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Bug #351

Segfaults and lincs warnings with vsites during EM

Added by Jochen Hub about 10 years ago. Updated about 10 years ago.

Status:
Closed
Priority:
Normal
Assignee:
Erik Lindahl
Category:
mdrun
Target version:
Affected version - extra info:
Affected version:
Difficulty:
uncategorized
Close

Description

energy minimization crashes with a segfault or, on 405 from a few weeks ago reports lincs warnings (and then also eventually crashes).

gdb reports a non-initialized pointer here:

Program received signal EXC_BAD_ACCESS, Could not access memory.
Reason: KERN_PROTECTION_FAILURE at address: 0x00000014
0x000a7c6a in get_vsite_pbc (iparams=0x3ca000, ilist=0x81f21c, atom=0x0, md=0x403400, cgs=0x81f694, a2cg=0x163f000) at vsite.c:1503
1503 if (atom[a].ptype != eptVSite || pbc_set[a]) {

where atom[a] yields the bad memory access.

Best,
Jochen

files.tar.gz (683 KB) files.tar.gz all input files for grompp Jochen Hub, 10/05/2009 06:00 PM

History

#1 Updated by Jochen Hub about 10 years ago

Created an attachment (id=393)
all input files for grompp

#2 Updated by Berk Hess about 10 years ago

This bug was introduced with the recent fix of the vsite code
for charge groups consisting only of multiple vsites.
I fixed it.

Berk

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