\section{Installing from Source} \label{s:installation: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. \subsection{Obtaining the source code} There are two ways to obtain the source code for \nekpp: \begin{itemize} \item Download the latest source-code archive from the \href{http://www.nektar.info/downloads}{Nektar++ downloads page}. \item Clone the git repository \begin{itemize} \item 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. \begin{lstlisting}[style=BashInputStyle] git clone http://gitlab.nektar.info/clone/nektar/nektar.git nektar++ \end{lstlisting} \item Using authenticated access. This will allow you to directly contribute back into the code. \begin{lstlisting}[style=BashInputStyle] git clone git@gitlab.nektar.info:nektar/nektar.git nektar++ \end{lstlisting} \begin{tipbox} You can easily switch to using the authenticated access from anonymous access at a later date. \end{tipbox} \end{itemize} \end{itemize} \subsection{Linux} \subsubsection{Prerequisites} \nekpp uses a number of external programs and libraries for some or all of its functionality. Some of these are \emph{required} and must be installed prior to compiling Nektar++, most of which are available as pre-built \emph{system} packages on most Linux distributions or can be installed manually by a \emph{user}. Others are optional and required only for specific features, or can be downloaded and compiled for use with Nektar++ \emph{automatically} (but not installed system-wide). \begin{center} \begin{tabular}{lccccl} \toprule & & \multicolumn{3}{c}{Installation} & \\ \cmidrule(r){3-5} Package & Req. & Sys. & User & Auto. & Note \\ \midrule C++ compiler & \cmark & \cmark & & & gcc, icc, etc \\ CMake $>2.8.7$ & \cmark & \cmark & \cmark & & Ncurses GUI optional \\ BLAS & \cmark & \cmark & \cmark & & Or MKL, ACML, OpenBLAS \\ LAPACK & \cmark & \cmark & \cmark & & \\ Boost $>=1.52$ & \cmark & \cmark & \cmark & \cmark & Compile with iostreams \\ ModMETIS & \cmark & & & \cmark & \\ FFTW $>3.0$ & & \cmark & \cmark & \cmark & For high-performance FFTs\\ ARPACK $>2.0$ & & \cmark & \cmark & & For arnoldi algorithms\\ OpenMPI & & \cmark & & & For parallel execution\\ GSMPI & & & & \cmark & For parallel execution\\ HDF5 & & \cmark & \cmark & \cmark & For large-scale parallel I/O\\ PETSc & & & \cmark & \cmark & Alternative linear solvers\\ Scotch & & \cmark & \cmark & \cmark & Alternative mesh partitioning\\ VTK $>5.8$ & & \cmark & \cmark & & Visualisation utilities\\ \bottomrule \end{tabular} \end{center} \begin{warningbox} Boost version 1.51 has a bug which prevents \nekpp working correctly. Please use a newer version. \end{warningbox} \subsubsection{Quick Start} Open a terminal. If you have downloaded the tarball, first unpack it: \begin{lstlisting}[style=BashInputStyle] tar -zxvf nektar++-(*\nekver*).tar.gz \end{lstlisting} Change into the \inlsh{nektar++} source code directory \begin{lstlisting}[style=BashInputStyle] mkdir -p build && cd build ccmake ../ make install \end{lstlisting} \subsubsection{Detailed instructions} From a terminal: \begin{enumerate} \item If you have downloaded the tarball, first unpack it \begin{lstlisting}[style=BashInputStyle] tar -zxvf nektar++-(*\nekver*).tar.gz \end{lstlisting} \item Change into the source-code directory, create a \inltt{build} subdirectory and enter it \begin{lstlisting}[style=BashInputStyle] mkdir -p build && cd build \end{lstlisting} \item Run the CMake GUI and configure the build by pressing \inltt{c} \begin{lstlisting}[style=BashInputStyle] ccmake ../ \end{lstlisting} \begin{itemize} \item Select the components of Nektar++ (prefixed with \inltt{NEKTAR\_BUILD\_}) you would like to build. Disabling solvers which you do not require will speed up the build process. \item Select the optional libraries you would like to use (prefixed with \inltt{NEKTAR\_USE\_}) for additional functionality. \item Select the libraries not already available on your system which you wish to be compiled automatically (prefixed with \inltt{THIRDPARTY\_BUILD\_}) \end{itemize} A full list of configuration options can be found in Section~\ref{s:installation:source:cmake}. \begin{notebox} Selecting \inltt{THIRDPARTY\_BUILD\_} options will request CMake to automatically download thirdparty libraries and compile them within