.server/bin/omero config set omero.data.dir "$OMERO_DATA_DIR"
********************************************************************************

        ERROR: Could not import omero.cli! (/lib64/libstdc++.so.6: version `CXXABI_1.3.8' not found (required by /usr/lib64/python2.7/site-packages/IcePy.so))

        This means that your installation is incomplete. Contact
        the OME mailing lists for more information:

        https://www.openmicroscopy.org/support/

        If you are building from source, please supply the build log
        as well as which version you are building from. If you
        downloaded a distribution, please provide which link you
        used.

********************************************************************************

        Debugging Info:
        --------------
        CWD=/home/omero
        VERSION=2.7.5 (default, Aug  4 2017, 00:39:18)  [GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
        OMERO_HOME=None
        PYTHONPATH=['/home/omero/OMERO.server/lib/python', '/home/omero/OMERO.server/var/lib', '/home/omero/OMERO.server-5.4.3-ice36-b77/bin', '/usr/lib/python2.7/site-packages/cffi-1.9.1-py2.7-linux-x86_64.egg', '/usr/lib/python2.7/site-packages/pycparser-2.17-py2.7.egg', '/usr/lib/python2.7/site-packages/enum34-1.1.6-py2.7.egg', '/usr/lib/python2.7/site-packages/lvm2py-1.0-py2.7.egg', '/usr/lib/python2.7/site-packages/mdstat-1.0.4-py2.7.egg', '/usr/lib/python2.7/site-packages/pip-9.0.1-py2.7.egg', '/usr/lib64/python27.zip', '/usr/lib64/python2.7', '/usr/lib64/python2.7/plat-linux2', '/usr/lib64/python2.7/lib-tk', '/usr/lib64/python2.7/lib-old', '/usr/lib64/python2.7/lib-dynload', '/usr/lib64/python2.7/site-packages', '/usr/lib64/python2.7/site-packages/gtk-2.0', '/usr/lib/python2.7/site-packages', '/home/omero/OMERO.server/lib/fallback']


Everything was loaded with g++ 4.8.5, but I'm not sure what was compiled during the installation process. (Am I using a compiler that is too far out of date?). I'm kinda at a loss for where the need for a module in the C++ library. Any help or pointers to get over this last bit of installation will be most appreciated.

--clay

Hi Clay,

claybreshears wrote:I downloaded the OMERO.server zip file: https://downloads.openmicroscopy.org/om ... 36-b77.zip. Following the installation steps from the website, all the needed prerequisite software was downloaded and installed.

Can you tell us which instructions you are following? i.e. what OS platform/version are you using?

~Josh

Sure thing.

I was following the instructions from https://docs.openmicroscopy.org/omero/5 ... ice36.html.

The OS installed on the machine is CentOS Linux release 7.4.1708 (Core)
(from /etc/centos-release)

The kernel is 3.10.0-693.5.2.el7.x86_64
(from uname -r)

Did you start from a fresh server, or were there packages/software already installed before you followed our instructions? Can you run the following as the omero user and as root:

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python -c 'import Ice; print Ice.stringVersion(), Ice.__file__'


Thanks, Simon

It was a fairly fresh server. Some packages were already installed on the system. (I've got notes as to what installed and what didn't at the office; I'm starting from home to overcome the 8 hours time difference first thing. )

Running that command as root and the omero system user, I got 'Segmentation fault (core dumped)' each time.

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[root@compute-0-6 ~]# python -c 'import Ice; print Ice.stringVersion(), Ice.__file__'
Segmentation fault (core dumped)
[root@compute-0-6 ~]# su - omero
Last login: Wed Mar  7 09:12:07 PST 2018 from XXX.XXX.com on pts/2
[omero@oda-compute-0-6 ~]$ python -c 'import Ice; print Ice.stringVersion(), Ice.__file__'
Segmentation fault (core dumped)


If you could give us a list of packages that were already installed, and any other non-standard system settings, that would be useful. The output of

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rpm -qa

might be useful too if there's nothing you want to keep private.

Simon

Hi Clay,

also to try to help with the time difference, you might want to read through some of these threads:

• https://stackoverflow.com/questions/203 ... ersion-cxx
• https://bugzilla.mozilla.org/show_bug.cgi?id=1055792 and the linked:
• https://pixinsight.com/forum/index.php?topic=11301.0

We don't have experience with this issue in particular, but it could be related.

All the best,
~Josh

Attached is the 2356 line text file with the results of

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rpm -qa | sort > rpm.sort

and then zipped to allow attachment.

I don't know of any obvious "interesting" settings. The system is on an NFS file system, but all the work I'm doing for installation and caching images is being done on local disks. The omero system user is also only on the local system, not seen by the larger set of servers.

I'll look into the URLs that Josh has listed to see if there might be something to try there.

--clay

At the end it was so simple. Need to add the right library path to LD_LIBRARY_PATH.

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export LD_LIBRARY_PATH=/usr/local/lib64:$LD_LIBRARY_PATH

To paraphrase Foghorn Leghorn, I feel like I was "doin' a lot of choppin', but no chips were flyin'".

Thanks for all the assistance.

--clay

HI Clay

Thanks for the update, and glad you got it working. I'm still intrigued as to why you needed /usr/local/lib64/, it's empty on all our CentOS-7 OMERO servers. If you ever figure out the underlying cause let us know and we can add it to our docs if appropriate.

Simon