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++:

• Download the latest source-code archive from the Nektar++ downloads page.
• Clone the git repository
  • Using anonymous access. This does not require credentials but any changes to the code cannot be pushed to the public repository. Use this initially if you would like to try using Nektar++ or make local changes to the code.
    git clone https://gitlab.nektar.info/nektar/nektar.git nektar++
  • Using authenticated access. This will allow you to directly contribute back into the code.
    git clone git@gitlab.nektar.info:nektar/nektar.git nektar++
    Tip: You can easily switch to using the authenticated access from anonymous access at a later date by running
    git remote set-url origin git@gitlab.nektar.info:nektar/nektar.git

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).

1.3.2.2 Quick Start

Open a terminal.

If you have downloaded the tarball, first unpack it:

Change into the nektar++ source code directory

1.3.2.3 Detailed instructions

From a terminal:

1. If you have downloaded the tarball, first unpack it
   tar -zxvf nektar++-5.3.0.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 ../
   • Select the components of Nektar++ (prefixed with NEKTAR_BUILD_) you would like to build. Disabling solvers which you do not require will speed up the build process.
   • Select the optional libraries you would like to use (prefixed with NEKTAR_USE_) for additional functionality.
   • Select the libraries not already available on your system which you wish to be compiled automatically (prefixed with THIRDPARTY_BUILD_). Some of these will be automatically enabled if not found on your system.
   • Choose the installation location by adjusting CMAKE_INSTALL_PREFIX. By default, this will be a dist subdirectory within the build directory, which is satisfactory for most users initially.

   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).

1.3.3.2 Quick Start

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

If you have downloaded the tarball, first unpack it:

Change into the nektar++ source code directory

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++-5.3.0.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.

   • Select the components of Nektar++ (prefixed with NEKTAR_BUILD_) you would like to build. Disabling solvers which you do not require will speed up the build process.
   • Select the optional libraries you would like to use (prefixed with NEKTAR_USE_) for additional functionality.
   • Select the libraries not already available on your system which you wish to be compiled automatically (prefixed with THIRDPARTY_BUILD_)
   • Choose the installation location by adjusting CMAKE_INSTALL_PREFIX. By default, this will be a dist subdirectory within the build directory, which is satisfactory for most users initially.

   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 there are some complexities with building additional features on this platform at present. As such, only builds with a minimal amount of additional build packages are currently supported. These can either be installed by the user, or automatically as part of the build process. Support has recently been added for building with MPI on Windows. This enables parallel computations to be carried out with Nektar++ on Windows where only sequential computations were previously supported.

1.3.4.1 Detailed instructions

1. Install Microsoft Visual Studio 2019 (preferred), 2017 or 2015 (both known to work). This can be obtained from Microsoft free of charge by using their Community developer tools from https://visualstudio.microsoft.com/vs/community/.
2. Install CMake from http://www.cmake.org/download/. For building on Windows you are strongly recommended to use a recent version of CMake, e.g 3.16+. Minimum required CMake versions for building Nektar++ on Windows with Visual Studio are CMake 3.5.1+ (VS2015), 3.7+ (VS2017), or 3.15+ (VS2019). When prompted, select the option to add CMake to the system PATH.
3. (Optional) As highlighted above, it is possible to have Boost built from source as a third-party library during the Nektar++ build. However, it is currently recommended to install the Boost binaries that can be found at http://sourceforge.net/projects/boost/files/boost-binaries. By default these install into
   C:\local\boost_<version>. We recommend installing a specific version of the binaries depending on the version of Visual Studio you are using, these are known to be working with the Nektar++ build:
   • For Visual Studio 2015, install boost 1.61 using the package boost_1_61_0-
msvc-14.0-64.exe from http://sourceforge.net/projects/boost/files/boost-binaries/1.61.0/
   • For Visual Studio 2017, install boost 1.68 using the package boost_1_68_0-
msvc-14.1-64.exe from http://sourceforge.net/projects/boost/files/boost-binaries/1.68.0/
   • For Visual Studio 2019, install boost 1.72 using the package boost_1_72_0-
msvc-14.2-64.exe from http://sourceforge.net/projects/boost/files/boost-binaries/1.72.0/

