as05-28Sep21
CSCI596 (Scientific Computing and Visualization) Assignment 5
Hybrid MPI+OpenMP Parallel Molecular Dynamics
Due: October 13 (Wed), 2021
1. Write a hybrid MPI+OpenMP parallel molecular dynamics (MD) program (name it hmd.c),
starting from the MPI parallel MD program, pmd.c, following the lecture note on “hybrid
MPI+OpenMP parallel MD”. Submit the source code of hmd.c, with your modifications
from pmd.c clearly marked.
2. (Verification) Run your hmd.c on two 4-core nodes (in total of 8 cores) with 2 MPI
processes, each with 4 OpenMP threads, using the following input parameters: InitUcell =
{24,24,12}, Density = 0.8, InitTemp = 1.0, DeltaT = 0.005, StepLimit =
100, StepAvg = 10. Use the following number of MPI processes and that of OpenMP
threads, vproc = {1,1,2}, nproc = 2, vthrd = {2,2,1}, nthrd = 4, in the header
file. Note the global number of atoms is: 4 atoms/unit cell ´ (24´24´12 unit cells) ´ 2 MPI
processes = 55,296. Submit the standard output from the run. Make sure that the total
energy is the same as that calculated by pmd.c using the same input parameters (shown
below) at least for ~5-6 digits.
al = 4.103942e+01 4.103942e+01 2.051971e+01
lc = 16 16 8
rc = 2.564964e+00 2.564964e+00 2.564964e+00
nglob = 55296
0.050000 0.877345 -5.137153 -3.821136
0.100000 0.462056 -4.513097 -3.820013
0.150000 0.510836 -4.587287 -3.821033
0.200000 0.527457 -4.611958 -3.820772
0.250000 0.518668 -4.598798 -3.820796
0.300000 0.529023 -4.614343 -3.820808
0.350000 0.532890 -4.620133 -3.820798
0.400000 0.536070 -4.624899 -3.820794
0.450000 0.539725 -4.630387 -3.820799
0.500000 0.538481 -4.628514 -3.820792
CPU & COMT = 3.836388e+00 2.632065e-02
3. (Scalability) Run your hmd.c on an 8-core node with one MPI process and the number of
threads varying from 1, 2, 4, to 8, with input parameters: InitUcell = {24,24,24},
Density = 0.8, InitTemp = 1.0, DeltaT = 0.005, StepLimit = 100, StepAvg =
101. Plot the strong-scaling parallel efficiency as a function of the number of threads and
submit the plot.
(Potential Final Project)
Optimize the performance of the hybrid MPI+OpenMP MD code. For example, we could
enclose the entire MD loop in a parallel clause in the main function to avoid the excessive fork-
join overhead. We could also use a lock variable for synchronization.