the \nekpp directory. If you have administrative access to your machine, it is recommended to install the libraries system-wide through your package-management system. \end{notebox} \item Press \inltt{c} to configure the build. If errors arise relating to missing libraries, review the \inltt{THIRDPARTY\_BUILD\_} selections in the configuration step above or install the missing libraries manually or from system packages. \item When configuration completes without errors, press \inltt{c} again until the option \inltt{g} to generate build files appears. Press \inltt{g} to generate the build files and exit CMake. \item Compile the code \begin{lstlisting}[style=BashInputStyle] make install \end{lstlisting} During the build, missing third-party libraries will be automatically downloaded, configured and built in the \nekpp \inlsh{build} directory. % Hacky way to get an lstlisting to an argument of a macro \newsavebox\installationLinuxTip \begin{lrbox}{\installationLinuxTip}\begin{minipage}{0.8\linewidth} \begin{lstlisting}[style=BashInputStyle] make -j4 install \end{lstlisting} \end{minipage} \end{lrbox} \begin{tipbox} If you have multiple processors/cores on your system, compilation can be significantly increased by adding the \inlsh{-jX} option to make, where X is the number of simultaneous jobs to spawn. For example, use \noindent\usebox\installationLinuxTip on a quad-core system. \end{tipbox} \item Test the build by running unit and regression tests. \begin{lstlisting}[style=BashInputStyle] ctest \end{lstlisting} \end{enumerate} \subsection{OS X} \subsubsection{Prerequisites} \nekpp uses a number of external programs and libraries for some or all of its functionality. Some of these are \emph{required} and must be installed prior to compiling Nektar++, most of which are available on \emph{MacPorts} (www.macports.org) or can be installed manually by a \emph{user}. Others are optional and required only for specific features, or can be downloaded and compiled for use with Nektar++ \emph{automatically} (but not installed system-wide). \begin{notebox} To compile \nekpp 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 \href{http://connect.apple.com/}{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). \end{notebox} \begin{center} \begin{tabular}{lccccl} \toprule & & \multicolumn{3}{c}{Installation} & \\ \cmidrule(r){3-5} Package & Req. & MacPorts & User & Auto. & Note \\ \midrule Xcode & \cmark & & & & Provides developer tools \\ CMake $>2.8.7$ & \cmark & \texttt{cmake} & \cmark & & Ncurses GUI optional \\ BLAS & \cmark & & & & Part of Xcode \\ LAPACK & \cmark & & & & Part of Xcode \\ Boost $>=1.52$ & \cmark & \texttt{boost} & \cmark & \cmark & Compile with iostreams \\ TinyXML & \cmark & \texttt{tinyxml} & \cmark & \cmark & \\ ModMETIS & \cmark & & & \cmark & \\ FFTW $>3.0$ & & \texttt{fftw-3} & \cmark & \cmark & For high-performance FFTs\\ ARPACK $>2.0$ & & \texttt{arpack} & \cmark & & For arnoldi algorithms\\ OpenMPI & & \texttt{openmpi} & & & For parallel execution\\ GSMPI & & & & \cmark & For parallel execution\\ HDF5 & & \cmark & \cmark & \cmark & For large-scale parallel I/O\\ PETSc & & \texttt{petsc} & \cmark & \cmark & Alternative linear solvers\\ Scotch & & \texttt{scotch} & \cmark & \cmark & Alternative mesh partitioning\\ VTK $>5.8$ & & \texttt{vtk} & \cmark & & Visualisation utilities\\ \bottomrule \end{tabular} \end{center} \newsavebox\installationOSXMacPortsTip \begin{lrbox}{\installationOSXMacPortsTip}\begin{minipage}{0.8\linewidth} \begin{lstlisting}[style=BashInputStyle] sudo port install cmake \end{lstlisting} \end{minipage} \end{lrbox} \begin{tipbox} CMake, and some other software, is available from MacPorts (\url{http://macports.org}) and can be installed using, for example, \noindent\usebox\installationOSXMacPortsTip Package names are given in the table above. Similar packages also exist in other package managers such as Homebrew. \end{tipbox} \subsubsection{Quick Start} Open a terminal (Applications->Utilities->Terminal). If you have downloaded the tarball, first unpack it: \begin{lstlisting}[style=BashInputStyle] tar -zxvf nektar++-(*\nekver*).tar.gz \end{lstlisting} Change into the \inlsh{nektar++} source code directory \begin{lstlisting}[style=BashInputStyle] mkdir -p build && cd build