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<div>Hi José<br>
<br>
</div>
<div>It looks like you're building your OMERO server from source, is this correct? Did you obtain it from GitHub or a source.zip? Have you previously been able to run an official released server on this system?<br>
<br>
</div>
<div>Thanks, Simon<br>
</div>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On 24 March 2015 at 17:08, José Salavert Torres <span dir="ltr">
<<a href="mailto:josator@ebi.ac.uk" target="_blank">josator@ebi.ac.uk</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div style="word-wrap:break-word">I attached new logs from a clean startup after checking.
<span class="">
<div><br>
<div></div>
</div>
<br>
<span style="font-size:10pt">The University of Dundee is a registered Scottish Charity, No: SC015096</span>
</span></div>
<br>
<div style="word-wrap:break-word">
<div>
<div></div>
<div><br>
</div>
<div><br>
<div>
<blockquote type="cite">
<div>On 24 Mar 2015, at 14:01, Sebastien Besson (Staff) <<a href="mailto:s.besson@dundee.ac.uk" target="_blank">s.besson@dundee.ac.uk</a>> wrote:</div>
<br>
<div>
<div style="word-wrap:break-word">Hi José,
<div><br>
</div>
<div>have you tried following the suggestion from the troubleshooting section of the </div>
<div>documentation</div>
<div><a href="http://www.openmicroscopy.org/site/support/omero5.1/sysadmins/troubleshooting.html#server-fails-to-start" target="_blank">http://www.openmicroscopy.org/site/support/omero5.1/sysadmins/troubleshooting.html#server-fails-to-start</a></div>
<div>If not, can you try and let us know if that clears the problem in master.err?</div>
<div><br>
</div>
<div>Best regards,</div>
<div>Sebastien</div>
<div><br>
</div>
<div>
<div>
<blockquote type="cite">
<div>On 24 Mar 2015, at 13:50, José Salavert Torres <<a href="mailto:josator@ebi.ac.uk" target="_blank">josator@ebi.ac.uk</a>> wrote:</div>
<br>
<div>
<div style="word-wrap:break-word">
<div>I did that already with:</div>
<div><br>
</div>
<div>omero admin stop</div>
<div>omero admin start</div>
<div><br>
</div>
<div>and the problem persists.</div>
<div><br>
</div>
<div>How can this lock be released?</div>
<br>
<div>
<blockquote type="cite">
<div>On 24 Mar 2015, at 13:43, Josh Moore <<a href="mailto:josh@glencoesoftware.com" target="_blank">josh@glencoesoftware.com</a>> wrote:</div>
<br>
<div><span style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;float:none;display:inline!important">On
Tue, Mar 24, 2015 at 1:36 PM, José Salavert Torres <</span><a href="mailto:josator@ebi.ac.uk" style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px" target="_blank">josator@ebi.ac.uk</a><span style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;float:none;display:inline!important">>
wrote:</span><br style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px">
<blockquote type="cite" style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px">
I have extracted with grep the error messages:<br>
</blockquote>
<br style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px">
<span style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;float:none;display:inline!important">Thanks,
José. The most related error message I see is from master.err:</span><br style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px">
<br style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px">
<span style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;float:none;display:inline!important">!!
03/23/15 11:23:45.482 OMERO.IceStorm: error: ServiceManager:</span><br style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px">
<span style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;float:none;display:inline!important">exception
while starting service OMERO.IceStorm:</span><br style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px">
<span style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;float:none;display:inline!important"> FileUtil.cpp:385:
IceUtil::FileLockedException:</span><br style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px">
<span style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;float:none;display:inline!important"> could
not lock file:</span><br style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px">
<span style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;float:none;display:inline!important">`/net/isilonP/public/rw/pdbe/mol2cell/omero/development/openmicroscopy/dist/var/master/servers/OMERO.IceStorm/dbs/OMERO.IceStorm/__Freeze/lock'</span><br style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px">
