README.kernel

These kernel directories contain Gromacs input files that have manipulated to only
call one type of interaction kernel per directory. Each directory will call both
the potential-and-force kernel (at steps 0 and 2) as well as the force-only 
kernel (at step 1). 

There is one caveat: When you run in parallel or with >1 thread, the domain 
decomposition interferes a bit with the manipulation above, which results in more
kernels being called. This is not a problem in normal executions when the kernels
pass the test, since the vast majority of interactions will have been computed
by the specific kernel the directory is named after.

If a kernel fails, start your debugging by executing the gmxtest.pl script using 
only a single thread (-nt 1). This will make sure each kernel only causes a failure
in a single directory. If you have an error you your potentials, the error must
be in the potential-and-force kernel. Similar, if you get errors in your forces
already at step 0, this too indicates the error is in the combined kernel.
If all properties match the reference values at step 0, but give incorrect results
for step 1 (this will only be the forces), the error is in the force-only kernel.