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Bug #3444

do_dssp does not work(gmx 2020 and 2020.1)

Added by yujie liu 9 months ago. Updated 6 months ago.

Status:
Resolved
Priority:
Normal
Category:
-
Target version:
Affected version - extra info:
2020 and 2020.1
Affected version:
Difficulty:
simple
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Description

This "gmx -do_dssp" tool will report an error "Segmentation fault" and no xpm and xvg file generated. I tesetd 2.0.4 and later version of dssp. Then I checked gmx_do_dssp.cpp code and found some parts of matrix changed a alot, I think this code may have a problem. Hope developer can solve this issue.
Thanks!

md.tpr (1.24 MB) md.tpr yujie liu, 03/18/2020 08:30 AM
md.xtc (13.1 MB) md.xtc yujie liu, 03/18/2020 08:32 AM

Associated revisions

Revision f3c08f93 (diff)
Added by Paul Bauer 7 months ago

Fix segmentation fault in do_dssp

A matrix would be initial allocated with zero size, so that a
following call to increase the size of one element would lead to memory
corruption on a subsequent try to set a value in the matrix.

Fixes #3444

Change-Id: I1892c09a8aa4c2f92156f7b1a76623df9ac62e56

Revision 7cd10c44 (diff)
Added by Paul Bauer 6 months ago

Proper fix for gmx do_dssp

The tool was still broken after the previous fix, even though it didn't
crash any more.

Fixed now by providing the correct sizes for the matrix.

Fixes #3444

Change-Id: I6b59bbdd5e69ff2c311ff4c8457037c9310b081f

History

#1 Updated by Mark Abraham 9 months ago

Can you share an input that works, e.g. with 2019.x please?

#2 Updated by yujie liu 9 months ago

Mark Abraham wrote:

Can you share an input that works, e.g. with 2019.x please?

I uploaded a sample of xtc and tpr file, when I use gmx do_dssp -f md.xtc -s md.tpr by using gmx 2020 or 2020.1 will have error "Segmentation fault", but using other gmx version, such as gmx2018 or gmx 2019 is correct.

#3 Updated by Christian Blau 9 months ago

  • Assignee set to Christian Blau

#4 Updated by Christian Blau 9 months ago

  • Priority changed from High to Normal

#5 Updated by Paul Bauer 7 months ago

  • Status changed from New to Resolved

#6 Updated by Paul Bauer 6 months ago

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