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As you know, there is a CellML 1.0 version of the epicardial version of the
ten Tusscher model, which we have. I computed that model for one-second
worth of cardiac activity, plotting the trans-membrane potential. From
there, we could extrapolate to 70 minutes by saying that the frequency of
the stimulus is 1 Hz. Like David, I have set the maximum time step to 0.1
ms. Here are some rough figures:

Simulation time: 1037.4 s (i.e. ~17 min 17 sec)
Computation time: 684.6 s (i.e. ~11 min 24 sec)

The computer on which I have run this is an IBM ThinkPad T42p (2 GHZ
processor with 2 GB of RAM). These figures can obviously vary quite a bit,
since it's based on a one-second simulation and is subject to whatever my
system does at the time... Still, that should give you a rough idea
indeed...

Alan.

> -----Original Message-----
> From: cellml-discussion-bounces at cellml.org
> [mailto:cellml-discussion-bounces at cellml.org] On Behalf Of
> David Nickerson
> Sent: 30 October 2006 10:14
> To: For those interested in contributing to the development of CellML.
> Subject: Re: [cellml-discussion] pcenv development priorities
>
> Just thought it might be useful to establish some benchmarks
> for comparison of performance amongst the various tools.
>
> I have attached my version of the ten Tusscher et. al (2004)
> human ventricular cell electrophysiology model, its in CellML
> 1.1 and uses relative URIs for all the imports. If there was
> an easy way to flatten the model Alan could try it in COR and
> we could also give it a go in JSim....and others...
>
> If you extract the attached file, there is a CellML model
> model/2004_tenTusscher/experiments/increasing-frequency-epicardial.xml
> which describes the boundary conditions etc. and simulation
> metadata for a simulation running the epicardial variant of
> the ten Tusscher model for 70 minutes with a periodic
> stimulus protocol with a frequency that varies from 0.25 to 3Hz.
>
> I run this simulation as specified in the simulation metadata
> using the BDF multistep method with Newton iteration from the
> CVODES integrator (using the dense direct linear solver). The
> full solution (every time varying variable) is saved every
> 1ms and the integration has a maximum time step of 0.1ms. My
> resulting HDF5 data file is 2.9GB and the timing, memory
> usage, and integrator stats were:
>
> Wall clock time : 1.57464269e+03 s
> CPU time : 1.54678467e+03 s (user 1.52703543e+03/system
> 1.97492340e+01)
> Total allocated space: 22786048 bytes
> in use: 22362384 bytes
> free: 423664 bytes
>
> Final integrator statistics for this run:
> (MM: BDF; IM: Newton; LS: Dense; max-step: 1.0000e-01)
> CVode real workspace length = 266
> CVode integer workspace length = 62
> Number of steps = 44973141
> Number of f-s = 47068790
> Number of setups = 3852394
> Number of nonlinear iterations = 47068785
> Number of nonlinear convergence failures = 19131
> Number of error test failures = 283742
>
> Linear solver real workspace length = 578
> Linear solver integer workspace length = 17
> Number of Jacobian evaluations = 814797
> Number of f evals. in linear solver = 13851549
>
> I also used the Unix command time to get total execution time:
> 1530.279u 19.817s 26:18.03 98.2% 0+0k 0+0io 0pf+0w
>
> So it took just almost 26.5 minutes to run this simulation
> (the difference between the time command output and the times
> reported above is the setup time prior to the integration
> loop - i.e. generating and compiling the C code).
>
> Hopefully this proves useful in establishing some idea of the
> relative performance of various tools/integrators.
>
>
> David.
>
> PS - the attached model seems to work for me, but its possible I have
> either missed some relative links or left out some required files...
>
>
> Andrew Miller wrote:
> > David Nickerson wrote:
> >> Hi all,
> >>
> >> From today's meeting minutes the following priorities
> were set for the
> >> development of pcenv:
> >>
> >> 1. Make an official release of what we have now,
> instead of just
> >> snapshot releases.
> >> 2. Try to improve integration performance, by using
> CVODE from the
> >> SUNDIALS project.
> >> 3. Investigate the possibility of getting Mac OSX
> support - Intel
> >> only to start with.
> >> 4. Get editing support for MathML and the CellML
> structure working.
> >> 5. Add CellML Metadata support to the backend, and
> editing support
> >> for this to the UI.
> >>
> >>
> >> I'm just wondering if 2 is more important than 1?
> >>
> >> From feedback so far, the performance of pcenv is very
> poor compared to
> >> other tools. There is currently (to my knowledge) no firm
> idea if this
> >> is due to the underlying technology being used by pcenv,
> or simply due
> >> to the numerical integrators being used not being as good
> as what most
> >> people are currently using.
> >>
> > Please refer to my messages on the 27th of this month,
> where I discuss
> > the results of profiling it in callgrind.
> >
> > The major performance bottleneck is the the evaluation of
> the Jacobian
> > function (I use the standard O(n^2) method for generating a dense
> > Jacobian in an array, and most of the time is spent evaluating the
> > variables). Although COR is closed source and so I cannot
> see exactly
> > what it is doing. Given that COR apparently isn't doing any
> optimisation
> > here, it must be taking a comparable amount of time per Jacobian
> > computation, so the difference must be in the number of
> calls to compute
> > the Jacobian.
> >> Seems it would be good to address this question now,
> because if using
> >> something like CVODE still results in the same poor
> performance then I
> >> think some serious thinking needs to be done about the underlying
> >> technology before an official release of pcenv should be made.
> > I understand that you already have CVODE working with CCGS,
> so perhaps
> > you can give some indication of how well CCGS generated
> code works with
> > CVODE?
> >
> > Best regards,
> > Andrew
> >
> > _______________________________________________
> > cellml-discussion mailing list
> > cellml-discussion at cellml.org
> > http://www.cellml.org/mailman/listinfo/cellml-discussion
>
> --
> David Nickerson, PhD
> Research Fellow
> Division of Bioengineering
> Faculty of Engineering
> National University of Singapore
> Email: david.nickerson at nus.edu.sg
>

---

• [cellml-discussion] pcenv development priorities, David Nickerson, 10/30/2006
  • [cellml-discussion] pcenv development priorities, Andrew Miller, 10/30/2006
    • [cellml-discussion] pcenv development priorities, David Nickerson, 10/30/2006
      • [cellml-discussion] pcenv development priorities, Alan Garny, 10/30/2006
    • [cellml-discussion] pcenv development priorities, Poul Nielsen, 10/30/2006
      • [cellml-discussion] pcenv development priorities, Andrew Miller, 10/30/2006
    • [cellml-discussion] pcenv development priorities, David Nickerson, 10/30/2006
      • [cellml-discussion] pcenv development priorities, Alan Garny, 10/30/2006
        • [cellml-discussion] pcenv development priorities, David Nickerson, 10/30/2006
          • [cellml-discussion] pcenv development priorities, Alan Garny, 10/31/2006
          • [cellml-discussion] pcenv development priorities, Andrew Miller, 10/31/2006
            • [cellml-discussion] pcenv development priorities, David Nickerson, 10/31/2006
              • [cellml-discussion] pcenv development priorities, Andrew Miller, 10/31/2006
              • [cellml-discussion] pcenv development priorities, Alan Garny, 10/31/2006

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