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    <div class="moz-cite-prefix">Yes, it will still take very long.<br>
      <br>
      Supporting more than 2^31 total eigenvector elements requires code
      changes through all our matrix and I/O routines. I don't think
      this is worth the effort with the current diagonalization times.
      If we add OpenMP parallelization, we can reconsider doing this.<br>
      For now I will add checks that ensure we don't ask for more than
      2^31 matrix or eigenvector elements.<br>
      <br>
      Cheers,<br>
      <br>
      Berk<br>
      <br>
      On 2016-07-05 14:36, Adrien Nicolaï wrote:<br>
    </div>
    <blockquote
      cite="mid:14190B95-5A50-4EFE-97AE-29B9879099D0@u-bourgogne.fr"
      type="cite">
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      Dear Berk,
      <div class=""><br class="">
      </div>
      <div class="">Yes I changed the default value from 50 to 3N
        because I need all the modes for further analyses. And it looks
        like it’s still taking “forever” to get the 50 first modes
        diagonalised...</div>
      <div class=""><br class="">
      </div>
      <div class="">Best,</div>
      <div class=""><br class="">
      </div>
      <div class="">
        <div class="">
          <div style="color: rgb(0, 0, 0); letter-spacing: normal;
            orphans: auto; text-align: start; text-indent: 0px;
            text-transform: none; white-space: normal; widows: auto;
            word-spacing: 0px; -webkit-text-stroke-width: 0px;
            word-wrap: break-word; -webkit-nbsp-mode: space;
            -webkit-line-break: after-white-space;" class="">
            <div style="color: rgb(0, 0, 0); letter-spacing: normal;
              orphans: auto; text-align: start; text-indent: 0px;
              text-transform: none; white-space: normal; widows: auto;
              word-spacing: 0px; -webkit-text-stroke-width: 0px;
              word-wrap: break-word; -webkit-nbsp-mode: space;
              -webkit-line-break: after-white-space;" class="">
              <div class="">
                <div style="margin: 0px; font-family: Menlo;" class="">************************************************************</div>
                <div style="margin: 0px; font-family: Menlo;" class="">Adrien
                  Nicolaï / Maître de conférences</div>
                <div style="margin: 0px; font-family: Menlo;" class="">Laboratoire
                  Interdisciplinaire Carnot de Bourgogne, UMR 6303 CNRS</div>
                <div style="margin: 0px; font-family: Menlo;" class="">Département
                  NANO - Equipe Physique appliquée aux protéines</div>
                <div style="margin: 0px; font-family: Menlo;" class="">Université
                  de Bourgogne Franche-Comté / Faculté des Sciences et
                  Techniques Mirande</div>
                <div style="margin: 0px; font-family: Menlo;" class="">9,
                  Av. Savary - B.P. 47 870 21078. DIJON CEDEX - France</div>
                <div style="margin: 0px; font-family: Menlo;" class="">Email
                  : <a moz-do-not-send="true"
                    href="mailto:adrien.nicolai@u-bourgogne.fr" class="">adrien.nicolai@u-bourgogne.fr</a></div>
                <div style="margin: 0px; font-family: Menlo;" class="">Tél:
                  03 80 39 60 93</div>
                <div style="margin: 0px; font-family: Menlo;" class="">URL
                  : <a moz-do-not-send="true"
href="https://icb.u-bourgogne.fr/fr/axes-scientifiques/nano/physique-appliquee-aux-proteines.html"
                    class="">https://icb.u-bourgogne.fr/fr/axes-scientifiques/nano/physique-appliquee-aux-proteines.html</a></div>
                <div style="margin: 0px; font-family: Menlo;" class="">************************************************************</div>
              </div>
            </div>
          </div>
        </div>
        <br class="">
        <div>
          <blockquote type="cite" class="">
            <div class="">On 05 Jul 2016, at 14:26, Berk Hess &lt;<a
                moz-do-not-send="true" href="mailto:hess@kth.se"
                class=""><a class="moz-txt-link-abbreviated" href="mailto:hess@kth.se">hess@kth.se</a></a>&gt; wrote:</div>
            <br class="Apple-interchange-newline">
            <div class="">
              <div text="#000000" bgcolor="#FFFFFF" class="">
                <div class="moz-cite-prefix">This is using the sparse
                  matrix code. The default value for -last (end) is 50,
                  which should work. I assume you increased it.<br
                    class="">
                  <br class="">
                  We should fix the code by casting the column and row
                  size to size_t before multiplying them.<br class="">
                  <br class="">
                  Cheers,<br class="">
                  <br class="">
                  Berk<br class="">
                  <br class="">
                  On 2016-07-05 14:21, Erik Lindahl wrote:<br class="">
                </div>
                <blockquote
                  cite="mid:B8FA0AF1-E3EF-41DA-8053-6206A2B075B7@gmail.com"
                  type="cite" class=""> Seems like a bug - we should use
                  a size_t to calculate the size of the matrix storage
                  required.