ccmake ../ make install \end{lstlisting} \subsubsection{Detailed instructions} From a terminal (Applications->Utilities->Terminal): \begin{enumerate} \item If you have downloaded the tarball, first unpack it \begin{lstlisting}[style=BashInputStyle] tar -zxvf nektar++-(*\nekver*).tar.gz \end{lstlisting} \item Change into the source-code directory, create a \inltt{build} subdirectory and enter it \begin{lstlisting}[style=BashInputStyle] mkdir -p build && cd build \end{lstlisting} \item Run the CMake GUI and configure the build \begin{lstlisting}[style=BashInputStyle] ccmake ../ \end{lstlisting} Use the arrow keys to navigate the options and \inlsh{ENTER} to select/edit an option. \begin{itemize} \item Select the components of Nektar++ (prefixed with \inltt{NEKTAR\_BUILD\_}) you would like to build. Disabling solvers which you do not require will speed up the build process. \item Select the optional libraries you would like to use (prefixed with \inltt{NEKTAR\_USE\_}) for additional functionality. \item Select the libraries not already available on your system which you wish to be compiled automatically (prefixed with \inltt{THIRDPARTY\_BUILD\_}) \item \end{itemize} A full list of configuration options can be found in Section~\ref{s:installation:source:cmake}. \begin{notebox} Selecting \inltt{THIRDPARTY\_BUILD\_} options will request CMake to automatically download thirdparty libraries and compile them within the \nekpp directory. If you have administrative access to your machine, it is recommended to install the libraries system-wide through MacPorts. \end{notebox} \item Press \inltt{c} to configure the build. If errors arise relating to missing libraries (variables set to \inlsh{NOTFOUND}), review the \inltt{THIRDPARTY\_BUILD\_} selections in the previous step or install the missing libraries manually or through MacPorts. \item When configuration completes without errors, press \inltt{c} again until the option \inltt{g} to generate build files appears. Press \inltt{g} to generate the build files and exit CMake. \item Compile the code \begin{lstlisting}[style=BashInputStyle] make install \end{lstlisting} During the build, missing third-party libraries will be automatically downloaded, configured and built in the \nekpp \inlsh{build} directory. % Hacky way to get an lstlisting to an argument of a macro \newsavebox\installationMacTip \begin{lrbox}{\installationMacTip}\begin{minipage}{0.8\linewidth} \begin{lstlisting}[style=BashInputStyle] make -j4 install \end{lstlisting} \end{minipage} \end{lrbox} \begin{tipbox} If you have multiple processors/cores on your system, compilation can be significantly increased by adding the \inlsh{-jX} option to make, where X is the number of simultaneous jobs to spawn. For example, \noindent\usebox\installationMacTip \end{tipbox} \item Test the build by running unit and regression tests. \begin{lstlisting}[style=BashInputStyle] ctest \end{lstlisting} \end{enumerate} \subsection{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. \begin{center} \begin{tabular}{lcccl} \toprule & & \multicolumn{2}{c}{Installation} & \\ \cmidrule(r){3-4} Package & Req. & User & Auto. & Note \\ \midrule MS Visual Studio & \cmark & \cmark & & 2012 and 2013 known working\\ CMake $\geq 3.0$ & \cmark & \cmark & & \\ BLAS & \cmark & \cmark & \cmark & \\ LAPACK & \cmark & \cmark & \cmark & \\ Boost $\geq 1.55$ & \cmark & \cmark & \cmark & Compile with iostreams\\ ModMETIS & \cmark & \cmark & \cmark & \\ \bottomrule \end{tabular} \end{center} \subsubsection{Detailed instructions} \begin{enumerate} \item Install Microsoft Visual Studio 2013 (preferred) or 2012 (known to work). This can be obtained from Microsoft free of charge by using their Express developer tools from \url{http://www.visualstudio.com/en-us/products/visual-studio-express-vs.aspx}. \item Install WinRAR from \url{http://www.rarlab.com/download.htm}. \item Install CMake 3.0+ from \url{http://www.cmake.org/download/}. When prompted, select the option to add CMake to the system PATH. \item (Optional) Install Git from \url{http://git-scm.com/download/win} to use the development versions of \nekpp. 