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

Erik Lindahl erik.lindahl at gmail.com
Thu Mar 1 21:57:34 CET 2018

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.



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
Science for Life Laboratory, Box 1031, 17121 Solna, Sweden
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