[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
Tue Aug 4 20:12:47 BST 2015
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$ bin/omero admin stop
Waiting on shutdown. Use CTRL-C to exit
.....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$ 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$ 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$ 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$ 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" /></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" /></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
[cid:image001.png at 01D0CEBD.05BB34C0]
And here’s the error msg I get
[cid:image002.png at 01D0CEBD.05BB34C0]
[cid:image003.png at 01D0CEBD.05BB34C0]
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 ?
[cid:image004.png at 01D0CEBD.05BB34C0]
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
The University of Dundee is a registered Scottish Charity, No: SC015096
_______________________________________________
ome-users mailing list
ome-users at lists.openmicroscopy.org.uk<mailto:ome-users at lists.openmicroscopy.org.uk>
http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
The University of Dundee is a registered Scottish Charity, No: SC015096
The University of Dundee is a registered Scottish Charity, No: SC015096
_______________________________________________
ome-users mailing list
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