dear gromacs users,<br>
i tried to profile the execution of grompp using <br>
the callgrind profiling tool.<br>
<br>
the command is as below.<br>
>callgrind -v -dump-every-bb = 10000000 grompp -f run4.mdp -c run3.gro -p CAVITY2.top -o run4.tpr <br>
<br>
the program aborted with the following output.<br>
<br>
=7186== Callgrind-0.10.1, a call-graph generating cache profiler.<br>
==7186== Copyright (C) 2002-2005, and GNU GPL'd, by J.Weidendorfer et al.<br>
==7186== Using LibVEX rev 1575, a library for dynamic binary translation.<br>
==7186== Copyright (C) 2004-2005, and GNU GPL'd, by OpenWorks LLP.<br>
==7186== Using valgrind-3.1.1, a dynamic binary instrumentation framework.<br>
==7186== Copyright (C) 2000-2005, and GNU GPL'd, by Julian Seward et al.<br>
==7186== For more details, rerun with: -v<br>
==7186==<br>
==7186==<br>
==7186== For interactive control, run 'callgrind_control -h'.<br>
:-) G R O M A C
S (-:<br>
<br>
Gravel Rubs Often Many Awfully Cauterized Sores<br>
<br>
:-) VERSION 3.3.1 (-:<br>
<br>
<br>
Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.<br>
Copyright (c) 1991-2000, University of Groningen, The Netherlands.<br>
Copyright (c) 2001-2006, The GROMACS development team,<br>
check out <a href="http://www.gromacs.org/" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">http://www.gromacs.org</a> for more information.<br>
<br>
This program is free software; you can redistribute it and/or<br>
modify it under the terms of the GNU General Public License<br>
as published by the Free Software Foundation; either version 2<br>
of the License, or (at your option) any later version.<br>
<br>
:-) grompp (-:<br>
<br>
Option Filename Type Description<br>
------------------------------
<div id="mb_1">------------------------------<br>
-f run4.mdp Input, Opt! grompp input file with MD parameters<br>
-po mdout.mdp Output grompp input file with MD parameters<br>
-c run3.gro Input Generic structure: gro g96 pdb tpr tpb tpa<br>
xml<br>
-r conf.gro Input, Opt. Generic structure: gro g96 pdb tpr tpb tpa<br>
xml<br>
-rb conf.gro Input, Opt. Generic structure: gro g96 pdb tpr tpb tpa<br>
xml<br>
-n index.ndx Input, Opt. Index file<br>
-deshuf deshuf.ndx Output, Opt. Index file<br>
-p CAVITY2.top Input Topology file<br>
-pp processed.top Output, Opt. Topology file<br>
-o run4.tpr Output Generic run input: tpr tpb tpa xml<br>
-t traj.trr Input, Opt. Full precision trajectory: trr trj<br>
-e ener.edr Input, Opt. Generic energy: edr ene<br>
<br>
Option Type Value Description<br>
------------------------------------------------------<br>
-[no]h bool no Print help info and quit<br>
-[no]X bool no Use dialog box GUI to edit command line options<br>
-nice int 0 Set the nicelevel<br>
-[no]v bool yes Be loud and noisy<br>
-time real -1 Take frame at or first after this time.<br>
-np int 1 Generate statusfile for # nodes<br>
-[no]shuffle bool no Shuffle molecules over nodes<br>
-[no]sort bool no Sort molecules according to X coordinate<br>
-[no]rmvsbds bool yes Remove constant bonded interactions with virtual<br>
sites<br>
-load string Releative load capacity of each node on a<br>
parallel machine. Be sure to use quotes
around<br>
the string, which should contain a number
for<br>
each node<br>
-maxwarn int 10 Number of warnings after which input processing<br>
stops<br>
-[no]check14 bool no Remove 1-4 interactions without Van der Waals<br>
-[no]renum bool yes Renumber atomtypes and minimize number of<br>
atomtypes<br>
<br>
creating statusfile for 1 node...<br>
