[gmx-developers] Understanding disparity in field values of "t_state" class

[Mark Abraham]

Hi,

What Erik said, plus also this behaviour varies whether there is more than
one rank, whether there are virtual sites, and with GROMACS version.

Mark

On Thu, Mar 1, 2018 at 9:57 PM Erik Lindahl <erik.lindahl at gmail.com> wrote:

> Hi Sanyam,
>
> Not entirely sure what your debugger reports, but it is likely due either
> to padding (which we do to avoid false sharing between threads), or
> over-allocation (which we do to avoid repeatedly re-allocating and freeing
> memory when particles drift between nodes during domain decomposition).
>
> This is also why we have separate fields to keep track of the number of
> atoms vs. the number of allocated entries.
>
> Cheers,
>
> Erik
>
> On Thu, Mar 1, 2018 at 9:52 PM, Sanyam Kapoor <sanyam at nyu.edu> wrote:
>
>> Hello everyone,
>>
>> I was trying to understand fields in the t_state class and it looks like
>> there is some disparity during the run which I cannot make sense of. I ran
>> the code for two topologies experiments with the following arguments
>>
>> mdrun -s m.tpr -rerun m.gro -e m.edr -g m.log
>>
>> 1. A topology which had *1960 atoms *but the *fields for coordinates (x)
>> and velocities (v) had 1968* items.
>> 2. A topology which had *1793 atoms *but the *fields for coordinates (x)
>> and velocities (v) had 1808* items.
>>
>> These numbers that I am reporting have been retrieved while debugging for
>> the fields natoms, x and v of t_state.
>>
>> The comments for t_state state that the lists should have been of the
>> same size as number of atoms. However this doesn't seem to be the case.
>> Could somebody verify if this is expected? If yes, why so?
>>
>> Thank you!
>> --
>> Regards,
>> Sanyam Kapoor
>> Masters in Computer Science
>> Courant Institute, New York University
>> https://www.sanyamkapoor.com
>>
>> --
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>
>
>
> --
> Erik Lindahl <erik.lindahl at dbb.su.se>
> Professor of Biophysics, Dept. Biochemistry & Biophysics, Stockholm
> University
> Science for Life Laboratory, Box 1031, 17121 Solna, Sweden
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