Parallel FFT-based Poisson solver for isolated three-dimensional systems

Reuben D. Budiardja; Christian Y. Cardall

doi:10.1016/j.cpc.2011.05.014

Parallel FFT-based Poisson solver for isolated three-dimensional systems

Reuben D. Budiardja, Christian Y. Cardall

Theoretical and Computational Physics

Research output: Contribution to journal › Article › peer-review

13 Scopus citations

Abstract

We describe an implementation to solve Poissons equation for an isolated system on a unigrid mesh using FFTs. The method solves the equation globally on mesh blocks distributed across multiple processes on a distributed-memory parallel computer. Test results to demonstrate the convergence and scaling properties of the implementation are presented. The solver is offered to interested users as the library PSPFFT. Program summary: Program title: PSPFFT Catalogue identifier: AEJK-v1-0 Program summary URL: http://cpc.cs.qub.ac.uk/ summaries/AEJK-v1-0.html Program obtainable from: CPC Program Library, Queens University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 110 243 No. of bytes in distributed program, including test data, etc.: 16 332 181 Distribution format: tar.gz Programming language: Fortran 95 Computer: Any architecture with a Fortran 95 compiler, distributed memory clusters Operating system: Linux, Unix Has the code been vectorized or parallelized?: Yes, using MPI. An arbitrary number of processors may be used (subject to some constraints). The program has been tested on from 1 up to ∼ 13 000 processors. RAM: Depends on the problem size, approximately 170 MBytes for 48³ cells per process. Classification: 4.3, 6.5 External routines: MPI (http://www.mcs.anl.gov/mpi/), FFTW (http://www.fftw.org) , Silo (https://wci.llnl.gov/codes/silo/) (only necessary for running test problem). Nature of problem: Solving Poissons equation globally on unigrid mesh distributed across multiple processes on distributed memory system. Solution method: Numerical solution using multidimensional discrete Fourier Transform in a parallel Fortran 95 code. Unusual features: This code can be compiled as a library to be readily linked and used as a blackbox Poisson solver with other codes. Running time: Depends on the size of the problem, but typically less than 1 second per solve.

Original language	English
Pages (from-to)	2265-2275
Number of pages	11
Journal	Computer Physics Communications
Volume	182
Issue number	10
DOIs	https://doi.org/10.1016/j.cpc.2011.05.014
State	Published - Oct 2011

Funding

This research used resources of the Oak Ridge Leadership Facility at the Oak Ridge National Laboratory, which is supported by the Office of Science of the U.S. Department of Energy (DOE) . C.Y.C. acknowledges support from the Office of Nuclear Physics and the Office of Advanced Scientific Computing Research of DOE . Oak Ridge National Laboratory is managed by UT-Battelle, LLC, for the DOE. R.D.B. acknowledges support from NSF-OCI-0749204 .

Keywords

Poisson solver
Poissons equation

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10.1016/j.cpc.2011.05.014

Cite this

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title = "Parallel FFT-based Poisson solver for isolated three-dimensional systems",

abstract = "We describe an implementation to solve Poissons equation for an isolated system on a unigrid mesh using FFTs. The method solves the equation globally on mesh blocks distributed across multiple processes on a distributed-memory parallel computer. Test results to demonstrate the convergence and scaling properties of the implementation are presented. The solver is offered to interested users as the library PSPFFT. Program summary: Program title: PSPFFT Catalogue identifier: AEJK-v1-0 Program summary URL: http://cpc.cs.qub.ac.uk/ summaries/AEJK-v1-0.html Program obtainable from: CPC Program Library, Queens University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 110 243 No. of bytes in distributed program, including test data, etc.: 16 332 181 Distribution format: tar.gz Programming language: Fortran 95 Computer: Any architecture with a Fortran 95 compiler, distributed memory clusters Operating system: Linux, Unix Has the code been vectorized or parallelized?: Yes, using MPI. An arbitrary number of processors may be used (subject to some constraints). The program has been tested on from 1 up to ∼ 13 000 processors. RAM: Depends on the problem size, approximately 170 MBytes for 483 cells per process. Classification: 4.3, 6.5 External routines: MPI (http://www.mcs.anl.gov/mpi/), FFTW (http://www.fftw.org) , Silo (https://wci.llnl.gov/codes/silo/) (only necessary for running test problem). Nature of problem: Solving Poissons equation globally on unigrid mesh distributed across multiple processes on distributed memory system. Solution method: Numerical solution using multidimensional discrete Fourier Transform in a parallel Fortran 95 code. Unusual features: This code can be compiled as a library to be readily linked and used as a blackbox Poisson solver with other codes. Running time: Depends on the size of the problem, but typically less than 1 second per solve.",

