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PEPC - Pretty Efficient Parallel Coulomb-solver

Authors:

Paul Gibbon, Mathias Winkel, Benedikt Steinbusch, Robert Speck, Junxian Chew, Dirk Brömmel, Lukas Arnold
Forschungszentrum Juelich GmbH
Juelich Supercomputing Centre

Webpage:

http://www.fz-juelich.de/ias/jsc/pepc

DOI:

10.5281/zenodo.7965548

E-Mail:

[email protected]

CI:

pipeline status

CB:

Continuous Benchmarking

0. LICENSE

This file is part of PEPC - The Pretty Efficient Parallel Coulomb Solver.

Copyright (C) 2002-2024
Juelich Supercomputing Centre,
Forschungszentrum Juelich GmbH,
Germany

PEPC is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

PEPC is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details.

You should have received a copy of the GNU Lesser General Public License along with PEPC. If not, see http://www.gnu.org/licenses/.

1. REQUIREMENTS

  • A reasonably modern Fortran compiler with support for Fortran 2003 object orientation, e.g.:
    • GCC >= 4.6
    • Intel >= 12.1
    • IBM XL Fortran >= 12
  • A C compiler and a C preprocessor with support for variadic macros.
  • An MPI library with support for MPI_THREAD_MULTIPLE. PEPC will complain about missing support at run time.
  • Support for POSIX threads (pthreads).

2. COMPILATION

For compiling this program, the machine-dependent compiler names and flags have to be set in a definition file called makefile.defs in the root directory.

Several exemplary definitions are available in the subdirectory ./makefiles. For example, for GCC you can simply run

ln -sf ./makefiles/makefile.defs.GCC ./makefile.defs

from the root directory to create a symbolic link the the appropriate definitions. Some compiler or machine specific hints are contained in the files within this directory, please have look there.

After providing the makefile.defs file, you can simply call

make help

to show information/recommendation on machine specifics.

After setting the proper environment (modules, paths) call

make pepc-mini

to build the pepc-mini frontend into the ./bin/ directory. Parallel make (i.e. make -j <n>) should work.

There are several different frontends available at the moment:

  • pepc-b:
    laser/beam-plasma with magnetic fields
  • pepc-essential/pepc-benchmark:
    simple setup w/ a Coulomb explosion
    also used for benchmarking
  • pepc-darwin-2d:
    2D version w/ Darwin appoximation for electrodynamics
  • pepc-mini:
    pure electrostatics
    simple molecular dynamics
    no diagnostics
    minimum requirements to get PEPC running
  • pepc-neighbour:
    tree-based nearest neighbour search
  • pepc-kh, pepc-kh-essential:
    Kevin-Helmholtz setup (essential following text-books)
  • pepc-v/pepc-dvh:
    vortex dynamics using the vortex particle method/diffused vortex hydrodynamics method
  • pepc-breakup:
    Townsend avalanche breakdown simulation

To build an alternative frontend, just call

make pepc-essential

or

make pepc-benchmark

All frontends can be built using

make (-j <n>) all

At the current stage, there is no real documentation available for the different frontends. However, you might simply want to take a look at the respective sourcecode to find out what they are doing.

3. RUNNING THE PROGRAM

Usually, the frontend's source directories contain a sample input deck for the frontends. For running pepc-essential it is for example called params. It contains user-adjustable parameters and can be fed to the executable as first command line parameter:

cd bin
mpirun -np 32 pepc-essential ../src/frontends/pepc/essential/params

4. DOCUMENTATION

Rudimentary doxygen documentation is available by calling

make doc

from the root directory. A users guide is in preparation.

5. REPORTING PROBLEMS

Please submit an issue with PEPC's issue tracker if you encounter a problem. There are a number of templates available depending on the problem you want to report:

Please note that our rescources are limited and that we will prioritise any requests. We do, however, appreciate any contribution.

6. DIRECTORY STRUCTURE / ADDING OWN FUNCTIONALITY

Inside the ./src/ directory, you will find four subdirectories:

  • "treecode": PEPC kernel, everything that is necessary for the pure algorithmic part of the treecode
  • "interaction_specific": interaction specific backends. The different subdirectories herein (currently mainly: coulomb, darwin, and vortex) provide data structures and functions for the different applications. See inline documentation in the sourcecode (especially inside the coulomb-subdir, which should be well documented) to find out about what the functions should do and which of them are necessary. The only files that must be provided in this directory are (names may not be changed, public functions and datastructures inside these files are mandatory):
    • module_interaction_specific.f90: data structures and functions for manipulating them
    • module_calc_force.f90: functions for actual force-law and multipole acceptance criterion etc.
    • makefile.backend: backend specific modifications to treecode makefile, may be empty
  • "utils": source code of utilities (mainly for treecode diagnostics, vtk-output etc.)
  • "frontends": different applications that utilize the treecode for their respective very specific purpose. The file makefile.frontend configures which source files, interaction ("BACKEND" / "BACKENDTYPE"), and tree walk ("WALK") will be included/used.

In case you want to use PEPC for developing a treecode-based N-body code, you might start by copying and modifying the pepc-mini frontend, which is a very simple coulomb-MD programme. It uses the coulomb backend, that implements an expansion of the plummer potential 1/sqrt(r^2+eps^2) up to quadrupole order.

Take care that your frontend-directory is called "pepc-something" with no further minus sign ("-") to be automatically recognized in the build system.

If you want to provide a new interaction-specific backend (for using other multipole orders and/or force laws), just copy and modify the coulomb subdirectory there. The backends do not have to be registered in some makefile, but are selected inside the makefile.frontend and later included by the main makefile. In case you only need to modify the interaction specific types but not the functions that are dealing with them (for example for adding velocity, mass, etc.), take a look at the coulomb-backend how to adjust the "type". There, this is done for the pepc-mini frontend, that uses other types than for example pepc-b while still using the same force expression. See also variable "BACKENDTYPE" in pepc-mini's makefile.include.

7. CONTRIBUTING

Please refer to the separate file CONTRIBUTING.md for more information.