<span style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;float:none;display:inline!important"> syscall
exception: Resource temporarily unavailable</span><br style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px">
<br style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px">
<span style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;float:none;display:inline!important">When
was the last time the server was restarted? If before that time,</span><br style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px">
<span style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;float:none;display:inline!important">can
it be restarted and then master.err checked for the same problem?</span><br style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px">
<br style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px">
<span style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;float:none;display:inline!important">Cheers,</span><br style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px">
<span style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;float:none;display:inline!important">~Josh.</span><br style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px">
<br style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px">
<br style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px">
<br style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px">
<blockquote type="cite" style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px">
On 24 Mar 2015, at 11:24, Josh Moore <<a href="mailto:josh@glencoesoftware.com" target="_blank">josh@glencoesoftware.com</a>> wrote:<br>
<br>
Hi José,<br>
<br>
<br>
On Tue, Mar 24, 2015 at 10:59 AM, José Salavert Torres<br>
<<a href="mailto:josator@ebi.ac.uk" target="_blank">josator@ebi.ac.uk</a>> wrote:<br>
<br>
Sorry, I can not execute the second command, I do not have root permissions<br>
on the OMERO machine.<br>
<br>
<br>
Hmmm....do you have access to the server logs? Can you put us in<br>
contact with your server administrator?<br>
<br>
Thanks,<br>
~Josh<br>
<br>
(I had to build and manually install every dependency).<br>
<br>
omero admin diagnostics<br>
<br>
================================================================================<br>
OMERO Diagnostics 5.1.0-m2-ice35-SNAPSHOT<br>
================================================================================<br>
<br>
Commands: java -version 1.6.0 (/usr/bin/java)<br>
Commands: python -V 2.6.6<br>
(/nfs/public/rw/pdbe/mol2cell/software/python2.6-virt-env/bin/python -- 2<br>
others)<br>
Commands: icegridnode --version 3.5.1<br>
(/nfs/public/rw/pdbe/mol2cell/software/Ice-3.5.1/bin/icegridnode)<br>
Commands: icegridadmin --version 3.5.1<br>
(/nfs/public/rw/pdbe/mol2cell/software/Ice-3.5.1/bin/icegridadmin)<br>
Commands: psql --version 8.4.20 (/usr/bin/psql)<br>
<br>
Server: icegridnode running<br>
Server: Blitz-0 active (pid = 4104, enabled)<br>
Server: DropBox active (pid = 4116, enabled)<br>
Server: FileServer active (pid = 4123, enabled)<br>
Server: Indexer-0 active (pid = 4125, enabled)<br>
Server: MonitorServer active (pid = 4124, enabled)<br>
Server: OMERO.Glacier2 active (pid = 4126, enabled)<br>
Server: OMERO.IceStorm inactive (disabled)<br>
Server: PixelData-0 active (pid = 4129, enabled)<br>
Server: Processor-0 active (pid = 4127, enabled)<br>
Server: Tables-0 inactive (disabled)<br>
Server: TestDropBox inactive (enabled)<br>
<br>
Log dir:<br>
/nfs/public/rw/pdbe/mol2cell/omero/development/openmicroscopy/dist/var/log<br>
exists<br>
<br>
Log files: Blitz-0.log 17.0 MB errors=1<br>
warnings=912<br>
Log files: Blitz-0.log.1 524.0 MB errors=65<br>
warnings=9855<br>
Log files: Blitz-0.log.2 524.0 MB errors=3900<br>
warnings=6595<br>
Log files: DropBox.log 41.0 KB errors=20<br>
warnings=19<br>
Log files: FileServer.log 7.0 KB errors=2<br>
warnings=0<br>
Log files: Indexer-0.log 2.0 MB errors=162<br>
warnings=590<br>
Log files: MonitorServer.log 20.0 KB errors=3<br>
warnings=0<br>
Log files: OMEROweb.log 1.0 MB errors=316<br>
warnings=294<br>
Log files: OMEROweb_request.log 176.0 KB errors=205<br>
warnings=290<br>
Log files: PixelData-0.log 419.0 KB errors=23<br>
warnings=290<br>
Log files: Processor-0.log 109.0 KB errors=46<br>
warnings=30<br>
Log files: Tables-0.log n/a<br>
Log files: TestDropBox.log n/a<br>
Log files: master.err 78.0 KB errors=53<br>
warnings=53<br>
Log files: master.out 0.0 KB errors=1<br>
warnings=0<br>
Log files: Total size 1070.65 MB<br>
<br>
<br>
Environment:OMERO_HOME=(unset)<br>
Environment:OMERO_NODE=(unset)<br>
Environment:OMERO_MASTER=(unset)<br>
Environment:OMERO_TEMPDIR=(unset)<br>