                  <div class=""><br class="">
                  </div>
                  <div class="">However, before you get your hopes up:
                    The reason why this happens is that you are asking
                    the code to do a full diagonalization of a matrix
                    that is 63255^2. That will take at least ~100GB of
                    memory, and probably take several months. I would
                    recommend that you use some cutoff-based
                    electrostatics/VdW instead to enable sparse matrix
                    diagonalization.</div>
                  <div class=""><br class="">
                  </div>
                  <div class="">Cheers,</div>
                  <div class=""><br class="">
                  </div>
                  <div class="">Erik</div>
                  <div class=""><br class="">
                  </div>
                  <div class=""><br class="">
                  </div>
                  <div class=""><br class="">
                  </div>
                  <div class=""><br class="">
                    <div class="">
                      <blockquote type="cite" class="">
                        <div class="">On 05 Jul 2016, at 14:02, Adrien
                          Nicolaï &lt;<a moz-do-not-send="true"
                            class="moz-txt-link-abbreviated"
                            href="mailto:adrien.nicolai@u-bourgogne.fr">adrien.nicolai@u-bourgogne.fr</a>&gt;

                          wrote:</div>
                        <br class="Apple-interchange-newline">
                        <div class="">
                          <div style="word-wrap: break-word;
                            -webkit-nbsp-mode: space;
                            -webkit-line-break: after-white-space;"
                            class="">Dear GROMACS developers,
                            <div class=""><br class="">
                            </div>
                            <div class="">I’m performing a Normal mode
                              analysis using the GROMACS 5.1 software.
                              The system I study is a dimer of a protein
                              surrounded by water molecules and is
                              comprised of 21075 atoms (corresponding to
                              63225 modes). After a proper minimisation
                              using the L-BFGS algorithm and a normal
                              mode calculation in double precision, I
                              tried to diagonalise the entire hessian
                              matrix using the nmeig command.</div>
                            <div class=""><br class="">
                            </div>
                            <div class="">The use of the gmx_d nmeig
                              command leads to the following error:</div>
                            <div class=""><br class="">
                            </div>
                            <div class="">
                              <div class="" style="margin: 0px;
                                font-size: 14px; line-height: normal;
                                font-family: Menlo; color: rgb(255, 255,
                                255); background-color: rgb(0, 0, 0);"><b
                                  class="">Reading double precision
                                  matrix generated by GROMACS VERSION
                                  5.1</b></div>
                              <div class="" style="margin: 0px;
                                font-size: 14px; line-height: normal;
                                font-family: Menlo; color: rgb(255, 255,
                                255); background-color: rgb(0, 0, 0);
                                min-height: 16px;"><br class="">
                              </div>
                              <div class="" style="margin: 0px;
                                font-size: 14px; line-height: normal;
                                font-family: Menlo; color: rgb(255, 255,
                                255); background-color: rgb(0, 0, 0);"><b
                                  class="">-------------------------------------------------------</b></div>
                              <div class="" style="margin: 0px;
                                font-size: 14px; line-height: normal;
                                font-family: Menlo; color: rgb(255, 255,
                                255); background-color: rgb(0, 0, 0);"><b
                                  class="">Program gmx nmeig, VERSION
                                  5.1</b></div>
                              <div class="" style="margin: 0px;
                                font-size: 14px; line-height: normal;
                                font-family: Menlo; color: rgb(255, 255,
                                255); background-color: rgb(0, 0, 0);"><b
                                  class="">Source code file:
                                  /tmp3/gromacs-5.1-20150825/gromacs-5.1/src/gromacs/utility/smalloc.c,
                                  line: 182</b></div>
                              <div class="" style="margin: 0px;