   If you use these libraries, you will need to:

   • Add a BOOST_HOME environment variable. To do so, click the Start menu and type ‘env’, you should be presented with an “Edit the system environment variables” option. Alternatively, from the Start menu, navigate to Settings > System > About > System info (under Related Settings on the right hand panel), select Advanced System Settings, and in the Advanced tab click the Environment Variables button. In the System variables box, click New. In the New System Variable window, type BOOST_HOME next to Variable name and C:\local\<boost_dir> next toVariable value, where <boost_dir> corresponds to the directory that boost has been installed to, based on the boost version you have installed. (e.g. boost_1_61_0, boost_1_68_0, boost_1_72_0).
4. (Optional) Install Git for Windows from https://gitforwindows.org/ to use the development versions of Nektar++. You can accept the default set of components in the Select Components panel. When prompted, in the “Adjusting your PATH environment” panel, select the option “Git from the command line and also from 3rd-party software”. You do not need to select the option to add Unix tools to the PATH.
5. If you’ve downloaded the source code archive (as described in Section 1.3.1), unpack nektar++-5.3.0.zip.
   Note: Some Windows versions do not recognise the path of a folder which has ++ in the name. If you are not using Windows 10 and think that your Windows version cannot handle paths containing special characters, you should rename nektar++-5.3.0 to nektar-5.3.0.

6. Create a build directory within the nektar++-5.3.0 subdirectory. If you cloned the source code from the git repository, your Nektar++ subdirectory will be called nektar rather than nektar++-5.3.0
7. Open a Visual Studio terminal (Developer Command Prompt for VS [2015/2017/2019] or x64 Native Tools Command Prompt. From the Start menu, this can be found under Visual Studio [2015/2017/2019].
8. Change directory into the build directory and run CMake to generate the build files. You need to set the generator to the correct Visual Studio version using the -G switch on the command line, e.g. for VS2019:
   cd C:\path\to\nektar\builds 
   cmake -G "Visual Studio 16 2019" ..

   You can see the list of available generators using cmake –help. For VS2017 use “Visual Studio 15 2017 Win64” and for VS2015 use “Visual Studio 14 2015 Win64”.

   If you want to build a parallel version of Nektar++ with MPI support, you need to add the -DNEKTAR_USE_MPI=ON switch to the cmake command, e.g.:

   cmake -G "Visual Studio 16 2019" -D NEKTAR_USE_MPI=ON ..
   Note: If you installed Boost binaries, as described above, you should ensure at this stage that the version of Boost that you installed has been correctly detected by CMake. You should see a number of lines of output from CMake saying – – Found boost <library name> library: followed by paths to one or more files which should be located in the directory where you installed your Boost binaries. If you do not see this output, CMake has failed to detect the installed Boost libraries and the build process will instead try to build Boost from source as part of building Nektar++.
   

   If you experience any issues with CMake finding pre-installed Boost, binaries ensure that you are working in a Visual Studio command prompt that was opened after you installed boost and set up the BOOST_HOME environment variable.

