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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Hi Simon,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">I tried to follow the instruction everything was going well until I restarted the server, Debian 6 will not restart, it’s waiting omero-web to start and frozed
the server.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">I have to hack the server and remove Omero-web from the start up. (probably because it tries to use the same port as NGINX<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">You’ll find attach the logs that may be usefull for you to help me.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">What I would like to do, is simply be able to use omero though the web page, my customer don t need to use NGINX and I would like to remove it and use it has
it was before…<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">I’m not very good with Omero, but would like to learn it<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">JMarc<o:p></o:p></span></p>
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<p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">From:</span></b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif""> ome-users [mailto:ome-users-bounces@lists.openmicroscopy.org.uk]
<b>On Behalf Of </b>Simon Li<br>
<b>Sent:</b> 5 août 2015 13:54<br>
<b>To:</b> OME User Support List<br>
<b>Subject:</b> Re: [ome-users] upgrade from 5.0.0-ice34-b19 to 5.1.2-ice35-b5<o:p></o:p></span></p>
</div>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
<div>
<div>
<p class="MsoNormal" style="margin-bottom:12.0pt">Since Nginx is already installed, is there any reason you can't use it?<br>
<br>
<a href="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/install-web/install-fastcgi.html</a><br>
<a href="https://www.openmicroscopy.org/site/support/omero5.1/sysadmins/unix/server-linux-walkthrough.html">https://www.openmicroscopy.org/site/support/omero5.1/sysadmins/unix/server-linux-walkthrough.html</a><o:p></o:p></p>
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<p class="MsoNormal">Simon<o:p></o:p></p>
</div>
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<p class="MsoNormal"><o:p> </o:p></p>
<div>
<p class="MsoNormal">On 5 August 2015 at 18:43, Jean-Marc Champagne <<a href="mailto:jean-marc.champagne@mhi-rc.org" target="_blank">jean-marc.champagne@mhi-rc.org</a>> wrote:<o:p></o:p></p>
<p class="MsoNormal" style="margin-bottom:12.0pt">You are right,<br>
<br>
root 3574 0.0 0.0 62356 1332 ? Ss 11:32 0:00 nginx: master process /usr/sbin/nginx<br>
www-data 3575 0.0 0.0 64792 2416 ? S 11:32 0:00 \_ nginx: worker process<br>
www-data 3576 0.0 0.0 64792 1916 ? S 11:32 0:00 \_ nginx: worker process<br>
www-data 3577 0.0 0.0 64792 1916 ? S 11:32 0:00 \_ nginx: worker process<br>
www-data 3578 0.0 0.0 64792 1916 ? S 11:32 0:00 \_ nginx: worker process<br>
root 9805 0.0 0.0 7832 868 pts/0 S+ 13:39 0:00 | \_ grep nginx<br>
<br>
how to I set it up ? to remove NGInx and use apache2 instead<br>
<br>
<br>
JMarc<br>
-----Original Message-----<br>
From: ome-users [mailto:<a href="mailto:ome-users-bounces@lists.openmicroscopy.org.uk">ome-users-bounces@lists.openmicroscopy.org.uk</a>] On Behalf Of Kenneth Gillen (Staff)<br>
Sent: 5 août 2015 13:34<br>
To: OME User Support List<br>
Subject: Re: [ome-users] upgrade from 5.0.0-ice34-b19 to 5.1.2-ice35-b5<br>
<br>
Hi Jean-Marc,<o:p></o:p></p>
<div>
<div>
<p class="MsoNormal">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).<br>
<br>
If you run the following command at the shell:<br>
<br>
ps auxf | grep nginx<br>
<br>
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.<br>
<br>
All the best,<br>
