MD_OPENMP\ Molecular Dynamics using OpenMP {#md_openmp-molecular-dynamics-using-openmp align=”center”} ===============================
MD_OPENMP is a C++ program which carries out a molecular dynamics simulation, using OpenMP for parallel execution.
On an Apple PowerPC G5 with two processors, the following results were observed for a run with 400 steps and 1000 particles:
Threads Time ——— —————— 1 183.517 secconds 2 94.037 seconds 4 93.164 seconds
In the BASH shell, the program could be run with 2 threads using the commands:
export OMP_NUM_THREADS=2
./md_openmp
The computer code and data files described and made available on this web page are distributed under the GNU LGPL license.
MD_OPENMP is available in a C version and a C++ version and a FORTRAN77 version and a FORTRAN90 version.
DIJKSTRA_OPENMP, a C++ program which uses OpenMP to parallelize a simple example of Dijkstra’s minimum distance algorithm for graphs.
FFT_OPENMP, a C++ program which demonstrates the computation of a Fast Fourier Transform in parallel, using OpenMP.
HEATED_PLATE_OPENMP, a C++ program which solves the steady (time independent) heat equation in a 2D rectangular region, using OpenMP to run in parallel.
HELLO_OPENMP, a C++ program which prints out “Hello, world!” using the OpenMP parallel programming environment.
MD, a C++ program which carries out a molecular dynamics simulation, and is intended as a starting point for implementing an OpenMP parallel version.
MD_PARFOR, a MATLAB program which is intended to be run in parallel using MATLAB’s “PARFOR” feature.
MD1, a FORTRAN90 program which carries out a molecular dynamics simulation.
MD2, a FORTRAN90 program which carries out a molecular dynamics simulation.
MD3, a FORTRAN90 program which carries out a molecular dynamics simulation.
MD3GLUE, a FORTRAN90 program which carries out a molecular dynamics simulation.
MDBNCH, a FORTRAN77 program which is a benchmark molecular simulation calculation.
MULTITASK_OPENMP, a C++ program which demonstrates how to “multitask”, that is, to execute several unrelated and distinct tasks simultaneously, using OpenMP for parallel execution.
MXM_OPENMP, a C++ program which computes a dense matrix product C=A*B, using OpenMP for parallel execution.
OPENMP, C++ programs which illustrate the use of OpenMP.
OPENMP_RCC, C++ programs which illustrate how a C program, using OpenMP, can be compiled and run in batch mode on the FSU High Performance Computing (HPC) cluster operated by the Research Computing Center (RCC).
POISSON_OPENMP, a C++ program which computes an approximate solution to the Poisson equation in a rectangle, using the Jacobi iteration to solve the linear system, and OpenMP to carry out the Jacobi iteration in parallel.
PRIME_OPENMP, a C++ program which counts the number of primes between 1 and N, using OpenMP for parallel execution.
QUAD_OPENMP, a C++ program which approximates an integral using a quadrature rule, and carries out the computation in parallel using OpenMP.
RANDOM_OPENMP, a C++ program which illustrates how a parallel program using OpenMP can generate multiple distinct streams of random numbers.
SATISFY_OPENMP, a C++ program which demonstrates, for a particular circuit, an exhaustive search for solutions of the circuit satisfy problem, using OpenMP for parallel execution.
SCHEDULE_OPENMP, a C++ program which demonstrates the default, static, and dynamic methods of “scheduling” loop iterations in OpenMP to avoid work imbalance.
SGEFA_OPENMP, a C++ program which reimplements the SGEFA/SGESL linear algebra routines from LINPACK for use with OpenMP.
ZIGGURAT_OPENMP, a C++ program which demonstrates how the ZIGGURAT library can be used to generate random numbers in an OpenMP parallel program.
MD_LOCAL runs the program locally.
MD_ITHACA runs the program through ITHACA’s batch system.
You can go up one level to the C++ source codes.
Last revised on 02 September 2009.