[ome-users] upgrade from 5.0.0-ice34-b19 to 5.1.2-ice35-b5
Jean-Marc Champagne
jean-marc.champagne at mhi-rc.org
Wed Aug 5 15:53:48 BST 2015
Before I downgraded ICE, The database was upgraded and now I receive
omero at sripl-ig-oms01:/home/OMS/apps/OMERO/OMERO.server$ psql -h localhost -U db_omero_usr omero_database < sql/psql/OMERO5.1__1/OMERO5.0__0.sql
Password for user db_omero_usr:
BEGIN
CREATE FUNCTION
ERROR: ASSERTION ERROR: Wrong database version
How do I know for sure it works fine ?
Jean-Marc Champagne
Analyste informatique et infrastructure
Tel: +1-514-461-1300 x 3311
Fax: +1-514-461-1301
Site web/Website: www.mhicc.org<http://www.mhicc.org>
[cid:image001.jpg at 01C86108.4D83E020]
4100 Molson St., Suite 300, Montreal, Quebec H1Y 3N1 CANADA
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From: ome-users [mailto:ome-users-bounces at lists.openmicroscopy.org.uk] On Behalf Of Sebastien Besson (Staff)
Sent: 5 août 2015 07:23
To: users OME
Subject: Re: [ome-users] upgrade from 5.0.0-ice34-b19 to 5.1.2-ice35-b5
Hi Jean-Marc,
assuming you haven’t upgraded your database to 5.1 yet, you’ll need to
run the PSQL command you pasted in your email before starting the
server (likely as the postgres user given your setup).
Best,
Sebastien
On 4 Aug 2015, at 21:13, Jean-Marc Champagne <jean-marc.champagne at mhi-rc.org<mailto:jean-marc.champagne at mhi-rc.org>> wrote:
I have copied the files to omero.server/etc/grid from the zip file and ran bin/omero admin diagnostics results below, Do I need to run psql -h localhost -U db_user omero_database < sql/psql/OMERO5.1__1/OMERO5.0__0.sql
I tried to run omero at sripl-ig-oms01:/home/OMS/apps/OMERO/OMERO.server$<mailto:omero at sripl-ig-oms01:/home/OMS/apps/OMERO/OMERO.server$> psql -l
psql: FATAL: role "omero" does not exist from my omero user
result from postgres user Is this normal ?
postgres at sripl-ig-oms01:/home/OMS/apps/OMERO/OMERO.server$<mailto:postgres at sripl-ig-oms01:/home/OMS/apps/OMERO/OMERO.server$> psql -l
List of databases
Name | Owner | Encoding | Collate | Ctype | Access privileges
----------------+----------+----------+-------------+-------------+-----------------------
omero_database | db_user | UTF8 | en_CA.UTF-8 | en_CA.UTF-8 |
postgres | postgres | UTF8 | en_CA.UTF-8 | en_CA.UTF-8 |
template0 | postgres | UTF8 | en_CA.UTF-8 | en_CA.UTF-8 | =c/postgres +
| | | | | postgres=CTc/postgres
template1 | postgres | UTF8 | en_CA.UTF-8 | en_CA.UTF-8 | postgres=CTc/postgres+
| | | | | =c/postgres
(4 rows)
================================================================================
OMERO Diagnostics 5.1.2-ice34-b45
================================================================================
WARNING:omero.util.UpgradeCheck:UPGRADE AVAILABLE:Please upgrade to 5.1.3 See http://trac.openmicroscopy.org.uk/omero for the latest version
Commands: java -version 1.7.0 (/usr/bin/java -- 2 others)
Commands: python -V 2.7.3 (/usr/bin/python)
Commands: icegridnode --version 3.4.2 (/usr/bin/icegridnode)
Commands: icegridadmin --version 3.4.2 (/usr/bin/icegridadmin)
Commands: psql --version 9.4.4 (/usr/bin/psql -- 2 others)
Server: icegridnode running
Server: Blitz-0 active (pid = 4008, enabled)
Server: DropBox active (pid = 4009, enabled)
Server: FileServer active (pid = 4012, enabled)
Server: Indexer-0 active (pid = 4014, enabled)
Server: MonitorServer active (pid = 4016, enabled)
Server: OMERO.Glacier2 active (pid = 4017, enabled)
Server: OMERO.IceStorm active (pid = 4019, enabled)
Server: PixelData-0 active (pid = 4020, enabled)
