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    On 7/09/2011 1:01 PM, Nathalia Garces wrote:
    <blockquote
cite="mid:CALFwwEvcXckEjpQ4kT=awcnmw4fagy_gpoiOviQ2rcedNZfDKQ@mail.gmail.com"
      type="cite">
      <div style="text-align: left;"><font class="Apple-style-span"
          face="arial, helvetica, sans-serif">Hello,</font></div>
      <div>
        <div style="text-align: left;"><font class="Apple-style-span"
            face="arial, helvetica, sans-serif"><br>
          </font></div>
        <div style="text-align: left;"><font class="Apple-style-span"
            face="arial, helvetica, sans-serif">The last 6 months I've
            been working with gromacs (4.5.3 and 4.5.4) in Ubuntu (10.4)
            and it has worked fine. The problem started when I changed
            the linux distribution to Scientific Linux (5.3)... I
            followed the same steps to download/configure gromacs&nbsp;but
            something's wrong or missing because&nbsp;the simulations that I
            had been running on UBUNTU crashed in SL. <br>
          </font></div>
      </div>
    </blockquote>
    <br>
    Maybe you just got lucky. The success of poorly-conditioned
    numerical integration procedures can vary with what the user ate for
    lunch. Well, not quite, but you get the idea. :)<br>
    <br>
    You can make a better assessment by transferring a fully
    equilibrated .tpr from your working machine to your non-working
    machine and seeing whether that runs.<br>
    <br>
    <blockquote
cite="mid:CALFwwEvcXckEjpQ4kT=awcnmw4fagy_gpoiOviQ2rcedNZfDKQ@mail.gmail.com"
      type="cite">
      <div>
        <div style="text-align: left;"><font class="Apple-style-span"
            face="arial, helvetica, sans-serif"><br>
          </font></div>
        <div style="text-align: left;"><font class="Apple-style-span"
            face="arial, helvetica, sans-serif">The command I use is
            very simple:</font></div>
        <div style="text-align: left;"><font class="Apple-style-span"
            face="arial, helvetica, sans-serif"><br>
          </font></div>
        <div style="text-align: left;"><i><font class="Apple-style-span"
              face="arial, helvetica, sans-serif">&nbsp;mdrun -v -s topol.tpr</font></i></div>
        <div style="text-align: left;"><font class="Apple-style-span"
            face="arial, helvetica, sans-serif"><br>
          </font></div>
        <div style="text-align: left;"><font class="Apple-style-span"
            face="arial, helvetica, sans-serif">In Ubuntu the simulation
            ends fine but in SL</font><span class="Apple-style-span"
            style="font-family: arial, helvetica, sans-serif; ">&nbsp;the
            application starts to write on prompt a</span>t early steps
          (around 100)</div>
        <div style="text-align: left;"><font class="Apple-style-span"
            face="arial, helvetica, sans-serif"><br>
          </font></div>
        <div>
          <div style="text-align: left;"><i><font
                class="Apple-style-span" face="arial, helvetica,
                sans-serif">Step XX, time 0.XX (ps) &nbsp;LINCS WARNING</font></i></div>
          <div style="text-align: left;"><i><font
                class="Apple-style-span" face="arial, helvetica,
                sans-serif">relative constraint deviation after LINCS:</font></i></div>
          <div style="text-align: left;"><i><font
                class="Apple-style-span" face="arial, helvetica,
                sans-serif">rms XX, max XX (between atoms XX and XX)</font></i></div>
          <div style="text-align: left;"><i><font
                class="Apple-style-span" face="arial, helvetica,
                sans-serif">bonds that rotated more than 30 degrees:</font></i></div>
        </div>
        <div>
          <div style="text-align: left;"><i><font
                class="Apple-style-span" face="arial, helvetica,
                sans-serif">...</font></i></div>
          <i><span class="Apple-style-span" style="font-style: normal; "><i><font
                  class="Apple-style-span" face="arial, helvetica,
                  sans-serif">Wrote pdb files with previous and current
                  coordinates</font></i></span></i></div>
        <div style="text-align: left;">
          <i><font class="Apple-style-span" face="arial, helvetica,
              sans-serif"><br>
            </font></i></div>
        <div style="text-align: left;"><font class="Apple-style-span"
            face="arial, helvetica, sans-serif">Until the simulation
            ends (around 250) with a message of</font></div>
        <div style="text-align: left;"><font class="Apple-style-span"
            face="arial, helvetica, sans-serif"><br>
          </font></div>
        <div><i>
            <div style="text-align: left;"><font
                class="Apple-style-span" face="arial, helvetica,
                sans-serif">Segmentation fault</font></div>
          </i></div>
        <div style="text-align: left;"><font class="Apple-style-span"
            face="arial, helvetica, sans-serif"><br>
          </font></div>
        <div style="text-align: left;"><font class="Apple-style-span"
            face="arial, helvetica, sans-serif"><br>
          </font></div>
        <div style="text-align: left;"><font class="Apple-style-span"
            face="arial, helvetica, sans-serif">I tried different ways
            to configure gromacs but none of them seems to resolve the
            problem</font></div>
        <div style="text-align: left;">
          <font class="Apple-style-span" face="arial, helvetica,
            sans-serif">1)&nbsp;./configure --prefix=&lt;my path&gt;</font></div>
        <div style="text-align: left;"><font class="Apple-style-span"
            face="arial, helvetica, sans-serif">make</font></div>
        <div style="text-align: left;"><font class="Apple-style-span"
            face="arial, helvetica, sans-serif">make install</font></div>
        <div style="text-align: left;"><font class="Apple-style-span"
            face="arial, helvetica, sans-serif"><br>
          </font></div>
        <div style="text-align: left;"><font class="Apple-style-span"
            face="arial, helvetica, sans-serif">2)&nbsp;./configure
            --with-fft=fftw3 --prefix=&lt;my path&gt;&nbsp;&nbsp;--without-x</font></div>
        <div>
          <div style="text-align: left;">
