White Papers

WRF decomposes the domain into tasks or patches. Each patch can be further decomposed into tiles that are
processed separately, but by default there is only one tile for every run. If the single tile is too large to fit into the cache
of the CPU and/or core, it slows down computation due to WRF’s memory bandwidth sensitivity. In order to reduce the
size of the tile, it is possible to increase the number of tiles by defining “numtile = x” in input file or defining environment
variable “WRF_NUM_TILES = x”. For both CONUS 12km and CONUS 2.5km the number of tiles are chosen based on
best performance. The tiles value depend on workload and hardware configuration. Table 2 shows more detail on the
number of tiles used in this study for best performance.
Table2: Parameters used in WRF for best performance
CONUS12km CONUS2.5km
Total
no. of
cores
MPI
Processes
OMP
Processes
TILES MPI
Processes
OMP
Processes
TILES
E5-2699
v4
44 22 2 22 44 1 56
E5-2698
v4
40 20 2 20 40 1 80
E5-2697A
v4
32 16 2 16 32 1 64
E5-2690
v4
28 14 2 14 28 1 56
E5-2650
v4
24 12 2 12 24 1 56
NAMD is one of the HPC applications used in molecular dynamics research. It is a portable, parallel and object oriented
molecular dynamics code designed for high-performance simulations of large bio molecular systems. NAMD is
developed using charm++. Molecular Dynamics simulations of bio molecular systems are an important technique for
our understanding of biological systems. This study has been performed with three NAMD benchmarks ApoA1 (92,224
Atoms), F1ATPase (327,506 Atoms) and STMV (virus, 1,066,628 Atoms). In the context of number of atoms, these
benchmarks lie in the category of small, medium and large size datasets.
Intel Broadwell processors