[Dock-fans] Single processor optimization

[Scott Brozell]

Hi,

On Sat, 10 May 2008, Francesco Pietra wrote:

> --- On Sat, 5/10/08, Sudipto Mukherjee <sudmukh at yahoo.com> wrote:
> 
> > I'm not clear why you are using continuous scoring
> > while docking, especially with a large protein. An energy
> > grid would make the dock run orders of magnitude faster.
> 
> Grid flex docking (standard grid size) results immediately in
> 
> what () : std::bad alloc
> 
> Why the operator () fails is not entirely clear. Scott is the opinion (I believe) that it means running out memory. Why however it is satisfied for continuous score of 29.3% of the available memory? It is now the first time I am insisting with the continuous score, both in the hope to get the complex for this new ligand and anyway to see what happens.
> 

The story is that grid_score fails because the memory needed for the grids
and the spheres exceeds the available memory.
continuous score eliminates the grids, but the spheres can still
consume lots of memory.
I thought this was verified by you and clear.
And note to those not routinely following your threads that your
docking application is atypical.

> > The Redpaper describes using IBM's MASSV libraries for
> > optimizing programs on Blue Gene. As far as I know, there
> > are no similar libraries we can use with gcc. 
> 
> What about AMD or Intel libraries, which are free for noncommercial use? I could compile Dock with icc (with Amber and OpenMPI I use ifort and icc)
> 

AMD Core Math Library (ACML) is compatible with gfortran, Intel, PGI, etc.
Sometime we shall provide config files for acml.
But the continuous score code is written very inefficiently, and
there are obvious improvements before considering acml.
Are you planning significant continuous score calculations ?


> > ----- Original Message ----
> > From: Francesco Pietra <chiendarret at yahoo.com>
> > 
> > To the developers: since most of the time with this
> > CPU-bound code is spent on scoring (Redpaper above), is
> > there any plan to implement a monitoring of the progress of
> > the scoring, no matter how approximate it might be?

Please clarify the question.
Are you suggesting output like
that from amber score with the -v flag ?

Scott