Environment:PATH=/nfs/public/rw/pdbe/mol2cell/software/python2.6-virt-env/bin:/nfs/public/rw/pdbe/mol2cell/software/IMOD/IMOD/bin:/nfs/public/rw/pdbe/mol2cell/software/bin:/nfs/public/rw/pdbe/mol2cell/omero/development/openmicroscopy/dist/bin:/nfs/public/rw/pdbe/mol2cell/software/hdf5-1.8.14-linux-centos6-x86_64-gcc447-shared/bin:/nfs/public/rw/pdbe/mol2cell/software/Ice-3.5.1/bin:/usr/lib64/ccache:/usr/local/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin:/net/isilonP/public/rw/homes/pdb_em/bin<br>
Environment:PYTHONPATH=/nfs/public/rw/pdbe/mol2cell/omero/development/openmicroscopy/dist/lib/python:/nfs/public/rw/pdbe/mol2cell/software/python2.6-virt-env/lib/python2.6:/nfs/public/rw/pdbe/mol2cell/software/Ice-3.5.1/python::/net/isilonP/public/rw/homes/pdb_em/python-2.6-libraries<br>
Environment:ICE_HOME=/nfs/public/rw/pdbe/mol2cell/software/Ice-3.5.1<br>
Environment:LD_LIBRARY_PATH=/nfs/public/rw/pdbe/mol2cell/software/IMOD/IMOD/lib:/nfs/public/rw/pdbe/mol2cell/software/Ice-3.5.1/lib64:/nfs/public/rw/pdbe/mol2cell/software/hdf5-1.8.14-linux-centos6-x86_64-gcc447-shared/lib:<br>
Environment:DYLD_LIBRARY_PATH=/nfs/public/rw/pdbe/mol2cell/software/Ice-3.5.1/lib:<br>
<br>
OMERO SSL port:4064<br>
OMERO TCP port:4063<br>
OMERO data<br>
dir:'/nfs/public/rw/pdbe/mol2cell/omero/development/var/OMERO.data' Exists?<br>
True Is writable? True<br>
OMERO temp dir:'/net/isilonP/public/rw/homes/pdb_em/omero/tmp' Exists? True<br>
Is writable? True (Size: 0)<br>
<br>
JVM settings: Blitz -Xmx602m -XX:MaxPermSize=512m<br>
JVM settings: Indexer -Xmx401m -XX:MaxPermSize=512m<br>
JVM settings: Pixeldata -Xmx602m -XX:MaxPermSize=512m<br>
JVM settings: Repository -Xmx401m -XX:MaxPermSize=512m<br>
<br>
OMERO.web status... [RUNNING] (PID 4375)<br>
<br>
<br>
<br>
<br>
<br>
On 23 Mar 2015, at 18:54, Josh Moore <<a href="mailto:josh@glencoesoftware.com" target="_blank">josh@glencoesoftware.com</a>> wrote:<br>
<br>
Hi José,<br>
<br>
On Mon, Mar 23, 2015 at 2:11 PM, José Salavert Torres <<a href="mailto:josator@ebi.ac.uk" target="_blank">josator@ebi.ac.uk</a>><br>
wrote:<br>
<br>
Dear OMERO users:<br>
<br>
I was able to do the import before but now without changing configuration or<br>
anything it fails from any machine (even localhost). However Romero insight<br>
is working properly. Can you help me?:<br>
<br>
...<br>
<br>
2015-03-23 10:40:43,444 2219 [ main] ERROR<br>
ome.formats.importer.ImportLibrary - Error on import<br>
java.lang.RuntimeException: Cannot exclusively use the managed repository.<br>
at<br>
ome.formats.importer.ImportLibrary.checkManagedRepo(ImportLibrary.java:709)<br>
~[blitz.jar:na]<br>
at<br>
ome.formats.importer.ImportLibrary.createImport(ImportLibrary.java:316)<br>
~[blitz.jar:na]<br>
at<br>
ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:465)<br>
~[blitz.jar:na]<br>
at<br>
ome.formats.importer.ImportLibrary.importCandidates(ImportLibrary.java:271)<br>
~[blitz.jar:na]<br>
at<br>
ome.formats.importer.cli.CommandLineImporter.start(CommandLineImporter.java:216)<br>
[blitz.jar:na]<br>
at<br>
ome.formats.importer.cli.CommandLineImporter.main(CommandLineImporter.java:752)<br>
[blitz.jar:na]<br>
2015-03-23 10:40:43,444 2219 [ main] INFO<br>
ome.formats.importer.ImportLibrary - Exiting on error<br>
<br>
<br>
This looks like there is some server error. Could you provide use the output<br>
of:<br>
<br>
$ bin/omero admin diagnostics<br>
<br>
as well as:<br>
<br>
<br>
$ bin/omero -s root@localhost fs repos<br>
<br>
e.g.<br>
<br>
# | Id | UUID | Type | Path<br>
---+-------+--------------------------------------+---------+-------------------------------------------------------------------<br>
0 | 17 | ce1e2766-089f-4555-a52a-f75746fd44da | Public |<br>
/repositories/OMERO-5.0-latest-deploy<br>
1 | 18 | ScriptRepo | Script |<br>
/opt/hudson/workspace/OMERO-5.1-merge-deploy/src/dist/lib/scripts<br>
2 | 10901 | a5a2b4b3-d146-4ccc-98fa-7353a1ba023b | Managed |<br>
/repositories/OMERO-5.1-merge-deploy/ManagedRepository<br>
3 | 18651 | 34b38044-0ff6-4019-8f97-4e0093f5a3c3 | Public |<br>
/repositories/OMERO-5.0-latest-deploy<br>
4 | 18701 | 640d985e-0ba5-47a6-bacb-42b7cf60354b | Public |<br>
/repositories/OMERO-5.1-merge-deploy<br>
(5 rows)<br>
<br>
Cheers,<br>
~Josh<br>
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<span style="font-size:10pt">The University of Dundee is a registered Scottish Charity, No: SC015096</span>
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<span style="font-size:10pt;">The University of Dundee is a registered Scottish Charity, No: SC015096</span>
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