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Tommy Yu
Tommy Yu
CellML Discussion List
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- From: alan.garny at physiol.ox.ac.uk (Alan Garny)
- Subject: [cellml-discussion] Binary and source snapshots for PCEnv on Win32 and Linux
- Date: Fri, 27 Oct 2006 06:33:44 +0100
Hi Andrew,
> I have been putting some work into improving the performance
> of PCEnv. I now only compute the variables that can affect
> the rates when computing the Jacobian (but this doesn't make
> any difference for the Zhang SAN model, because it uses all
> variables to compute the rates, directly or indirectly). I
> also got about a 20% performance increase by compiling the
> generated code with -ffast-maths, which would be giving
> similar machine code to what you are writing (it makes things
> less IEEE754 compliant, but CIS still works without it).
>
> You didn't say what error control parameters you were using.
> I presume you are running this with error controls in PCEnv
> matched to the ones used in COR?
By error control parameters, you mean the relative and absolute tolerances?
If so, then I use 10^-7 and 10^-9 respectively, which I believe are small
enough to get converging results.
> > After that, I restarted PCEnv, reopened my CellML file and
> it opened
> > 'fine', except that I couldn't see anything in the 'middle' window.
> I think this is a metadata related issue which only happens
> on Win32. I will look into why this is happening.
> > I could,
> > however, run it, which I did using Implicit Gear (M=1).
> > This turned out to
> > be much faster, but still very slow compared with COR
> The GSL developers have tried hard to make their GEAR1
> accurately reproduce the results (and algorithm) from the
> original GEAR1.F integrator, so I don't think we can expect
> it to match the improved BDF/Newton algorithm from CVODE. I
> will look into how hard it would be to produce a derivative
> of the GSL Gear module which behaves like the CVODE version.
Why not try CVODE itself? That would allow to determine whether your bottle
neck is currently in the integrator or elsewhere.
Alan.
- [cellml-discussion] Binary and source snapshots for PCEnv on Win32 and Linux, Andrew Miller, 10/27/2006
- [cellml-discussion] Binary and source snapshots for PCEnv on Win32 and Linux, Alan Garny, 10/27/2006
- [cellml-discussion] Binary and source snapshots for PCEnv onWin32 and Linux, David Nickerson, 10/27/2006
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