[gmx-users] problem with profiling grompp using callgrind

ganapathy senthilkumar rgskumar1983 at gmail.com
Tue May 9 07:54:05 CEST 2006


 dear gromacs users,
        i tried to profile the execution of grompp using
the callgrind profiling tool.

the command is as below.
>callgrind -v -dump-every-bb = 10000000 grompp -f run4.mdp -c run3.gro -p
CAVITY2.top -o run4.tpr

the program aborted with the following output.

=7186== Callgrind-0.10.1, a call-graph generating cache profiler.
==7186== Copyright (C) 2002-2005, and GNU GPL'd, by J.Weidendorfer et al.
==7186== Using LibVEX rev 1575, a library for dynamic binary translation.
==7186== Copyright (C) 2004-2005, and GNU GPL'd, by OpenWorks LLP.
==7186== Using valgrind-3.1.1, a dynamic binary instrumentation framework.
==7186== Copyright (C) 2000-2005, and GNU GPL'd, by Julian Seward et al.
==7186== For more details, rerun with: -v
==7186==
==7186==
==7186== For interactive control, run 'callgrind_control -h'.
                        :-)  G  R  O  M  A  C  S  (-:

                Gravel Rubs Often Many Awfully Cauterized Sores

                            :-)  VERSION 3.3.1  (-:


      Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
      Copyright (c) 1991-2000, University of Groningen, The Netherlands.
            Copyright (c) 2001-2006, The GROMACS development team,
            check out http://www.gromacs.org for more information.

        This program is free software; you can redistribute it and/or
          modify it under the terms of the GNU General Public License
        as published by the Free Software Foundation; either version 2
            of the License, or (at your option) any later version.

                                :-)  grompp  (-:

Option    Filename  Type        Description
------------------------------ ------------------------------
  -f      run4.mdp  Input, Opt!  grompp input file with MD parameters
-po      mdout.mdp  Output      grompp input file with MD parameters
  -c      run3.gro  Input        Generic structure: gro g96 pdb tpr tpb tpa
                                  xml
  -r      conf.gro  Input, Opt.  Generic structure: gro g96 pdb tpr tpb tpa
                                  xml
-rb      conf.gro  Input, Opt.  Generic structure: gro g96 pdb tpr tpb tpa
                                  xml
  -n      index.ndx  Input, Opt.  Index file
-deshuf  deshuf.ndx  Output, Opt. Index file
  -p    CAVITY2.top  Input        Topology file
-pp  processed.top  Output, Opt. Topology file
  -o      run4.tpr  Output      Generic run input: tpr tpb tpa xml
  -t      traj.trr  Input, Opt.  Full precision trajectory: trr trj
  -e      ener.edr  Input, Opt.  Generic energy: edr ene

      Option  Type  Value  Description
------------------------------------------------------
      -[no]h  bool    no  Print help info and quit
      -[no]X  bool    no  Use dialog box GUI to edit command line options
      -nice    int      0  Set the nicelevel
      -[no]v  bool    yes  Be loud and noisy
      -time  real    -1  Take frame at or first after this time.
        -np    int      1  Generate statusfile for # nodes
-[no]shuffle  bool    no  Shuffle molecules over nodes
  -[no]sort  bool    no  Sort molecules according to X coordinate
-[no]rmvsbds  bool    yes  Remove constant bonded interactions with virtual
                            sites
      -load string        Releative load capacity of each node on a
                            parallel machine. Be sure to use quotes around
                            the string, which should contain a number for
                            each node
    -maxwarn    int    10  Number of warnings after which input processing
                            stops
-[no]check14  bool    no  Remove 1-4 interactions without Van der Waals
  -[no]renum  bool    yes  Renumber atomtypes and minimize number of
                            atomtypes