Server: Processor-0 active (pid = 4101, enabled)
Server: Tables-0 active (pid = 4105, enabled)
Server: TestDropBox inactive (enabled)
Log dir: /home/OMS/apps/OMERO/OMERO.server-5.1.2-ice34-b45/var/log exists
Log files: Blitz-0.log 419.0 KB errors=108 warnings=10
Log files: DropBox.log 20.0 KB errors=8 warnings=9
Log files: FileServer.log 3.0 KB
Log files: Indexer-0.log 159.0 KB errors=92 warnings=0
Log files: MonitorServer.log 9.0 KB
Log files: OMEROweb.log 72.0 KB
Log files: OMEROweb_request.log 0.0 KB
Log files: PixelData-0.log 152.0 KB errors=79 warnings=0
Log files: Processor-0.log 127.0 KB errors=64 warnings=35
Log files: Tables-0.log 135.0 KB errors=64 warnings=36
Log files: TestDropBox.log n/a
Log files: master.err 5.0 KB errors=3 warnings=16
Log files: master.out 0.0 KB
Log files: Total size 1.11 MB
Environment:OMERO_HOME=(unset)
Environment:OMERO_NODE=(unset)
Environment:OMERO_MASTER=(unset)
Environment:OMERO_USERDIR=(unset)
Environment:OMERO_TMPDIR=(unset)
Environment:PATH=/usr/local/bin:/usr/bin:/bin:/usr/local/games:/usr/games:/usr/lib/jvm/java-6-sun/bin:/usr/share/Ice-3.4.2:/usr/lib/postgresql/9.1/bin:/home/OMS/apps/OMERO/OMERO.server/bin
Environment:PYTHONPATH=/usr/lib/pymodules/python2.7:
Environment:ICE_HOME=/usr/share/Ice-3.4.2
Environment:LD_LIBRARY_PATH=/usr/share/java:/usr/lib:
Environment:DYLD_LIBRARY_PATH=(unset)
OMERO SSL port:4064
OMERO TCP port:4063
OMERO data dir:'/home/OMS/OMERO.data' Exists? True Is writable? True
OMERO temp dir:'/home/omero/omero/tmp' Exists? True Is writable? True (Size: 0)
JVM settings: Blitz -Xmx3799m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions
JVM settings: Indexer -Xmx2532m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions
JVM settings: Pixeldata -Xmx3799m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions
JVM settings: Repository -Xmx2532m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions
OMERO.web status... [RUNNING] (PID 3544)
Jean-Marc Champagne
Analyste informatique et infrastructure
Tel: +1-514-461-1300 x 3311
Fax: +1-514-461-1301
Site web/Website: www.mhicc.org<http://www.mhicc.org/>
<image001.jpg>
4100 Molson St., Suite 300, Montreal, Quebec H1Y 3N1 CANADA
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From: ome-users [mailto:ome-users-bounces at lists.openmicroscopy.org.uk] On Behalf Of Sebastien Besson (Staff)
Sent: 4 août 2015 15:46
To: users OME
Subject: Re: [ome-users] upgrade from 5.0.0-ice34-b19 to 5.1.2-ice35-b5
Hi Jean-Marie,
No worries. Indeed, what I meant is that the default.xml, windefault.xml and
templates.xml files located under your OMERO.server/etc/grid should be the
same as the ones extracted from the OMERO.server zip bundle.
Either you can replace these files under OMERO.server/etc/grid/ or you can
start from scratch by removing the 5.1.3 OMERO.server and running something
like
$ unzip OMERO.server-5.1.2-ice34-b45.zip
$ ln -s OMERO.server-5.1.2-ice34-b45 OMERO.server
$ cp OMERO.server-old/etc/grid/config.xml OMERO.server/etc/grid
and then start the new server.
Let us know if this works
Sebastien
[1] https://www.openmicroscopy.org/site/support/omero5.1/sysadmins/server-upgrade.html#copy-new-binaries
On 4 Aug 2015, at 20:34, Jean-Marc Champagne <jean-marc.champagne at mhi-rc.org<mailto:jean-marc.champagne at mhi-rc.org>> wrote:
Sorry, I’m not sure I understand what you are telling me (confused)
You want me to unzip the file again into OMERO.server/etc/grid/*.xml and only copy the OMERO.server/etc/grid/config.xml from Omero.server-old ?
