Re: [SOSlib-discuss] sparse Jacobi matrix, DENSE_ELEM, removing 0s

[Rainer M. <ra...@tb...>]

Current CVS now makes use of the sparse Jacobi matrix list (was really 
simple to implement using libSBML's generic list functions), as well as 
the new arithmetic compiler for all r.h.s. functions where applicable.

Currently you need to activate these via defines e.g. during `make' on 
command-line, as follows:

make clean
make DEFS="-DSPARSE -DARITHMETIC_TEST"
make install

Maybe some you want to try and benchmark these new features.


Rainer


Rainer Machne wrote:
> Hi there,
> 
> For large models with a very sparse Jacobi matrix, it is much more 
> efficient to NOT print out all the DENSE_ELEM[] = 0 commands for the gcc 
> compiler.
> 
> So I have added this to construction of the forward and adjoint Jacobi 
> evaluation function. From looking at the results and the CVODES examples 
> I think that it is OK, to just not initialize or set the DENSE_ELEM 
> things for the 0 entries.
> 
> 
> However, I guess that could also be very useful for the hard-coded 
> R.H.S. functions (used by both evaluateAST and the arithmeticCompiler).
> 
> So instead of looping through the neq*neq matrix, we could generate some 
> sort of list, which contains the correct Jacobi matrix equation (only 
> for non-0 entris) and the indices i,j to which Jacobi element it refers 
> to. Then just loop through this list instead of through neq*neq.
> 
> 
> What do you think? Worth a try?
> 
> Rainer
> 
> 
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