Project

General

Profile

Bug #2430

gmx trjconv gets invalid pointer if tpr is not provided

Added by Viveca Lindahl over 1 year ago. Updated over 1 year ago.

Status:
Closed
Priority:
Normal
Assignee:
-
Category:
analysis tools
Target version:
Affected version - extra info:
Affected version:
Difficulty:
uncategorized
Close

Description

gmx trjconv -f traj_comp.xtc

results in an segmentation fault, presumably because it's being assumed that a tpr file has been provided while it is not necessarily. Adding "-s topol.tpr" avoids the error. As can be see in the valgrind output (attached) the error occurs in "done_top(t_topology*) (topology.cpp:176)"

valgrind-gmx-trjconv-no-tpr.log (33.8 KB) valgrind-gmx-trjconv-no-tpr.log Viveca Lindahl, 02/28/2018 02:26 PM
topol.tpr (11.8 KB) topol.tpr Viveca Lindahl, 02/28/2018 02:29 PM

Related issues

Has duplicate GROMACS - Bug #2476: gmx trjconv segfaults when converting gro file to xtc when no tpr is givenClosed

Associated revisions

Revision 6a2e469b (diff)
Added by Paul Bauer over 1 year ago

Only free topology when allocated

Fix trjconv so that the topology only gets free'd when it has been
previously allocated.

Fixes #2430

Change-Id: Idc9a4219d988e1794ef86f7cc79f0d00750394ca

History

#1 Updated by Viveca Lindahl over 1 year ago

here is the tpr I used, but it seems to be a general issue.

#2 Updated by Gerrit Code Review Bot over 1 year ago

Gerrit received a related patchset '1' for Issue #2430.
Uploader: Paul Bauer ()
Change-Id: gromacs~master~Idc9a4219d988e1794ef86f7cc79f0d00750394ca
Gerrit URL: https://gerrit.gromacs.org/7678

#3 Updated by Paul Bauer over 1 year ago

  • Status changed from New to Resolved

#4 Updated by Mark Abraham over 1 year ago

  • Status changed from Resolved to Closed
  • Target version set to 2019

#5 Updated by Viveca Lindahl about 1 year ago

  • Has duplicate Bug #2476: gmx trjconv segfaults when converting gro file to xtc when no tpr is given added

Also available in: Atom PDF