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

[Berk Hess]

Hi,

state->natoms is the count. But note that this will not match the 
topology when you are using domain decomposition.

In your case it looks like the mismatch is due to padding for SIMD 
operations. The extra elements will not be used to generate results.

Cheers,

Berk

On 03/01/2018 10:04 PM, Sanyam Kapoor wrote:
> @Mark Sorry to have left the version information out. I'm currently 
> pinned to version *v2018*.
>
> @Erik I can't seem to find another count variable. Do you mind 
> pointing me to it? Also, just to put it out, I'm trying to inspect 
> this after the threads have been joined (right before the return). Is 
> there a way for me to find one-to-one correspondence between the atom 
> number and this state structure?
>
> Thank you so much for the prompt responses!
>
> On Thu, Mar 1, 2018 at 3:59 PM Mark Abraham <mark.j.abraham at gmail.com 
> <mailto:mark.j.abraham at gmail.com>> wrote:
>
>     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 <mailto: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
>         <mailto: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
>
>             --
>             Gromacs Developers mailing list
>
>             * Please search the archive at
>             http://www.gromacs.org/Support/Mailing_Lists/GMX-developers_List
>             before posting!
>
>             * Can't post? Read
>             http://www.gromacs.org/Support/Mailing_Lists
>
>             * For (un)subscribe requests visit
>             https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-developers
>             or send a mail to gmx-developers-request at gromacs.org
>             <mailto:gmx-developers-request at gromacs.org>.
>
>
>
>
>         -- 
>         Erik Lindahl <erik.lindahl at dbb.su.se
>         <mailto:erik.lindahl at dbb.su.se>>
>         Professor of Biophysics, Dept. Biochemistry & Biophysics,
>         Stockholm University
>         Science for Life Laboratory, Box 1031, 17121 Solna, Sweden
>         --
>         Gromacs Developers mailing list
>
>         * Please search the archive at
>         http://www.gromacs.org/Support/Mailing_Lists/GMX-developers_List
>         before posting!
>
>         * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
>         * For (un)subscribe requests visit
>         https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-developers
>         or send a mail to gmx-developers-request at gromacs.org
>         <mailto:gmx-developers-request at gromacs.org>.
>
>     --
>     Gromacs Developers mailing list
>
>     * Please search the archive at
>     http://www.gromacs.org/Support/Mailing_Lists/GMX-developers_List
>     before posting!
>
>     * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
>     * For (un)subscribe requests visit
>     https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-developers
>     or send a mail to gmx-developers-request at gromacs.org
>     <mailto:gmx-developers-request at gromacs.org>.
>
> -- 
> Regards,
> Sanyam Kapoor
> Masters in Computer Science
> Courant Institute, New York University
> https://www.sanyamkapoor.com
>
>

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-developers/attachments/20180301/dd4dfab7/attachment-0001.html>