[gmx-users] "Range checking error" issue
Matteo Guglielmi
matteo.guglielmi at epfl.ch
Sat May 26 20:03:54 CEST 2007
Mark Abraham wrote:
> Matteo Guglielmi wrote:
>> I did what you suggest and even more, I decreased the timestep to 0.001
>>
>> Well the problem doesn't go away.
>>
>> I've been reading mails from this discussion list... I'm not the only
>> who's experiencing this kind of problem (ci variable range error)...
>> actually few gmx users suggest it comes only from parallel runs which
>> is my case BTW.
>
> I've seen it most often when equilibration hasn't happened properly,
> but you'd think 1.5ns would be enough to avoid a crash.
>
>> I'm running parallel runs on different clusters... it's happening
>> everywhere.
>
> Do serial runs do it?
>
> Have you looked at your trajectory visually to see where things start
> going wrong?
>
> Mark
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I did no try any serial run yet... trajectory looks fine... but log
files might explain
why parallel runs keep crashing.
Usually I run gromacs on a dual Xeon 5140 cpus machine (2x2-cores) in
double precision.
I did compile gromacs using the intel compilers - 9.1 series:
[matteo at lcbcpc02 ~]$ icc -V
Intel(R) C Compiler for Intel(R) EM64T-based applications, Version
9.1 Build 20070320 Package ID: l_cc_c_9.1.049
Copyright (C) 1985-2007 Intel Corporation. All rights reserved.
[matteo at lcbcpc02 ~]$ icpc -V
Intel(R) C++ Compiler for Intel(R) EM64T-based applications, Version
9.1 Build 20070320 Package ID: l_cc_c_9.1.049
Copyright (C) 1985-2007 Intel Corporation. All rights reserved.
[matteo at lcbcpc02 ~]$ ifort -V
Intel(R) Fortran Compiler for Intel(R) EM64T-based applications, Version
9.1 Build 20070320 Package ID: l_fc_c_9.1.045
Copyright (C) 1985-2007 Intel Corporation. All rights reserved.
#### compilatition setup detalis ###
export F77='ifort'
export CC='icc'
export CFLAGS='-axT -unroll -ip -O3'
export FFLAGS='-axT -unroll -ip -O3'
export CPPFLAGS="-I${HOME}/Software/fftw-3.1.2/include"
export LDFLAGS="-L${HOME}/Software/fftw-3.1.2/lib"
./configure --enable-double --with-fft=fftw3 --program-suffix=''
--enable-fortran --enable-threads --prefix=${HOME}/Software/gromacs-3.3.1
make
make install
make distclean
./configure --enable-mpi --enable-double --with-fft=fftw3
--program-suffix='' --enable-fortran --enable-threads
--prefix=${HOME}/Software/gromacs-3.3.1
make mdrun
make install-mdrun
#################################
I use openMPI 1.2.1 which was compiled with the same intel compilers
I've shown before.
All my systems were pre-geometry optimized:
emtol = 70
integrator = steep
constraints = none
#### md0.log ###
[matteo at lcbcpc02 ~]$ cat md0.log | grep Grid
ns_type = Grid
Grid: 10 x 12 x 13 cells
#### md1.log ###
[matteo at lcbcpc02 ~]$ cat md1.log | grep Grid
Grid: 10 x 12 x 13 cells
Grid: 10 x 12 x 12 cells
[matteo at lcbcpc02 ~]$ tail -40 md1.log
Rel. Constraint Deviation: Max between atoms RMS
Before LINCS 0.009211 7638 7640 0.001295
After LINCS 0.000000 10707 10709 0.000000
Rel. Constraint Deviation: Max between atoms RMS
Before LINCS 0.008704 9341 9344 0.001308
After LINCS 0.000000 12623 12625 0.000000
Rel. Constraint Deviation: Max between atoms RMS
Before LINCS 0.009517 8162 8163 0.001276
After LINCS 0.000000 8355 8357 0.000000
Rel. Constraint Deviation: Max between atoms RMS
Before LINCS 0.009805 7638 7640 0.001325
After LINCS 0.000000 10207 10210 0.000000
Rel. Constraint Deviation: Max between atoms RMS
Before LINCS 0.009253 12747 12750 0.001259
After LINCS 0.000000 8377 8379 0.000000
Grid: 10 x 12 x 12 cells
-------------------------------------------------------
Program mdrun_mpi, VERSION 3.3.1
Source code file: nsgrid.c, line: 226
Range checking error:
Explanation: During neighborsearching, we assign each particle to a grid
based on its coordinates. If your system contains collisions or parameter
errors that give particles very high velocities you might end up with some
coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot
put these on a grid, so this is usually where we detect those errors.
Make sure your system is properly energy-minimized and that the potential
energy seems reasonable before trying again.
Variable ci has value 1476. It should have been within [ 0 .. 1440 ]
Please report this to the mailing list (gmx-users at gromacs.org)
-------------------------------------------------------
"Ease Myself Into the Body Bag" (P.J. Harvey)
#########################
The same holds for md2.log and md3.log!
So... the grid size seems to move from:
10 x 12 x 13 (=1560)
to:
10 x 12 x 12 (=1440)
putting "Variable ci has value 1476..." out of bounds.
Is it normal?
Any help is greatly appreciated,
MG.
### Full input file #####
; PREPROCESSING
title = 2masn
cpp = /usr/bin/cpp
;include = -I./
define = -DPOSRES
; RUN CONTROL
integrator = md
tinit = 0
dt = 0.001
nsteps = 1500000
init_step = 0
comm_mode = Angular
nstcomm = 1
comm_grps = Pore
; ENERGY MINIMIZATION
;emtol = 100
;emstep = 0.01
; OUTPUT CONTROL
nstxout = 500000
nstvout = 500000
nstfout = 500000
nstcheckpoint = 1000
nstlog = 5000
nstxtcout = 5000
xtc_grps = System
energygrps = Pore Membrane Ions Water
nstenergy = 5000
; NEIGHBOR SEARCHING
nstlist = 5
ns_type = grid
pbc = xyz
rlist = 1.0
; ELECTROSTATICS
coulombtype = PME
rcoulomb = 1.0
; VDW
vdwtype = Cut-off
rvdw = 1.4
; EWALD
fourierspacing = 0.09
fourier_nx =
fourier_ny =
fourier_nz =
pme_order = 4
ewald_rtol = 1e-5
ewald_geometry = 3d
optimize_fft = yes
; TEMPERATURE COUPLING
tcoupl = berendsen
tc_grps = Solute Solvent
tau_t = 0.1 0.4
ref_t = 300 300
; PRESSURE COUPLING
pcoupl = berendsen
pcoupltype = anisotropic
tau_p = 5.0 5.0 5.0 5.0 5.0 5.0
compressibility = 4.53e-5 4.53e-5 4.53e-5 0.0 0.0 0.0
ref_p = 1.025 1.025 1.025 1.025 1.025 1.025
; SIMULATED ANNEALING
;annealing = single single
;annealing_npoints = 2 2
;annealing_time = 0 500 0 500
;annealing_temp = 200 300 200 300
; VELOCITY GENERATION
gen_vel = yes
gen_temp = 300
gen_seed = 173529
; BONDS
constraints = hbonds
constraint_algorithm = lincs
unconstrained_start = no
lincs_order = 4
lincs_iter = 2
lincs_warnangle = 30
#############################
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