[gmx-developers] Adding computing kernels in shared linked library

Mark Abraham Mark.Abraham at anu.edu.au
Thu Aug 25 01:43:17 CEST 2011

On 25/08/2011 12:52 AM, Sebastian Jodłowski wrote:
> I'm trying to add some features (e.g. interactions with membrane) into
> nb_generic_kernel. I've written all my stuff, tested it hardly and
> everything seems to work perfectly - all results are correct. Next
> step, which I would like to performe, is to extract my kernels and
> move them to the external library. So I added my lib(for now empty
> lib) to gromacs makefiles(all of them), and inlcuded my lib header in
> the nb_generic.c. In that place gromacs compiled and linked properly.
> I cut my kernel code from the nb_generic_kernel() body and above it I
> created function my_kernel() which consist body of my kernel. All
> parametres are passed via pointers and kernel is called in its earlier
> body's place in nb_generic_kernel(). Then I tested it again -
> everything works great. So I finally moved my_kernel into the library.
> Gromacs compiled and linked properly so I started testing. The results
> are already wrong at the stage of minimization. I performed 100 steps
> of minimization and version without external library calls 78144 times
> my_kernel wherease with external library my_kernel is called 69696.
> (What the hell?)The results start to differ at about 60% (45000th
> calls of my_kernel).

Sounds like you're managing to do a non-reproducible calculation 
non-reproducibly. Perhaps mdrun -reprod will help.


>   I have no idead what's going on and I spent
> several days looking for the bug and couldn't find it. I would like to
> notice that i don't know how gromacs minimization works and have no to
> time for studing these code(but I pretty good analised how computing
> of forces works).
> Has anybody ever met something similar? Or has any experience with
> writing libraries for gromacs?
> Greetings
> Sebastian Jodlowski

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