<br>
Kenny<br>
<br>
--<br>
<br>
Kenneth Gillen<br>
<br>
<br>
OME System Administrator<br>
<br>
Wellcome Trust Centre for Gene Regulation & Expression School of Life Sciences CTIR 2 University of Dundee Dow Street Dundee DD1 5EH United Kingdom<br>
<br>
Tel: <a href="tel:%2B44%20%280%29%201382%20388797">+44 (0) 1382 388797</a><br>
Skype: kennethgillen<br>
<br>
<a href="http://www.twitter.com/openmicroscopy" target="_blank">http://www.twitter.com/openmicroscopy</a><br>
<br>
<br>
<br>
<br>
<br>
<br>
On 05/08/2015 17:55, "ome-users on behalf of Jean-Marc Champagne"<br>
<<a href="mailto:ome-users-bounces@lists.openmicroscopy.org.uk">ome-users-bounces@lists.openmicroscopy.org.uk</a> on behalf of
<a href="mailto:jean-marc.champagne@mhi-rc.org">jean-marc.champagne@mhi-rc.org</a>> wrote:<br>
<br>
><a href="mailto:omero@sripl-ig-oms01:/home/OMS/apps/OMERO/OMERO.server$">omero@sripl-ig-oms01:/home/OMS/apps/OMERO/OMERO.server$</a> bin/omero admin<br>
>diagnostics<br>
><br>
>=======================================================================<br>
>===<br>
>======<br>
>OMERO Diagnostics 5.1.2-ice34-b45<br>
>=======================================================================<br>
>===<br>
>======<br>
><br>
>WARNING:omero.util.UpgradeCheck:UPGRADE AVAILABLE:Please upgrade to<br>
>5.1.3 See <a href="http://trac.openmicroscopy.org.uk/omero" target="_blank">http://trac.openmicroscopy.org.uk/omero</a> for the latest<br>
>version<br>
><br>
>Commands: java -version 1.7.0 (/usr/bin/java -- 3<br>
>others)<br>
>Commands: python -V 2.7.3 (/usr/bin/python)<br>
>Commands: icegridnode --version 3.4.2<br>
>(/usr/bin/icegridnode)<br>
>Commands: icegridadmin --version 3.4.2<br>
>(/usr/bin/icegridadmin)<br>
>Commands: psql --version 9.4.4 (/usr/bin/psql -- 2<br>
>others)<br>
><br>
>Server: icegridnode running<br>
>Server: Blitz-0 active (pid = 3977, enabled)<br>
>Server: DropBox active (pid = 3990, enabled)<br>
>Server: FileServer active (pid = 3991, enabled)<br>
>Server: Indexer-0 active (pid = 3993, enabled)<br>
>Server: MonitorServer active (pid = 3995, enabled)<br>
>Server: OMERO.Glacier2 active (pid = 3997, enabled)<br>
>Server: OMERO.IceStorm active (pid = 3999, enabled)<br>
>Server: PixelData-0 active (pid = 4013, enabled)<br>
>Server: Processor-0 active (pid = 4015, enabled)<br>
>Server: Tables-0 active (pid = 4017, enabled)<br>
>Server: TestDropBox inactive (enabled)<br>
><br>
>Log dir: /home/OMS/apps/OMERO/OMERO.server-5.1.2-ice34-b45/var/log<br>
>exists<br>
><br>
>Log files: Blitz-0.log 2.0 MB errors=146<br>
>warnings=14<br>
>Log files: DropBox.log 24.0 KB errors=10<br>
>warnings=11<br>
>Log files: FileServer.log 3.0 KB<br>
>Log files: Indexer-0.log 251.0 KB errors=140<br>
>warnings=0<br>
>Log files: MonitorServer.log 10.0 KB<br>
>Log files: OMEROweb.log 180.0 KB<br>
>Log files: OMEROweb_request.log 0.0 KB<br>
>Log files: PixelData-0.log 219.0 KB errors=114<br>
>warnings=0<br>
>Log files: Processor-0.log 147.0 KB errors=74<br>
>warnings=40<br>
>Log files: Tables-0.log 156.0 KB errors=74<br>
>warnings=41<br>
>Log files: TestDropBox.log n/a<br>
>Log files: master.err 9.0 KB errors=3<br>
>warnings=22<br>
>Log files: master.out 0.0 KB<br>
>Log files: Total size 3.31 MB<br>
><br>
><br>
>Environment:OMERO_HOME=(unset)<br>
>Environment:OMERO_NODE=(unset)<br>
>Environment:OMERO_MASTER=(unset)<br>
>Environment:OMERO_USERDIR=(unset)<br>
>Environment:OMERO_TMPDIR=(unset)<br>
>Environment:PATH=/usr/local/bin:/usr/bin:/bin:/usr/local/games:/usr/games:<br>
>/usr/lib/jvm/java-6-sun/bin:/usr/share/Ice-3.4.2:/usr/lib/postgresql/9.<br>
>1/b<br>
>in:/home/OMS/apps/OMERO/OMERO.server/bin:/usr/lib/jvm/java-7/bin:/usr/s<br>
>har<br>
