1.3 Installing from Source

This section explains how to build Nektar++ from the source-code package.

Nektar++ uses a number of third-party libraries. Some of these are required, others are optional. It is generally more straightforward to use versions of these libraries supplied pre-packaged for your operating system, but if you run into difficulties with compilation errors or failing regression tests, the Nektar++ build system can automatically build tried-and-tested versions of these libraries for you. This requires enabling the relevant options in the CMake configuration.

1.3.1 Obtaining the source code

There are two ways to obtain the source code for Nektar++:

1.3.2 Linux

1.3.2.1 Prerequisites

Nektar++ uses a number of external programs and libraries for some or all of its functionality. Some of these are required and must be installed prior to compiling Nektar++, most of which are available as pre-built system packages on most Linux distributions or can be installed manually by a user. Typically, the development packages, with a -dev or -devel suffix, are required to compile codes against these libraries. Others are optional and required only for specific features, or can be downloaded and compiled for use with Nektar++ automatically (but not installed system-wide).

Installation

Package Req. Sys. User Auto.

Note

C++ compiler

gcc, icc, etc, supporting C++11

CMake > 2.8.11

Ncurses GUI optional

BLAS

Or MKL, ACML, OpenBLAS

LAPACK

Boost >= 1.56

Compile with iostreams

TinyXML

For reading XML input files

Scotch

Required for multi-level static condensation, highly recommended

METIS

Alternative mesh partitioning

FFTW > 3.0

For high-performance FFTs

ARPACK > 2.0

For arnoldi algorithms

MPI

For parallel execution (OpenMPI, MPICH, Intel MPI, etc)

GSMPI

For parallel execution

HDF5

For large-scale parallel I/O (requires CMake >3.1)

OpenCascade CE

For mesh generation and optimisation

PETSc

Alternative linear solvers

PT-Scotch

Required when MPI enabled

Tetgen

For 3D mesh generation

Triangle

For 2D mesh generation

VTK > 5.8

Not required to convert field output files to VTK, only mesh files

1.3.2.2 Quick Start

Open a terminal.

If you have downloaded the tarball, first unpack it:

tar -zxvf nektar++-5.0.0.tar.gz

Change into the nektar++ source code directory

mkdir -p build && cd build 
ccmake ../ 
make install

1.3.2.3 Detailed instructions

From a terminal:

  1. If you have downloaded the tarball, first unpack it
    tar -zxvf nektar++-5.0.0.tar.gz 
        
  2. Change into the source-code directory, create a build subdirectory and enter it
    mkdir -p build && cd build
  3. Run the CMake GUI and configure the build by pressing c
    ccmake ../

    A full list of configuration options can be found in Section 1.3.5.

    Note: Selecting THIRDPARTY_BUILD_ options will request CMake to automatically download thirdparty libraries and compile them within the Nektar++ directory. If you have administrative access to your machine, it is recommended to install the libraries system-wide through your package-management system.

    If you have installed additional system packages since running CMake, you may need to wipe your build directory and rerun CMake for them to be detected.

  4. Press c to configure the build. If errors arise relating to missing libraries, review the THIRDPARTY_BUILD_ selections in the configuration step above or install the missing libraries manually or from system packages.
  5. When configuration completes without errors, press c again until the option g to generate build files appears. Press g to generate the build files and exit CMake.
  6. Compile the code
    make install

    During the build, missing third-party libraries will be automatically downloaded, configured and built in the Nektar++ build directory.

    Tip: If you have multiple processors/cores on your system, compilation can be significantly increased by adding the -jX option to make, where X is the number of simultaneous jobs to spawn. For example, use

    make -j4 install

    on a quad-core system.

  7. Test the build by running unit and regression tests.
    ctest

1.3.3 OS X

1.3.3.1 Prerequisites

Nektar++ uses a number of external programs and libraries for some or all of its functionality. Some of these are required and must be installed prior to compiling Nektar++, most of which are available on MacPorts (www.macports.org) or can be installed manually by a user. Others are optional and required only for specific features, or can be downloaded and compiled for use with Nektar++ automatically (but not installed system-wide).

Note: To compile Nektar++ on OS X, Apple’s Xcode Developer Tools must be installed. They can be installed either from the App Store (only on Mac OS 10.7 and above) or downloaded directly from http://connect.apple.com/ (you are required to have an Apple Developer Connection account). Xcode includes Apple implementations of BLAS and LAPACK (called the Accelerate Framework).

Installation

Package Req. MacPorts User Auto.

Note

Xcode

Provides developer tools

CMake > 2.8.11 cmake

Ncurses GUI optional

BLAS

Part of Xcode

LAPACK

Part of Xcode

Boost >= 1.56 boost

Compile with iostreams

TinyXML tinyxml

Scotch scotch

Required for multi-level static condensation, highly recommended

METIS metis

Alternative mesh partitioning

FFTW > 3.0 fftw-3

For high-performance FFTs

ARPACK > 2.0 arpack

For arnoldi algorithms

OpenMPI openmpi

For parallel execution

GSMPI

For parallel execution

HDF5

For large-scale parallel I/O (requires CMake >3.1)

OpenCascade CE

For mesh generation and optimisation

PETSc petsc

Alternative linear solvers

PT-Scotch

Required when MPI enabled

Tetgen

For 3D mesh generation

Triangle

For 2D mesh generation

VTK > 5.8 vtk

Not required to convert field output files to VTK, only mesh files

Tip: CMake, and some other software, is available from MacPorts (http://macports.org) and can be installed using, for example,

sudo port install cmake

Package names are given in the table above. Similar packages also exist in other package managers such as Homebrew.

