Hi Gernot 
You're seeting the ~20 work vectors for the nonlinear & multigrid
solver (PMG) plus the 4 that I use for internal storage
20 * 161^3 * 8 =3D 636 MB
4 * 161^3 * 8 =3D 128 MB
We can definitely reduce the amount of memory actually allocated for
some of the calculations based on the calculation type. We're going
to be doing a fair amount of optimization of APBS for speed and memory
in the next year so this will be on the list.
Thanks!
 Nathan
On 3/17/06, Gernot Kieseritzky <gernotf@...> wrote:
> Hi all!
> I have a question regarding the memory demand of APBS. I noticed that
> APBS consumes roughly 10x as much memory as e.g. Bashford's solvate progr=
am.
>
> I don't quite understand what this extra memory is spend for. In my test
> calculation I used a grid setup of 161x161x161 which eats up roughly one
> 1 GB of memory using APBS. Since on my 64bit opteron system the size of
> a double value is 8 bytes, and I need to store the dielectric constant,
> kappa, the charge and a solution I would get the following minimum
> memory demand:
>
> 8 bytes x 161^3 x 4 =3D 127.36 MB
>
> Ok, I know APBS stores three x/y/zshifted dielectric maps which makes
> 191 MB. The multigrid algorithm APBS will have to store coarser copies
> of those data structures, but, since, they are coarsened, I estimate an
> additional factor of 2: ~400 MB.
>
> So, what happens with the remaining 600 MB?
>
> Greetings,
> Gernot
>
>
> 
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Assistant Professor, Dept. of Biochemistry and Molecular Biophysics
Center for Computational Biology, Washington University in St. Louis
Web: http://cholla.wustl.edu/