Jean-Marc Champagne
Analyste informatique et infrastructure
Tel: +1-514-461-1300 x 3311
Fax: +1-514-461-1301
Site web/Website: www.mhicc.org<http://www.mhicc.org/>
<image001.jpg>
4100 Molson St., Suite 300, Montreal, Quebec H1Y 3N1 CANADA
Ce courriel peut contenir de l’information privilégiée, confidentielle ou protégée contre la divulgation. Si ce courriel a été reçu par erreur, veuillez en aviser l’expéditeur et détruire toute copie en votre possession. Toute utilisation, divulgation, distribution ou impression du contenu de ce courriel est strictement interdite.
This e-mail may contain information that is privileged, confidential and/or exempt from disclosure. If this e-mail has been received in error, please notify the sender and destroy all copies of this e-mail. Any use, disclosure, distribution, or printing of the contents of this e-mail is strictly prohibited.
From: ome-users [mailto:ome-users-bounces at lists.openmicroscopy.org.uk] On Behalf Of Sebastien Besson (Staff)
Sent: 4 août 2015 15:25
To: users OME
Subject: Re: [ome-users] upgrade from 5.0.0-ice34-b19 to 5.1.2-ice35-b5
Hi Jean-Marc,
The etc/grid/config.xml file contains the OMERO server configuration properties and should
be the only file you need to copy in-between server upgrades.
Several adjustments were also made to these templates for 5.1.0. Could you copy back all xml
files from the downloaded server zip under etc/ and try starting the server again?
Looking at your config, you seem to have a mismatch between the database owner which is
db_user and the configuration omero.db.user which is db_omero_user as well.
Best,
Sebastien
On 4 Aug 2015, at 20:12, Jean-Marc Champagne <jean-marc.champagne at mhi-rc.org<mailto:jean-marc.champagne at mhi-rc.org>> wrote:
I used the procedure I found on the site
http://www.openmicroscopy.org/site/support/omero4/sysadmins/unix/server-install-linux.html
sudo apt-get install zeroc-ice33 but it’s not available anymore
After a restart of the server I tried again with apt-get install zeroc-ice34 and it installed it properly
installed Ice
using
sudo apt-get install zeroc-ice34
omero at sripl-ig-oms01:/home/OMS/apps/OMERO$ icegridnode --version 3.4.2
python -c 'import Ice; print Ice.stringVersion()' 3.4.2
cp OMERO.server-old/etc/grid/config.xml OMERO.server/etc/grid/
omero at sripl-ig-oms01:/home/OMS/apps/OMERO/OMERO.server$<mailto:omero at sripl-ig-oms01:/home/OMS/apps/OMERO/OMERO.server$> bin/omero admin stop
Waiting on shutdown. Use CTRL-C to exit
.....omero at sripl-ig-oms01:/home/OMS/apps/OMERO/OMERO.server$<mailto:.....omero at sripl-ig-oms01:/home/OMS/apps/OMERO/OMERO.server$> bin/omero admin start
WARNING: lock files in /home/OMS/OMERO.data
----------------------------------------
/home/OMS/OMERO.data/.omero/repository/4dba782d-12bc-4a98-a950-0aa63c6b71ef/.lock
/home/OMS/OMERO.data/.omero/repository/355ef21e-e9dd-4e2d-a696-3e019425da87/.lock
/home/OMS/OMERO.data/.omero/repository/bd756a09-5b59-4060-abd4-4cec15f73977/.lock
/home/OMS/OMERO.data/.omero/repository/0f86610b-2563-4aae-a964-070d1c539469/.lock
----------------------------------------
removed the files manually
omero at sripl-ig-oms01:/home/OMS/apps/OMERO/OMERO.server$<mailto:omero at sripl-ig-oms01:/home/OMS/apps/OMERO/OMERO.server$> bin/omero admin restart
Waiting on shutdown. Use CTRL-C to exit
.No descriptor given. Using etc/grid/default.xml
Waiting on startup. Use CTRL-C to exit
postgres at sripl-ig-oms01:/home/OMS/apps/OMERO/OMERO.server$<mailto:postgres at sripl-ig-oms01:/home/OMS/apps/OMERO/OMERO.server$> psql -l
