[gmx-users] problem with profiling grompp using callgrind
David van der Spoel
spoel at xray.bmc.uu.se
Tue May 9 08:28:42 CEST 2006
ganapathy senthilkumar wrote:
> 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 <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
> <http://2.3.5.so/>
> 00162000-00163000 r-xp 00019000 fd:00 945102 /lib/ld-2.3.5.so
> <http://2.3.5.so/>
> 00163000-00164000 rwxp 0001a000 fd:00 945102 /lib/ld-2.3.5.so
> <http://2.3.5.so/>
> 0016a000-0028e000 r-xp 00000000 fd:00 945103 /lib/libc-2.3.5.so
> <http://2.3.5.so/>
> 0028e000-00290000 r-xp 00124000 fd:00 945103 /lib/libc-2.3.5.so
> <http://2.3.5.so/>
> 00290000-00292000 rwxp 00126000 fd:00 945103 /lib/libc-2.3.5.so
> <http://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
> <http://2.3.5.so/>
> 002b8000-002b9000 r-xp 00021000 fd:00 945104 /lib/libm-2.3.5.so
> <http://2.3.5.so/>
> 002b9000-002ba000 rwxp 00022000 fd:00 945104 /lib/libm-2.3.5.so
> <http://2.3.5.so/>
> 002bc000-002be000 r-xp 00000000 fd:00 945105 /lib/libdl-2.3.5.so
> <http://2.3.5.so/>
> 002be000-002bf000 r-xp 00001000 fd:00 945105 /lib/libdl-2.3.5.so
> <http://2.3.5.so/>
> 002bf000-002c0000 rwxp 00002000 fd:00 945105 /lib/libdl-2.3.5.so
> <http://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 <http://2.3.5.so/>
> 0400d000-0400e000 r-xp 00008000 fd:00 943829
> /lib/libnss_files-2.3.5.so <http://2.3.5.so/>
> 0400e000-0400f000 rwxp 00009000 fd:00 943829
> /lib/libnss_files-2.3.5.so <http://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
> <http://2.3.5.so/>
> 07f8f000-07f90000 r-xp 00011000 fd:00 945114 /lib/libnsl-2.3.5.so
> <http://2.3.5.so/>
> 07f90000-07f91000 rwxp 00012000 fd:00 945114 /lib/libnsl-2.3.5.so
> <http://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?
this seems more like a bug that is dependent on memory allocation. I'm
no aware of any known bug in grompp. Maybe you can recompile all of
grompp with the -g flag and retry. For memory debugging simpler tools
like Electric Fence usually work. For profiling, you'd probably want to
profile mdrun, although there is a bugzilla about grompp being
excessively slow for large systems with OPLS and dummies.
>
> thank you in advance
>
> regards
> ganapathy senthilkumar
>
>
> ------------------------------------------------------------------------
>
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--
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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