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

[Roger Leigh]

On 13/06/2014 15:25, John Webber (NBI) wrote:
> Not sure I am getting very far with this error!
>
> I have re-run the process a few times today for the purpose of testing.
>
> I have a number of images that are being uploaded to Omero as part of this "bulk upload process".  This jobs is failing at DIFFERENT stages each time I run the job - sometimes it uploads 1 or 2 images before it fails, sometimes it will upload 5 or 6 before it fails.  It is therefore extremely had to track down the issue.
>
> When I ran the job, I saw the following error:
>
>       -! 06/13/14 12:33:54.390 warning: Proxy keep alive failed.
>
> Which appears after the session information, i.e.
>
>       Using session c4bef719-ae6f-4d85-b4bb-ffc09ee189b9 (webberj at localhost:4064). Idle timeout: 10.0 min. Current group: system
>       -! 06/13/14 12:33:54.390 warning: Proxy keep alive failed.
>
> At this point, a core dump is generated.
>
> As per Roger's email below, I have run an strace, but the resulting logfile is too big to send! I've looked through the logfile but am not sure what I am looking for in order to just snip a section out of it!  Is there something specific in the log that I should look for, or can I transfer this file another way?

Looking through the log, the first SIGSEGV is in thread 29086.
Immediately before, it's using fd=38 (client/logback-classic.jar) and a
bit further back fd=5 (ice-glacier2.jar).  After this point, it
repeatedly segfaults, presumably inside it's own SEGV handler.

It also spawns threads 29101 and 29105, both of which also subsequently
segfault; not clear why but the jvm may be a horrible mess by this point.

This /might/ point to an issue in client-logback.jar, but that's not
certain.

> The /var/log/messages file just has the following lines:
>
> Jun 13 12:29:42 v0246 abrt[29178]: Saved core dump of pid 28122 (/usr/lib/jvm/java-1.7.0-openjdk-1.7.0.55.x86_64/jre/bin/java) to /var/spool/abrt/ccpp-2014-06-13-12:29:35-28122 (750710784 bytes) Jun 13 12:29:42 v0246 abrtd: Directory 'ccpp-2014-06-13-12:29:35-28122' creation detected Jun 13 12:29:42 v0246 abrt[29178]: /var/spool/abrt is 1527378116 bytes (more than 1279MiB), deleting 'ccpp-2014-06-13-11:58:33-27089'
> Jun 13 12:29:51 v0246 kernel: end_request: I/O error, dev fd0, sector 0 Jun 13 12:29:51 v0246 kernel: end_request: I/O error, dev fd0, sector 0

The latter looks erroneous (just no floppy disc present; not sure what's
trying to access it).  The former may be useful for getting a
stacktrace; if it's different from the one you posted, might potentially
be useful to get a backtrace of each thread.


Regards,
Roger

--
Dr Roger Leigh -- Open Microscopy Environment
Wellcome Trust Centre for Gene Regulation and Expression,
College of Life Sciences, University of Dundee, Dow Street,
Dundee DD1 5EH Scotland UK   Tel: (01382) 386364

The University of Dundee is a registered Scottish Charity, No: SC015096