Name | Owner | Encoding | Collate | Ctype | Access privileges
----------------+----------+----------+-------------+-------------+-----------------------
omero_database | db_user | UTF8 | en_CA.UTF-8 | en_CA.UTF-8 |
postgres | postgres | UTF8 | en_CA.UTF-8 | en_CA.UTF-8 |
template0 | postgres | UTF8 | en_CA.UTF-8 | en_CA.UTF-8 | =c/postgres +
| | | | | postgres=CTc/postgres
template1 | postgres | UTF8 | en_CA.UTF-8 | en_CA.UTF-8 | postgres=CTc/postgres+
| | | | | =c/postgres ((does not work with OMERO user))
List of databases
(4 rows)
psql: FATAL: role "omero" does not exist
The database upgrade , reindex and vacuum) were done before, How can I verify that the data is good
cp OMERO.server-old/etc/grid/config.xml OMERO.server/etc/grid/config.xml
Waiting on shutdown. Use CTRL-C to exit
.No descriptor given. Using etc/grid/default.xml
Waiting on startup. Use CTRL-C to exit
Verified config.xml
vi OMERO.server/etc/grid/config.xml
omero at sripl-ig-oms01:/home/OMS/apps/OMERO/OMERO.server$<mailto:omero at sripl-ig-oms01:/home/OMS/apps/OMERO/OMERO.server$> bin/omero admin restart
Waiting on shutdown. Use CTRL-C to exit
.No descriptor given. Using etc/grid/default.xml
Waiting on startup. Use CTRL-C to exit
omero at sripl-ig-oms01:/home/OMS/apps/OMERO/OMERO.server$<mailto:omero at sripl-ig-oms01:/home/OMS/apps/OMERO/OMERO.server$> vi etc/grid/config.xml
<icegrid><!--
This file was generated at Tue Aug 4 14:54:52 2015 by the OmeroConfig system.
Do not edit directly but see bin/omero config for details.
This file may be included into your IceGrid application.
--><properties id="__ACTIVE__"><property name="omero.config.profile" value="default" /><property name="omero.config.version" value="5.1.0" /><property name="omero.data.dir" value="/home/OMS/OMERO.data" /><property name="omero.db.name" value="omero_database" /><property name="omero.db.pass" value="password in clear" /><property name="omero.db.user" value="db_omero_usr" /><property name="omero.ldap.base" value="OU=ALL,dc=RG,dc=local" /><property name="omero.ldap.config" value="true" /><property name="omero.ldap.group_filter" value="(&(objectClass=group)" /><property name="omero.ldap.group_mapping" value="name=cn" /><property name="omero.ldap.new_user_group" value=":query:(cn=IG_OMERO_USRs))" /><property name="omero.ldap.password" value="other password clear" /><property name="omero.ldap.sync_on_login" value="true" /><property name="omero.ldap.urls" value="ldap://192.168.22.1:389" /><property name="omero.ldap.user_filter" value="(objectClass=user)" /><property name="omero.ldap.user_mapping" value="omeName=sAMAccountName,firstName=givenName,lastName=sn,email=mail" /><property name="omero.ldap.username" value="cn=LDAP AD. Search,ou=devices,ou=Users,ou=RG,ou=ALL,dc=RG,dc=local" /><property name="omero.security.password_provider" value="chainedPasswordProvider" /><property name="omero.security.trustStore" value="/home/OMS/OMERO.data/keystore/keystore.jks" /><property name="omero.web.debug" value="True" /><property name="omero.web.application_server" value="fastcgi-tcp" /><property name="omero.web.application_host" value="http://webpage<http://webpage/>" /></properties><properties id="default"><property name="omero.config.version" value="5.1.0" /><property name="omero.config.profile" value="default" /><property name="omero.data.dir" value="/home/OMS/OMERO.data" /><property name="omero.db.name" value="omero_database" /><property name="omero.db.pass" value="Password in clear" /><property name="omero.db.user" value="db_omero_usr" /><property