checking input for internal consistency...<br>
WARNING 1 [file run4.mdp, line unknown]:<br>
For energy conservation with switch/shift potentials, rlist should be 0.1<br>
to 0.3 nm larger than rcoulomb/rvdw.<br>
calling /lib/cpp...<br>
processing topology...<br>
Generated 141 of the 1176 non-bonded parameter combinations<br>
Excluding 3 bonded neighbours for POP 32<br>
turning H bonds into constraints...<br>
Excluding 2 bonded neighbours for SOL 1051<br>
turning H bonds into constraints...<br>
Excluding 3 bonded neighbours for POP 32<br>
Excluding 2 bonded neighbours for SOL 1051<br>
Excluding 3 bonded neighbours for POP 32<br>
Excluding 2 bonded neighbours for SOL 1051<br>
Excluding 3 bonded neighbours for POP 32<br>
Excluding 2 bonded neighbours for SOL 1051<br>
*** glibc detected *** grompp: realloc(): invalid pointer: 0x04120008 ***<br>
======= Backtrace: =========<br>
/lib/libc.so.6(__libc_realloc+0x2e6)[0x1cff15]<br>
grompp[0x80a926d]<br>
======= Memory map: ========<br>
0011f000-00120000 r-xp 0011f000 00:00 0<br>
00148000-00162000 r-xp 00000000 fd:00 945102 /lib/ld-<a href="http://2.3.5.so/" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">2.3.5.so</a><br>
00162000-00163000 r-xp 00019000 fd:00 945102 /lib/ld-<a href="http://2.3.5.so/" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">2.3.5.so</a><br>
00163000-00164000 rwxp 0001a000 fd:00 945102 /lib/ld-<a href="http://2.3.5.so/" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">2.3.5.so</a><br>
0016a000-0028e000 r-xp 00000000 fd:00 945103 /lib/libc-<a href="http://2.3.5.so/" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">2.3.5.so</a><br>
0028e000-00290000 r-xp 00124000 fd:00 945103 /lib/libc-<a href="http://2.3.5.so/" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">2.3.5.so</a><br>
00290000-00292000 rwxp 00126000 fd:00 945103 /lib/libc-<a href="http://2.3.5.so/" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">2.3.5.so</a><br>
00292000-00294000 rwxp 00292000 00:00 0<br>
00296000-002b8000 r-xp 00000000 fd:00 945104 /lib/libm-<a href="http://2.3.5.so/" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">2.3.5.so</a><br>
002b8000-002b9000 r-xp 00021000 fd:00 945104 /lib/libm-<a href="http://2.3.5.so/" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">2.3.5.so</a><br>
002b9000-002ba000 rwxp 00022000 fd:00 945104 /lib/libm-<a href="http://2.3.5.so/" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">2.3.5.so</a><br>
002bc000-002be000 r-xp 00000000 fd:00 945105 /lib/libdl-<a href="http://2.3.5.so/" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">2.3.5.so</a><br>
002be000-002bf000 r-xp 00001000 fd:00 945105 /lib/libdl-<a href="http://2.3.5.so/" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">2.3.5.so</a><br>
002bf000-002c0000 rwxp 00002000 fd:00 945105 /lib/libdl-<a href="http://2.3.5.so/" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">2.3.5.so</a><br>
002d7000-003a7000 r-xp 00000000 fd:00 1482512 /usr/X11R6/lib/libX11.so.6.2<br>
003a7000-003ab000 rwxp 000cf000 fd:00 1482512 /usr/X11R6/lib/libX11.so.6.2<br>
003ad000-003bb000 r-xp 00000000 fd:00 1482513 /usr/X11R6/lib/libXext.so.6.4<br>
003bb000-003bc000 rwxp 0000e000 fd:00 1482513 /usr/X11R6/lib/libXext.so.6.4<br>
003be000-003c5000 r-xp 00000000 fd:00 1476469 /usr/X11R6/lib/libXp.so.6.2<br>
003c5000-003c6000 rwxp 00006000 fd:00 1476469 /usr/X11R6/lib/libXp.so.6.2<br>
004d4000-004dd000 r-xp 00000000 fd:00 945107 /lib/libgcc_s-4.0.0-20050520.so.1<br>
004dd000-004de000 rwxp 00009000 fd:00 945107 /lib/libgcc_s-4.0.0-20050520.so.1<br>