>e/Ice-3.4.2:/etc/postgresql/9.4/main/postgresql.conf/bin:/home/OMS/apps<br>
>/OM<br>
>ERO/OMERO.server/bin<br>
>Environment:PYTHONPATH=/usr/lib/pymodules/python2.7<br>
>Environment:ICE_HOME=/usr/share/Ice-3.4.2<br>
>Environment:LD_LIBRARY_PATH=/usr/share/java:/usr/lib:/usr/share/java:/u<br>
>sr/<br>
>lib:<br>
>Environment:DYLD_LIBRARY_PATH=(unset)<br>
><br>
>OMERO SSL port:4064<br>
>OMERO TCP port:4063<br>
>OMERO data dir:'/home/OMS/OMERO.data' Exists? True Is<br>
>writable? True<br>
>OMERO temp dir:'/home/omero/omero/tmp' Exists? True Is<br>
>writable? True (Size: 0)<br>
><br>
>JVM settings: Blitz -Xmx3799m -XX:MaxPermSize=1g<br>
>-XX:+IgnoreUnrecognizedVMOptions<br>
>JVM settings: Indexer -Xmx2532m -XX:MaxPermSize=1g<br>
>-XX:+IgnoreUnrecognizedVMOptions<br>
>JVM settings: Pixeldata -Xmx3799m -XX:MaxPermSize=1g<br>
>-XX:+IgnoreUnrecognizedVMOptions<br>
>JVM settings: Repository -Xmx2532m -XX:MaxPermSize=1g<br>
>-XX:+IgnoreUnrecognizedVMOptions<br>
><br>
>OMERO.web status... [RUNNING] (PID 6739)<br>
><br>
><br>
>_______________________________________________________________________<o:p></o:p></p>
</div>
</div>
<p class="MsoNormal">>___ ________________________________________<o:p></o:p></p>
<div>
<div>
<p class="MsoNormal">><br>
><a href="mailto:omero@sripl-ig-oms01:/home/OMS/apps/OMERO/OMERO.server$">omero@sripl-ig-oms01:/home/OMS/apps/OMERO/OMERO.server$</a> bin/omero<br>
>config get omero.data.dir=/home/OMS/OMERO.data<br>
><a href="http://omero.db.name" target="_blank">omero.db.name</a>=omero_database<br>
>omero.db.pass=xxxxxxxx<br>
>omero.db.user=db_omero_usr<br>
>omero.ldap.base=OU=ALL,dc=RG,dc=local<br>
>omero.ldap.config=true<br>
>omero.ldap.group_filter=(&(objectClass=group)<br>
>omero.ldap.group_mapping=name=cn<br>
>omero.ldap.new_user_group=:query:(cn=IG_OMERO_USRs))<br>
>omero.ldap.password=xxxxxxx<br>
>omero.ldap.sync_on_login=true<br>
>omero.ldap.urls=ldap://<a href="http://192.168.22.1:389" target="_blank">192.168.22.1:389</a><br>
>omero.ldap.user_filter=(objectClass=user)<br>
>omero.ldap.user_mapping=omeName=sAMAccountName,firstName=givenName,last<br>
>Nam<br>
>e=sn,email=mail<br>
>omero.ldap.username=cn=LDAP AD.<br>
>Search,ou=devices,ou=Users,ou=RG,ou=ALL,dc=RG,dc=local<br>
>omero.security.password_provider=chainedPasswordProvider<br>
>omero.security.trustStore=/home/OMS/OMERO.data/keystore/keystore.jks<br>
>omero.web.application_host=<a href="http://omero-web.inflammgen.local" target="_blank">http://omero-web.inflammgen.local</a><br>
>omero.web.application_server=fastcgi-tcp<br>
>omero.web.debug=True<br>
>_______________________________________________________________________<o:p></o:p></p>
</div>
</div>
<p class="MsoNormal">>___ _______________________________________<o:p></o:p></p>
<div>
<div>
<p class="MsoNormal">><br>
>We are not using NGINX<br>
><br>
>Attached, OMEROweb.log and OMEROweb_request.log is empty<br>
><br>
>JMarc<br>
><br>
>-----Original Message-----<br>
>From: ome-users [mailto:<a href="mailto:ome-users-bounces@lists.openmicroscopy.org.uk">ome-users-bounces@lists.openmicroscopy.org.uk</a>]<br>
>On Behalf Of Aleksandra Tarkowska (Staff)<br>
>Sent: 5 août 2015 11:22<br>
>To: OME User Support List<br>
>Subject: Re: [ome-users] upgrade from 5.0.0-ice34-b19 to 5.1.2-ice35-b5<br>
><br>
>Hi Jean-Marc,<br>
><br>
>Could you please send:<br>
> - output of bin/omero admin diagnostics,<br>
> - nginx config,<br>
> - output of bin/omero config get --hide-password,<br>
> - all var/log/OMEROweb*.log,<br>
> - nginx error and access logs<br>
><br>
>Kind regards<br>
>Ola<br>
><br>
><br>
><br>
><br>
><br>
>On 05/08/2015 16:12, "Jean-Marc Champagne"<br>
><<a href="mailto:jean-marc.champagne@mhi-rc.org">jean-marc.champagne@mhi-rc.org</a>> wrote:<br>
