[gmx-developers] Kernel Reduction

Berk Hess hessb at mpip-mainz.mpg.de
Thu Apr 19 14:53:10 CEST 2007

Delon Levi wrote:

> I have a run of GROMACS that uses the following cores:
>   nb_kernel112
>   nb_kernel100
>   nb_kernel110
>   nb_kernel111
>   nb_kernel101
> All of these cores are basically running the same Coulombic/Van der 
> Waals kernel.   Sometimes there are 3 interactions in the inner loop 
> calculated, sometimes 9 (noted that with nb_kernel100 and nb_kernel101 
> van der Waals is not calculated).  What I want to do is just call
> nb_kernel110 (which does 1 interaction in the inner loop) and have the 
> data structures formatted so that only nb_kernel110 is called.  Is 
> there a relatively easy way to get the code to do this, or something 
> equivalent where 1 simple core is called?

Not for your system.
A non-zero last digit means solvent optimization, so you apparently
have water in your system. You can get rid of the solvent optimization
by setting the environment variable GMX_NO_SOLV_OPT
The second 0 means no LJ. This is because water H's (and maybe other
atoms in your system) have no LJ. You can not avoid these loops,
unless you edit src/mdlib/ns.c to not check for the LJ parameters.


> Delon
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