\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++. \begin{lstlisting}[style=BashInputStyle] git clone http://gitlab.nektar.info/clone/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.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 Package & Req. & \multicolumn{3}{c}{Installation} & Note \\ \cline{3-5} & & Sys. & User & Auto. & \\ \midrule C++ compiler & \checkmark & \checkmark & & & gcc, icc, etc \\ CMake $>2.8.7$ & \checkmark & \checkmark & \checkmark & & Ncurses GUI optional \\ BLAS & \checkmark & \checkmark & \checkmark & & Or MKL, ACML, OpenBLAS \\ LAPACK & \checkmark & \checkmark & \checkmark & & \\ Boost $>1.49$ & \checkmark & \checkmark & \checkmark & \checkmark & Compile with iostreams \\ ModMETIS & \checkmark & & & \checkmark & \\ FFTW $>3.0$ & & \checkmark & \checkmark & \checkmark & For high-performance FFTs\\ ARPACK $>2.0$ & & \checkmark & \checkmark & & For arnoldi algorithms\\ OpenMPI & & \checkmark & & & For parallel execution\\ GSMPI & & & & \checkmark & For parallel execution\\ PetSC & & & \checkmark & \checkmark & Alternative linear solvers\\ Scotch & & \checkmark & \checkmark & \checkmark & Alternative mesh partitioning\\ VTK $>5.8$ & & \checkmark & \checkmark & & 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++-4.0.0.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++-4.0.0.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} \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{OSX} \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 OSX, 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 Package & Req. & \multicolumn{3}{c}{Installation} & Note \\ \cline{3-5} & & MacPorts & User & Auto. & \\ \midrule Xcode & \checkmark & & & & gcc, icc, etc \\ CMake $>2.8.7$ & \checkmark & \checkmark & \checkmark & & Ncurses GUI optional \\ BLAS & \checkmark & & & & Part of Xcode \\ LAPACK & \checkmark & & & & Part of Xcode \\ Boost $>1.49$ & \checkmark & \checkmark & \checkmark & \checkmark & Compile with iostreams \\ ModMETIS & \checkmark & & & \checkmark & \\ FFTW $>3.0$ & & \checkmark & \checkmark & \checkmark & For high-performance FFTs\\ ARPACK $>2.0$ & & \checkmark & \checkmark & & For arnoldi algorithms\\ OpenMPI & & \checkmark & & & For parallel execution\\ GSMPI & & & & \checkmark & For parallel execution\\ PetSC & & \checkmark & \checkmark & \checkmark & Alternative linear solvers\\ Scotch & & & \checkmark & \checkmark & Alternative mesh partitioning\\ VTK $>5.8$ & & \checkmark & \checkmark & & 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 \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++-4.0.0.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++-4.0.0.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} The following software must be pre-installed on your system: \begin{itemize} \item Microsoft Visual Studio 2008 \begin{itemize} \item Visual Studio 2008 Service Pack 1 is required \end{itemize} \item Python Compiler 2.7.2+ (download from \url{http://www.http//python.org/download/}) \item CMake 2.8.7+ (download from \url{http://www.cmake.org/HTML/index.html}) \begin{itemize} \item When prompted, select the option to add CMake to the system PATH. \end{itemize} \item WinRAR (download from \url{http://www.rarlab.com/download.htm}) \end{itemize} \newcommand{\nekver}{\input{../../VERSION}} \subsubsection{Unpack the tarballs} \begin{itemize} \item Unpack the \inlsh{nektar++-\nekver.tar.gz} file using WinRAR \item Create a \inlsh{ThirdParty} directory within the \inlsh{nektar++-\nekver} subdirectory. \begin{notebox} Some windows version 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 \inlsh{nektar++-\nekver} to \inlsh{nektar-\nekver}. \end{notebox} \end{itemize} \subsubsection{Building ThirdParty libraries} Download ThirdParty packages from \inlsh{www.nektar.info/thirdparty} as requried below. \begin{itemize} \item \textbf{TinyXML} Extract the \inlsh{tinyxml\_2\_4\_3.zip} archive into the ThirdParty directory using WinRAR. This will create a \inlsh{tinyxml} sub-directory. \item \textbf{Loki} Extract the \inlsh{loki-0.1.3.tar.bz2} archive into the ThirdParty directory using WinRAR. This will create a \inlsh{loki-0.1.3} sub-directory. \item \textbf{Mod-METIS} Extract the \inlsh{modmetis-4.0.tar.bz2} archive into the ThirdParty directory using WinRAR. This will create a \inlsh{modmetis-4.0} sub-directory. \begin{itemize} \item Open a command-line terminal and change to \inlsh{ThirdParty\textbackslash modmetis-4.0\textbackslash build}. \item Run \begin{lstlisting}[style=BashInputStyle] cmake ..\ vcbuild "ModifiedMetis.sln" vcbuild "INSTALL.vcproj" \end{lstlisting} \end{itemize} \item \textbf{NIST SparseBLAS} Extract the \inlsh{spblastk0.9b} archive into the ThirdParty directory using WinRAR. This will create a \inlsh{spblastk0.9b} sub-directory. \begin{itemize} \item From a command-line terminal change to \inlsh{ThirdParty\textbackslash spblastk0.9b\textbackslash build}. \item Run \begin{lstlisting}[style=BashInputStyle] cmake ..