libSBML-5.10.2 experimental SMBLReader crashes JVM when reading a file
Sys info / error message:
os.arch: amd64
os.name: Windows 7
os.version: 6.1
java.vendor: Oracle Corporation
java.vendor.url: http://java.oracle.com/
java.version: 1.7.0_55
A fatal error has been detected by the Java Runtime Environment:
EXCEPTION_ACCESS_VIOLATION (0xc0000005) at pc=0x000007feed80006d, pid=3100, tid=3676
JRE version: Java(TM) SE Runtime Environment (7.0_55-b13) (build 1.7.0_55-b13)
Java VM: Java HotSpot(TM) 64-Bit Server VM (24.55-b03 mixed mode windows-amd64 compressed oops)
Problematic frame:
C [sbmlj.dll+0x11006d]
Failed to write core dump. Minidumps are not enabled by default on client versions of Windows
D:\workspace\CrashDemo\hs_err_pid3100.log
If you would like to submit a bug report, please visit:
The crash happened outside the Java Virtual Machine in native code.
See problematic frame for where to report the bug.
NOTICE NOTICE NOTICE
The comments associated with this ticket were lost in late 2014.
The SBML Team manually recovered the comments. The text is appended below.
NOTICE NOTICE NOTICE
Comment By: GerardW (gerardw)
Date: 2014-08-19 14:02
additional attachments
Attachment: gw_Solver_Suite.xml (4.5 MB; text/xml) hs_err_pid3100.log (16.1 kB; application/octet-stream)
Comment By: Sarah Keating (sarahkeating)
Date: 2014-08-19 21:09
Hi Gerard
Thanks for the report. This issue occurs when libSBML tries to read the 'req' listOfChangedMaths element. It will work if you prefix all these elements/attributes rather than leave them not prefixed.
I agree that libsbml needs to deal with this a little more kindly and I will look into it properly when I get back from the meeting I'm currently at.
Was the test file written out using libSBML ??
Thanks
Sarah
Comment By: GerardW (gerardw)
Date: 2014-08-20 17:28
Yes,
I'm working on updating Virtual Cell to use the current 5.10.2 (via the downloaded libSBML.jar and *dll)
P.S. Apologies for the "shouting" on the original post -- it was artifact of the JVM error message (which starts with #)
Comment By: Sarah Keating (sarahkeating)
Date: 2014-08-21 17:13
This is now fixed in the libsbml-experimental branch of svn and will be in the next release.