MD_OPENMP
Molecular Dynamics using OpenMP

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

Usage:

In the BASH shell, the program could be run with 2 threads using the commands:

        export OMP_NUM_THREADS=2
        ./md_openmp
      

Licensing:

The computer code and data files described and made available on this web page are distributed under the GNU LGPL license.

Languages:

MD_OPENMP is available in a C version and a C++ version and a FORTRAN77 version and a FORTRAN90 version.

Related Data and Programs:

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.

MXV_OPENMP, a C++ program which compares the performance of plain vanilla Fortran and the FORTRAN90 intrinsic routine MATMUL, for the matrix multiplication problem y=A*x, with and without parallelization by OpenMP.

OPENMP, C++ programs which illustrate the use of OpenMP.

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.

Reference:

1. Peter Arbenz, Wesley Petersen,
   Introduction to Parallel Computing - A practical guide with examples in C,
   Oxford University Press,
   ISBN: 0-19-851576-6,
   LC: QA76.58.P47.
2. Rohit Chandra, Leonardo Dagum, Dave Kohr, Dror Maydan, Jeff McDonald, Ramesh Menon,
   Parallel Programming in OpenMP,
   Morgan Kaufmann, 2001,
   ISBN: 1-55860-671-8,
   LC: QA76.642.P32.
3. Barbara Chapman, Gabriele Jost, Ruud vanderPas, David Kuck,
   Using OpenMP: Portable Shared Memory Parallel Processing,
   MIT Press, 2007,
   ISBN13: 978-0262533027,
   LC: QA76.642.C49.

Source Code:

• md_openmp.cpp, the source code;

Examples and Tests:

MD_LOCAL runs the program locally.

• md_local.sh, commands to compile the program and run with 1, 2, 4, and 8 threads.
• md_local_output.txt, the output file.

MD_ITHACA runs the program through ITHACA's batch system.

• md_ithaca.sh, commands to compile the program and run with 1, 2, 4, and 8 threads.
• md_ithaca_output.txt, the output file.

List of Routines:

• MAIN is the main program for MD_OPENMP.
• COMPUTE computes the forces and energies.
• DIST computes the displacement and distance between two particles.
• INITIALIZE initializes the positions, velocities, and accelerations.
• TIMESTAMP prints the current YMDHMS date as a time stamp.
• UPDATE updates positions, velocities and accelerations.

You can go up one level to the C++ source codes.