[ome-users] Core dump attempting to perfrom bulk upload to Omero

John Webber (NBI) John.Webber at nbi.ac.uk
Thu May 22 17:17:16 BST 2014


I have an upload process running on our existing Omero server (omero version 4.4.8, Ice version 3.3) which uses the Omero CLI to upload images into Omero.  This is working correctly for a bulk upload process that we have written.

I am currently testing the same process on a new server which is built with Omero 5.0 and Ice 3.5.  I am seeing the following error, but not after a consistent time:

Using session feccfbae-b08e-4298-9f3c-5f31139af486 (webberj at localhost:4064). Idle timeout: 10.0 min. Current group: system
Previous session expired for webberj on localhost:4064
InternalException: Failed to connect: exception ::Glacier2::CannotCreateSessionException
    reason = Server not fully initialized

A core dump is then generated.  The following are the log entries (/var/log/messages) when this occurs:

May 22 16:38:24 v0246 abrt[9252]: Saved core dump of pid 6130 (/usr/lib/jvm/java-1.7.0-openjdk- to /var/spool/abrt/ccpp-2014-05-22-16:38:12-6130 (668704768 bytes)
May 22 16:38:24 v0246 abrtd: Directory 'ccpp-2014-05-22-16:38:12-6130' creation detected
May 22 16:38:25 v0246 abrt[9252]: /var/spool/abrt is 1433007648 bytes (more than 1279MiB), deleting 'ccpp-2014-05-22-15:14:52-4857'
May 22 16:38:25 v0246 abrtd: Size of '/var/spool/abrt' >= 1000 MB, deleting 'ccpp-2014-05-22-15:14:52-4857'
May 22 16:38:25 v0246 abrt[9252]: Lock file '/var/spool/abrt/ccpp-2014-05-22-15:14:52-4857/.lock' is locked by process 1467
May 22 16:38:25 v0246 abrt[9252]: '/var/spool/abrt/ccpp-2014-05-22-15:14:52-4857' does not exist
May 22 16:38:34 v0246 kernel: end_request: I/O error, dev fd0, sector 0
May 22 16:38:34 v0246 kernel: end_request: I/O error, dev fd0, sector 0
May 22 16:39:52 v0246 abrtd: Sending an email...
May 22 16:39:52 v0246 abrtd: Email was sent to: root at localhost

The email that is sent as a result of this crash  is very long, but I have attached the first part of an example to this email.

Does anyone have any ideas why Omero / Ice is crashing in this way?  Does this look like an Omero Issue, an Ice issue or a Java issue?


John Webber
Computing and Information Services
NBI Partnership Ltd
Norwich Research park
Colney Lane

E-Mail: john.webber at nbi.ac.uk<mailto:john.webber at nbi.ac.uk>
Web:     http://www.nbi.ac.uk<http://www.nbi.ac.uk/>
Tel:         +44(0)1603 450 818

Helpdesk (Tel):  1234      HPC Support (Web):       http://hpc.nbi.ac.uk<http://hpc.nbi.ac.uk/>  (NBI  internal)
                                                HPC Support (Tel):           2003  (NBI internal)

The NBI Partnership Ltd provides non-scientific services to the Institute of Food Research, the John Innes Centre, The Genome Analysis Centre and The Sainsbury Laboratory

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.openmicroscopy.org.uk/pipermail/ome-users/attachments/20140522/65645831/attachment.html>
-------------- next part --------------
An embedded and charset-unspecified text was scrubbed...
Name: information from email.txt
URL: <http://lists.openmicroscopy.org.uk/pipermail/ome-users/attachments/20140522/65645831/attachment.txt>

More information about the ome-users mailing list