[gmx-users] floating point exception for grompp -e ener.edr on some clusters
David van der Spoel
spoel at xray.bmc.uu.se
Mon Nov 19 08:26:10 CET 2007
chris.neale at utoronto.ca wrote:
>> Very dificult to debug without access to the machine. It could be due
>> to a weird bug that only shows up with certain compilers or it could
>> be a compiler problem. We have most experience with gcc, and its
>> quirks. Most of the gcc related problems have been worked around. If
>> you can try with a different compiler that would be something to try.
>> Alternative is to compile grompp with CFLAGS=-g and run it in the
>> debugger to see where this happens.
>
> Thanks for the assistance. I will continue to try to get gcc to work for
> me.
>
> I have attempted the CFLAGS=-g (full output at end of email). The error
> message is now:
>
> Program received signal SIGFPE, Arithmetic exception.
> 0x12001449c in do_enx (fp=0, fr=0x12010a9c0) at enxio.c:310
> 310 enxio.c: No such file or directory.
> in enxio.c
Try adding the following in enxio.c at line 305:
for(i=fr->e_alloc; (i<fr->nre); i++) {
fr->ener[i].e = fr->ener[i].eav =
fr->ener[i].esum = fr->ener[i].esum2 = 0;
}
The code should come *in-between* the following two lines:
srenew(fr->ener,fr->nre);
fr->e_alloc = fr->nre;
Alphas are very sensitive about not-initialized variables.
>
> I also tried with CFLAGS=-ggdb but I didn't get any additional
> information about the error.
>
> I have also tried to compile while 'export CC=gcc3' or 'export CC=gcc'
> but I have an error in trxio.c during compilation in both cases:
>
> $ which gcc3
> /usr/bin/gcc3
> $ gcc3 --version
> 3.0.4
>
> $ which gcc
> /usr/bin/gcc
> $ gcc --version
> 2.96
>
> $ tail output.make
> if /bin/sh ../../libtool --tag=CC --mode=compile gcc3 -DHAVE_CONFIG_H
> -I. -I. -I../../src -I/usr/X11R6/include -I../../include
> -DGMXLIBDIR=\"/scratch/cneale/exe/gromacs-3.3.1/exec/share/top\"
> -I/home/cneale/exe/fftw-3.1.2/exec/include -O3 -fomit-frame-pointer
> -finline-functions -Wall -Wno-unused -funroll-all-loops -MT trxio.lo -MD
> -MP -MF ".deps/trxio.Tpo" -c -o trxio.lo trxio.c; \
> then mv -f ".deps/trxio.Tpo" ".deps/trxio.Plo"; else rm -f
> ".deps/trxio.Tpo"; exit 1; fi
> gcc3 -DHAVE_CONFIG_H -I. -I. -I../../src -I/usr/X11R6/include
> -I../../include
> -DGMXLIBDIR=\"/scratch/cneale/exe/gromacs-3.3.1/exec/share/top\"
> -I/home/cneale/exe/fftw-3.1.2/exec/include -O3 -fomit-frame-pointer
> -finline-functions -Wall -Wno-unused -funroll-all-loops -MT trxio.lo -MD
> -MP -MF .deps/trxio.Tpo -c trxio.c -o trxio.o
> trxio.c: In function `read_next_frame':
> trxio.c:690: Internal error: Segmentation fault
>
>
> For reference I have first posted the g_energy output while run under
> gdb and then I have posted the first ~30 lines from the output of the
> configure routine while CC=gcc3
>
> ################################################
>
> $ gdb ../../exe/gromacs-3.3.1/exec/bin/g_energy_debug_gdb
> GNU gdb Red Hat Linux (5.1-4)
> Copyright 2001 Free Software Foundation, Inc.
> GDB is free software, covered by the GNU General Public License, and you
> are
> welcome to change it and/or distribute copies of it under certain
> conditions.
> Type "show copying" to see the conditions.
> There is absolutely no warranty for GDB. Type "show warranty" for details.
> This GDB was configured as "alpha-redhat-linux"...
> (gdb) run -f sys1800_md689.edr
> Starting program:
> /mnt/scratch/cneale/micelle/2huge_16/../../exe/gromacs-3.3.1/exec/bin/g_energy_debug_gdb
> -f sys1800_md689.edr
> :-) G R O M A C S (-:
>
> Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
>
> :-) 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.
