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Re: [cellml-discussion] CellML file optimization


Chronological Thread 
  • From: Jonathan Cooper <jonathan.cooper AT cs.ox.ac.uk>
  • To: cellml-discussion AT lists.cellml.org
  • Subject: Re: [cellml-discussion] CellML file optimization
  • Date: Tue, 29 Sep 2015 08:53:15 +0100
  • Authentication-results: mx3.auckland.ac.nz; dkim=neutral (message not signed) header.i=none
  • Organization: University of Oxford
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    Hi Jesús,<br />
    <br />
    Indeed, the CellML support within the Chaste software
    (<a href="http://www.cs.ox.ac.uk/chaste";>http://www.cs.ox.ac.uk/chaste</a>) is probably the most advanced in
    this respect. We have our own Python toolkit for converting CellML
    to C++ which performs many optimisations (among other useful
    things), and you could probably adapt it for your needs fairly
    easily. The best recent description is at
    <a href="http://dx.doi.org/10.3389/fphys.2014.00511";>http://dx.doi.org/10.3389/fphys.2014.00511</a><br />
    <br />
    Best wishes,<br />
    Jonathan<br />
    <br />
    <div>On 29/09/2015 08:35, Alan Garny wrote:<br />
    </div>
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        <p><!--filtered-->Hi
            Jesús,<!--filtered--><!--filtered--><!--filtered--></p>
        <p><!--filtered--><!--filtered--> <!--filtered--><!--filtered--></p>
        <p><!--filtered-->You
            might be interested in looking at Jonathan Cooper’s work on
            optimising CellML files using partial evaluation and lookup
            tables (see <!--filtered-->here<!--filtered-->
            and <!--filtered-->here<!--filtered-->).
            (Note, however, that he doesn’t use the CellML API.)<!--filtered--><!--filtered--><!--filtered--></p>
        <p><!--filtered--><!--filtered--> <!--filtered--><!--filtered--></p>
        <p><!--filtered-->Cheers,
            Alan.<!--filtered--><!--filtered--><!--filtered--></p>
        <p><!--filtered--><!--filtered--> <!--filtered--><!--filtered--></p>
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              <p><b><!--filtered-->From:<!--filtered--></b><!--filtered-->
                  <a href="mailto:cellml-discussion-request AT lists.cellml.org">cellml-discussion-request AT lists.cellml.org</a>
                  [<a href="mailto:cellml-discussion-request AT lists.cellml.org">mailto:cellml-discussion-request AT lists.cellml.org</a>] <b>On
                    Behalf Of </b>Jesús Carro Fernández<br />
                  <b>Sent:</b> 29 September 2015 00:11<br />
                  <b>To:</b> <a href="mailto:cellml-discussion AT cellml.org">cellml-discussion AT cellml.org</a><br />
                  <b>Cc:</b> Joel Castro Mur<br />
                  <b>Subject:</b> [cellml-discussion] CellML file
                  optimization<!--filtered--><!--filtered--><!--filtered--></p>
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          <p><!--filtered-->Hi!<br />
              Do you know if any one has developed a tool for the
              optimization of CellML models? Some volunteers in the
              DENIS project have been trying to help us making our
              program faster. In the project, we export (using
              CeLeDSExporter) models from CellML to C++ and we create a
              executable prepared for volunteer computing. One of the
              improvements they have proposed is to transform constants
              in the divisor by constants in the numerator. Doing it on
              the CellML version of the Carro et al (2010) model, the
              execution time is reduced by 48%. Doing it by hand is easy
              but we could make mistakes and it&#39;s tedious.<br />
              <br />
              Do you have any idea on how to do it automatically?<br />
              <br />
              They have proposed us more modifications in the C++ code,
              but we would like to add them directly to the exportation
              process.<br />
              <br />
              Thank you very much!<br />
              <br />
              Best,<!--filtered--><!--filtered--><!--filtered--></p>
          <div>
            <p>-- <!--filtered--><!--filtered--></p>
            <p><strong><!--filtered-->Jesús
                  Carro Fernández<!--filtered--></strong><!--filtered-->
              <!--filtered--><br />
              <!--filtered-->Escuela
                Politécnica Superior<!--filtered--><!--filtered--><!--filtered--></p>
            <p><!--filtered-->Campus
                Universitario de Villanueva de Gállego<!--filtered--><br />
              <!--filtered-->Autov.
                A-23 Zaragoza-Huesca, km. 299<!--filtered--><br />
              <!--filtered-->50830
                Villanueva de Gállego - Zaragoza<!--filtered--><br />
              <!--filtered-->Tfno.:
                (34) 976 060 100<!--filtered--><!--filtered--><!--filtered--></p>
            <p><!--filtered--><!--filtered--><a href="http://www.usj.es";>www.usj.es</a><!--filtered--><!--filtered--><!--filtered--><!--filtered--></p>
            <p><!--filtered--><!--filtered--><!--filtered--></p>
            <p><!--filtered-->P<!--filtered-->
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