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. \item (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 \url{http://sourceforge.net/projects/boost/files/boost-binaries/1.57.0/}. By default these install into \inlsh{C:\textbackslash local\textbackslash boost\_1\_57\_0}. If you use these libraries, you will need to: \begin{itemize} \item Rename \texttt{libs-msvc12.0} to \texttt{lib} \item Inside the \texttt{lib} directory, create duplicates of \texttt{boost\_zlib.dll} and \texttt{boost\_bzip2.dll} called \texttt{zlib.dll} and \texttt{libbz2.dll}. \end{itemize} \item Unpack \inlsh{nektar++-\nekver.tar.gz} using WinRAR. \begin{notebox} Some Windows versions do not recognise the path of a folder which has \inltt{++} in the name. If you think that your Windows version can not handle path containing special characters, you should rename \inlsh{nektar++-\nekver} to \inlsh{nektar-\nekver}. \end{notebox} \item Create a \inlsh{builds} directory within the \inlsh{nektar++-\nekver} subdirectory. \item Open a Visual Studio terminal. From the start menu, this can be found in \emph{All Programs > Visual Studio 2013 > Visual Studio Tools > Developer Command Prompt for VS2013}. \item Change directory into the \texttt{builds} directory and run the CMake graphical utility: \begin{lstlisting}[style=BashInputStyle] cd C:\path\to\nektar\builds cmake-gui .. \end{lstlisting} \item Select the build system you want to generate build scripts for. Note that \emph{Visual Studio 2013} is listed as \emph{Visual Studio 12} in the drop-down list. If you have a 64-bit installation of Windows 7, you should select the \emph{Win64} variant, otherwise 32-bit executables will be generated. Select the option to use the native compilers. \item Click the \emph{Configure} button, then the \emph{Generate} button. \item Return to the command line and issue the command: \begin{lstlisting}[style=BashInputStyle] msbuild INSTALL.vcxproj /p:Configuration=Release \end{lstlisting} To build in parallel with, for example, 12 processors, issue: \begin{lstlisting}[style=BashInputStyle] msbuild INSTALL.vcxproj /p:Configuration=Release /m:12 \end{lstlisting} \item After the installation process is completed, the executables will be available in \inlsh{builds\textbackslash dist\textbackslash bin}. \item To use these executables, you need to modify your system \inlsh{PATH} to include the library directories where DLLs are stored. To do this, navigate to \emph{Control Panel > System and Security > System}, select \emph{Advanced System Settings}, and in the \emph{Advanced} tab click the \emph{Environment Variables}. In the \emph{System Variables} box, select \emph{Path} and click \emph{Edit}. To the end of this list, add the \textbf{full paths} to directories: \begin{itemize} \item \inlsh{builds\textbackslash dist\textbackslash lib\textbackslash nektar++-\nekver} \item \inlsh{builds\textbackslash dist\textbackslash bin} \item Optionally, if you installed Boost from the binary packages, \inlsh{C:\textbackslash local\textbackslash boost\_1\_57\_0 \textbackslash lib} \end{itemize} \item To run the test suite, open a \textbf{new} command line window, change to the \inlsh{builds} directory, and then issue the command \begin{lstlisting}[style=BashInputStyle] ctest -C Release \end{lstlisting} \end{enumerate} \subsection{CMake Option Reference} \label{s:installation:source:cmake} 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. \subsubsection{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 \nekpp package can be selected using the following options: \begin{itemize} \item \inlsh{NEKTAR\_BUILD\_DEMOS} (Recommended) Compiles the demonstration programs. These are primarily used by the regression testing suite to verify the \nekpp library, but also provide an example of the basic usage of the framework. \item \inlsh{NEKTAR\_BUILD\_DOC} Compiles the Doxygen documentation for the code. This will be put in \begin{lstlisting}[style=BashInputStyle] $BUILDDIR/doxygen/html \end{lstlisting} \item \inlsh{NEKTAR\_BUILD\_LIBRARY} (Required) Compiles the Nektar++ framework libraries. This is required for all other options. \item \inlsh{NEKTAR\_BUILD\_SOLVERS} (Recommended) Compiles the solvers distributed with the \nekpp framework. If enabling \inlsh{NEKTAR\_BUILD\_SOLVERS}, individual solvers can be enabled or disabled. See Part~\ref{p:applications} for the list of available solvers. You can disable solvers which are not