Polymec

Copyright (c) 2012-2019, Jeffrey N. Johnson All rights reserved.

Polymec is a set of libraries that can be used to construct models for physical systems. These libraries are designed to allow a computational scientist to construct low-maintenance science applications with robust capabilities.

Features

• A comprehensive set of C tools appropriate for high performance computing, including containers, spatial data structures, and interfaces to important libraries and facilities.
• A layered structure allowing different levels of buy-in: using only basic data structures, adopting a framework for simulator apps, and everything between.
• Stiffly-accurate, implicit time integrators that use high-quality preconditioners without a lot of application-specific classes.
• A strategy that favors a small code footprint and good scalability, likely at the expense of implementations that run optimally on serial computers.

License

Polymec is licensed under the Mozilla Public License (MPL) version 2.0, which is defined in the LICENSE file, and also available at http://mozilla.org/MPL/2.0/. This license allows you to use Polymec in a commercial code as long as certain requirements are satisfied. Please read or read about the license.

The 3rd-party libraries used by Polymec have their own licenses which are described within the various source trees in the 3rdparty directory. Source files have been minimally modified within these trees; typically they contain files extracted directly from distribution tarballs. You'll find instructions for obtaining each library in its directory.

Installing Polymec

You can use polymec on Linux or macOS systems.

Software Requirements

The polymec libraries require the following software:

• A C compiler that adheres to (or aspires to) the C11 standard. GCC 4.9+ and Clang 3.4+ work well.
• A reasonable C++ compiler, for the C++ build/link test
• MPI (OpenMPI or MPICH), for parallelism
• A working set of LAPACK/BLAS libraries, for dense linear algebra
• The Bourne Again SHell (bash), for bootstrapping
• CMake 3.10+, for configuring and generating build files
• GNU Make or Ninja, for performing the actual build
• A recent version of Perl, for HDF5's installation process

The following are helpful, but not required:

• A recent version of Git, for code development
• Valgrind, for finding memory-related issues
• A Python 3.x interpreter, for running some of the targets
• Doxygen, for generating reference documentation)

You can easily install these using your favorite package manager.

Building

To build polymec on a UNIX-like system, change to your polymec-dev directory and type the following commands:

./bootstrap build_dir

where build_dir is the directory in which you want to build. Then just follow the onscreen directions: you change to that build directory, edit config.sh to define your build, and then start the build using your generator's build process. For the default generator (UNIX makefiles), this is just make. For Ninja (recommended if you have it), it's ninja.

Installing

To install polymec, use the install command for the generator you've selected. For example, if you're using a generator that writes UNIX makefiles, run

make install [-j #threads]

from your build directory.

Other Targets

These targets all work with Make and Ninja.

• test - Runs all unit tests for the library. Use ctest -j #threads instead, though, to run the tests in parallel.
• memcheck - Runs all unit tests for the library using Valgrind if you're on Linux and it's available. Tests run in parallel.
• clean - Removes all build assets but retains configuration options.
• stats - Prints some interesting code statistics to the screen. Requires Python 3.x.
• coverage - Generates a code coverage report. This only works if you enable the COVERAGE build option in config.sh, and if gcov and lcov are available.
• doc - Generates HTML and man reference documentation pages using Doxygen. Only available when CMake finds Doxygen.