Description
The purpose of this assignment is to (1) get familiar with the message-passing scheme used in
the parallel molecular dynamics (MD) program, pmd.c, and (2) gain hands-on experience for
asynchronous messages and communicators in the message passing interface (MPI).
(Part I—Asynchronous Messages)
Modify pmd.c such that, for each message exchange, it first calls MPI_Irecv, then MPI_Send,
and finally MPI_Wait. The asynchronous messages make the deadlock-avoidance scheme
unnecessary, and thus there is no need to use different orders of send and receive calls for evenand odd-parity processes. In addition to just MPI_Send, insert other computations that do not
depend on the received messages between MPI_Irecv and MPI_Wait.
• Submit the modified source code, with your modifications clearly marked.
• Run both the original pmd.c and the modified program on 16 cores (requesting 4 nodes with
4 cores per node in your Slurm script), and compare the execution time for InitUcell =
{3,3,3}, StepLimit = 1000, and StepAvg = 1001 in pmd.in (keep all the other parameter
values as they are as downloaded from the course home page) and vproc = {2,2,4} (i.e.,
nproc = 16) in pmd.h. Which program runs faster? Submit the timing data.
(Part II—Communicators)
Following the lecture note on “In situ analysis of molecular dynamics simulation data using
communicators,” modify pmd.c such that as many number of processes as that for MD
simulations is spawned to calculate the probability density function (PDF) for the atomic
velocity.
• Submit the modified source code, with your modifications clearly marked.
• Run the modified program on 16 cores (requesting 2 nodes with 8 cores per node in your
Slurm script), with which 8 cores perform MD simulation and the other 8 cores calculate
PDF. In pmd.h, choose vproc[3] = {2,2,2} and nproc = 8. Also, specify InitUcell =
{5,5,5}, StepLimit = 30, and StepAvg = 10 in pmd.in. Submit the plot of calculated PDFs
at time steps 10, 20, and 30.
