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

[Roger Leigh]

On 12/06/14 11:05, John Webber (NBI) wrote:
> Hi Simon,
>
> Sorry for not responding to your message till today - busy week!
>
> As per your email below, I have entered "bt" for a stack trace, but AM surprised, not at the unexpectedly long output, but the unexpectedly short output - see below:
>
> (gdb) bt
> #0  0x0000003d7a432925 in raise (sig=6) at ../nptl/sysdeps/unix/sysv/linux/raise.c:64
> #1  0x0000003d7a434105 in abort () at abort.c:92
> #2  0x00007f5dd33088c5 in os::abort (dump_core=true)
>      at /usr/src/debug/java-1.7.0-openjdk/openjdk/hotspot/src/os/linux/vm/os_linux.cpp:1594
> #3  0x00007f5dd347678f in VMError::report_and_die (this=0x7f5d874f2860)
>      at /usr/src/debug/java-1.7.0-openjdk/openjdk/hotspot/src/share/vm/utilities/vmError.cpp:1078
> #4  0x00007f5dd330da92 in JVM_handle_linux_signal (sig=11, info=0x7f5d874f2a30, ucVoid=0x7f5d874f2900,
>      abort_if_unrecognized=-2024855584)
>      at /usr/src/debug/java-1.7.0-openjdk/openjdk/hotspot/src/os_cpu/linux_x86/vm/os_linux_x86.cpp:531
> #5  <signal handler called>
> #6  inflateEnd (strm=0x7f5d9c001cc0) at inflate.c:1162
> #7  0x00007f5dd1ff512e in Java_java_util_zip_Inflater_end (env=0x7f5d880141d8, cls=<value optimized out>,
>      addr=140040025939136) at ../../../src/share/native/java/util/zip/Inflater.c:188

Dear John,

This is only speculative, but it appears that the crash here is while
unpacking a zip file, which I would presume to be a .jar file or similar
while setting up the JVM or using a classloader.  This is deep in the
JVM internals, so unlikely to be an issue with any of the java code
itself.  This might be a JVM bug triggered by a corrupt jar.
Identifying which might be tricky, but should be possible if you were to
repeat this using "strace -f -o logfile -e trace=file,process", for example.

If this is the case, it might be worth re-downloading the zipfile for
omero to double-check if the jars are the same.  Of course, it's also
possible that one might be corrupt in our zipfile, in which case we'll
need to fix that once we know which is at fault.

If this can be reduced to triggering with just one file (or a small
number of files), if you could zip them up and upload them using
qa.openmicroscopy.org, we can try to reproduce this as well.  It may be
that this is caused by using a specific file type.


Kind 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