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<div class="moz-cite-prefix">Hi,<br>
<br>
state->natoms is the count. But note that this will not match
the topology when you are using domain decomposition.<br>
<br>
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.<br>
<br>
Cheers,<br>
<br>
Berk<br>
<br>
On 03/01/2018 10:04 PM, Sanyam Kapoor wrote:<br>
</div>
<blockquote
cite="mid:CAPRc5XeLXk372Nm3FWRYdpM0RgBPZLakZOsOF3-X6-1vBXzHcA@mail.gmail.com"
type="cite">
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<div dir="ltr">@Mark Sorry to have left the version information
out. I'm currently pinned to version <b>v2018</b>.
<div><br>
</div>
<div>@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?</div>
<div><br>
</div>
<div>Thank you so much for the prompt responses!<br>
<br>
<div class="gmail_quote">
<div dir="ltr">On Thu, Mar 1, 2018 at 3:59 PM Mark Abraham
<<a moz-do-not-send="true"
href="mailto:mark.j.abraham@gmail.com">mark.j.abraham@gmail.com</a>>
wrote:<br>
</div>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr">Hi,
<div><br>
</div>
<div>What Erik said, plus also this behaviour varies
whether there is more than one rank, whether there are
virtual sites, and with GROMACS version.</div>
</div>
<div dir="ltr">
<div><br>
</div>
<div>Mark</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr">On Thu, Mar 1, 2018 at 9:57 PM Erik
Lindahl <<a moz-do-not-send="true"
href="mailto:erik.lindahl@gmail.com" target="_blank">erik.lindahl@gmail.com</a>>
wrote:<br>
</div>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr">Hi Sanyam,
<div><br>
</div>
<div>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).</div>
<div><br>
</div>
<div>This is also why we have separate fields to
keep track of the number of atoms vs. the number
of allocated entries.</div>
<div><br>
</div>
<div>Cheers,</div>
<div><br>
</div>
<div>Erik</div>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On Thu, Mar 1, 2018 at 9:52
PM, Sanyam Kapoor <span dir="ltr"><<a
moz-do-not-send="true"
href="mailto:sanyam@nyu.edu" target="_blank">sanyam@nyu.edu</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0
0 .8ex;border-left:1px #ccc
solid;padding-left:1ex">
<div dir="ltr">Hello everyone,
<div><br>
</div>
<div>I was trying to understand fields in the
<font face="monospace">t_state</font> 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</div>
<div><br>
</div>
<div><font face="monospace">mdrun -s m.tpr
-rerun m.gro -e m.edr -g m.log</font></div>
<div><br>
</div>
<div>1. A topology which had <b>1960 atoms </b>but
the <b>fields for coordinates (x) and
velocities (v) had 1968</b> items.</div>
<div>2. A topology which had <b>1793 atoms </b>but
the <b>fields for coordinates (x) and
velocities (v) had 1808</b> items.</div>
<div><br>
</div>
<div>These numbers that I am reporting have
been retrieved while debugging for the
fields <font face="monospace">natoms</font>,
<font face="monospace">x</font> and <font
face="monospace">v</font> of <font
face="monospace">t_state</font>.</div>
<div><br>
</div>
<div>The comments for <span
style="font-family:monospace">t_state</span> 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?</div>
<div><br>
</div>
<div>Thank you!</div>
</div>
<span
class="m_1224751365729588764m_-2800472018907322967HOEnZb"><font
color="#888888">-- <br>
<div dir="ltr"
class="m_1224751365729588764m_-2800472018907322967m_7924609721254566729gmail_signature"
data-smartmail="gmail_signature">Regards,<br>
Sanyam Kapoor<br>
Masters in Computer Science<br>
Courant Institute, New York University<br>
<a moz-do-not-send="true"
href="https://www.sanyamkapoor.com"
target="_blank">https://www.sanyamkapoor.com</a></div>
</font></span><br>
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<div class="gmail_extra">-- <br>
<div
class="m_1224751365729588764m_-2800472018907322967gmail_signature"
data-smartmail="gmail_signature">
<div dir="ltr">
<div>
<div dir="ltr">
<div>
<div dir="ltr">
<div>
<div dir="ltr">
<div>Erik Lindahl <<a
moz-do-not-send="true"
href="mailto:erik.lindahl@dbb.su.se"
target="_blank">erik.lindahl@dbb.su.se</a>></div>
<div>Professor of Biophysics, Dept.
Biochemistry & Biophysics,
Stockholm University</div>
<div>Science for Life Laboratory,
Box 1031, 17121 Solna, Sweden</div>
</div>
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</div>
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-- <br>
<div dir="ltr" class="gmail_signature"
data-smartmail="gmail_signature">Regards,<br>
Sanyam Kapoor<br>
Masters in Computer Science<br>
Courant Institute, New York University<br>
<a moz-do-not-send="true" href="https://www.sanyamkapoor.com">https://www.sanyamkapoor.com</a></div>
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