name="omero.ldap.base" value="OU=ALL,dc=RG,dc=local" /><property name="omero.ldap.config" value="true" /><property name="omero.ldap.group_filter" value="(&(objectClass=group)" /><property name="omero.ldap.group_mapping" value="name=cn" /><property name="omero.ldap.new_user_group" value=":query:(cn=IG_OMERO_USRs))" /><property name="omero.ldap.password" value="otherpasswordinclear" /><property name="omero.ldap.sync_on_login" value="true" /><property name="omero.ldap.urls" value="ldap://192.168.22.1:389" /><property name="omero.ldap.user_filter" value="(objectClass=user)" /><property name="omero.ldap.user_mapping" value="omeName=sAMAccountName,firstName=givenName,lastName=sn,email=mail" /><property name="omero.ldap.username" value="cn=LDAP AD. Search,ou=devices,ou=Users,ou=RG,ou=ALL,dc=RG,dc=local" /><property name="omero.security.password_provider" value="chainedPasswordProvider" /><property name="omero.security.trustStore" value="/home/OMS/OMERO.data/keystore/keystore.jks" /><property name="omero.web.debug" value="True" /><property name="omero.web.application_server" value="fastcgi-tcp" /><property name="omero.web.application_host" value="http://webpage<http://webpage/>" /></properties><include file="generated.xml" /></icegrid>
Sorry for the delay, I was trying to figure out what was the problem
Now it says .NO descriptor givin using etc/grid/default.xml which I copied from OMERO.server-old/etc/grid/default.xml
JMarc
From: ome-users [mailto:ome-users-bounces at lists.openmicroscopy.org.uk] On Behalf Of Simon Li
Sent: 4 août 2015 13:47
To: OME User Support List
Subject: Re: [ome-users] upgrade from 5.0.0-ice34-b19 to 5.1.2-ice35-b5
From your previous output:
echo $ICE_HOME /usr/share/Ice-3.4.2 (does not exist)
How did you install Ice when you setup your older OMERO.server? Is there any way it could have been inadvertently removed?
On 4 August 2015 at 18:26, Jean-Marc Champagne <jean-marc.champagne at mhi-rc.org<mailto:jean-marc.champagne at mhi-rc.org>> wrote:
Yes it is my own server that is use only for Omero, before the upgrade I had OMERO.server-5.0.0-ice34-b19 installed and it was working fine,
Then I tried to install Omero.server-5.1.2-ice35-b45 which was installed fine but I had
ERROR: Ice version mismatch!
Your OMERO code has been compiled using Ice version 3.5.1
but you seem to have Ice version 3.4.2 installed. If you need
help understanding this issue, please send this error message
to the OME community:
environment variable are set has
echo $JAVA_HOME /usr/lib/jvm/java-7
#export JAVA_HOME=/usr/lib/jvm/java-6-sun
lrwxrwxrwx 1 root root 24 Feb 26 2012 default-java -> java-1.6.0-openjdk-amd64
a lrwxrwxrwx 1 root root 20 Jul 12 2013 java-1.6.0-openjdk-amd64 -> java-6-openjdk-amd64v
v -rw-r--r-- 1 root root 2387 Jul 12 2013 .java-1.6.0-openjdk-amd64.jinfo
a lrwxrwxrwx 1 root root 20 Jul 3 2013 java-1.7.0-openjdk-amd64 -> java-7-openjdk-amd64
i -rw-r--r-- 1 root root 2439 Jul 3 2013 .java-1.7.0-openjdk-amd64.jinfo
l drwxr-xr-x 5 root root 4096 Feb 27 2014 java-6-openjdk-amd64
a drwxr-xr-x 3 root root 4096 Feb 27 2014 java-6-openjdk-common
b lrwxrwxrwx 1 root root 19 Jun 9 2011 java-6-sun -> java-6-sun-1.6.0.26
l drwxr-xr-x 8 root root 4096 Feb 27 2014 java-6-sun-1.6.0.26
e -rw-r--r-- 1 root root 2793 Jun 9 2011 .java-6-sun.jinfo
drwxr-xr-x 7 root root 4096 Feb 27 2014 java-7-openjdk-amd64
drwxr-xr-x 3 root root 4096 Feb 27 2014 java-7-openjdk-common
drwxr-xr-x 8 root root 4096 Jul 31 15:28 java-7-oracle
lrwxrwxrwx 1 root root 4096 aug 4 10:48 java-7
-rw-r--r-- 1 root root 2586 Jul 31 15:28 .java-7-oracle.jinfo