\ vcbuild "NistSparseBlasToolkit.sln" vcbuild "INSTALL.vcproj" \end{lstlisting} \end{itemize} \item \textbf{BLAS/LAPACK} Extract the \inlsh{blaslapack-dll.zip} archive into the ThirdParty directory using WinRAR. This will create \inlsh{blas\_win32.*} and \inlsh{lapack\_win32.*} files in the ThirdParty directory. \item \textbf{ZLib} Extract the \inlsh{zlib-1.2.3.tar.bz2} archive using WinRAR. This will create a \inlsh{zlib-1.2.3} sub-directory. \item \textbf{Boost} Extract the \inlsh{boost\_1\_49\_0.tar.bz2} archive using WinRAR. This will create a {{{boost\_1\_49\_0}}} sub-directory. \begin{itemize} \item Open a command-line terminal and change to the \inlsh{boost\_1\_49\_0} directory and run: \begin{lstlisting}[style=BashInputStyle] bootstrap.bat b2.exe -s ZLIB_SOURCE=..\..\..\..\zlib-1.2.3 \ --prefix=..\boost toolset=msvc-9.0 install \end{lstlisting} \end{itemize} \begin{notebox} Boost might not be able to find the \inlsh{zlib-1.2.3} directory specified by the relative path in the command line above. If this happens, you can replace the relative path with the absolute path of the \inlsh{zlib-1.2.3} directory (surround it in quotes). \end{notebox} \end{itemize} \subsubsection{Building Nektar++} Change to the \inlsh{nektar++-\nekver\textbackslash builds} directory. \begin{lstlisting}[style=BashInputStyle] cmake ..\ vcbuild "Nektar++.sln" vcbuild "INSTALL.vcproj" \end{lstlisting} To modify the default configuration use \inlsh{cmake -i ..\textbackslash} or use the CMake-gui application. \subsubsection{Notes on building on windows 7 64 bit with Visual Studio 10} To get a build working on a windows 7 64 bit machine with VS10, the following modifications were helpful or necessary: \begin{itemize} \item Instead of vcbuild (which doesn't exist in VS10) use msbuild. \item You may need to run \\ \inlsh{C:\textbackslash Program Files (x86)\textbackslash Microsoft Visual Studio 10.0\textbackslash VC\textbackslash vcvarsall.bat} \\ first to set up some registry entries to run msbuild. Try without first. \item You will probably wish to put msbuild into your path \item project files created by cmake are likely to have the extension .vcxproj rather than .vcproj. \item When running b2.exe, provide the full path to zlib. Not doing so will only cause an error later when running cmake for Nektar++ \item When running b2.exe, use toolset=msvc-10.0 instead of toolset=msvc-9.0 \item When using cmake for nektar++, it is helpful to use the cmake gui \item Using the cmake gui, set the BOOST\_ROOT variable to the appropriate path for boost * Set Boost\_USE\_STATIC\_LIBS = ON (I did this by editing CMakeLists.txt, but setting it from the gui should work) \item When running msbuild "Nektar++.sln" I got error can't find zlib.lib. As a workaround, copy the files zlibd.lib (two of them) and rename the copies zlib.lib. However, I believe these are the debug builds, so it would be better to work out how to build in release mode. \item At this stage, when running msbuild "Nektar++.sln", I got boost link errors. To fix them, look for the line \begin{lstlisting}[style=BashInputStyle] ADD_DEFINITIONS(-DBOOST_ALL_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK \ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_THREAD_DYN_LINK) \end{lstlisting} in the \inlsh{CMakeLists.txt} file and comment it out (and run cmake again) \item At this point, when building Nektar, linking against boost is fine, but I got a compile error in TestData.cpp. This could be fixed by editing TestData.cpp and replacing the line \begin{lstlisting} m_doc = new TiXmlDocument(pFilename.file_string().c_str()); \end{lstlisting} with \begin{lstlisting} m_doc =new TiXmlDocument(pFilename.string().c_str()); \end{lstlisting} \end{itemize} \begin{notebox} The step of building INSTALL.vcproj causes executables and dlls to be copied into a directory \inlsh{<path>\textbackslash nektar\textbackslash builds-test\textbackslash dist\textbackslash bin}. The executables should be run from here so that they can find the dlls they need. \end{notebox} If you wish to put a breakpoint in to step through Nektar++, you may need to run from the folder the executable was built in so that the pdb files are in the expected place. Then a workaround is to copy the dlls into that folder. \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 Chapter~\ref{s:solvers} 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\_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\_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\_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\_FFTW} Build Nektar++ 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\_ARPACK} Build Nektar++ with support for ARPACK. This provides routines used for linear stability analyses. Alternative Arnoldi algorithms are also implemented directly in Nektar++. \item \inlsh{NEKTAR\_USE\_VTK} Build Nektar++ 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 Nektar++ is run in parallel. \item \inlsh{TINYXML} Library for reading and writing XML files. \end{itemize}