Sai Pooja wrote:
Hi,
I am running a very short md run for 100 steps and I get the Infinite
giga flopses error. I stored info at every step to check if the
simulation is running. And the log file has all the variables for each
time-step with reasonable values. I don't understand the meaning of the
message at the end of the log file.
nodetime = 0! Infinite Giga flopses!
Finished mdrun on node 0 Tue Jun 8 10:16:31 2010
This is not the first time I have encountered this problem with short md
runs.
This isn't really a "problem," per se. Gromacs is fast. If you look at the
benchmarks in the Gromacs 4 paper, you can get several hundred steps of MD per
second for a relatively small system. So essentially your run probably finished
in less than a second, and mdrun recorded that as "zero" time. Division by zero
= infinite performance :)
If you think there's something else actually wrong, please at least provide a
description of how large your system is, how long the run actually took to
complete, if you're running in parallel, etc.
-Justin
Parameter file
; VARIOUS PREPROCESSING OPTIONS
title =NPT simulation for a 2D WCA system
cpp =/lib/cpp
; RUN CONTROL PARAMETERS
integrator = md
dt = 0.0001
nsteps = 100
; OUTPUT CONTROL OPTIONS
nstxout = 0 ; No output, except for last frame
(coordinates)
nstvout = 0 ; No output, except for last frame
(velocities)
nstfout = 0 ; No output, except for last frame (forces)
nstlog = 1 ; Write every nth step to the log
nstenergy = 0 ; Write energies at every n step
nstxtcout = 0 ; Do not write a compressed tr
; NEIGHBORSEARCHING PARAMETERS
nstlist = 10
ns-type = Grid
pbc = xyz
rlist = 0.9
; OPTIONS FOR ELECTROSTATICS AND VDW
coulombtype = Cut-off
rcoulomb = 1.1225
vdw-type = Cut-off
rvdw = 1.1225
; Temperature coupling
tcoupl = v-rescale
tc-grps = AR
tau_t = 0.1
ref_t = 0.1
ld_seed =-1
; Pressure coupling
pcoupl = Berendsen
pcoupltype = semiisotropic
tau-p = 0.1 0.1
compressibility = 1e-5 0 ;Dont know
ref-p = 58 0
;Generate velocities for startup run
gen_vel =yes
gen_temp =1
gen_seed =-1
;Non equilibrium MD steps
freezegrps =AR
freezedim =N N Y
Error: At the end of log file
nodetime = 0! Infinite Giga flopses!
Finished mdrun on node 0 Tue Jun 8 10:16:31 2010
Regards
Pooja
--
Quaerendo Invenietis-Seek and you shall discover.
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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