[ome-users] upgrade from 5.0.0-ice34-b19 to 5.1.2-ice35-b5
Sebastien Besson (Staff)
s.besson at dundee.ac.uk
Wed Aug 5 16:04:27 BST 2015
Hi Jean-Marc,
can you paste the output of:
$ psql -h localhost -U db_omero_usr omero_database -c 'select * from dbpatch';
Sebastien
> On 5 Aug 2015, at 15:53, Jean-Marc Champagne <jean-marc.champagne at mhi-rc.org> wrote:
>
> 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
>
>
>
> <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,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,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: 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> 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 runpsql -h localhost -U db_user omero_database < sql/psql/OMERO5.1__1/OMERO5.0__0.sql
>
>
>
> I tried to runomero 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$ 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 Seehttp://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
>
>
>
> <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,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,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 15:46
> 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> 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
>
>
>
> <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,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,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> 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$ 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"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> wrote:
>
> Yes it is my own server that is use only for Omero, before the upgrade I had OMERO.server-5.0.0-ice34-b19installed 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 $LD_LIBRARY_PATH /usr/share/java:/usr/lib:
>
>
>
>
>
> From: ome-users [mailto:ome-users-bounces at lists.openmicroscopy.org.uk] On Behalf Of Simon Li
> Sent: 4 août 2015 13:15
>
>
> To: OME User Support List
> Subject: Re: [ome-users] upgrade from 5.0.0-ice34-b19 to 5.1.2-ice35-b5
>
>
>
> It looks like Debian 6 has the very old zeroc-ice33 in it's repos. Is this your own server, or was it setup by someone else? If OMERO was variables e.g. PATH, PYTHONPATH.
>
> Simon
>
>
>
> On 4 August 2015 at 18:11, Jean-Marc Champagne <jean-marc.champagne at mhi-rc.org> wrote:
>
> It’s installed on Debian 6
>
> Linux version 3.2.0-4-amd64 (debian-kernel at lists.debian.org) (gcc version 4.6.3 (Debian 4.6.3-14) ) #1 SMP Debian 3.2.54-2
>
>
>
> omero at sripl-ig-oms01:/home/OMS/apps/OMERO/OMERO.server$ icegridnode --version
>
> -bash: icegridnode: command not found
>
>
>
> 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] 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> 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 sheis refering to ?
>
>
>
>
>
> <image004.png>
>
> JMarc
>
>
>
> From: ome-users [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> 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$ 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-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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> 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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> The University of Dundee is a registered Scottish Charity, No: SC015096
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> ome-users at lists.openmicroscopy.org.uk
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