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Bug #1711

gmx x2top seg fault

Added by Justin Lemkul about 2 years ago. Updated 9 months ago.

Status:
Closed
Priority:
Normal
Assignee:
Category:
preprocessing (pdb2gmx,grompp)
Target version:
Affected version - extra info:
Affected version:
Difficulty:
uncategorized
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Description

As reported on gmx-users:

https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2015-March/096288.html

gdb backtrace indicates line 1054 (in version 5.0.4, line 1050 in current master) is to blame:

Program received signal SIGSEGV, Segmentation fault.
0x00007ffff66be7e0 in gen_pad (nnb=0x7fffffffaf40, atoms=0x6523c0, rtp=0x7ffff7dd2ac0, plist=0x7fffffff97f0, excls=0x680120, hb=0x0, 
    bAllowMissing=1) at /home/jalemkul/code/gromacs/gromacs-5.0.4/src/gromacs/gmxpreprocess/gen_ad.c:1054
1054            for (j = 0; j < hbang->nb; j++)
(gdb) bt
#0  0x00007ffff66be7e0 in gen_pad (nnb=0x7fffffffaf40, atoms=0x6523c0, rtp=0x7ffff7dd2ac0, plist=0x7fffffff97f0, excls=0x680120, hb=0x0, 
    bAllowMissing=1) at /home/jalemkul/code/gromacs/gromacs-5.0.4/src/gromacs/gmxpreprocess/gen_ad.c:1054
#1  0x00007ffff66ac889 in gmx_x2top (argc=1, argv=0x7fffffffe240)
    at /home/jalemkul/code/gromacs/gromacs-5.0.4/src/gromacs/gmxpreprocess/x2top.c:589
#2  0x00007ffff6715d1d in gmx::(anonymous namespace)::CMainCommandLineModule::run (this=0x644610, argc=7, argv=0x7fffffffe240)
    at /home/jalemkul/code/gromacs/gromacs-5.0.4/src/gromacs/commandline/cmdlinemodulemanager.cpp:119
#3  0x00007ffff6717487 in gmx::CommandLineModuleManager::run (this=0x7fffffffe120, argc=7, argv=0x7fffffffe240)
    at /home/jalemkul/code/gromacs/gromacs-5.0.4/src/gromacs/commandline/cmdlinemodulemanager.cpp:545
#4  0x000000000040ed9a in main (argc=8, argv=0x7fffffffe238) at /home/jalemkul/code/gromacs/gromacs-5.0.4/src/programs/gmx.cpp:58

The bug appears to have been introduced in commit 7ba0a841df25e54d36586e31003fbfe93bd2588d


Related issues

Related to GROMACS - Bug #1276: pdb2gmx ignores angles when no bonds are present Closed 06/05/2013

Associated revisions

Revision fadb3ecb (diff)
Added by Erik Lindahl almost 2 years ago

Avoid accessing hackblocks for x2top

Previous fixes for generating dihedrals would cause us to access
the hackblock even when using x2top, which we should not do.

Fixes #1711.

Change-Id: Id0ea6d524d80b87fe257c9fd4f1c48c4be828654

History

#1 Updated by Rossen Apostolov almost 2 years ago

  • Related to Bug #1276: pdb2gmx ignores angles when no bonds are present added

#2 Updated by Erik Lindahl almost 2 years ago

  • Status changed from New to Accepted
  • Assignee set to Erik Lindahl

#3 Updated by Gerrit Code Review Bot almost 2 years ago

Gerrit received a related patchset '1' for Issue #1711.
Uploader: Erik Lindahl ()
Change-Id: Id0ea6d524d80b87fe257c9fd4f1c48c4be828654
Gerrit URL: https://gerrit.gromacs.org/4773

#4 Updated by Erik Lindahl almost 2 years ago

  • Status changed from Accepted to Fix uploaded

#5 Updated by Erik Lindahl over 1 year ago

  • Status changed from Fix uploaded to Resolved

#6 Updated by Erik Lindahl over 1 year ago

  • Status changed from Resolved to Closed

#7 Updated by Mark Abraham 9 months ago

  • Target version changed from 5.x to 5.0.7

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