[gmx-users] 100 step md run: Infinite giga flopses error

[Sai Pooja]

Thanks Justin. I think you are right. I always encounter this problem with
extremely small runs.

On Tue, Jun 8, 2010 at 11:04 AM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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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-- 
Quaerendo Invenietis-Seek and you shall discover.
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