            <div style="text-align: left; "><font
                class="Apple-style-span" face="arial, helvetica,
                sans-serif">make</font></div>
            <div style="text-align: left; "><font
                class="Apple-style-span" face="arial, helvetica,
                sans-serif">make install</font></div>
            <div style="text-align: left; "><font
                class="Apple-style-span" face="arial, helvetica,
                sans-serif"><br>
              </font></div>
            <div style="text-align: left; "><font
                class="Apple-style-span" face="arial, helvetica,
                sans-serif">3)./configure --program-suffix=
                --disable-float --prefix=&lt;my
                path&gt;&nbsp;--exec-prefix=&lt;my
                path&gt;&nbsp;--enable-all-static --with-fft=fftw3
                --without-x</font></div>
            <div style="text-align: left;"><font
                class="Apple-style-span" face="arial, helvetica,
                sans-serif">
                <div style="font-family: arial; text-align: left; "><font
                    class="Apple-style-span" face="arial, helvetica,
                    sans-serif">make</font></div>
                <div style="font-family: arial; text-align: left; "><font
                    class="Apple-style-span" face="arial, helvetica,
                    sans-serif">make install</font></div>
              </font></div>
          </div>
        </div>
      </div>
    </blockquote>
    <br>
    You will need an FFTW install with float/double precision matching
    that of the GROMACS configure command.<br>
    <br>
    <blockquote
cite="mid:CALFwwEvcXckEjpQ4kT=awcnmw4fagy_gpoiOviQ2rcedNZfDKQ@mail.gmail.com"
      type="cite">
      <div>
        <div>
          <div style="text-align: left;">
            <div style="text-align: left;"><font
                class="Apple-style-span" face="arial, helvetica,
                sans-serif">
                <div style="font-family: arial; text-align: left; "><font
                    class="Apple-style-span" face="arial, helvetica,
                    sans-serif"><br>
                  </font></div>
                <div style="text-align: left; ">Moreover,&nbsp;I downloaded
                  the benchmark posted in the gromacs web page to test
                  the simulations with other ".tpr" files. I run the
                  first simulation (implicit solvent) in UBUNTU and
                  worked OK but the one on SL crashed (around step 460)
                  with the first two options of configuration. The last
                  configuration enabled the simulation to run OK( I
                  decided to stop it at 4000 steps)...</div>
                <div style="text-align: left; ">This bewilders me
                  because the last configuration permitted the benchmark
                  to run OK but not my file. I don't think my file has
                  an unstable system because it works all right in
                  UBUNTU (and also Debian!)</div>
              </font></div>
          </div>
        </div>
      </div>
    </blockquote>
    <br>
    One possibility is some kind of dynamic linking failure from all
    your different installations. If you always install to a --prefix
    that you can delete later, then you can be sure that this kind of
    problem cannot occur when you are testing different installations.<br>
    <br>
    <blockquote
cite="mid:CALFwwEvcXckEjpQ4kT=awcnmw4fagy_gpoiOviQ2rcedNZfDKQ@mail.gmail.com"
      type="cite">
      <div>
        <div>
          <div style="text-align: left;">
            <div style="text-align: left;"><font
                class="Apple-style-span" face="arial, helvetica,
                sans-serif"><br>
              </font><font class="Apple-style-span" face="arial,
                helvetica, sans-serif"><span class="Apple-style-span"
                  style="font-family: arial;">
                  <div style="text-align: left; ">
                    <font class="Apple-style-span" face="arial,
                      helvetica, sans-serif">In addition, I&nbsp;</font>upgraded
                    my linux distribution to the latest SL 5.x release
                    but it didn't make any change!</div>
                  <div style="text-align: left; ">
                    <br>
                  </div>
                  <div style="text-align: left; "><br>
                  </div>
                  <div style="text-align: left; ">I hope you can help me
                    with some guide on how to proceed a GOOD instalation
                    in SL or to let me know what is my problem and what
                    I am missing. <br>
                  </div>
                </span></font></div>
          </div>
        </div>
      </div>
    </blockquote>
    <br>
    Be sure you are following all the advice on the installation page of
    the GROMACS webpages.<br>
    <br>
    Mark<br>
    <br>
    <blockquote
cite="mid:CALFwwEvcXckEjpQ4kT=awcnmw4fagy_gpoiOviQ2rcedNZfDKQ@mail.gmail.com"
      type="cite">
      <div>
        <div>
          <div style="text-align: left;">
            <div style="text-align: left; "><font
                class="Apple-style-span" face="arial, helvetica,
                sans-serif"><span class="Apple-style-span"
                  style="font-family: arial; ">
                  <div style="text-align: left; ">&nbsp;</div>
                  <div style="text-align: left; "><br>
                  </div>
                </span></font></div>
          </div>
          <span class="Apple-style-span" style="font-family: arial,
            sans-serif; font-size: 13px; background-color: rgb(255, 255,
            255); ">Thank you for four answer,</span><font
            class="Apple-style-span" face="arial, helvetica, sans-serif"><span
              class="Apple-style-span" style="background-color: rgb(255,
              255, 255); "><span class="Apple-style-span"
                style="white-space: pre;"><br>
              </span></span><br>
          </font></div>
        <div><font class="Apple-style-span" face="arial, helvetica,
            sans-serif">Nathalia Garces</font></div>
      </div>
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      <br>
    </blockquote>
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