<div dir="ltr">If you are on release-2018 I think you have the PaddedRVecVectors, and then it is handled by hiding the allocation size inside the class.<div><br></div><div>Note that the exact size of the *allocation* is not relevant to determine a unique physical *state* for your system. The extra positions are not used, it's merely an optimization to make the memory behave better. The physics will be the same even if we restore the state to another structure without, or with different, padding.</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 10:04 PM, Sanyam Kapoor <span dir="ltr"><<a 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">@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!<div><div class="h5"><br><br><div class="gmail_quote"><div dir="ltr">On Thu, Mar 1, 2018 at 3:59 PM Mark Abraham <<a href="mailto:mark.j.abraham@gmail.com" target="_blank">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 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"></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 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_-8147218920324783739m_1224751365729588764m_-2800472018907322967HOEnZb"><font color="#888888">-- <br><div dir="ltr" class="m_-8147218920324783739m_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 href="https://www.sanyamkapoor.com" target="_blank">https://www.sanyamkapoor.com</a></div>
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