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Bug #2701

GMX Helix Segmentation Fault

Added by Budheswar Dehury 6 months ago. Updated 5 months ago.

Status:
Closed
Priority:
High
Assignee:
Category:
analysis tools
Target version:
Affected version - extra info:
The same problem also lies with GROMACS 2018.2 version
Affected version:
Difficulty:
hard
Close

Description

Dear GROMACS Development Team,

Hello everybody. I am doing analysis of helix properties using GMX helix command in Gromacs 2016.4 as well as in 2018.2. While running the command I have the following issue after executing the following command..

GROMACS: gmx helix, version 2016.4
Executable: /usr/bin/gmx
Data prefix: /usr
Working dir: /storage/home/local/bude-loc/Desktop/PS2/Seed1/TM1
Command line:
gmx helix -f ../md1.xtc -s ../md.tpr -n index.ndx

Reading file ../md.tpr, VERSION 2018.2 (single precision)
Reading frame 0 time 490000.000 Please select a group containing the entire backbone
Group 0 ( System) has 201382 elements
Group 1 ( Protein) has 22327 elements
Group 2 ( Protein-H) has 11159 elements
Group 3 ( C-alpha) has 1414 elements
Group 4 ( Backbone) has 4242 elements
Group 5 ( MainChain) has 5651 elements
Group 6 ( MainChain+Cb) has 6978 elements
Group 7 ( MainChain+H) has 6986 elements
Group 8 ( SideChain) has 15341 elements
Group 9 ( SideChain-H) has 5508 elements
Group 10 ( Prot-Masses) has 22327 elements
Group 11 ( non-Protein) has 179055 elements
Group 12 ( Other) has 179055 elements
Group 13 ( POPC) has 40468 elements
Group 14 ( TIP3) has 138315 elements
Group 15 ( SOD) has 146 elements
Group 16 ( CLA) has 126 elements
Group 17 ( a_10635-11031) has 397 elements
Select a group: 17
Selected 17: 'a_10635-11031'
Checking group a_10635-11031
There are 25 residues
There are 23 complete backbone residues (from 2 to 24)
nall=397
Reading file ../md.tpr, VERSION 2018.2 (single precision)
helix from: 8 through 23

The same problem also in case of 2018.2 . Though the other helix properties including gmx helixorient and gmx bundle works fine in both the versions...

I have attached the last ns trajectory with 10 snapshots for your kind perusal and necessary input.

Thanking You
With Warm regards
Budheswar

md.gro (13.3 MB) md.gro GRO Budheswar Dehury, 10/17/2018 02:17 PM
index.ndx (5.2 MB) index.ndx Index Budheswar Dehury, 10/17/2018 02:17 PM
md.tpr (11.3 MB) md.tpr TPR Budheswar Dehury, 10/17/2018 02:17 PM
md1.xtc (15.1 MB) md1.xtc Trajectory Budheswar Dehury, 10/17/2018 02:17 PM

Associated revisions

Revision 76c65770 (diff)
Added by Paul Bauer 6 months ago

Fix segmentation fault in gmx helix

Changed the logic in tpxio to only try to access the mtop
datastructure if it is actually present.

Fixes #2701

Change-Id: I268af10dc125a57758f5f3e79e4b14a25050b3b3

Revision 93bea6f4 (diff)
Added by Paul Bauer 6 months ago

Actually fix gmx helix segmentation fault

The residue indexing in hxprops was wrong because the residue indices
used for residue name lookup were wrong.

Added some documentation to clarify what this code does.

Fixes #2701

Change-Id: Ie6c002be6ff2139f6af27c7b891a180338ae5b20

History

#1 Updated by Gerrit Code Review Bot 6 months ago

Gerrit received a related patchset '1' for Issue #2701.
Uploader: Paul Bauer ()
Change-Id: gromacs~release-2018~I268af10dc125a57758f5f3e79e4b14a25050b3b3
Gerrit URL: https://gerrit.gromacs.org/8566

#2 Updated by Paul Bauer 6 months ago

  • Status changed from New to Resolved

#3 Updated by Paul Bauer 6 months ago

  • Status changed from Resolved to Closed

Fixed in 2018.

#4 Updated by Paul Bauer 6 months ago

  • Status changed from Closed to Accepted

not fixed yet, there is a separate memory violation going on that was masked by the first, more obvious one.

#5 Updated by Gerrit Code Review Bot 6 months ago

Gerrit received a related patchset '2' for Issue #2701.
Uploader: Paul Bauer ()
Change-Id: gromacs~release-2018~Ie6c002be6ff2139f6af27c7b891a180338ae5b20
Gerrit URL: https://gerrit.gromacs.org/8633

#6 Updated by Paul Bauer 6 months ago

  • Status changed from Accepted to Resolved

#7 Updated by Paul Bauer 5 months ago

  • Status changed from Resolved to Closed

#8 Updated by Mark Abraham 5 months ago

  • Target version set to 2018.4

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