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Bug #430

g_chi bus error with -p option

Added by Justin Lemkul over 9 years ago. Updated over 9 years ago.

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

The use of the -p option with g_chi (both version 4.0.7 and git version as of 6/9/2010) exits with a Bus error, preventing a complete chi.log file from being written (although order.xvg) is written. The problem is reproducible with both .gro and .xtc files. I can upload a test case if necessary, but everything I've thrown at g_chi produces the error faithfully.

test.tar.gz (706 KB) test.tar.gz The .tpr and .gro files Justin Lemkul, 06/10/2010 01:30 PM

History

#1 Updated by Justin Lemkul over 9 years ago

I should also add that this bug is reproducible on a Linux machine (AMD64) running Gromacs-4.0.7. I took a quick look into the code and it seems as though the -p flag is never used, and thus no attempt is ever made to open a file or write anything to it. I could be missing something, though.

#2 Updated by David van der Spoel over 9 years ago

Could you please send example input and command line? I can not reproduce the error. If I use

g_chi -s -f -p

I do get an order.pdb as expected. The -p option is used, and a pdbfn is sent to the function order_param.

#3 Updated by Justin Lemkul over 9 years ago

Created an attachment (id=466)
The .tpr and .gro files

#4 Updated by Justin Lemkul over 9 years ago

The attachment contains a .gro and .tpr file necessary to reproduce the problem. With the command:

g_chi -s md_0_10.tpr -f md_40_50.tpr -p

the program exits with the following:

94 residues with dihedrals found
453 dihedrals found
Reading frames from gro file 'DEP domain of Dvl2 with 4:1 DHPA in water', 15359 atoms.
Last frame 0 time 0.000
j after resetting (nr. active dihedrals) = 281
WARNING: not all dihedrals found in topology (only 281 out of 453)!
Now calculating transitions...
Total number of transitions: 0
Bus error

I get an incomplete chi.log file, and an intact order.xvg, but no order.pdb. The error is a segmentation fault on my AMD64 machine, but I don't know if that's significant at all.

#5 Updated by Justin Lemkul over 9 years ago

I get an incomplete chi.log file, and an intact order.xvg, but no order.pdb.
The error is a segmentation fault on my AMD64 machine, but I don't know if
that's significant at all.

I can reproduce the error with an .xtc trajectory as well, in case that's an issue. The latest git code I tried was from early yesterday (6/9/10), so if I should try a newer version, please let me know.

#6 Updated by David van der Spoel over 9 years ago

Fixed in git master.

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