[gmx-users] Running multiple kernels

Justin M. Shorb shorb at wisc.edu
Tue Apr 10 21:11:09 CEST 2007


I have been running a modified version of gromacs 3.3 and would like to 
run two kernel loops: one which is 330 and one which is 300. In the 
src/gmxlib/nonbonded/nb_kerneltype.h file it strictly says to use 
wrapper routines that are included in the gmx_nonbonded.h file, which I 
cannot find. I assume that in switching versions the filename has 
changed, and perhaps was meant to point me to nonbonded.c ? Given that 
nb_kerneltype.h says that it is part of the gromacs 4.0 version, I 
would not be surprised if a version misnomer occured. However, I would 
be more than happy if you can point me to where this file should be 

In a similar light, is it possible to build and call two separate 
kernels within one run of gromacs, or would the tabulated files end up 
on top of each other? The nb_kerneltype.h seems to say you can use a 
build routine (probably setup_kernels() in nonbonded.c, but I want to 
make sure I'm not missing the gmx_nonbonded.h file somewhere).

My plan currently is to use setup_kernels() to explicitly setup both 
kernels needed in the nb_kernel_list (which I believe is the list of 
kernels to be setup ranging from 1 to eNB_NBKERNEL_NR) and then simply 
force the kernel 300 to be created as well as the generic propagation 
kernel (typically 330). Then it should be a matter of choosing a 
different nrnb_ind index to run the alternate kernel in the 
do_nonbonded() routine.

Are there double counting things that should be taken into account? And 
more importantly, is there an efficient subroutine written for such a 
matter that is being overlooked (hidden in a *.h file somewhere)?

Thanks in advance,
Justin M. Shorb			Phone: (608) 262-0483
Skinner Group				shorb at wisc.edu
University of Wisconsin-Madison,  Department of Chemistry
1101 University Ave., Madison, WI, 53706
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