[gmx-users] floating point exception for grompp -e ener.edr on some clusters
chris.neale at utoronto.ca
chris.neale at utoronto.ca
Mon Nov 19 01:25:15 CET 2007
> 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
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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