Issue1416

classification

Title:	jython crashes when running a Jmol-based script
Type:	crash	Severity:	normal
Components:		Versions:	2.5.0
		Milestone:

process

Status:	closed	Resolution:	invalid
Dependencies:		Superseder:
Assigned To:		Nosy List:	connolly, nriley
Priority:		Keywords:

Created on 2009-07-30.21:26:28 by connolly, last changed 2009-07-30.21:41:09 by nriley.

Files
File name	Uploaded	Description	Edit	Remove
,jython-crash	connolly, 2009-07-30.21:26:28	trace of jython crash

Messages
msg4966 (view)	Author: Dan Connolly (connolly)	Date: 2009-07-30.21:26:28
I'm using jython to drive Jmol and it crashes with SIGSEGV. A trace is attached. I'm trying to prune it down to a simpler case, but I can't seem to reproduce the problem any other way. To reproduce my environment, here are the files: Jmol.jar is from jmol 11.6.21, i.e. http://sourceforge.net/projects/jmol/files/Jmol/Version%2011.6.21/jmol-11.6.21-binary.zip/download 3255e1ed8e152b87ca004ddc2e1f0c11 Jmol.jar My code (i.e. pdbparts_j.py and a few other modules) is in http://svn.neurocommons.org/svn/trunk/packages/pdb/ .revision 1178 The input file, 1A1M.xml.gz is http://www.rcsb.org/pdb/files/1A1M.xml.gz The script also reads from 1A1M.pdb, i.e. http://www.rcsb.org/pdb/files/1A1M.pdb 298621766c09c38162ec461756124e0c 1A1M.pdb cfeb781816003bb99256134f4e5588ea 1A1M.xml.gz
msg4967 (view)	Author: Dan Connolly (connolly)	Date: 2009-07-30.21:29:43
forgot some version info: > java -version java version "1.5.0_15" Java(TM) 2 Runtime Environment, Standard Edition (build 1.5.0_15-b04) Java HotSpot(TM) 64-Bit Server VM (build 1.5.0_15-b04, mixed mode) > uname -a Linux norbert 2.6.22.17-0.1-default #1 SMP 2008/02/10 20:01:04 UTC x86_64 x86_64 x86_64 GNU/Linux
msg4968 (view)	Author: Nicholas Riley (nriley)	Date: 2009-07-30.21:41:00
This appears to be a JVM bug; it worked for me when I tried it on Sun 1.6.0_14 on 64-bit Linux (RHEL5). http://pylonshq.com/pasties/203fc9cae067efd71fe9333230d0f350

History
Date	User	Action	Args
2009-07-30 21:41:09	nriley	set	status: open -> closed
2009-07-30 21:41:00	nriley	set	resolution: invalid messages: + msg4968 nosy: + nriley
2009-07-30 21:29:43	connolly	set	messages: + msg4967
2009-07-30 21:26:28	connolly	create