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Bug #1503

Segfault/Doublefree Corruption using g_chi

Added by Justin Lecher about 3 years ago. Updated almost 3 years ago.

Status:
Closed
Priority:
Normal
Category:
-
Target version:
-
Affected version - extra info:
4.6.4, 4.6.5
Affected version:
Difficulty:
uncategorized
Close

Description

As a test project you can simply follow the following tutorial

www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/index.html

If the following command

g_chi -s em.gro -f md_0_1.xtc -o -p -chi_prod -maxchi 1 -rama -shift -jc -corr -ot -oh -rt -cp -viol -all

is run on the final trajectory, gmx segfaults.

Removing "-maxchi 1" seems to work around.

This is reproducible with gmx 4.6.4, 4.6.5 and 5.0-rc1

abrt - abrt.log (67.9 KB) Justin Lecher, 05/16/2014 12:31 PM

gmx.log View - run.log (3.87 KB) Justin Lecher, 05/16/2014 12:31 PM

zf.md.gro (62.6 KB) Alexey Shvetsov, 05/19/2014 10:54 AM

zf.md.xtc (539 KB) Alexey Shvetsov, 05/19/2014 10:54 AM

Associated revisions

Revision 820e4e53 (diff)
Added by David van der Spoel almost 3 years ago

Fix memory-usage error in g_chi

Out of array bounds writing error as pointed out by valgrind
is fixed by this patch, preventing a SEGV.

Fixes #1503

Change-Id: I57959f4751f3eb645ff66bbcd4418607af56c1a4

History

#1 Updated by Rossen Apostolov about 3 years ago

  • Assignee set to David van der Spoel

#2 Updated by David van der Spoel about 3 years ago

Can you please upload em.gro and the xtc file?

#3 Updated by Alexey Shvetsov about 3 years ago

I can reproduce same issue with this two attached files

#4 Updated by Gerrit Code Review Bot almost 3 years ago

Gerrit received a related patchset '1' for Issue #1503.
Uploader: David van der Spoel ()
Change-Id: I57959f4751f3eb645ff66bbcd4418607af56c1a4
Gerrit URL: https://gerrit.gromacs.org/3579

#5 Updated by David van der Spoel almost 3 years ago

  • Status changed from New to Fix uploaded

#6 Updated by Erik Lindahl almost 3 years ago

  • Status changed from Fix uploaded to Resolved

#7 Updated by Erik Lindahl almost 3 years ago

  • Status changed from Resolved to Closed

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