>
> :-)
> /mnt/scratch/cneale/micelle/2huge_16/../../exe/gromacs-3.3.1/exec/bin/g_energy_debug_gdb
> (-:
>
> Option Filename Type Description
> ------------------------------------------------------------
> -f sys1800_md689.edr Input Generic energy: edr ene
> -f2 ener.edr Input, Opt. Generic energy: edr ene
> -s topol.tpr Input, Opt. Generic run input: tpr tpb tpa xml
> -o energy.xvg Output xvgr/xmgr file
> -viol violaver.xvg Output, Opt. xvgr/xmgr file
> -pairs pairs.xvg Output, Opt. xvgr/xmgr file
> -ora orienta.xvg Output, Opt. xvgr/xmgr file
> -ort orientt.xvg Output, Opt. xvgr/xmgr file
> -oda orideva.xvg Output, Opt. xvgr/xmgr file
> -odr oridevr.xvg Output, Opt. xvgr/xmgr file
> -odt oridevt.xvg Output, Opt. xvgr/xmgr file
> -oten oriten.xvg Output, Opt. xvgr/xmgr file
> -corr enecorr.xvg Output, Opt. xvgr/xmgr file
> -vis visco.xvg Output, Opt. xvgr/xmgr file
> -ravg runavgdf.xvg Output, Opt. xvgr/xmgr file
>
> Option Type Value Description
> ------------------------------------------------------
> -[no]h bool no Print help info and quit
> -nice int 19 Set the nicelevel
> -b time 0 First frame (ps) to read from trajectory
> -e time 0 Last frame (ps) to read from trajectory
> -[no]w bool no View output xvg, xpm, eps and pdb files
> -[no]xvgr bool yes Add specific codes (legends etc.) in the output
> xvg files for the xmgrace program
> -[no]fee bool no Do a free energy estimate
> -fetemp real 300 Reference temperature for free energy
> calculation
> -zero real 0 Subtract a zero-point energy
> -[no]sum bool no Sum the energy terms selected rather than
> display
> them all
> -[no]dp bool no Print energies in high precision
> -[no]mutot bool no Compute the total dipole moment from the
> components
> -skip int 0 Skip number of frames between data points
> -[no]aver bool no Print also the X1,t and sigma1,t, only if
> only 1
> energy is requested
> -nmol int 1 Number of molecules in your sample: the
> energies
> are divided by this number
> -ndf int 3 Number of degrees of freedom per molecule.
> Necessary for calculating the heat capacity
> -[no]fluc bool no Calculate autocorrelation of energy
> fluctuations
> rather than energy itself
> -[no]orinst bool no Analyse instantaneous orientation data
> -[no]ovec bool no Also plot the eigenvectors with -oten
> -acflen int -1 Length of the ACF, default is half the
> number of
> frames
> -[no]normalize bool yes Normalize ACF
> -P enum 0 Order of Legendre polynomial for ACF (0
> indicates
> none): 0, 1, 2 or 3
> -fitfn enum none Fit function: none, exp, aexp, exp_exp, vac,
> exp5, exp7 or exp9
> -ncskip int 0 Skip N points in the output file of correlation
> functions
> -beginfit real 0 Time where to begin the exponential fit of the
> correlation function
> -endfit real -1 Time where to end the exponential fit of the
> correlation function, -1 is till the end
>
> Opened sys1800_md689.edr as single precision energy file
>
> Select the terms you want from the following list
> -----------------------------------------------------
> Angle Proper-Dih. Ryckaert-Bell. LJ-14 Coulomb-14
> LJ-(SR) LJ-(LR) Coulomb-(SR) Coul.-recip. Potential
> Kinetic-En. Total-Energy Temperature Pressure-(bar) Box-X
> Box-Y Box-Z Volume Density-(SI) pV
> Vir-XX Vir-XY Vir-XZ Vir-YX Vir-YY
> Vir-YZ Vir-ZX Vir-ZY Vir-ZZ Pres-XX-(bar)
> Pres-XY-(bar) Pres-XZ-(bar) Pres-YX-(bar) Pres-YY-(bar) Pres-YZ-(bar)
> Pres-ZX-(bar) Pres-ZY-(bar) Pres-ZZ-(bar) #Surf*SurfTen Pcoupl-Mu-XX
> Pcoupl-Mu-YY Pcoupl-Mu-ZZ Mu-X Mu-Y Mu-Z
> T-DPC T-SOL Lamb-DPC Lamb-SOL
>
> Total-Energy
>
>
> Back Off! I just backed up energy.xvg to ./#energy.xvg.1#
> Reading frame 0 time 35250.000
> Program received signal SIGFPE, Arithmetic exception.
> 0x12001449c in do_enx (fp=0, fr=0x12010a9c0) at enxio.c:310
> 310 enxio.c: No such file or directory.
> in enxio.c
> (gdb)
>
> Note that backtrace does not suggest any additional information. I get
> the seme basic error with grompp -e and g_energy and eneconv.
>
> ##################################################
>
> $ head -30 output.configure
>
> checking build system type... alphaev6-unknown-linux-gnu
> checking host system type... alphaev6-unknown-linux-gnu
> checking for a BSD-compatible install... /usr/bin/install -c
> checking whether build environment is sane... yes
> checking for gawk... gawk
> checking whether make sets $(MAKE)... yes
> checking how to create a ustar tar archive... pax
> checking for C compiler default output file name... a.out
> checking whether the C compiler works... yes
> checking whether we are cross compiling... no
> checking for suffix of executables...
> checking for suffix of object files... o
> checking whether we are using the GNU C compiler... yes
> checking whether gcc3 accepts -g... yes
> checking for gcc3 option to accept ANSI C... none needed
> checking for style of include used by make... GNU
> checking dependency style of gcc3... gcc3
> checking for fort... fort
> checking whether we are using the GNU Fortran 77 compiler... no
> checking whether fort accepts -g... yes
> checking how to get verbose linking output from fort... -v
> checking for Fortran libraries of fort...
> -L/home/cneale/exe/fftw-3.1.2/exec/lib -lUfor -lfor -lFutil -lcpml -lots
> -L/usr/lib/gcc-lib/alpha-redhat-linux/2.96
> -L/usr/lib/gcc-lib/alpha-redhat-linux/2.96/../../..
> checking for dummy main to link with Fortran libraries... none
> checking for Fortran name-mangling scheme... lower case, underscore,
> extra underscore
> checking how to run the C preprocessor... gcc3 -E
> checking whether gcc3 accepts -O3... yes
>
>
> Thanks,
> Chris.
>
>
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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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