creating statusfile for 1 node...
checking input for internal consistency...
WARNING 1 [file run4.mdp, line unknown]:
  For energy conservation with switch/shift potentials, rlist should be 0.1
  to 0.3 nm larger than rcoulomb/rvdw.
calling /lib/cpp...
processing topology...
Generated 141 of the 1176 non-bonded parameter combinations
Excluding 3 bonded neighbours for POP 32
turning H bonds into constraints...
Excluding 2 bonded neighbours for SOL 1051
turning H bonds into constraints...
Excluding 3 bonded neighbours for POP 32
Excluding 2 bonded neighbours for SOL 1051
Excluding 3 bonded neighbours for POP 32
Excluding 2 bonded neighbours for SOL 1051
Excluding 3 bonded neighbours for POP 32
Excluding 2 bonded neighbours for SOL 1051
*** glibc detected *** grompp: realloc(): invalid pointer: 0x04120008 ***
======= Backtrace: =========
/lib/libc.so.6(__libc_realloc+0x2e6)[0x1cff15]
grompp[0x80a926d]
======= Memory map: ========
0011f000-00120000 r-xp 0011f000 00:00 0
00148000-00162000 r-xp 00000000 fd:00 945102    /lib/ld-2.3.5.so
00162000-00163000 r-xp 00019000 fd:00 945102    /lib/ld-2.3.5.so
00163000-00164000 rwxp 0001a000 fd:00 945102    /lib/ld-2.3.5.so
0016a000-0028e000 r-xp 00000000 fd:00 945103    /lib/libc-2.3.5.so
0028e000-00290000 r-xp 00124000 fd:00 945103    /lib/libc-2.3.5.so
00290000-00292000 rwxp 00126000 fd:00 945103    /lib/libc-2.3.5.so
00292000-00294000 rwxp 00292000 00:00 0
00296000-002b8000 r-xp 00000000 fd:00 945104    /lib/libm-2.3.5.so
002b8000-002b9000 r-xp 00021000 fd:00 945104    /lib/libm-2.3.5.so
002b9000-002ba000 rwxp 00022000 fd:00 945104    /lib/libm-2.3.5.so
002bc000-002be000 r-xp 00000000 fd:00 945105    /lib/libdl-2.3.5.so
002be000-002bf000 r-xp 00001000 fd:00 945105    /lib/libdl-2.3.5.so
002bf000-002c0000 rwxp 00002000 fd:00 945105    /lib/libdl-2.3.5.so
002d7000-003a7000 r-xp 00000000 fd:00 1482512
/usr/X11R6/lib/libX11.so.6.2
003a7000-003ab000 rwxp 000cf000 fd:00 1482512
/usr/X11R6/lib/libX11.so.6.2
003ad000-003bb000 r-xp 00000000 fd:00 1482513
/usr/X11R6/lib/libXext.so.6.4
003bb000-003bc000 rwxp 0000e000 fd:00 1482513
/usr/X11R6/lib/libXext.so.6.4
003be000-003c5000 r-xp 00000000 fd:00 1476469    /usr/X11R6/lib/libXp.so.6.2
003c5000-003c6000 rwxp 00006000 fd:00 1476469    /usr/X11R6/lib/libXp.so.6.2
004d4000-004dd000 r-xp 00000000 fd:00 945107    /lib/libgcc_s-
4.0.0-20050520.so.1
004dd000-004de000 rwxp 00009000 fd:00 945107    /lib/libgcc_s-
4.0.0-20050520.so.1
005cb000-005d3000 r-xp 00000000 fd:00 1482523    /usr/X11R6/lib/libSM.so.6.0
005d3000-005d4000 rwxp 00007000 fd:00 1482523    /usr/X11R6/lib/libSM.so.6.0
005d6000-005ed000 r-xp 00000000 fd:00 1482522
/usr/X11R6/lib/libICE.so.6.3
005ed000-005ee000 rwxp 00016000 fd:00 1482522
/usr/X11R6/lib/libICE.so.6.3
005ee000-005f0000 rwxp 005ee000 00:00 0
005f2000-00847000 r-xp 00000000 fd:00 1475394
/usr/X11R6/lib/libXm.so.3.0.2
00847000-00860000 rwxp 00255000 fd:00 1475394
/usr/X11R6/lib/libXm.so.3.0.2
00860000-00861000 rwxp 00860000 00:00 0
04000000-04001000 r-xp 00000000 fd:00 260368
/usr/local/lib/valgrind/x86-linux/vgpreload_core.so
04001000-04002000 rwxp 00000000 fd:00 260368
/usr/local/lib/valgrind/x86-linux/vgpreload_core.so
04002000-04003000 rwxp 04002000 00:00 0
04004000-0400d000 r-xp 00000000 fd:00 943829    /lib/libnss_files-2.3.5.so
0400d000-0400e000 r-xp 00008000 fd:00 943829    /lib/libnss_files-2.3.5.so
0400e000-0400f000 rwxp 00009000 fd:00 943829    /lib/libnss_files-2.3.5.so
04019000-0401a000 rwxp 04019000 00:00 0
0401a000-0406c000 r-xp 00000000 fd:00 1481939    /usr/X11R6/lib/libXt.so.6.0
0406c000-04070000 rwxp 00052000 fd:00 1481939    /usr/X11R6/lib/libXt.so.6.0
04070000-04071000 rwxp 04070000 00:00 0
04071000-04087000 r-xp 00000000 fd:00 1482558
/usr/X11R6/lib/libXmu.so.6.2
04087000-04088000 rwxp 00015000 fd:00 1482558
/usr/X11R6/lib/libXmu.so.6.2
04088000-04229000 rwxp 04088000 00:00 0
07f7d000-07f8f000 r-xp 00000000 fd:00 945114    /lib/libnsl-2.3.5.so
07f8f000-07f90000 r-xp 00011000 fd:00 945114    /lib/libnsl-2.3.5.so
07f90000-07f91000 rwxp 00012000 fd:00 945114    /lib/libnsl-2.3.5.so
07f91000-07f93000 rwxp 07f91000 00:00 0
08048000-081c9000 r-xp 00000000 fd:00 2024902
/usr/local/gromacs/bin/grompp
081c9000-081d0000 rwxp 00181000 fd:00 2024902
/usr/local/gromacs/bin/grompp
081d0000-08202000 rwxp 081d0000 00:00 0
08202000-082bf000 rwxp 08202000 00:00 0
61d4a000-6224a000 rwxp 61d4a000 00:00 0
6224a000-6224c000 --xp 6224a000 00:00 0
6224c000-6225c000 rwxp 6224c000 00:00 0
6225c000-6225e000 --xp 6225c000 00:00 0
6225e000-633a4000 rwxp 6225e000 00:00 0
b0000000-b0125000 r-xp 00000000 fd:00 650893
/usr/local/lib/valgrind/x86-linux/callgrind
b0125000-b012e000 rwxp 00125000 fd:00 650893
/usr/local/lib/valgrind/x86-linux/callgrind
b012e000-b074c000 rwxp b012e000 00:00 0
bea85000-bea93000 rwxp bea85000 00:00 0
bfa7f000-bfa95000 rw-p bfa7f000 00:00 0          [stack]
==7186==
==7186== Events    : Ir
==7186== Collected : 110292439
==7186==
==7186== I  refs:      110,292,439
Aborted

the program ran perfectly without the profiling tool and generated the
output files.

can anybody help me with a solution or a workaround plzzzz.

does anyone know of other profiling tools that work well with gromacs?

thank you in advance

regards
ganapathy senthilkumar
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