<div dir="ltr">Thank you so much everyone!</div><br><div class="gmail_quote"><div dir="ltr">On Thu, Mar 1, 2018 at 4:23 PM Erik Lindahl &lt;<a href="mailto:erik.lindahl@gmail.com">erik.lindahl@gmail.com</a>&gt; wrote:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Exactly.<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 10:20 PM, Sanyam Kapoor <span dir="ltr">&lt;<a href="mailto:sanyam@nyu.edu" target="_blank">sanyam@nyu.edu</a>&gt;</span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div>That is right. It is the PaddedRVecVectors.</div><div><br></div>Just to clarify if I understand correctly, I can safely use the first <b>natoms</b> positions from the PaddedRVecVectors without worrying about the rest. Is that correct?</div><div class="m_-201586047408431528HOEnZb"><div class="m_-201586047408431528h5"><br><div class="gmail_quote"><div dir="ltr">On Thu, Mar 1, 2018 at 4:11 PM Berk Hess &lt;<a href="mailto:hess@kth.se" target="_blank">hess@kth.se</a>&gt; wrote:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
  
    
  
  <div text="#000000" bgcolor="#FFFFFF">
    <div class="m_-201586047408431528m_2016350812731892465m_-23557831742712923moz-cite-prefix">Hi,<br>
      <br>
      state-&gt;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</div></div><div text="#000000" bgcolor="#FFFFFF"><div class="m_-201586047408431528m_2016350812731892465m_-23557831742712923moz-cite-prefix"><br>
      <br>
      On 03/01/2018 10:04 PM, Sanyam Kapoor wrote:<br>
    </div></div><div text="#000000" bgcolor="#FFFFFF">
    <blockquote type="cite">
      
      <div dir="ltr">@Mark Sorry to have left the version information
        out. I&#39;m currently pinned to version <b>v2018</b>.
        <div><br>
        </div>
        <div>@Erik I can&#39;t seem to find another count variable. Do you
          mind pointing me to it? Also, just to put it out, I&#39;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
              &lt;<a href="mailto:mark.j.abraham@gmail.com" target="_blank">mark.j.abraham@gmail.com</a>&gt;
              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 &lt;<a href="mailto:erik.lindahl@gmail.com" target="_blank">erik.lindahl@gmail.com</a>&gt;
                  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">&lt;<a href="mailto:sanyam@nyu.edu" target="_blank">sanyam@nyu.edu</a>&gt;</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&#39;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_-201586047408431528m_2016350812731892465m_-23557831742712923m_1224751365729588764m_-2800472018907322967HOEnZb"><font color="#888888">-- <br>
                            <div dir="ltr" class="m_-201586047408431528m_2016350812731892465m_-23557831742712923m_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>
                          </font></span><br>
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                    </div>
                    <br>
                    <br clear="all">
                    <div><br>
                    </div>
                  </div>
                  <div class="gmail_extra">-- <br>
                    <div class="m_-201586047408431528m_2016350812731892465m_-23557831742712923m_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 &lt;<a href="mailto:erik.lindahl@dbb.su.se" target="_blank">erik.lindahl@dbb.su.se</a>&gt;</div>
                                    <div>Professor of Biophysics, Dept.
                                      Biochemistry &amp; Biophysics,
                                      Stockholm University</div>
                                    <div>Science for Life Laboratory,
                                      Box 1031, 17121 Solna, Sweden</div>
                                  </div>
                                </div>
                              </div>
                            </div>
                          </div>
                        </div>
                      </div>
                    </div>
                  </div>
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      -- <br>
      <div dir="ltr" class="m_-201586047408431528m_2016350812731892465m_-23557831742712923gmail_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>
      <br>
      <fieldset class="m_-201586047408431528m_2016350812731892465m_-23557831742712923mimeAttachmentHeader"></fieldset>
      <br>
    </blockquote>
    <br>
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