Project

General

Profile

Bug #1920

Updated by Mark Abraham over 4 years ago

GROMACS version 5.1.2 (but 5.0.6 gives the same result) under Ubuntu 14.04.3 LTS

The error appears when executing:

gmx dielectric -ffn aexp

on a dipcorr.xvg file longer than a few timesteps. For example:

<pre>
$ gmx dielectric -ffn aexp

Read data set containing 2 colums and 1001 rows
Assuming (from data) that timestep is 10, nxtail = 50
Creating standard deviation numbers ...
nbegin = 1, x[nbegin] = 10, tbegin = 5
*** Error in `gmx': malloc(): smallbin double linked list corrupted: 0x000000000078b730 ***
Aborted (core dumped)
</pre>


After reducing the dipcorr.xvg file to a few timesteps (dipcorr.xvg copied to correl.xvg and edited by hand), the command works correctly:

<pre>
$ gmx dielectric -ffn aexp -f correl.xvg

Read data set containing 2 colums and 11 rows
Assuming (from data) that timestep is 10, nxtail = 11
Creating standard deviation numbers ...
nbegin = 1, x[nbegin] = 10, tbegin = 5
Step chi^2 Lambda A1 A2 A3 A4
irow = 2, icol = 2
-nan -nan
-nan 0.000
Numerical Recipes run-time error...
GAUSSJ: Singular Matrix-2
Fit failed!
DATA INTEGRAL: 0.0, tauD(old) = 0.0 ps, tau_slope = 0.0, tau_slope,D = 0.0 ps
tau_D from tau1 = 2.33e-38 , eps(Infty) = 80.000
nbegin = 1, x[nbegin] = 10, tbegin = 5
Making smooth transition from 1 through 4
SMOOTH integral = 1.09961e+01
FIT INTEGRAL (tau_M): 11.0, tau_D = 16.5
Doing FFT of 32 points
MAXEPS = 3.40426e+01 at frequency 1.25000e+01 GHz (tauD = 12.7 ps)

gcq#17: "I Calculate My Birthright" (P.J. Harvey)

</pre>



I have tried to recompile gromacs 5.1.2 with debugging options, and to execute gmx under gdb:

<pre>
$ gdb gmx

GNU gdb (Ubuntu 7.7.1-0ubuntu5~14.04.2) 7.7.1
Copyright (C) 2014 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law. Type "show copying"
and "show warranty" for details.
This GDB was configured as "x86_64-linux-gnu".
Type "show configuration" for configuration details.
For bug reporting instructions, please see:
<http://www.gnu.org/software/gdb/bugs/>.
Find the GDB manual and other documentation resources online at:
<http://www.gnu.org/software/gdb/documentation/>.
For help, type "help".
Type "apropos word" to search for commands related to "word"...
Reading symbols from gmx...done.

(gdb) run dielectric

Starting program: /home/roberto/MD/gromacs-5.1.2/build1/bin/gmx dielectric
[Thread debugging using libthread_db enabled]
Using host libthread_db library "/lib/x86_64-linux-gnu/libthread_db.so.1".
:-) GROMACS - gmx dielectric, VERSION 5.1.2 (-:

GROMACS is written by:
Emile Apol Rossen Apostolov Herman J.C. Berendsen Par Bjelkmar
Aldert van Buuren Rudi van Drunen Anton Feenstra Sebastian Fritsch
Gerrit Groenhof Christoph Junghans Anca Hamuraru Vincent Hindriksen
Dimitrios Karkoulis Peter Kasson Jiri Kraus Carsten Kutzner
Per Larsson Justin A. Lemkul Magnus Lundborg Pieter Meulenhoff
Erik Marklund Teemu Murtola Szilard Pall Sander Pronk
Roland Schulz Alexey Shvetsov Michael Shirts Alfons Sijbers
Peter Tieleman Teemu Virolainen Christian Wennberg Maarten Wolf
and the project leaders:
Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel

Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2015, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.

GROMACS is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
of the License, or (at your option) any later version.

GROMACS: gmx dielectric, VERSION 5.1.2
Executable: /home/roberto/MD/gromacs-5.1.2/build1/bin/gmx
Data prefix: /home/roberto/MD/gromacs-5.1.2 (source tree)
Command line:
gmx dielectric

++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
D. van der Spoel and P. J. van Maaren and H. J. C. Berendsen
A systematic study of water models for molecular simulation. Derivation of
models optimized for use with a reaction-field.
J. Chem. Phys. 108 (1998) pp. 10220-10230
-------- -------- --- Thank You --- -------- --------

WARNING: non-polarizable models can never yield an infinite
dielectric constant that is different from 1. This is incorrect
in the reference given above (Spoel98a).