9. Assuming the configuration completes successfully and you see the message Build files have been written to: ..., you should now be ready to issue the build 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
10. After the build and installation process has completed, the executables will be available in build\dist\bin.
11. To use these executables, you need to modify your system PATH to include the bin directory and library directories where DLLs are stored. To do this, click the Start menu and type ‘env’, you should be presented with an “Edit the system environment variables” option. Alternatively, navigate to Settings > System > About > System info (under Related Settings on the right hand panel), select Advanced System Settings, and in the Advanced tab click the Environment Variables button. In the System Variables box, select Path and click Edit. Add the full paths to the following directories to the end of the list of paths shown in the “Edit environment variable” window:
    • nektar++-5.3.0\build\dist\lib\nektar++-5.3.0
    • nektar++-5.3.0\build\dist\bin
    • nektar++-5.3.0\ThirdParty
    • C:\local\boost_<boost_version>\<boost_lib_dir> where boost_<boost_version> is the directory where the boost binaries were installed to and <boost_lib_dir> is the name of the library directory within this location, e.g. lib64-msvc-14.2 or similar depending on the version of Boost binaries you installed.
12. To run the test suite, open a new command line window, change to the build 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:

• NEKTAR_BUILD_DEMOS (Recommended)

  Compiles the demonstration programs. These are primarily used by the regression testing suite to verify the Nektar++ library, but also provide an example of the basic usage of the framework.

• NEKTAR_BUILD_DOC

  Compiles the Doxygen documentation for the code. This will be put in

  $BUILDDIR/doxygen/html
• NEKTAR_BUILD_LIBRARY (Required)

  Compiles the Nektar++ framework libraries. This is required for all other options.

• NEKTAR_BUILD_PYTHON

  Installs the Python wrapper to Nektar++. Requires running the following command after installing Nektar++ in order to install the Python package for the current user:

  make nekpy-install-user

  Alternatively, the Python package can be installed for all users by running the following command with appropriate priviledges:

  make nekpy-install-system
• NEKTAR_BUILD_SOLVERS (Recommended)

  Compiles the solvers distributed with the Nektar++ framework.

  If enabling NEKTAR_BUILD_SOLVERS, individual solvers can be enabled or disabled. See Part III for the list of available solvers. You can disable solvers which are not required to reduce compilation time. See the NEKTAR_SOLVER_X option.

• NEKTAR_BUILD_TESTS (Recommended)

  Compiles the testing program used to verify the Nektar++ framework.

• NEKTAR_BUILD_TIMINGS

  Compiles programs used for timing Nektar++ operations.

• NEKTAR_BUILD_UNIT_TESTS

  Compiles tests for checking the core library functions.

• NEKTAR_BUILD_UTILITIES

  Compiles utilities for pre- and post-processing simulation data, including the mesh conversion and generation tool NekMesh and the FieldConvert post-processing utility.

• NEKTAR_SOLVER_X

  Enable compilation of the ’X’ solver.

• NEKTAR_UTILITY_X

  Enable compilation of the ’X’ utility.

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:

• NEKTAR_USE_ARPACK

  Build Nektar++ with support for ARPACK. This provides routines used for linear stability analyses. Alternative Arnoldi algorithms are also implemented directly in Nektar++.

• NEKTAR_USE_CCM

  Use the ccmio library provided with the Star-CCM package for reading ccm files. This option is required as part of NekMesh if you wish to convert a Star-CCM mesh into the Nektar format. It is possible to read a Tecplot plt file from Star-CCM but this output currently needs to be converted to ascii format using the Tecplot package.

• NEKTAR_USE_CWIPI

  Use the CWIPI library for enabling inter-process communication between two solvers. Solvers may also interface with third-party solvers using this package.

• NEKTAR_USE_FFTW

  Build Nektar++ with support for FFTW for performing Fast Fourier Transforms (FFTs). This is used only when using domains with homogeneous coordinate directions.

• NEKTAR_USE_HDF5

  Build Nektar++ with support for HDF5. This enables input/output in the HDF5 parallel file format, which can be very efficient for large numbers of processes. HDF5 output can be enabled by using a command-line option or in the SOLVERINFO section of the XML file. This option requires that Nektar++ be built with MPI support with NEKTAR_USE_MPI enabled and that HDF5 is compiled with MPI support.

• NEKTAR_USE_MESHGEN

  Build the NekMesh utility with support for generating meshes from CAD geometries. This enables use of the OpenCascade Community Edition library, as well as Triangle and Tetgen.

