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++-5.0.0.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 ../
   • 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++-5.0.0.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.

   • 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 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.

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:
   • Rename libs-msvc14.0 to lib
   • Inside the lib directory, create duplicates of boost_zlib.dll and boost_bzip2.dll called zlib.dll and libbz2.dll
   • Add a BOOST_HOME environment variable. To do so, 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, click New. In the New System Variable window, type BOOST_HOME next to Variable name and C:\local\boost_1_61_0 next toVariable value.
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:
    • builds\dist\lib\nektar++-5.0.0
    • builds\dist\bin
    • Optionally, if you installed Boost from the binary packages, C:\local\boost_1_61_0 \lib
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:

• 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_DISABLE_BACKUPS

  By default, Nektar++ solvers and the FieldConvert utility will not overwrite any generated field files or output files they find an existing file with the same name. Instead, the existing file will be either moved to a backup file or you will be prompted to overwrite them. If you do not want this behaviour, then enabling this option will cause all pre-existing output to be overwritten silently.

• 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.