Thanks Justin. I think you are right. I always encounter this problem with extremely small runs.<br><br><div class="gmail_quote">On Tue, Jun 8, 2010 at 11:04 AM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><div class="im"><br>
<br>
Sai Pooja wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi,<br>
<br>
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. <br>
nodetime = 0! Infinite Giga flopses!<br>
Finished mdrun on node 0 Tue Jun 8 10:16:31 2010<br>
<br>
This is not the first time I have encountered this problem with short md runs.<br>
<br>
</blockquote>
<br></div>
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 :)<br>
<br>
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.<br><font color="#888888">
<br>
-Justin</font><div><div></div><div class="h5"><br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Parameter file<br>
<br>
; VARIOUS PREPROCESSING OPTIONS title =NPT simulation for a 2D WCA system<br>
cpp =/lib/cpp<br>
<br>
; RUN CONTROL PARAMETERS<br>
integrator = md<br>
dt = 0.0001<br>
nsteps = 100<br>
<br>
; OUTPUT CONTROL OPTIONS<br>
nstxout = 0 ; No output, except for last frame (coordinates)<br>
nstvout = 0 ; No output, except for last frame (velocities)<br>
nstfout = 0 ; No output, except for last frame (forces)<br>
nstlog = 1 ; Write every nth step to the log<br>
nstenergy = 0 ; Write energies at every n step<br>
nstxtcout = 0 ; Do not write a compressed tr<br>
<br>
; NEIGHBORSEARCHING PARAMETERS<br>
nstlist = 10<br>
ns-type = Grid<br>
pbc = xyz<br>
rlist = 0.9<br>
<br>
; OPTIONS FOR ELECTROSTATICS AND VDW<br>
coulombtype = Cut-off<br>
rcoulomb = 1.1225<br>
vdw-type = Cut-off<br>
rvdw = 1.1225<br>
<br>
; Temperature coupling<br>
tcoupl = v-rescale<br>
tc-grps = AR<br>
tau_t = 0.1<br>
ref_t = 0.1<br>
ld_seed =-1<br>
<br>
; Pressure coupling<br>
pcoupl = Berendsen<br>
pcoupltype = semiisotropic<br>
tau-p = 0.1 0.1<br>
compressibility = 1e-5 0 ;Dont know<br>
ref-p = 58 0<br>
<br>
<br>
;Generate velocities for startup run<br>
gen_vel =yes<br>
gen_temp =1<br>
gen_seed =-1<br>
<br>
;Non equilibrium MD steps<br>
freezegrps =AR<br>
freezedim =N N Y<br>
<br>
Error: At the end of log file<br>
<br>
nodetime = 0! Infinite Giga flopses!<br>
Finished mdrun on node 0 Tue Jun 8 10:16:31 2010<br>
<br>
<br>
Regards<br>
Pooja<br>
<br>
-- <br>
Quaerendo Invenietis-Seek and you shall discover.<br>
<br>
</blockquote>
<br></div></div><div class="im">
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
========================================<br>
-- <br></div><div><div></div><div class="h5">
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</div></div></blockquote></div><br><br clear="all"><br>-- <br>Quaerendo Invenietis-Seek and you shall discover.<br>