[ome-users] upgrade from 5.0.0-ice34-b19 to 5.1.2-ice35-b5
Kenneth Gillen (Staff)
k.h.gillen at dundee.ac.uk
Wed Aug 5 18:34:20 BST 2015
Hi Jean-Marc,
If you¹re seeing a ³Welcome to nginx² screen, then chances are nginx is
running on the host (or a proxy in between you and the server).
If you run the following command at the shell:
ps auxf | grep nginx
This should tell you if nginx is indeed running. If you normally use
Apache, you may wish to try stopping nginx in case nginx has started up
and taken over the ports normally used by Apache.
All the best,
Kenny
--
Kenneth Gillen
OME System Administrator
Wellcome Trust Centre for Gene Regulation & Expression
School of Life Sciences
CTIR 2
University of Dundee
Dow Street
Dundee DD1 5EH
United Kingdom
Tel: +44 (0) 1382 388797
Skype: kennethgillen
http://www.twitter.com/openmicroscopy
On 05/08/2015 17:55, "ome-users on behalf of Jean-Marc Champagne"
<ome-users-bounces at lists.openmicroscopy.org.uk on behalf of
jean-marc.champagne at mhi-rc.org> wrote:
>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/b
>in:/home/OMS/apps/OMERO/OMERO.server/bin:/usr/lib/jvm/java-7/bin:/usr/shar
>e/Ice-3.4.2:/etc/postgresql/9.4/main/postgresql.conf/bin:/home/OMS/apps/OM
>ERO/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,lastNam
>e=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
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