required to reduce compilation time. See the \inlsh{NEKTAR\_SOLVER\_X} option. \item \inlsh{NEKTAR\_BUILD\_TESTS} (Recommended) Compiles the testing program used to verify the \nekpp framework. \item \inlsh{NEKTAR\_BUILD\_TIMINGS} Compiles programs used for timing \nekpp operations. \item \inlsh{NEKTAR\_BUILD\_UNIT\_TESTS} Compiles tests for checking the core library functions. \item \inlsh{NEKTAR\_BUILD\_UTILITIES} Compiles utilities for pre- and post-processing simulation data. \item \inlsh{NEKTAR\_SOLVER\_X} Enabled compilation of the 'X' solver. \end{itemize} A number of ThirdParty libraries are required by \nekpp. There are also optional libraries which provide additional functionality. These can be selected using the following options: \begin{itemize} \item \inlsh{NEKTAR\_USE\_ACML} Use the optimised BLAS library for AMD processors. \item \inlsh{NEKTAR\_USE\_ACCELERATE\_FRAMEWORK} Use the Mac Osx accelerate framework for BLAS and LAPACK methods. This option should only be required under in a Mac OSX environment. \item \inlsh{NEKTAR\_USE\_ARPACK} Build \nekpp with support for ARPACK. This provides routines used for linear stability analyses. Alternative Arnoldi algorithms are also implemented directly in \nekpp. \item \inlsh{NEKTAR\_USE\_BLAS\_LAPACK} (Required) Enables the use of Basic Linear Algebra Subroutines libraries for linear algebra operations. \item \inlsh{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. \item \inlsh{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. \item \inlsh{NEKTAR\_USE\_FFTW} Build \nekpp with support for FFTW for performing Fast Fourier Transforms (FFTs). This is used only when using domains with homogeneous coordinate directions. \item \inlsh{NEKTAR\_USE\_HDF5} Build \nekpp with support for HDF5. This enables input/output in the HDF5 parallel file format, which can be very efficient for large numbers of processors. HDF5 output can be enabled by using a command-line option or in the \inlsh{SOLVERINFO} section of the XML file. This option requires that \nekpp be built with MPI support with \inlsh{NEKTAR\_USE\_MPI} enabled. \item \inlsh{NEKTAR\_USE\_MKL} Use the Intel MKL library. This is typically available on cluster environments and should offer performance tuned for the specific cluster environment. \item \inlsh{NEKTAR\_USE\_MPI} (Recommended) Build Nektar++ with MPI parallelisation. This allows solvers to be run in serial or parallel. \item \inlsh{NEKTAR\_USE\_OPENBLAS} Use OpenBLAS for the BLAS library. OpenBLAS is based on the Goto BLAS implementation and generally offers better performance than a non-optimised system BLAS. However, the library must be installed on the system. \item \inlsh{NEKTAR\_USE\_PETSC} Build \nekpp with support for the PETSc package for solving linear systems. \item \inlsh{NEKTAR\_USE\_SCOTCH} Build \nekpp with support for the SCOTCH graph partitioning library. This provides an alternative mesh partitioning algorithm to METIS. However, METIS is still required as it is used by the multi-level static condensation algorithm. \item \inlsh{NEKTAR\_USE\_SMV} Build \nekpp with support for optimised sparse matrix-vector operations. \item \inlsh{NEKTAR\_USE\_VTK} Build \nekpp with support for VTK libraries. This is only needed for specialist utilities and is not needed for general use. \begin{notebox} The VTK libraries are not needed for converting the output of simulations to VTK format for visualization as this is handled internally. \end{notebox} \end{itemize} The \inlsh{THIRDPARTY\_BUILD\_X} options select which third-party libraries are automatically built during the \nekpp build process. Below are the choices of X: \begin{itemize} \item \inlsh{BOOST} The \emph{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. \item \inlsh{GSMPI} (MPI-only) Parallel communication library. \item \inlsh{LOKI} An implementation of a singleton. \item \inlsh{METIS} A graph partitioning library used for substructuring of matrices and mesh partitioning when \nekpp is run in parallel. \item \inlsh{PETSC} A package for the parallel solution of linear algebra systems. \item \inlsh{SCOTCH} An alternative graph partitioning library used for mesh partitioning when \nekpp is run in parallel. \item \inlsh{TINYXML} Library for reading and writing XML files. \end{itemize}