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?
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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