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Tommy Yu
Tommy Yu
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- From: Jesús Carro Fernández <jcarro AT usj.es>
- To: cellml-discussion AT lists.cellml.org
- Subject: Re: [cellml-discussion] CellML file optimization
- Date: Tue, 29 Sep 2015 11:36:07 +0200
- Authentication-results: mx3.auckland.ac.nz; dkim=neutral (message not signed) header.i=none
- Organization: Universidad San Jorge
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<font size="-1"><font face="Helvetica, Arial, sans-serif">Thank you
both!<br />
<br />
I will look all this information.<br />
<br />
Cheers,<br />
</font></font>
<div>
<p><!--filtered--> <strong>Jesús Carro
Fernández</strong> <!--filtered--> <br />
<!--filtered-->Escuela Politécnica
Superior<!--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<br />
<!--filtered--></p>
<p><!--filtered--><a href="http://www.usj.es";>www.usj.es</a><!--filtered--></p>
<p><!--filtered--></p>
<p><!--filtered-->P<!--filtered--> <!--filtered--> Antes de imprimir este mensaje,
asegúrese de que es necesario. El medio ambiente es cosa de
todos. <!--filtered--></p>
<p><!--filtered--> En cumplimiento de la LEY 34/2002,
de 11 de julio, de servicios de la sociedad de la información
y de comercio electrónico y de la Ley Orgánica 15/1999 de
Protección de Datos, le comunicamos que su que es titular la
Universidad San Jorge. Si no desea seguir recibiendo
comunicaciones, le rogamos remita un correo electrónico a <!--filtered--><a href="mailto:lopd AT usj.es">lopd AT usj.es</a><!--filtered-->. La información
contenida en este e-mail es confidencial y va dirigida
únicamente al receptor que aparece como destinatario. Si ha
recibido este e-mail por error, por favor, notifíquelo al
emisor inmediatamente y bórrelo de su sistema. Cualquier uso,
diseminación, remisión, impresión o almacenamiento de un
e-mail remitido erróneamente está estrictamente prohibido. <!--filtered--></p>
</div>
<div>On 29/09/15 09:53, Jonathan Cooper
wrote:<br />
</div>
<blockquote>
<!--filtered-->
Hi Jesús,<br />
<br />
Indeed, the CellML support within the Chaste software (<!--filtered--><a href="http://www.cs.ox.ac.uk/chaste";>http://www.cs.ox.ac.uk/chaste</a><!--filtered-->)
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 <!--filtered-->http://dx.doi.org/10.3389/fphys.2014.00511<!--filtered--><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>
<!--filtered-->
<div>
<!--filtered-->
<p><b><!--filtered-->From:<!--filtered--></b><!--filtered--> <!--filtered-->cellml-discussion-request AT lists.cellml.org<!--filtered-->
[<!--filtered-->mailto:cellml-discussion-request AT lists.cellml.org<!--filtered-->]
<b>On Behalf Of </b>Jesús Carro Fernández<br />
<b>Sent:</b> 29 September 2015 00:11<br />
<b>To:</b> <!--filtered-->cellml-discussion AT cellml.org<!--filtered--><br />
<b>Cc:</b> Joel Castro Mur<br />
<b>Subject:</b> [cellml-discussion] CellML file
optimization<!--filtered--><!--filtered--><!--filtered--></p>
</div>
</div>
<p><!--filtered--> <!--filtered--></p>
<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'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-->
<!--filtered-->Antes
de imprimir este mensaje, asegúrese de que es
necesario. El medio ambiente es cosa de todos. <!--filtered--><!--filtered--><!--filtered--></p>
<p><!--filtered--><!--filtered-->En cumplimiento de la LEY
34/2002, de 11 de julio, de servicios de la sociedad
de la información y de comercio electrónico y de la
Ley Orgánica 15/1999 de Protección de Datos, le
comunicamos que su que es titular la Universidad San
Jorge. Si no desea seguir recibiendo comunicaciones,
le rogamos remita un correo electrónico a <!--filtered--><!--filtered--><!--filtered--><!--filtered--><!--filtered--><a href="mailto:lopd AT usj.es">lopd AT usj.es</a><!--filtered--><!--filtered-->.
La información contenida en este e-mail es
confidencial y va dirigida únicamente al receptor que
aparece como destinatario. Si ha recibido este e-mail
por error, por favor, notifíquelo al emisor
inmediatamente y bórrelo de su sistema. Cualquier uso,
diseminación, remisión, impresión o almacenamiento de
un e-mail remitido erróneamente está estrictamente
prohibido. <!--filtered--><!--filtered--><!--filtered--></p>
</div>
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- [cellml-discussion] CellML file optimization, Jesús Carro Fernández, 09/29/2015
- RE: [cellml-discussion] CellML file optimization, Alan Garny, 09/29/2015
- Re: [cellml-discussion] CellML file optimization, Jonathan Cooper, 09/29/2015
- Re: [cellml-discussion] CellML file optimization, Jesús Carro Fernández, 09/29/2015
- Re: [cellml-discussion] CellML file optimization, Jonathan Cooper, 09/29/2015
- RE: [cellml-discussion] CellML file optimization, Alan Garny, 09/29/2015
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