#373 Java SBMLReader crashes JVM

[GerardW]

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

An error report file with more information is saved as:

D:\workspace\CrashDemo\hs_err_pid3100.log

If you would like to submit a bug report, please visit:

http://bugreport.sun.com/bugreport/crash.jsp

The crash happened outside the Java Virtual Machine in native code.

See problematic frame for where to report the bug.

[Frank Bergmann]

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.