<html>
<head>
<meta content="text/html; charset=ISO-8859-1"
http-equiv="Content-Type">
</head>
<body bgcolor="#FFFFFF" text="#000000">
<div class="moz-cite-prefix">Hi Colin,</div>
<blockquote
cite="mid:5C43AF4F-CD1F-48B1-AD9B-9243C0AD7B50@dundee.ac.uk"
type="cite">
<pre wrap="">Hi Julien,</pre>
</blockquote>
<blockquote
cite="mid:5C43AF4F-CD1F-48B1-AD9B-9243C0AD7B50@dundee.ac.uk"
type="cite">
<pre wrap="">
</pre>
<blockquote type="cite">
<pre wrap="">So, I re-tested without NFS and ... it worked ! Tables ran correctly and, moreover, it solved another problem : the pyramid creation system also worked.
I also checked the .lock file on the binary repository. It changes when it's on a local drive, but not when it's on NFS. It's definitely our problem.
</pre>
</blockquote>
<pre wrap="">
Thanks for letting us know and we're glad things are now working for you.</pre>
</blockquote>
Actually, we have to use the NFS partition! We don't have anywhere
else to put our data. So it's working but ... it's not working
>_<<br>
I was able to solve our Tables problem by moving the .omero
directory on the local drive and by creating a symlink on the NFS
partition (I found the solution <a
href="http://lists.openmicroscopy.org.uk/pipermail/ome-users/2012-September/003287.html">here</a>).<br>
But the pyramid creation problem still remains. I'll do another mail
for this one.<br>
<br>
So, we can consider the Tables problem with NFS solved, at least!<br>
<br>
Thanks for the help :)<br>
<br>
JJ<br>
<blockquote
cite="mid:5C43AF4F-CD1F-48B1-AD9B-9243C0AD7B50@dundee.ac.uk"
type="cite">
<pre wrap="">
</pre>
<blockquote type="cite">
<pre wrap="">By the way, there isn't any Exception in our Blitz-0.log.
</pre>
</blockquote>
<pre wrap="">
There should be something logged there. If you still have the relevant log and you are able to send it to us (direct email to me would be fine) and point then it might be useful to us in improving our logging.</pre>
</blockquote>
PS : Really, there was absolutely nothing in it. But I can send it
to you anyway.<br>
<blockquote
cite="mid:5C43AF4F-CD1F-48B1-AD9B-9243C0AD7B50@dundee.ac.uk"
type="cite">
<pre wrap="">
Cheers,
Colin
On 17 May 2013, at 13:32, Julien Jourde <a class="moz-txt-link-rfc2396E" href="mailto:julien.jourde@pasteur.fr"><julien.jourde@pasteur.fr></a> wrote:
</pre>
<blockquote type="cite">
<pre wrap="">Le 16/05/13 10:59, Josh Moore a écrit :
</pre>
<blockquote type="cite">
<pre wrap="">On May 13, 2013, at 2:58 PM, Julien Jourde wrote:
</pre>
<blockquote type="cite">
<pre wrap="">Le 13/05/13 12:22, Colin Blackburn a écrit :
Hi Colin,
</pre>
<blockquote type="cite">
<pre wrap="">Hi Julien,
</pre>
</blockquote>
</blockquote>
<pre wrap="">Hi Julien,
</pre>
</blockquote>
<pre wrap="">Hi Josh,
</pre>
<blockquote type="cite">
<pre wrap="">
</pre>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">
<pre wrap="">I'm running a 4-4-7 OMERO server and tables fail to startup. It's exactly the same problem as the one in the ticket 3690, which should be fixed :-/
</pre>
</blockquote>
<pre wrap="">Sorry, that's not the clearest ticket in suggesting a solution!
</pre>
<blockquote type="cite">
<pre wrap="">Any idea / advise / help is very welcome, thanks :)
</pre>
</blockquote>
<pre wrap="">It is possible that you have a lingering icegridregistry process running.
</pre>
</blockquote>
<pre wrap="">There is no lingering icegridregistry process running (I didn't find any at least).
</pre>
<blockquote type="cite">
<pre wrap="">You could try killing that process (and any other lingering ice processes). If that doesn't address the issue then deleting the entire var directory under your server install might also help. On your installation it looks like that would be:
/home/omero/apps/omero/OMERO.server-4.4.7-ice34-b246/var
</pre>
</blockquote>
<pre wrap="">Unfortunately, it didn't solve my problem :-/ But I noticed something strange comparing my production server (the one where Tables fails to startup) with my test server (the one without any problem) :
- I did the same installation on each server : I installed a 4-4-5 version, then I upgraded it to a 4-4-6 version and finally a 4-4-7 one.
- I wanted to have a look on the /MyBinaryRepository/.omero/repository/XXX-XXX-XXX/repo_uuid, to compare it with the one in my logs. That's where I noticed that there are 3 different "XXX-XXX-XXX" repositories on my test server (probably corresponding to the different versions of OMERO), but only one on my production server ! (for the production server, I moved my bynary repository to an NFS partition but between the 4-4-6 and the 4-4-7 versions).
</pre>
</blockquote>
<pre wrap="">Ah a smoking gun: NFS.
cF. <a class="moz-txt-link-freetext" href="https://www.openmicroscopy.org/site/support/omero4/sysadmins/unix/server-binary-repository.html#locking-and-remote-shares">https://www.openmicroscopy.org/site/support/omero4/sysadmins/unix/server-binary-repository.html#locking-and-remote-shares</a>
Would it be possible to re-test without NFS in the mix, i.e. by copying (a portion of) your binary repository back to a local drive and starting up a copy of the database again it? Are you in fact seeing NullPointerExceptions in your Blitz-0.log?