echo $ICE_HOME /usr/share/Ice-3.4.2 (does not exist)
drwxr-xr-x 2 root root 4096 Feb 27 2014 icedtea-web
echo $POSTGRES_HOME /usr/lib/postgresql/9.1 replaced by /usr/lib/postgresql/9.4
drwxr-xr-x 4 root root 4096 Feb 27 2014 9.1 */etc/postgresql/9.4/main/prostgresql.conf port 5432
drwxr-xr-x 4 root root 4096 Jul 28 12:11 9.4 */etc/postgresql/9.1/main/prostgresql.conf port 5433
echo $OMERO_PREFIX /home/OMS/apps/OMERO/OMERO.server
export OMERO_PREFIX=~/apps/OMERO/OMERO/OMERO.server
echo $PATH /usr/local/bin:/usr/bin:/bin:/usr/local/games:/usr/games:/usr/lib/jvm/java-6-sun/bin:/usr/share/Ice-3.4.2:/usr/lib/postgresql/9.1/bin:/home/OMS/apps/OMERO/OMERO.server/bin
export PATH=$PATH:$JAVA_HOME/bin:$ICE_HOME:$POSTGRES_HOME/bin:$OMERO_PREFIX/bin
export PYTHONPATH=/usr/lib/pymodules/python2.6:$PYTHONPATH
echo $PYTHONPATH /usr/lib/pymodules/python2.7:
export LD_LIBRARY_PATH=/usr/share/java:/usr/lib:$LD_LIBRARY_PATH
echo $LD_LIBRARY_PATH /usr/share/java:/usr/lib:
From: ome-users [mailto:ome-users-bounces at lists.openmicroscopy.org.uk<mailto:ome-users-bounces at lists.openmicroscopy.org.uk>] On Behalf Of Simon Li
Sent: 4 août 2015 13:15
To: OME User Support List
Subject: Re: [ome-users] upgrade from 5.0.0-ice34-b19 to 5.1.2-ice35-b5
It looks like Debian 6 has the very old zeroc-ice33 in it's repos. Is this your own server, or was it setup by someone else? If OMERO was previously running then ice may have been installed in a non-standard location, which means you'll need to setup some environment variables e.g. PATH, PYTHONPATH.
Simon
On 4 August 2015 at 18:11, Jean-Marc Champagne <jean-marc.champagne at mhi-rc.org<mailto:jean-marc.champagne at mhi-rc.org>> wrote:
It’s installed on Debian 6
Linux version 3.2.0-4-amd64 (debian-kernel at lists.debian.org<mailto:debian-kernel at lists.debian.org>) (gcc version 4.6.3 (Debian 4.6.3-14) ) #1 SMP Debian 3.2.54-2
omero at sripl-ig-oms01:/home/OMS/apps/OMERO/OMERO.server$<mailto:omero at sripl-ig-oms01:/home/OMS/apps/OMERO/OMERO.server$> icegridnode --version
-bash: icegridnode: command not found
omero at sripl-ig-oms01:/home/OMS/apps/OMERO/OMERO.server$<mailto:omero at sripl-ig-oms01:/home/OMS/apps/OMERO/OMERO.server$> python -c 'import Ice; print Ice.stringVersion()'
Traceback (most recent call last):
File "<string>", line 1, in <module>
ImportError: No module named Ice
Thanks for the quick reply
JMarc
From: ome-users [mailto:ome-users-bounces at lists.openmicroscopy.org.uk<mailto:ome-users-bounces at lists.openmicroscopy.org.uk>] On Behalf Of Simon Li
Sent: 4 août 2015 13:03
To: OME User Support List
Subject: Re: [ome-users] upgrade from 5.0.0-ice34-b19 to 5.1.2-ice35-b5
Hi Jean-Marc
What operating system are you using (including the full version)? The ice poackage might have a different name.
Can you run the following two commands in a console and paste the output?
icegridnode --version
python -c 'import Ice; print Ice.stringVersion()'
Thanks, Simon
On 4 August 2015 at 17:38, Jean-Marc Champagne <jean-marc.champagne at mhi-rc.org<mailto:jean-marc.champagne at mhi-rc.org>> wrote:
I re-installed it using Omero.server-5.1.2-ice34-b45 file downloaded from the Omero web site
<image001.png>
And here’s the error msg I get
<image002.png>
<image003.png>
I verified if Ice was installed to find out it was not using
dpkg -s zeroc-ice34
dpkg-query: package 'zeroc-ice34' is not installed and no information is available
Use dpkg --info (= dpkg-deb --info) to examine archive files,
and dpkg --contents (= dpkg-deb --contents) to list their contents.
