Gromacs/Acceleration and parallelization

Read this first.

On Combo, we have compiled several builds of Gromacs. List refers to How to use Combo and compilation options refer to How to compile Gromacs.

We now provide mdrun options for each build:

Gromacs 5.0.4 MPI, single, GPU

UNDER TESTS

Gromacs 5.0.4 MPI, double

mpirun -np M mdrun

Points to note:
* M is the total number of cores you wish to use
* Dunno why M=32 can only utilize one single node, i.e. M=48 utilizes one and half node observed from Ganglia

Gromacs 5.0.4 CUDA, single

mdrun (-nt N) (-pin on)

Points to note:
* For single machine only, i.e. N<=16

Gromacs 5.0.4 thread-MPI, double

mdrun (-nt N) (-pin on)

Points to note:
* For single machine only, i.e. N<=16

Benchmark