005cb000-005d3000 r-xp 00000000 fd:00 1482523 /usr/X11R6/lib/libSM.so.6.0<br>
005d3000-005d4000 rwxp 00007000 fd:00 1482523 /usr/X11R6/lib/libSM.so.6.0<br>
005d6000-005ed000 r-xp 00000000 fd:00 1482522 /usr/X11R6/lib/libICE.so.6.3<br>
005ed000-005ee000 rwxp 00016000 fd:00 1482522 /usr/X11R6/lib/libICE.so.6.3<br>
005ee000-005f0000 rwxp 005ee000 00:00 0<br>
005f2000-00847000 r-xp 00000000 fd:00 1475394 /usr/X11R6/lib/libXm.so.3.0.2<br>
00847000-00860000 rwxp 00255000 fd:00 1475394 /usr/X11R6/lib/libXm.so.3.0.2<br>
00860000-00861000 rwxp 00860000 00:00 0<br>
04000000-04001000 r-xp 00000000 fd:00 260368 /usr/local/lib/valgrind/x86-linux/vgpreload_core.so<br>
04001000-04002000 rwxp 00000000 fd:00 260368 /usr/local/lib/valgrind/x86-linux/vgpreload_core.so<br>
04002000-04003000 rwxp 04002000 00:00 0<br>
04004000-0400d000 r-xp 00000000 fd:00 943829 /lib/libnss_files-<a href="http://2.3.5.so/" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">2.3.5.so</a><br>
0400d000-0400e000 r-xp 00008000 fd:00 943829 /lib/libnss_files-<a href="http://2.3.5.so/" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">2.3.5.so</a><br>
0400e000-0400f000 rwxp 00009000 fd:00 943829 /lib/libnss_files-<a href="http://2.3.5.so/" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">2.3.5.so</a><br>
04019000-0401a000 rwxp 04019000 00:00 0<br>
0401a000-0406c000 r-xp 00000000 fd:00 1481939 /usr/X11R6/lib/libXt.so.6.0<br>
0406c000-04070000 rwxp 00052000 fd:00 1481939 /usr/X11R6/lib/libXt.so.6.0<br>
04070000-04071000 rwxp 04070000 00:00 0<br>
04071000-04087000 r-xp 00000000 fd:00 1482558 /usr/X11R6/lib/libXmu.so.6.2<br>
04087000-04088000 rwxp 00015000 fd:00 1482558 /usr/X11R6/lib/libXmu.so.6.2<br>
04088000-04229000 rwxp 04088000 00:00 0<br>
07f7d000-07f8f000 r-xp 00000000 fd:00 945114 /lib/libnsl-<a href="http://2.3.5.so/" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">2.3.5.so</a><br>
07f8f000-07f90000 r-xp 00011000 fd:00 945114 /lib/libnsl-<a href="http://2.3.5.so/" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">2.3.5.so</a><br>
07f90000-07f91000 rwxp 00012000 fd:00 945114 /lib/libnsl-<a href="http://2.3.5.so/" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">2.3.5.so</a><br>
07f91000-07f93000 rwxp 07f91000 00:00 0<br>
08048000-081c9000 r-xp 00000000 fd:00 2024902 /usr/local/gromacs/bin/grompp<br>
081c9000-081d0000 rwxp 00181000 fd:00 2024902 /usr/local/gromacs/bin/grompp<br>
081d0000-08202000 rwxp 081d0000 00:00 0<br>
08202000-082bf000 rwxp 08202000 00:00 0<br>
61d4a000-6224a000 rwxp 61d4a000 00:00 0<br>
6224a000-6224c000 --xp 6224a000 00:00 0<br>
6224c000-6225c000 rwxp 6224c000 00:00 0<br>
6225c000-6225e000 --xp 6225c000 00:00 0<br>
6225e000-633a4000 rwxp 6225e000 00:00 0<br>
b0000000-b0125000 r-xp 00000000 fd:00 650893 /usr/local/lib/valgrind/x86-linux/callgrind<br>
b0125000-b012e000 rwxp 00125000 fd:00 650893 /usr/local/lib/valgrind/x86-linux/callgrind<br>
b012e000-b074c000 rwxp b012e000 00:00 0<br>
bea85000-bea93000 rwxp bea85000 00:00 0<br>
bfa7f000-bfa95000 rw-p bfa7f000 00:00 0 [stack]<br>
==7186==<br>
==7186== Events : Ir<br>
==7186== Collected : 110292439<br>
==7186==<br>
==7186== I refs: 110,292,439<br>
Aborted<br>
<br>
the program ran perfectly without the profiling tool and generated the <br>
output files.<br>
<br>
can anybody help me with a solution or a workaround plzzzz.<br>
<br>
does anyone know of other profiling tools that work well with gromacs?<br>
<br>
thank you in advance <br>
<br>
regards <br>
ganapathy senthilkumar </div>