Read data set containing 2 colums and 1001 rows
Assuming (from data) that timestep is 10, nxtail = 50
Creating standard deviation numbers ...
nbegin = 1, x[nbegin] = 10, tbegin = 5
There are 50 data points, 0 parameters, initial chi2 = 0.0581182
params:
*** Error in `/home/roberto/MD/gromacs-5.1.2/build1/bin/gmx': malloc(): smallbin double linked list corrupted: 0x000000000064d060 ***

Program received signal SIGABRT, Aborted.
0x00007ffff4d87cc9 in __GI_raise (sig=sig@entry=6)
at ../nptl/sysdeps/unix/sysv/linux/raise.c:56
56 ../nptl/sysdeps/unix/sysv/linux/raise.c: No such file or directory.

(gdb) where

#0 0x00007ffff4d87cc9 in __GI_raise (sig=sig@entry=6)
at ../nptl/sysdeps/unix/sysv/linux/raise.c:56
#1 0x00007ffff4d8b0d8 in __GI_abort () at abort.c:89
#2 0x00007ffff4dc4394 in __libc_message (do_abort=do_abort@entry=1,
fmt=fmt@entry=0x7ffff4ed2b28 "*** Error in `%s': %s: 0x%s ***\n")
at ../sysdeps/posix/libc_fatal.c:175
#3 0x00007ffff4dcf0f7 in malloc_printerr (action=<optimized out>,
str=0x7ffff4ed2ef0 "malloc(): smallbin double linked list corrupted",
ptr=<optimized out>) at malloc.c:4996
#4 0x00007ffff4dd1e04 in _int_malloc (
av=av@entry=0x7ffff510f760 <main_arena>, bytes=bytes@entry=24)
at malloc.c:3359
#5 0x00007ffff4dd42cc in __libc_calloc (n=<optimized out>,
elem_size=<optimized out>) at malloc.c:3219
#6 0x00007ffff5cdaca4 in save_calloc (name=0x7ffff79db453 "status",
file=0x7ffff79db408 "/home/roberto/MD/gromacs-5.1.2/src/gromacs/correlationfunctions/expfit.cpp", line=458, nelem=1, elsize=24)
at /home/roberto/MD/gromacs-5.1.2/src/gromacs/utility/smalloc.c:180
#7 0x00007ffff5f06c54 in gmx_snew_impl<lm_status_struct> (
name=0x7ffff79db453 "status",
file=0x7ffff79db408 "/home/roberto/MD/gromacs-5.1.2/src/gromacs/correlationfunctions/expfit.cpp", line=458,
ptr=@0x7fffffffdc48: 0x7ffff4dc25c9 <fputc+185>, nelem=1)
at /home/roberto/MD/gromacs-5.1.2/src/gromacs/utility/smalloc.h:225
#8 0x00007ffff5f04b01 in lmfit_exp (nfit=50, x=0x659cc0, y=0x65bc10,
dy=0x65db60, parm=0x64c620, bVerbose=1, eFitFn=0, nfix=0)
at /home/roberto/MD/gromacs-5.1.2/src/gromacs/correlationfunctions/expfit.cpp:458
#9 0x00007ffff5f05b1e in do_lmfit (ndata=1001, c1=0x654e50, sig=0x655e00,
dt=10, x0=0x64fe20, begintimefit=5, endtimefit=500, oenv=0x64fc20,
bVerbose=1, eFitFn=0, fitparms=0x64c620, fix=0, fn_fitted=0x0)
at /home/roberto/MD/gromacs-5.1.2/src/gromacs/correlationfunctions/expfit.cpp:768
#10 0x00007ffff5d5d836 in gmx_dielectric (argc=1, argv=0x7fffffffe430)
at /home/roberto/MD/gromacs-5.1.2/src/gromacs/gmxana/gmx_dielectric.c:399
#11 0x00007ffff5bfd691 in gmx::(anonymous namespace)::CMainCommandLineModule::run (this=0x643ff0, argc=1, argv=0x7fffffffe430)
at /home/roberto/MD/gromacs-5.1.2/src/gromacs/commandline/cmdlinemodulemanager.cpp:125
#12 0x00007ffff5bfee26 in gmx::CommandLineModuleManager::run (
this=0x7fffffffe300, argc=1, argv=0x7fffffffe430)
at /home/roberto/MD/gromacs-5.1.2/src/gromacs/commandline/cmdlinemodulemanager.cpp:554
#13 0x00000000004115b3 in main (argc=2, argv=0x7fffffffe428)
at /home/roberto/MD/gromacs-5.1.2/src/programs/gmx.cpp:60

</pre>
Navigating in the WEB, the "double linked list corrupted" error appears to be a subtle error, related to a wrong malloc() allocation of a pointer to pointer, for example:

<pre>
a=(char **)malloc(nl);
</pre>


instead of
<pre>


a=(char **)malloc( nl * sizeof(char*) );
</pre>

Back