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N2 - We describe an implementation to solve Poissons equation for an isolated system on a unigrid mesh using FFTs. The method solves the equation globally on mesh blocks distributed across multiple processes on a distributed-memory parallel computer. Test results to demonstrate the convergence and scaling properties of the implementation are presented. The solver is offered to interested users as the library PSPFFT. Program summary: Program title: PSPFFT Catalogue identifier: AEJK-v1-0 Program summary URL: http://cpc.cs.qub.ac.uk/ summaries/AEJK-v1-0.html Program obtainable from: CPC Program Library, Queens University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 110 243 No. of bytes in distributed program, including test data, etc.: 16 332 181 Distribution format: tar.gz Programming language: Fortran 95 Computer: Any architecture with a Fortran 95 compiler, distributed memory clusters Operating system: Linux, Unix Has the code been vectorized or parallelized?: Yes, using MPI. An arbitrary number of processors may be used (subject to some constraints). The program has been tested on from 1 up to ∼ 13 000 processors. RAM: Depends on the problem size, approximately 170 MBytes for 483 cells per process. Classification: 4.3, 6.5 External routines: MPI (http://www.mcs.anl.gov/mpi/), FFTW (http://www.fftw.org) , Silo (https://wci.llnl.gov/codes/silo/) (only necessary for running test problem). Nature of problem: Solving Poissons equation globally on unigrid mesh distributed across multiple processes on distributed memory system. Solution method: Numerical solution using multidimensional discrete Fourier Transform in a parallel Fortran 95 code. Unusual features: This code can be compiled as a library to be readily linked and used as a blackbox Poisson solver with other codes. Running time: Depends on the size of the problem, but typically less than 1 second per solve.

AB - We describe an implementation to solve Poissons equation for an isolated system on a unigrid mesh using FFTs. The method solves the equation globally on mesh blocks distributed across multiple processes on a distributed-memory parallel computer. Test results to demonstrate the convergence and scaling properties of the implementation are presented. The solver is offered to interested users as the library PSPFFT. Program summary: Program title: PSPFFT Catalogue identifier: AEJK-v1-0 Program summary URL: http://cpc.cs.qub.ac.uk/ summaries/AEJK-v1-0.html Program obtainable from: CPC Program Library, Queens University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 110 243 No. of bytes in distributed program, including test data, etc.: 16 332 181 Distribution format: tar.gz Programming language: Fortran 95 Computer: Any architecture with a Fortran 95 compiler, distributed memory clusters Operating system: Linux, Unix Has the code been vectorized or parallelized?: Yes, using MPI. An arbitrary number of processors may be used (subject to some constraints). The program has been tested on from 1 up to ∼ 13 000 processors. RAM: Depends on the problem size, approximately 170 MBytes for 483 cells per process. Classification: 4.3, 6.5 External routines: MPI (http://www.mcs.anl.gov/mpi/), FFTW (http://www.fftw.org) , Silo (https://wci.llnl.gov/codes/silo/) (only necessary for running test problem). Nature of problem: Solving Poissons equation globally on unigrid mesh distributed across multiple processes on distributed memory system. Solution method: Numerical solution using multidimensional discrete Fourier Transform in a parallel Fortran 95 code. Unusual features: This code can be compiled as a library to be readily linked and used as a blackbox Poisson solver with other codes. Running time: Depends on the size of the problem, but typically less than 1 second per solve.

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Parallel FFT-based Poisson solver for isolated three-dimensional systems

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