</pre>
</blockquote>
<pre wrap="">So, I re-tested without NFS and ... it worked ! Tables ran correctly and, moreover, it solved another problem : the pyramid creation system also worked.
I also checked the .lock file on the binary repository. It changes when it's on a local drive, but not when it's on NFS. It's definitely our problem.
By the way, there isn't any Exception in our Blitz-0.log.
Cheers,
JJ
</pre>
<blockquote type="cite">
<pre wrap="">
Cheers,
~Josh.
</pre>
<blockquote type="cite">
<pre wrap="">Thanks for your help :)
Cheers,
JJ
</pre>
<blockquote type="cite">
<pre wrap="">Please do let us know whether this solves your problem.
Cheers,
Colin
On 13 May 2013, at 09:12, Julien Jourde <a class="moz-txt-link-rfc2396E" href="mailto:julien.jourde@pasteur.fr"><julien.jourde@pasteur.fr></a> wrote:
</pre>
<blockquote type="cite">
<pre wrap="">Hi ome list,
I'm running a 4-4-7 OMERO server and tables fail to startup. It's exactly the same problem as the one in the ticket 3690, which should be fixed :-/
Here are my logs :
2013-05-13 09:49:20,658 INFO [ omero.util.Server] (MainThread) Waiting 10000 ms on startup
2013-05-13 09:49:30,658 INFO [ omero.util.Server] (MainThread) Starting
2013-05-13 09:49:30,659 INFO [ omero.util.Server] (MainThread) Loaded dependency numpy (1.6.2)
2013-05-13 09:49:30,659 INFO [ omero.util.Server] (MainThread) Loaded dependency tables (2.4.0, hdf=1.8.5-patch1)
2013-05-13 09:49:30,663 INFO [ omero.util.Resources] (Thread-2 ) Starting
2013-05-13 09:49:30,791 INFO [ omero.utils] (MainThread) Failed to get session on attempt 1
2013-05-13 09:49:41,099 ERROR [ omero.util.Server] (MainThread) Failed initialization
Traceback (most recent call last):
File "/home/omero/apps/omero/OMERO.server-4.4.7-ice34-b246/lib/python/omero/util/__init__.py", line 437, in run
self.impl = self.impl_class(ctx)
File "/home/omero/apps/omero/OMERO.server-4.4.7-ice34-b246/lib/python/omero/tables.py", line 795, in __init__
self._get_repo()
File "/home/omero/apps/omero/OMERO.server-4.4.7-ice34-b246/lib/python/omero/tables.py", line 847, in _get_repo
self.repo_mgr = self._internal_repo_cast(self.repo_mgr)
File "/home/omero/apps/omero/OMERO.server-4.4.7-ice34-b246/lib/python/omero_Repositories_ice.py", line 907, in checkedCast
return _M_omero.grid.InternalRepositoryPrx.ice_checkedCast(proxy, '::omero::grid::InternalRepository', facetOrCtx, _ctx)
NotRegisteredException: exception ::Ice::NotRegisteredException
{
kindOfObject = object
id = InternalRepository-f5718416-9db9-486b-ba49-4c55d0562e6b
}
2013-05-13 09:49:41,100 INFO [ omero.util.Server] (MainThread) Cleanup
2013-05-13 09:49:41,101 INFO [ omero.util.Server] (MainThread) Stopped
2013-05-13 09:49:41,101 INFO [ omero.util.Server] (MainThread) ********************************************************************************
2013-05-13 09:49:41,101 INFO [ omero.tables.TablesI] (MainThread) Cleaning up
2013-05-13 09:49:41,101 INFO [ omero.tables.TablesI] (MainThread) Done
2013-05-13 09:49:41,113 WARNI [ stderr] (MainThread) 2013-05-13 09:49:41.113020 Tables-0: error: Traceback (most recent call last):
File "/usr/lib64/python2.6/site-packages/Ice/Ice.py", line 984, in main
status = self.doMain(args, initData)
File "/usr/lib64/python2.6/site-packages/Ice/Ice.py", line 1031, in doMain
return self.run(args)
File "/home/omero/apps/omero/OMERO.server-4.4.7-ice34-b246/lib/python/omero/util/__init__.py", line 441, in run
sys.exit(100)
SystemExit: 100
2013-05-13 09:49:41,123 INFO [ omero.util.Resources] (Thread-2 ) Halted
Any idea / advise / help is very welcome, thanks :)
</pre>
</blockquote>
</blockquote>
</blockquote>
</blockquote>
<pre wrap="">
--
Julien JOURDE
Plateforme d'Imagerie Dynamique(PFID)
Imagopole
Institut Pasteur
25-28 rue du Docteur Roux
75724 Paris cedex15
FRANCE
<a class="moz-txt-link-abbreviated" href="http://www.imagopole.org/">www.imagopole.org/</a>
tel:33 (0)1 45 68 82 18
fax:33(0)1 45 68 89 49
</pre>
</blockquote>
<pre wrap="">
</pre>
</blockquote>
<br>
<br>
<pre class="moz-signature" cols="72">--
Julien JOURDE
Plateforme d'Imagerie Dynamique(PFID)
Imagopole
Institut Pasteur
25-28 rue du Docteur Roux
75724 Paris cedex15
FRANCE
<a class="moz-txt-link-abbreviated" href="http://www.imagopole.org/">www.imagopole.org/</a>
tel:33 (0)1 45 68 82 18
fax:33(0)1 45 68 89 49</pre>
</body>
</html>