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

[Erik Lindahl]

Exactly.

Cheers,

Erik

On Thu, Mar 1, 2018 at 10:20 PM, Sanyam Kapoor <sanyam at nyu.edu> wrote:

> That is right. It is the PaddedRVecVectors.
>
> Just to clarify if I understand correctly, I can safely use the first
> *natoms* positions from the PaddedRVecVectors without worrying about the
> rest. Is that correct?
>
> On Thu, Mar 1, 2018 at 4:11 PM Berk Hess <hess at kth.se> wrote:
>
>> 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>
>> 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>
>>> 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
>>>>>
>>>>> --
>>>>> 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.
>>>>>
>>>>
>>>>
>>>>
>>>> --
>>>> 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
>>>> --
>>>> 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.
>>>
>>> --
>>> 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.
>>
>> --
>> 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.
>
> --
> 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.
>



-- 
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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-developers/attachments/20180301/86b20046/attachment.html>