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Bug #342

trjconv returns a memory allocation error when reading checkpoint files

Added by Peter Kasson over 10 years ago. Updated about 10 years ago.

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

Description

git-current trjconv is returning a memory allocation error when reading checkpoint files. Checked on two different .cpt files (both from slightly older Gromacs versions). On one of them, I could successfully read the cpt file with trjconv from the last CVS head.

Invocation syntax:
~/Desktop/software/gromacs/src/tools/trjconv -s production.tpr -f production.cpt -o foo.gro

Output snippet with error:
Select group for output
Opening library file /Users/kasson/Desktop/software/gromacs/share/top/aminoacids.dat
Group 0 ( System) has 173181 elements
Group 1 ( SOL) has 173181 elements
Select a group: 0
Selected 0: 'System'
trjconv(22811) malloc: * error for object 0xa0001c38: pointer being reallocated was not allocated
trjconv(22811) malloc: *
set a breakpoint in szone_error to debug

-------------------------------------------------------
Program trjconv, VERSION 4.0.99_development_20090605
Source code file: /Users/kasson/Desktop/software/gromacs/src/gmxlib/smalloc.c, line: 188

Fatal error:
Not enough memory. Failed to realloc 280 bytes for enerhist->ener_sum_sim, enerhist->ener_sum_sim=0xa0001c38
(called from file /Users/kasson/Desktop/software/gromacs/src/gmxlib/checkpoint.c, line 783)
For more information and tips for trouble shooting please check the GROMACS Wiki at
http://wiki.gromacs.org/index.php/Errors
-------------------------------------------------------

"You Look Better Upside Down" (Throwing Muses)
: Cannot allocate memory

testfiles.tgz (4.56 MB) testfiles.tgz tgz containing .tpr and .cpt files Peter Kasson, 08/04/2009 08:05 PM

History

#1 Updated by Peter Kasson over 10 years ago

Created an attachment (id=385)
tgz containing .tpr and .cpt files

#2 Updated by Berk Hess about 10 years ago

I fixed this bug.

Berk

#3 Updated by Berk Hess about 10 years ago

Having off_t only 4 bytes sounds strange though.
What kind of architecture/processor do you have?

Berk

#4 Updated by Berk Hess about 10 years ago

Oops, that last comment was for bug 341, not bug 342.

Sorry,

Berk

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