><br>
>>From the output everything looks fine, but when I try to login from<br>
>>the webpage <a href="http://omero-web.inflammgen.local/omero/webclient" target="_blank">
http://omero-web.inflammgen.local/omero/webclient</a> I get a<br>
>>page with Welcome to nginx !<br>
>><br>
>>What did I do wrong ? and how do I fix it ?<br>
>><br>
>><br>
>><br>
>><br>
>>can you paste the output of:<br>
>><br>
>>$ psql -h localhost -U db_omero_usr omero_database -c 'select * from<br>
>>dbpatch';<br>
>><br>
>>id | currentpatch | currentversion | permissions | finished<br>
>> | message<br>
>> | previouspatch | previousversion |<br>
>>external_id<br>
>>----+--------------+----------------+-------------+-------------------<o:p></o:p></p>
</div>
</div>
<p class="MsoNormal">>>----+--------------+----------------+-------------+-<br>
>>----+--------------+----------------+-------------+---<br>
>>-----+----------------------------------------------------------------<br>
>>-----+-<br>
>>-----+---<br>
>>--------------------------+---------------+-----------------+---------<br>
>>--------------------------+---------------+-----------------+-<o:p></o:p></p>
<div>
<div>
<p class="MsoNormal">>>--------------------------+---------------+-----------------+---<br>
>> 1 | 0 | OMERO5.0 | -52 | 2014-03-04<br>
>>11:53:52.471713 | Database ready.<br>
>> | 0 | OMERO5.0 |<br>
>> 2 | 1 | OMERO5.1 | -52 | 2015-07-28<br>
>>14:10:34.931488 | Database updated.<br>
>> | 0 | OMERO5.0 |<br>
>> 3 | 1 | OMERO5.1 | -52 | 2015-08-04<br>
>>14:25:00.12515 | DB check DBEnumCheck: done for Bio-Formats revision<br>
>>923bf020f921d8bfcef203f407fc94855e5b03f0 | 1 | OMERO5.1<br>
>> |<br>
>> 4 | 1 | OMERO5.1 | -52 | 2015-08-04<br>
>>14:25:00.162061 | DB check DBUnicodeUnitsCheck: done<br>
>> | 1 | OMERO5.1 |<br>
>>(4 rows)<br>
>>_______________________________________________<br>
>>ome-users mailing list<br>
>><a href="mailto:ome-users@lists.openmicroscopy.org.uk">ome-users@lists.openmicroscopy.org.uk</a><br>
>><a href="http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users" target="_blank">http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users</a><br>
><br>
><br>
>The University of Dundee is a registered Scottish Charity, No: SC015096<br>
>_______________________________________________<br>
>ome-users mailing list<br>
><a href="mailto:ome-users@lists.openmicroscopy.org.uk">ome-users@lists.openmicroscopy.org.uk</a><br>
><a href="http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users" target="_blank">http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users</a><br>
<br>
<br>
The University of Dundee is a registered Scottish Charity, No: SC015096 _______________________________________________<br>
ome-users mailing list<br>
<a href="mailto:ome-users@lists.openmicroscopy.org.uk">ome-users@lists.openmicroscopy.org.uk</a><br>
<a href="http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users" target="_blank">http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users</a><br>
_______________________________________________<br>
ome-users mailing list<br>
<a href="mailto:ome-users@lists.openmicroscopy.org.uk">ome-users@lists.openmicroscopy.org.uk</a><br>
<a href="http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users" target="_blank">http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users</a><br>
<br>
The University of Dundee is a registered Scottish Charity, No: SC015096<o:p></o:p></p>
</div>
</div>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<p class="MsoNormal"><br>
<span style="font-size:10.0pt">The University of Dundee is a registered Scottish Charity, No: SC015096</span>
<o:p></o:p></p>
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