Having trouble with server installation

Hi everyone.

I followed this document (https://docs.openmicroscopy.org/omero/5.6.2/sysadmins/unix/server-ubuntu1804-ice36.html) to install OMERO.server on my machine.

Everything was going well until I tried to run the server.

“omero admin start” command stopped with this error message:

icegridnode version is not compatible with 3.6.5: icegridnode: error while loading shared libraries: libdb_cxx-5.3.so: cannot open shared object file: No such file or directory

So I checked the diagnostics and the result is as below.

================================================================================
OMERO Diagnostics (admin) 5.7.1

Commands: java -version 11.0.8 (/usr/bin/java)
Commands: python -V 3.6.9 (/home/hhan72/omero/omero562/py3_venv/bin/python – 2 others)
Commands: icegridnode --version 5.3 (/opt/ice-3.6.5/bin/icegridnode)
Commands: icegridadmin --version 3.6.5 (/opt/ice-3.6.5/bin/icegridadmin)
Commands: psql --version 11.8 (/usr/bin/psql)
Commands: openssl version 1.1.111 (/usr/bin/openssl)

Server: icegridnode not started

Log dir: /home/hhan72/omero/omero562/OMERO.server/var/log
No logs available

Environment:OMERO_HOME=(unset)
Environment:OMERODIR=/home/hhan72/omero/omero562/OMERO.server
Environment:OMERO_NODE=(unset)
Environment:OMERO_MASTER=(unset)
Environment:OMERO_USERDIR=(unset)
Environment:OMERO_TMPDIR=(unset)
Environment:PATH=/home/hhan72/omero/omero562/py3_venv/bin:/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin
Environment:PYTHONPATH=(unset)
Environment:ICE_HOME=/opt/ice-3.6.5
Environment:LD_LIBRARY_PATH=/opt/ice-3.6.5/lib64:/opt/ice-3.6.5/lib:
Environment:DYLD_LIBRARY_PATH=(unset)

Cannot list deployed applications.
OMERO data dir:’/home/hhan72/omero/omero562/DATA’ Exists? True Is writable? True
OMERO temp dir:’/home/omero-server/omero/tmp’ Exists? True Is writable? True (Size: 0)

Jar: lib/server/formats-api.jar Bio-Formats API 6.5.1 7 July 2020 6f50e4d52c9d96112635fd8b2dde737f31041cf0
Jar: lib/server/formats-bsd.jar BSD Bio-Formats readers and writers 6.5.1 7 July 2020 6f50e4d52c9d96112635fd8b2dde737f31041cf0
Jar: lib/server/formats-gpl.jar Bio-Formats library 6.5.1 7 July 2020 6f50e4d52c9d96112635fd8b2dde737f31041cf0
Jar: lib/server/ome-codecs.jar OME Codecs 0.3.0 3 March 2020 8287f33d3bff3d08a9925fa45e0b225e27d71fe0
Jar: lib/server/ome-common.jar OME Common Java 6.0.4 21 October 2019 650939cfa026e33d2f38c1f56c74715dfb44b974
Jar: lib/server/ome-jai.jar OME JAI 0.1.0 28 June 2017 96ed34bf59f5ba3b51e3d60e342f30962a46c292
Jar: lib/server/ome-mdbtools.jar MDB Tools (Java port) 5.3.2 7 August 2018 68ffca2a95750cbb96f0d11785851aa4a554c0a4
Jar: lib/server/ome-poi.jar OME POI 5.3.3 6 August 2018 3887f4b2b21e195fa76ec4378858f6278aed5dcd
Jar: lib/server/ome-xml.jar OME XML library 6.1.0 7 April 2020 8f490f5987062978fafe77a3e35f7bd24d211281
Jar: lib/server/omero-blitz.jar jar 5.5.7
Jar: lib/server/omero-common.jar jar 5.5.6
Jar: lib/server/omero-gateway.jar jar 5.6.4
Jar: lib/server/omero-model.jar jar 5.6.1
Jar: lib/server/omero-renderer.jar jar 5.5.6
Jar: lib/server/omero-romio.jar jar 5.6.1
Jar: lib/server/omero-server.jar jar 5.6.0

Do you think downgrading icegridnode to 3.6.5 could solve this issue? I have no idea why it installed version 5.3 out of nowhere.

Thank you for all your assistance in advance.

Hi. It looks like you’re missing the libdb++-dev package. It’s part of the ‘Installing prerequisites’ step in the documentation. Just run all the apt-get ... steps again, in case you’re missing something else too.
Kind Regards,
Dominik

2 Likes