[ome-users] upgrade from 5.0.0-ice34-b19 to 5.1.2-ice35-b5
Simon Li
spli at dundee.ac.uk
Wed Aug 5 18:53:50 BST 2015
Since Nginx is already installed, is there any reason you can't use it?
https://www.openmicroscopy.org/site/support/omero5.1/sysadmins/unix/install-web/install-fastcgi.html
https://www.openmicroscopy.org/site/support/omero5.1/sysadmins/unix/server-linux-walkthrough.html
Simon
On 5 August 2015 at 18:43, Jean-Marc Champagne <jean-marc.champagne at mhi-rc.org<mailto: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<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<tel:%2B44%20%280%29%201382%20388797>
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<mailto:ome-users-bounces at lists.openmicroscopy.org.uk> on behalf of jean-marc.champagne at mhi-rc.org<mailto: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<http://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<http://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<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<mailto: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<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
>_______________________________________________
>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 _______________________________________________
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
_______________________________________________
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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.openmicroscopy.org.uk/pipermail/ome-users/attachments/20150805/52c97c03/attachment.html>
More information about the ome-users
mailing list