[gmx-users] Reducing Standard Error output

[Jack Shultz]

Thanks,

I just figured out removing the -v will reduce output. Interestingly I
only have this problem with 64-bit Windows hosts. I have not observed
it in any others and I have a fairly diverse environment on this
project. For now I can say removing the -v gets the app to finish the
run.

Jack

On Thu, Dec 3, 2009 at 10:36 AM, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:
> Hi Jack,
>
> The option -v is for verbose output.
> The LINCS warnings may indicate an issue regarding the stability of
> your system. They usually precede crashes. Maybe you need to
> equilibrate a bit further.
>
> Hope it helps,
>
> Tsjerk
>
> On Thu, Dec 3, 2009 at 1:26 PM, Jack Shultz <js at drugdiscoveryathome.com> wrote:
>> Our first run typically produces this output
>>
>> Getting Loaded...
>> Reading file md.tpr, VERSION 4.0.5 (single precision)
>> Loaded with Money
>>
>> starting mdrun 'Protein in water'
>> 500 steps,      1.0 ps.
>>
>> step 0
>> step 100, remaining runtime:    95 s          Fraction complete: 0.2
>>
>> step 200, remaining runtime:    70 s          Fraction complete: 0.4
>>
>> step 300, remaining runtime:    46 s          Fraction complete: 0.6
>>
>> step 400, remaining runtime:    23 s          Fraction complete: 0.8
>>
>> Writing final coordinates.
>>
>> step 500, remaining runtime:     0 s          Fraction complete: 1
>>
>>        Parallel run - timing based on wallclock.
>>
>>               NODE (s)   Real (s)      (%)
>>       Time:    119.000    119.000    100.0
>>                       1:59
>>               (Mnbf/s)   (GFlops)   (ns/day)  (hour/ns)
>> Performance:     55.372      3.138      0.728     32.990
>>
>> gcq#0: Thanx for Using GROMACS - Have a Nice Day
>>
>>
>> For our project's workflow we are extending the simulations using
>> these arguments,
>> -v -x -c -o -e -cpo next.cpt -cpi md.cpt -deffnm md
>>
>> but I notice there is much more standard error output than I was
>> expecting, in addition to a LINCS WARNING. Should I be worried about
>> that warning?
>> Is there a way we can turn off these error reports for each timestep?
>>
>> Step 785, time 1.57 (ps)  LINCS WARNING
>> relative constraint deviation after LINCS:
>> rms 0.051275, max 3.234419 (between atoms 2396 and 2397)
>> bonds that rotated more than 30 degrees:
>>  atom 1 atom 2  angle  previous, current, constraint length
>>   2396   2397  103.7    0.0973   0.4065      0.0960
>>
>> Step 786, time 1.572 (ps)  LINCS WARNING
>> relative constraint deviation after LINCS:
>> rms 0.000031, max 0.001926 (between atoms 2396 and 2397)
>> bonds that rotated more than 30 degrees:
>>  atom 1 atom 2  angle  previous, current, constraint length
>>   2396   2397   69.5    0.4065   0.0962      0.0960
>>
>>
>> --
>> Jack
>>
>> http://drugdiscoveryathome.com
>> http://hydrogenathome.org
>> --
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>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
> Computational Chemist
> Medicinal Chemist
> Neuropharmacologist
> --
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-- 
Jack

http://drugdiscoveryathome.com
http://hydrogenathome.org