Installation

Dependencies

Triumvirate as a compiled C++ library/program or as a Python package built from a source distribution has the following dependencies.

GSL & FFTW3

The GSL and FFTW3 libraries are required dependencies. If they have already been installed on your system, please ignore this subsection.

In a Conda environment, both libraries can be installed with

$ conda install -c conda-forge gsl fftw

Outside Conda environments, they can be installed using a package manager:

LinuxmacOS

# Debian-based OS (e.g. Ubuntu); or
$ [sudo] apt[-get] install [-y] libgsl(-dev|27) libfftw3-(dev|3)
# Red Hat--based OS (e.g. CentOS)
$ [sudo] yum install [-y] gsl[-devel] fftw3-devel

(select the appropriate option/version in the brackets above).

Another option is to build these libraries from the source, following the instructions from ‘GSL - GNU Scientific Library’ and ‘FFTW’. In this case, path environmental variables may need to be set/modified to ensure that they are included and linked during Triumvirate compilation.

To check the compilation options for using these libraries, pkg-config may be of help:

$ pkg-config --cflags --libs gsl fftw3

However, it is not guaranteed that pkg-config always detects the relevant settings, and it is important to ensure the set-up of pkg-config matches that of the dependencies (e.g. both are installed by Conda in the same Conda environment).

Hint

These library compilation options are automatically configured and set by the default Makefile in the package distribution(s) (located at the repository diretory root) during build processes.

OpenMP library

An OpenMP library is an optional dependency for OpenMP-enabled installation. If a compatible OpenMP library has been distributed with your compiler, please ignore this subsection.

For GCC compilers, the relevant library is libgomp (typically distributed with the compiler). On Linux systems, it can be additionally installed either in a Conda environment with

Linux

$ conda install -c conda-forge libgomp

or outside Conda environments using a package manager:

Linux

# Debian-based OS (e.g. Ubuntu); or
$ [sudo] apt[-get] install [-y] libgomp1
# Red Hat--based OS (e.g. CentOS)
$ [sudo] yum install [-y] libgomp

For LLVM compilers, the relevant library is libomp. It can be installed either in a Conda environment with

$ conda install -c conda-forge llvm-openmp

or outside Conda environments using the Homebrew package manager:

$ brew install libomp

Python package

Triumvirate as a Python package is distributed through PyPI and Conda. For dependency management, it is recommended that a virtual environment should be created for installing and using the package (e.g. a Conda environment created with conda create -n <env> and activated with conda activate <env>).

To install from PyPI, execute in shell:

$ python -m pip install triumvirate

To install using Conda, execute in shell:

$ conda install -c msw triumvirate

By default, the package is installed with OpenMP enabled if it is supported.

Hint

Conda packages are built with dependencies such as numpy and scipy sourced from the conda-forge channel. For consistency and avoidance of dependency conflicts, it is recommended that conda-forge should be set as the highest-priority channel,

$ conda config --prepend channels conda-forge

and optionally, it is good practice to use strict channel priority,

$ conda config --set channel_priority strict

C++ library & program

Triumvirate as either a static library or a binary executable can be built using make, provided that dependency requirements are satisfied (see ‘Dependencies’ above).

First, obtain the source by cloning the GitHub repository and change into its local directory path:

$ git clone git@github.com:MikeSWang/Triumvirate.git [--branch <branch-or-release>]
$ cd Triumvirate

Then, execute in shell:

$ make clean
$ make cppinstall|cpplibinstall|cppappbuild [useomp=(true|1)]

Here cppinstall builds both the static library and the binary executable, cpplibinstall only the former and cppappbuild only the latter. To enable OpenMP parallelisation (see ‘OpenMP support’ below), append useomp=true or useomp=1 to the end of the second line as shown above.

By default, the static library is compiled to build/lib/libtrv.a and the binary executable is compiled to build/bin/triumvirate in the repository directory.

Hint

The default Makefile (located at the repository diretory root) should work in most build environments, but may need to be modified as appropriate for the build environment.

Development mode

Both the Python package and the C++ library/program can be set up in development mode with make, provided that dependency requirements are satisfied (see ‘Dependencies’ above).

As in ‘C++ library & program’ above, first git clone the desired branch/release from the GitHub repository and change into the repository directory path:

$ git clone git@github.com:MikeSWang/Triumvirate.git --branch <branch-or-release>
$ cd Triumvirate

Then, execute in shell:

$ make clean
$ make ([py|cpp]install)|(cpp[libinstall|appbuild]) [useomp=(true|1)]

where cpplibinstall or cppappbuild respectively builds the C++ static library or binary executable only, cppinstall builds both, pyinstall builds the Python package only, and install builds all of the above. As before, to enable OpenMP parallelisation (see ‘OpenMP support’ below), append useomp=true or useomp=1 to the end of the second line as shown above.

Note

The latest release is on the main branch. The default Makefile (located at the repository diretory root) should work in most build environments, but may need to be modified as appropriate.

OpenMP support

When building from a source distribution with OpenMP parallelisation, the compiler must support OpenMP and the OpenMP library (see ‘OpenMP library’) must be compatible.

By default, Makefile in source distributions and setup.py in Python package distributions both assume the GCC compiler and OpenMP library and configure the OpenMP-enabled compilation options accordingly.

Using make

By default, OpenMP is disabled for make-based installation. To enable OpenMP parallelisation, pass useomp=true or useomp=1 to make.

To override the compilation settings used in the default Makefile, set the environmental variables as shown in the following examples for macOS:

GCCLLVM

# Set GCC compiler (version 12 assumed here).
$ export CXX=$(brew --prefix gcc)/bin/g++-12

These commands are also included in the default Makefile (though commented out as they are an alternative to the default GCC set-up).

Python setup

By default, OpenMP support is automatically detected for Python installation (except when building through make). To disable OpenMP parallelisation explicitly, set the environmental variable PY_NO_OMP with export PY_NO_OMP='' (and unset with unset PY_NO_OMP to re-enable it); to enforce OpenMP parallelisation explicitly, set the environmental variable PY_OMP (to any non-empty value).

To override the compilation settings used by setup.py (e.g. to use a different compiler suite to the default GCC), set the environmental variables as shown in the following examples (for macOS with Homebrew package manager):

GCCLLVM

# Set GCC compiler (version 12 assumed here).
$ export PY_CXX=$(brew --prefix gcc)/bin/g++-12

Parallelised building

Building the C++ library/program or the Python package from a source distribution can be parallelised.

When using make, pass the -j[N] option where the optional parameter N is the number of concurrent jobs (see also ‘GNU Make Manual’).

For the Python setup, set the environmental variable PY_BUILD_PARALLEL to -j[N] akin to the above, e.g. export PY_BUILD_PARALLEL=-j to use all available CPUs or export PY_BUILD_PARALLEL=-j4 to use four.