                                font-size: 14px; line-height: normal;
                                font-family: Menlo; color: rgb(255, 255,
                                255); background-color: rgb(0, 0, 0);
                                min-height: 16px;"><br class="">
                              </div>
                              <div class="" style="margin: 0px;
                                font-size: 14px; line-height: normal;
                                font-family: Menlo; color: rgb(255, 255,
                                255); background-color: rgb(0, 0, 0);"><b
                                  class="">Fatal error:</b></div>
                              <div class="" style="margin: 0px;
                                font-size: 14px; line-height: normal;
                                font-family: Menlo; color: rgb(255, 255,
                                255); background-color: rgb(0, 0, 0);"><b
                                  class="">Not enough memory. Failed to
                                  calloc -297566671 elements of size 8
                                  for eigenvectors</b></div>
                              <div class="" style="margin: 0px;
                                font-size: 14px; line-height: normal;
                                font-family: Menlo; color: rgb(255, 255,
                                255); background-color: rgb(0, 0, 0);"><b
                                  class="">(called from file
                                  /tmp3/gromacs-5.1-20150825/gromacs-5.1/src/gromacs/gmxana/gmx_nmeig.c,
                                  line 401)</b></div>
                              <div class="" style="margin: 0px;
                                font-size: 14px; line-height: normal;
                                font-family: Menlo; color: rgb(255, 255,
                                255); background-color: rgb(0, 0, 0);"><b
                                  class="">For more information and tips
                                  for troubleshooting, please check the
                                  GROMACS</b></div>
                              <div class="" style="margin: 0px;
                                font-size: 14px; line-height: normal;
                                font-family: Menlo; color: rgb(255, 255,
                                255); background-color: rgb(0, 0, 0);"><b
                                  class="">website at <a
                                    moz-do-not-send="true"
                                    href="http://www.gromacs.org/Documentation/Errors"
                                    class=""><a class="moz-txt-link-freetext" href="http://www.gromacs.org/Documentation/Errors">http://www.gromacs.org/Documentation/Errors</a></a></b></div>
                              <div class="" style="margin: 0px;
                                font-size: 14px; line-height: normal;
                                font-family: Menlo; color: rgb(255, 255,
                                255); background-color: rgb(0, 0, 0);"><b
                                  class="">-------------------------------------------------------</b></div>
                              <div class="" style="margin: 0px;
                                font-size: 14px; line-height: normal;
                                font-family: Menlo; color: rgb(255, 255,
                                255); background-color: rgb(0, 0, 0);"><b
                                  class="">: Cannot allocate memory</b></div>
                              <div class="" style="margin: 0px;
                                font-size: 14px; line-height: normal;
                                font-family: Menlo; color: rgb(255, 255,
                                255); background-color: rgb(0, 0, 0);"><b
                                  class="">Using begin = 1 and end =
                                  63225</b></div>
                              <div class="" style="margin: 0px;
                                font-size: 14px; line-height: normal;
                                font-family: Menlo; color: rgb(255, 255,
                                255); background-color: rgb(0, 0, 0);"><b
                                  class="">Sparse matrix storage format,
                                  nrow=63225, ncols=63225</b></div>
                              <div class="" style="margin: 0px;
                                font-size: 14px; line-height: normal;
                                font-family: Menlo; color: rgb(255, 255,
                                255); background-color: rgb(0, 0, 0);"><b
                                  class="">Starter(339849): Return
                                  code=1</b></div>
                              <div class="" style="margin: 0px;
                                font-size: 14px; line-height: normal;
                                font-family: Menlo; color: rgb(255, 255,
                                255); background-color: rgb(0, 0, 0);"><b
                                  class="">Starter end(339849)</b></div>
                            </div>
                            <div class=""><br class="">
