[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 18:54:52 BST 2015
Hi Jean-Marc,
>how to I set it up ? to remove NGInx and use apache2 instead
If you were using nginx before your upgrade, and it worked, there’s no
reason to do this.
Like I mentioned previously, if somehow nginx has been installed alongside
Apache, you may wish to try stopping nginx and starting up Apache again.
If you were using nginx all along, and Apache is not installed at all,
then having nginx running isn’t a problem at all.
If you could provide your OMERO nginx config file and access/error logs,
as Ola earlier asked, that would be useful.
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 18:43, "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:
>You are right,
>
>root 3574 0.0 0.0 62356 1332 ? Ss 11:32 0:00 nginx:
>master process /usr/sbin/nginx
>www-data 3575 0.0 0.0 64792 2416 ? S 11:32 0:00 \_
>nginx: worker process
>www-data 3576 0.0 0.0 64792 1916 ? S 11:32 0:00 \_
>nginx: worker process
>www-data 3577 0.0 0.0 64792 1916 ? S 11:32 0:00 \_
>nginx: worker process
>www-data 3578 0.0 0.0 64792 1916 ? S 11:32 0:00 \_
>nginx: worker process
>root 9805 0.0 0.0 7832 868 pts/0 S+ 13:39 0:00 |
>\_ grep nginx
>
>how to I set it up ? to remove NGInx and use apache2 instead
>
>
>JMarc
>-----Original Message-----
>From: ome-users [mailto:ome-users-bounces at lists.openmicroscopy.org.uk] On
>Behalf Of Kenneth Gillen (Staff)
>Sent: 5 août 2015 13:34
>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,
>
>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/s
>>har
>>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:/u
>>sr/
>>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,last
>>Nam
>>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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>>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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