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Bug #1920

malloc() error: smallbin double linked list corrupted

Added by Roberto Olmi over 3 years ago. Updated over 3 years ago.

Status:
Closed
Priority:
Normal
Category:
analysis tools
Target version:
Affected version - extra info:
Also 5.0.6 is affected
Affected version:
Difficulty:
uncategorized
Close

Description

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:

$ 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)

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

$ 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)

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

$ 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


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:
a=(char **)malloc(nl);

instead of


a=(char **)malloc( nl * sizeof(char*) );

dipcorr.xvg (23 KB) dipcorr.xvg full-size correlation file Roberto Olmi, 03/23/2016 01:31 PM
correl.xvg (991 Bytes) correl.xvg reduce correlation file Roberto Olmi, 03/23/2016 01:32 PM

Associated revisions

Revision 1e130c8c (diff)
Added by David van der Spoel over 3 years ago

Removed srenew that was making array smaller incorrectly.

An array y was first allocated to 6 entries, then reduced
to 3 entries using srenew, but after that the indices
3, 4 and 5 were used anyway. Removing the srenew fixes the probem.

Fixes #1920

Change-Id: I3f35f0af3f56d33435bf54a9c7cda6273fb3f05a

History

#1 Updated by Mark Abraham over 3 years ago

  • Description updated (diff)

#2 Updated by David van der Spoel over 3 years ago

  • Assignee set to David van der Spoel

Can you please upload a dipcorr file that gives this problem?

#3 Updated by Roberto Olmi over 3 years ago

gmx dielectric -ffn aexp gives the mentioned error.

gmx dielectric -ffn aexp -f correl.xvg, on the reduced file correl.xvg (first 200 ps), works well.

#4 Updated by Roberto Olmi over 3 years ago

#5 Updated by David van der Spoel over 3 years ago

I reproduced the problem on Linux (but it is fine on mac osx). Will have a look.

#6 Updated by Gerrit Code Review Bot over 3 years ago

Gerrit received a related patchset '1' for Issue #1920.
Uploader: David van der Spoel ()
Change-Id: I3f35f0af3f56d33435bf54a9c7cda6273fb3f05a
Gerrit URL: https://gerrit.gromacs.org/5740

#7 Updated by David van der Spoel over 3 years ago

  • Status changed from New to Resolved

#8 Updated by Szilárd Páll over 3 years ago

  • Target version set to 5.1.3

#9 Updated by David van der Spoel over 3 years ago

  • Status changed from Resolved to Closed

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