                            </div>
                            <div class="">Could you help me with the
                              meaning of this error? Is my system to big
                              for NMA using GROMACS 5.1?</div>
                            <div class=""><br class="">
                            </div>
                            <div class="">Thanks you in advance for your
                              help</div>
                            <div class=""><br class="">
                            </div>
                            <div class="">Best regards,</div>
                            <div class=""><br class="">
                            </div>
                            <div class="">
                              <div style="letter-spacing: normal;
                                orphans: auto; text-align: start;
                                text-indent: 0px; text-transform: none;
                                white-space: normal; widows: auto;
                                word-spacing: 0px;
                                -webkit-text-stroke-width: 0px;
                                word-wrap: break-word;
                                -webkit-nbsp-mode: space;
                                -webkit-line-break: after-white-space;"
                                class="">
                                <div style="letter-spacing: normal;
                                  orphans: auto; text-align: start;
                                  text-indent: 0px; text-transform:
                                  none; white-space: normal; widows:
                                  auto; word-spacing: 0px;
                                  -webkit-text-stroke-width: 0px;
                                  word-wrap: break-word;
                                  -webkit-nbsp-mode: space;
                                  -webkit-line-break:
                                  after-white-space;" class="">
                                  <div class="">
                                    <div style="margin: 0px;
                                      font-family: Menlo;" class="">************************************************************</div>
                                    <div style="margin: 0px;
                                      font-family: Menlo;" class="">Adrien
                                      Nicolaï / Maître de conférences</div>
                                    <div style="margin: 0px;
                                      font-family: Menlo;" class="">Laboratoire
                                      Interdisciplinaire Carnot de
                                      Bourgogne, UMR 6303 CNRS</div>
                                    <div style="margin: 0px;
                                      font-family: Menlo;" class="">Département
                                      NANO - Equipe Physique appliquée
                                      aux protéines</div>
                                    <div style="margin: 0px;
                                      font-family: Menlo;" class="">Université
                                      de Bourgogne Franche-Comté
                                      / Faculté des Sciences et
                                      Techniques Mirande</div>
                                    <div style="margin: 0px;
                                      font-family: Menlo;" class="">9,
                                      Av. Savary - B.P. 47 870 21078.
                                      DIJON CEDEX - France</div>
                                    <div style="margin: 0px;
                                      font-family: Menlo;" class="">Email
                                      : <a moz-do-not-send="true"
                                        href="mailto:adrien.nicolai@u-bourgogne.fr"
                                        class="">adrien.nicolai@u-bourgogne.fr</a></div>
                                    <div style="margin: 0px;
                                      font-family: Menlo;" class="">Tél:
                                      03 80 39 60 93</div>
                                    <div style="margin: 0px;
                                      font-family: Menlo;" class="">URL
                                      : <a moz-do-not-send="true"
href="https://icb.u-bourgogne.fr/fr/axes-scientifiques/nano/physique-appliquee-aux-proteines.html"
                                        class="">https://icb.u-bourgogne.fr/fr/axes-scientifiques/nano/physique-appliquee-aux-proteines.html</a></div>
                                    <div style="margin: 0px;
                                      font-family: Menlo;" class="">************************************************************</div>
                                  </div>
                                </div>
                              </div>
                            </div>
                            <br class="">
                          </div>
                          -- <br class="">
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                </blockquote>
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