1.3.3.2 Quick Start

Open a terminal (Applications->Utilities->Terminal).

If you have downloaded the tarball, first unpack it:

tar -zxvf nektar++-5.0.0.tar.gz

Change into the nektar++ source code directory

mkdir -p build && cd build 
ccmake ../ 
make install

1.3.3.3 Detailed instructions

From a terminal (Applications->Utilities->Terminal):

  1. If you have downloaded the tarball, first unpack it
    tar -zxvf nektar++-5.0.0.tar.gz 
        
  2. Change into the source-code directory, create a build subdirectory and enter it
    mkdir -p build && cd build
  3. Run the CMake GUI and configure the build
    ccmake ../

    Use the arrow keys to navigate the options and ENTER to select/edit an option.

    A full list of configuration options can be found in Section 1.3.5.

    Note: Selecting THIRDPARTY_BUILD_ options will request CMake to automatically download thirdparty libraries and compile them within the Nektar++ directory. If you have administrative access to your machine, it is recommended to install the libraries system-wide through MacPorts.

  4. Press c to configure the build. If errors arise relating to missing libraries (variables set to NOTFOUND), review the THIRDPARTY_BUILD_ selections in the previous step or install the missing libraries manually or through MacPorts.
  5. When configuration completes without errors, press c again until the option g to generate build files appears. Press g to generate the build files and exit CMake.
  6. Compile the code
    make install

    During the build, missing third-party libraries will be automatically downloaded, configured and built in the Nektar++ build directory.

    Tip: If you have multiple processors/cores on your system, compilation can be significantly increased by adding the -jX option to make, where X is the number of simultaneous jobs to spawn. For example,

    make -j4 install

  7. Test the build by running unit and regression tests.
    ctest

1.3.4 Windows

Windows compilation is supported, but the build process is somewhat convoluted at present. As such, only serial execution is supported with a minimal amount of additional build packages. These can either be installed by the user, or automatically in the build process.

Installation

Package Req. User Auto.

Note

MS Visual Studio

2012, 2013 and 2015 known working

CMake ≥ 3.0

BLAS

LAPACK

Boost ≥ 1.56

Compile with iostreams

1.3.4.1 Detailed instructions

  1. Install Microsoft Visual Studio 2015 (preferred), 2013 or 2012 (known to work). This can be obtained from Microsoft free of charge by using their Community developer tools from https://www.visualstudio.com/en-us/products/visual-studio-community-vs.aspx.
  2. Install CMake 3.0+ from http://www.cmake.org/download/. When prompted, select the option to add CMake to the system PATH.
  3. (Optional) Install Git from http://git-scm.com/download/win to use the development versions of Nektar++. When prompted, select the option to add Git to the system PATH. You do not need to select the option to add Unix tools to the PATH.
  4. (Optional) If you do not wish to build boost during the compilation process (which can take some time), then boost binaries can be found at http://sourceforge.net/projects/boost/files/boost-binaries/1.61.0/. By default these install into C:\local\boost_1_61_0. If you use these libraries, you will need to:
  5. Unpack nektar++-5.0.0.zip.

    Note: Some Windows versions do not recognise the path of a folder which has ++ in the name. If you think that your Windows version can not handle path containing special characters, you should rename nektar++-5.0.0 to nektar-5.0.0.

  6. Create a builds directory within the nektar++-5.0.0 subdirectory.
  7. Open a Visual Studio terminal. From the start menu, this can be found in All Programs > Visual Studio 2015 > Visual Studio Tools > Developer Command Prompt for VS2015.
  8. Change directory into the builds directory and run the CMake graphical utility:
    cd C:\path\to\nektar\builds 
    cmake-gui ..
  9. Select the build system you want to generate build scripts for. Note that Visual Studio 2015 is listed as Visual Studio 14 in the drop-down list. If you have a 64-bit installation of Windows, you should select the Win64 variant, otherwise 32-bit executables will be generated. Select the option to use the native compilers.
  10. Click the Configure button, then the Generate button.
  11. Return to the command line and issue the command:
    msbuild INSTALL.vcxproj /p:Configuration=Release

    To build in parallel with, for example, 12 processors, issue:

    msbuild INSTALL.vcxproj /p:Configuration=Release /m:12
  12. After the installation process is completed, the executables will be available in builds\dist\bin.
  13. To use these executables, you need to modify your system PATH to include the library directories where DLLs are stored. To do this, navigate to Control Panel > System and Security > System, select Advanced System Settings, and in the Advanced tab click the Environment Variables. In the System Variables box, select Path and click Edit. To the end of this list, add the full paths to directories:
  14. To run the test suite, open a new command line window, change to the builds directory, and then issue the command
    ctest -C Release

1.3.5 CMake Option Reference

This section describes the main configuration options which can be set when building Nektar++. The default options should work on almost all systems, but additional features (such as parallelisation and specialist libraries) can be enabled if needed.

1.3.5.1 Components

The first set of options specify the components of the Nektar++ toolkit to compile. Some options are dependent on others being enabled, so the available options may change.

Components of the Nektar++ package can be selected using the following options:

A number of ThirdParty libraries are required by Nektar++. There are also optional libraries which provide additional functionality. These can be selected using the following options:

The THIRDPARTY_BUILD_X options select which third-party libraries are automatically built during the Nektar++ build process. Below are the choices of X:

There are also a number of additional options to fine-tune the build: