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

Thu Mar 1 22:24:24 CET 2018

Thank you so much everyone!

On Thu, Mar 1, 2018 at 4:23 PM Erik Lindahl <erik.lindahl at gmail.com> wrote:

> 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
>>>>>>
>>>>>> --
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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
>>>>> --
>>>>> Gromacs Developers mailing list
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>>>>
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>>>
>>> --
>>> Regards,
>>> Sanyam Kapoor
>>> Masters in Computer Science
>>> Courant Institute, New York University
>>> https://www.sanyamkapoor.com
>>>
>>>
>>>
>>> --
>>> Gromacs Developers mailing list
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>>
>> --
>> Regards,
>> Sanyam Kapoor
>> Masters in Computer Science
>> Courant Institute, New York University
>> https://www.sanyamkapoor.com
>>
>> --
>> Gromacs Developers mailing list
>>
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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
> --
> Gromacs Developers mailing list
>
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-- 
Regards,
Sanyam Kapoor
Masters in Computer Science
Courant Institute, New York University
https://www.sanyamkapoor.com
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