I went to the community and Maria had the same problem which she use to fix the probleme… what is the long line she is refering to ?
<image004.png>
JMarc
From: ome-users [mailto:ome-users-bounces at lists.openmicroscopy.org.uk<mailto:ome-users-bounces at lists.openmicroscopy.org.uk>] On Behalf Of Sebastien Besson (Staff)
Sent: 1 août 2015 08:15
To: users OME
Subject: Re: [ome-users] upgrade from 5.0.0-ice34-b19 to 5.1.2-ice35-b5
Hi Jean-Marc,
as we already suggested in the previous thread [1] [2], if you have Ice 3.4
installed via your package manager, could you try downloading the Ice 3.4
server and retry to start the server?
The upgrade of your version of Ice depends on your Linux distribution. More
information is available on the Ice 3.5 downloads page [3].
Best,
Sebastien
[1] http://lists.openmicroscopy.org.uk/pipermail/ome-users/2015-July/005508.html
[2] http://lists.openmicroscopy.org.uk/pipermail/ome-users/2015-July/005509.html
[3] https://zeroc.com/download_3_5_1.html
On 31 Jul 2015, at 15:18, Jean-Marc Champagne <jean-marc.champagne at mhi-rc.org<mailto:jean-marc.champagne at mhi-rc.org>> wrote:
I ran http://www.openmicroscopy.org/site/support/omero5.1/sysadmins/server-upgrade.html#omero-web-configuration procedures, and had to upgrade postgres from 9.1 to 9.4 to be able to set it up.
psql -h localhost -U db_omero_usr omero_database < sql/psql/OMERO5.1__1/OMERO5.0__0.sql -p 5433
UPDATE 1
status
---------------------------------------------------------------------
+
+
+
YOU HAVE SUCCESSFULLY UPGRADED YOUR DATABASE TO VERSION OMERO5.1__1+
+
+
(1 row)
COMMIT
Reindex was fine and so was the vacuum analyse
But when started omero, I received this error
How do I upgrade ICE ?
Any help would be greatly appreciated…
postgres at sripl-ig-oms01:/home/OMS/apps/OMERO/OMERO.server$<mailto:postgres at sripl-ig-oms01:/home/OMS/apps/OMERO/OMERO.server$> bin/omero admin start
Traceback (most recent call last):
File "bin/omero", line 97, in <module>
import omero.cli
File "/home/OMS/apps/OMERO/OMERO.server-5.1.2-ice35-b45/lib/python/omero/__init__.py", line 43, in <module>
raise Exception(msg)
Exception:
ERROR: Ice version mismatch!
Your OMERO code has been compiled using Ice version 3.5.1
but you seem to have Ice version 3.4.2 installed. If you need
help understanding this issue, please send this error message
to the OME community:
http://www.openmicroscopy.org/site/community
Debugging Info:
--------------
VERSION=5.1.2-ice35-b45
PYTHONPATH=/home/OMS/apps/OMERO/OMERO.server-5.1.2-ice35-b45/lib/python:/home/OMS/apps/OMERO/OMERO.server-5.1.2-ice35-b45/var/lib:/home/OMS/apps/OMERO/OMERO.server-5.1.2-ice35-b45/bin:/usr/lib/pymodules/python2.7:/home/OMS/apps/OMERO/OMERO.server-5.1.2-ice35-b45:/usr/lib/python2.7:/usr/lib/python2.7/plat-linux2:/usr/lib/python2.7/lib-tk:/usr/lib/python2.7/lib-old:/usr/lib/python2.7/lib-dynload:/usr/local/lib/python2.7/dist-packages:/usr/lib/python2.7/dist-packages:/usr/lib/python2.7/dist-packages/PIL:/usr/lib/python2.7/dist-packages/gtk-2.0:/home/OMS/apps/OMERO/OMERO.server-5.1.2-ice35-b45/lib/fallback
JMarc
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The University of Dundee is a registered Scottish Charity, No: SC015096
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The University of Dundee is a registered Scottish Charity, No: SC015096
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