[gmx-users] floating point exception for grompp -e ener.edr on some clusters
David van der Spoel
spoel at xray.bmc.uu.se
Fri Nov 16 08:54:20 CET 2007
chris.neale at utoronto.ca wrote:
> Hello,
>
> I continue to have difficulties with my newest gromacs compilation
> (3.3.1). The errors that I report here are entirely absent from other
> clusters on which I have compiled gromacs.
>
> The error now is in grompp and looks like this:
> Opened sys1800_md689.edr as single precision energy file
> Reading frame 0 time 35250.000 Floating point exception
> (core dumped)
>
> Everything works fine if I remove the -e x.edr from the grompp command.
> If I copy all files over to a different cluster and run the original
> command there is no error so this is compilation dependent.
>
> Does anybody have any insight into why I would have this particular
> problem on one installation and not on another?
>
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.
> gmxcheck on the .edr file indicated that it is fine.
>
> Thanks,
> Chris.
>
> ###
>
> here is the entire output:
>
> $ /scratch/cneale/exe/gromacs-3.3.1/exec/bin/grompp -f sys1800_md690.mdp
> -c sys1800_md689_deshuffleddesorted.gro -t
> sys1800_md689_reshuffleresort.trr -p sys1800.top -n sys1800.ndx -deshuf
> deshuffle_md690.ndx -e sys1800_md689.edr -o sys1800_md690.tpr
> :-) G R O M A C S (-:
>
> God Rules Over Mankind, Animals, Cosmos and Such
>
> :-) 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.
>
> :-) /scratch/cneale/exe/gromacs-3.3.1/exec/bin/grompp (-:
>
> Option Filename Type Description
> ------------------------------------------------------------
> -f sys1800_md690.mdp Input, Opt! grompp input file with MD parameters
> -po mdout.mdp Output grompp input file with MD parameters
> -c sys1800_md689_deshuffleddesorted.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 sys1800.ndx Input, Opt! Index file
> -deshufshuffle_md690.ndx Output, Opt! Index file
> -p sys1800.top Input Topology file
> -pp processed.top Output, Opt. Topology file
> -o sys1800_md690.tpr Output Generic run input: tpr tpb tpa xml
> -t sys1800_md689_reshuffleresort.trr Input, Opt! Full precision
> trajectory: trr trj
> -e sys1800_md689.edr Input, Opt! Generic energy: edr ene
>
> Option Type Value Description
> ------------------------------------------------------
> -[no]h bool no Print help info and quit
> -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...
>
> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.4#
> checking input for internal consistency...
> calling cpp...
> processing topology...
> Generated 344865 of the 344865 non-bonded parameter combinations
> Generating 1-4 interactions: fudge = 0.5
> Generated 344761 of the 344865 1-4 parameter combinations
> Excluding 3 bonded neighbours for DPC 1800
> turning all bonds into constraints...
> Excluding 2 bonded neighbours for SOL 224404
> turning all bonds into constraints...
> processing coordinates...
> double-checking input for internal consistency...
> Cleaning up constraints and constant bonded interactions with virtual sites
> renumbering atomtypes...
> converting bonded parameters...
> # ANGLES: 48600
> # PDIHS: 16200
> # RBDIHS: 16200
> # LJ14: 46800
> # CONSTR: 39600
> # SETTLE: 224404
> # VSITE3: 224404
> Setting particle type to V for virtual sites
> Walking down the molecule graph to make shake-blocks
> initialising group options...
> processing index file...
> Making dummy/rest group for Acceleration containing 939016 elements
> Making dummy/rest group for Freeze containing 939016 elements
> Making dummy/rest group for Energy Mon. containing 939016 elements
> Number of degrees of freedom in T-Coupling group DPC is 84599.82
> Number of degrees of freedom in T-Coupling group SOL is 1346421.12
> Making dummy/rest group for User1 containing 939016 elements
> Making dummy/rest group for User2 containing 939016 elements
> Making dummy/rest group for XTC containing 939016 elements
> Making dummy/rest group for Or. Res. Fit containing 939016 elements
> Making dummy/rest group for QMMM containing 939016 elements
> T-Coupling has 2 element(s): DPC SOL
> Energy Mon. has 1 element(s): rest
> Acceleration has 1 element(s): rest
> Freeze has 1 element(s): rest
> User1 has 1 element(s): rest
> User2 has 1 element(s): rest
> VCM has 1 element(s): System
> XTC has 1 element(s): rest
> Or. Res. Fit has 1 element(s): rest
> QMMM has 1 element(s): rest
> Checking consistency between energy and charge groups...
> getting data from old trajectory ...
> Reading Coordinates, Velocities and Box size from old trajectory
> Will read whole trajectory
> trn version: GMX_trn_file (single precision)
> Last frame 1 time 35300.000
> Using frame at t = 35300 ps
> Starting time for run is 35300 ps
> Opened sys1800_md689.edr as single precision energy file
> Reading frame 0 time 35250.000 Floating point exception
> (core dumped)
>
>
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--
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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