• NEKTAR_USE_METIS

  Build Nektar++ with support for the METIS graph partitioning library. This provides both an alternative mesh partitioning algorithm to SCOTCH for parallel simulations.

• NEKTAR_USE_MPI (Recommended)

  Build Nektar++ with MPI parallelisation. This allows solvers to be run in serial or parallel.

• NEKTAR_USE_PETSC

  Build Nektar++ with support for the PETSc package for solving linear systems.

• NEKTAR_USE_PYTHON3 (Requires NEKTAR_BUILD_PYTHON)

  Enables the generation of Python3 interfaces.

• NEKTAR_USE_SCOTCH (Recommended)

  Build Nektar++ with support for the SCOTCH graph partitioning library. This provides both a mesh partitioning algorithm for parallel simulations and enabled support for multi-level static condensation, so is highly recommended and enabled by default. However for systems that do not support SCOTCH build requirements (e.g. Windows), this can be disabled.

• NEKTAR_USE_SYSTEM_BLAS_LAPACK (Recommended)

  On Linux systems, use the default BLAS and LAPACK library on the system. This may not be the implementation offering the highest performance for your architecture, but it is the most likely to work without problem.

• NEKTAR_USE_VTK

  Build Nektar++ with support for VTK libraries. This is only needed for specialist utilities and is not needed for general use.

  Note: The VTK libraries are not needed for converting the output of simulations to VTK format for visualization as this is handled internally.

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

• ARPACK

  Library of iterative Arnoldi algorithms.

• BLAS_LAPACK

  Library of linear algebra routines.

• BOOST

  The Boost libraries are frequently provided by the operating system, so automatic compilation is not enabled by default. If you do not have Boost on your system, you can enable this to have Boost configured automatically.

• CCMIO

  I/O library for the Star-CCM+ format.

• CWIPI

  Library for inter-process exchange of data between different solvers.

• FFTW

  Fast-Fourier transform library.

• GSMPI

  (MPI-only) Parallel communication library.

• HDF5

  Hierarchical Data Format v5 library for structured data storage.

• METIS

  A graph partitioning library used for mesh partitioning when Nektar++ is run in parallel.

• OCE

  OpenCascade Community Edition 3D modelling library.

• PETSC

  A package for the parallel solution of linear algebra systems.

• SCOTCH

  A graph partitioning library used for mesh partitioning when Nektar++ is run in parallel, and reordering routines that are used in multi-level static condensation.

• TETGEN

  3D tetrahedral meshing library.

• TINYXML

  Library for reading and writing XML files.

• TRIANGLE

  2D triangular meshing library.

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

• NEKTAR_TEST_ALL

  Enables an extra set of more substantial and long-running tests.

• NEKTAR_TEST_USE_HOSTFILE

  By default, MPI tests are run directly with the mpiexec command together with the number of cores. If your MPI installation requires a hostfile, enabling this option adds the command line argument -hostfile hostfile to the command line arguments when tests are run with ctest or the Tester executable.

We have recently added explicit support to SIMD (Single Instruction Multiple Data) x86 instruction set extensions (i.e. AVX2, AVX512). Selected operators (the matrix free operators) utilize the SIMD types, if none of them is enabled these operators default to scalar types. The various extensions available are marked as advanced options (to visualize them in the cmake gui you need to press the t-button):

• NEKTAR_ENABLE_SIMD_AVX2

  Enables 256 bit wide vector types and set the appropriate compiler flags (gcc only).

• NEKTAR_ENABLE_SIMD_AVX512

  Enables 512 bit wide vector types and set the appropriate compiler flags (gcc only).

Note that if you are not configuring cmake for the first time, you need to delete the cached variable CMAKE_CXX_FLAGS in order for the appropriate flags to be set. Alternatively you can manually set the flag to target the appropriate architecture.