[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 17:55:25 BST 2015
omero at sripl-ig-oms01:/home/OMS/apps/OMERO/OMERO.server$ bin/omero admin diagnostics
================================================================================
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 -- 3 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 = 3977, enabled)
Server: DropBox active (pid = 3990, enabled)
Server: FileServer active (pid = 3991, enabled)
Server: Indexer-0 active (pid = 3993, enabled)
Server: MonitorServer active (pid = 3995, enabled)
Server: OMERO.Glacier2 active (pid = 3997, enabled)
Server: OMERO.IceStorm active (pid = 3999, enabled)
Server: PixelData-0 active (pid = 4013, enabled)
Server: Processor-0 active (pid = 4015, enabled)
Server: Tables-0 active (pid = 4017, 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 2.0 MB errors=146 warnings=14
Log files: DropBox.log 24.0 KB errors=10 warnings=11
Log files: FileServer.log 3.0 KB
Log files: Indexer-0.log 251.0 KB errors=140 warnings=0
Log files: MonitorServer.log 10.0 KB
Log files: OMEROweb.log 180.0 KB
Log files: OMEROweb_request.log 0.0 KB
Log files: PixelData-0.log 219.0 KB errors=114 warnings=0
Log files: Processor-0.log 147.0 KB errors=74 warnings=40
Log files: Tables-0.log 156.0 KB errors=74 warnings=41
Log files: TestDropBox.log n/a
Log files: master.err 9.0 KB errors=3 warnings=22
Log files: master.out 0.0 KB
Log files: Total size 3.31 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:/usr/lib/jvm/java-7/bin:/usr/share/Ice-3.4.2:/etc/postgresql/9.4/main/postgresql.conf/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:/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 6739)
__________________________________________________________________________________________________________________
omero at sripl-ig-oms01:/home/OMS/apps/OMERO/OMERO.server$ bin/omero config get
omero.data.dir=/home/OMS/OMERO.data
omero.db.name=omero_database
omero.db.pass=xxxxxxxx
omero.db.user=db_omero_usr
omero.ldap.base=OU=ALL,dc=RG,dc=local
omero.ldap.config=true
omero.ldap.group_filter=(&(objectClass=group)
omero.ldap.group_mapping=name=cn
omero.ldap.new_user_group=:query:(cn=IG_OMERO_USRs))
omero.ldap.password=xxxxxxx
omero.ldap.sync_on_login=true
omero.ldap.urls=ldap://192.168.22.1:389
omero.ldap.user_filter=(objectClass=user)
omero.ldap.user_mapping=omeName=sAMAccountName,firstName=givenName,lastName=sn,email=mail
omero.ldap.username=cn=LDAP AD. Search,ou=devices,ou=Users,ou=RG,ou=ALL,dc=RG,dc=local
omero.security.password_provider=chainedPasswordProvider
omero.security.trustStore=/home/OMS/OMERO.data/keystore/keystore.jks
omero.web.application_host=http://omero-web.inflammgen.local
omero.web.application_server=fastcgi-tcp
omero.web.debug=True
_________________________________________________________________________________________________________________
We are not using NGINX
Attached, OMEROweb.log and OMEROweb_request.log is empty
JMarc
-----Original Message-----
From: ome-users [mailto:ome-users-bounces at lists.openmicroscopy.org.uk] On Behalf Of Aleksandra Tarkowska (Staff)
Sent: 5 août 2015 11:22
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,
Could you please send:
- output of bin/omero admin diagnostics,
- nginx config,
- output of bin/omero config get --hide-password,
- all var/log/OMEROweb*.log,
- nginx error and access logs
Kind regards
Ola
On 05/08/2015 16:12, "Jean-Marc Champagne"
<jean-marc.champagne at mhi-rc.org> wrote:
>From the output everything looks fine, but when I try to login from the
>webpage http://omero-web.inflammgen.local/omero/webclient I get a page
>with Welcome to nginx !
>
>What did I do wrong ? and how do I fix it ?
>
>
>
>
>can you paste the output of:
>
>$ psql -h localhost -U db_omero_usr omero_database -c 'select * from
>dbpatch';
>
>id | currentpatch | currentversion | permissions | finished
> | message
> | previouspatch | previousversion |
>external_id
>----+--------------+----------------+-------------+--------------------
>----+--------------+----------------+-------------+---
>-----+-----------------------------------------------------------------
>-----+---
>--------------------------+---------------+-----------------+----------
>--------------------------+---------------+-----------------+---
> 1 | 0 | OMERO5.0 | -52 | 2014-03-04
>11:53:52.471713 | Database ready.
> | 0 | OMERO5.0 |
> 2 | 1 | OMERO5.1 | -52 | 2015-07-28
>14:10:34.931488 | Database updated.
> | 0 | OMERO5.0 |
> 3 | 1 | OMERO5.1 | -52 | 2015-08-04
>14:25:00.12515 | DB check DBEnumCheck: done for Bio-Formats revision
>923bf020f921d8bfcef203f407fc94855e5b03f0 | 1 | OMERO5.1
> |
> 4 | 1 | OMERO5.1 | -52 | 2015-08-04
>14:25:00.162061 | DB check DBUnicodeUnitsCheck: done
> | 1 | OMERO5.1 |
>(4 rows)
>_______________________________________________
>ome-users mailing list
>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 _______________________________________________
ome-users mailing list
ome-users at lists.openmicroscopy.org.uk
http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
-------------- next part --------------
A non-text attachment was scrubbed...
Name: OMEROweb.log
Type: application/octet-stream
Size: 211530 bytes
Desc: OMEROweb.log
URL: <http://lists.openmicroscopy.org.uk/pipermail/ome-users/attachments/20150805/eba162ea/attachment.obj>
More information about the ome-users
mailing list