source.tex 25.8 KB
 Chris Cantwell committed Aug 08, 2014 1 \section{Installing from Source}  Chris Cantwell committed Aug 12, 2014 2 \label{s:installation:source}  Chris Cantwell committed Aug 08, 2014 3   Chris Cantwell committed Sep 04, 2014 4 This section explains how to build Nektar++ from the source-code package.  Chris Cantwell committed Aug 13, 2014 5 6  Nektar++ uses a number of third-party libraries. Some of these are required,  Chris Cantwell committed Sep 04, 2014 7 8 9 10 11 12 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.  Chris Cantwell committed Aug 13, 2014 13 14 15 16 17 18 19 20 21 22  \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  Chris Cantwell committed Sep 04, 2014 23  credentials but any changes to the code cannot be pushed to the  Michael Turner committed Jan 08, 2016 24  public repository. Use this initially if you would like to try using  Chris Cantwell committed Jul 14, 2015 25  Nektar++ or make local changes to the code.  Chris Cantwell committed Aug 13, 2014 26  \begin{lstlisting}[style=BashInputStyle]  Chris Cantwell committed Jan 20, 2015 27  git clone http://gitlab.nektar.info/clone/nektar/nektar.git nektar++  Chris Cantwell committed Aug 13, 2014 28 29 30 31  \end{lstlisting} \item Using authenticated access. This will allow you to directly contribute back into the code. \begin{lstlisting}[style=BashInputStyle]  Pavel Burovskiy committed Dec 05, 2014 32  git clone git@gitlab.nektar.info:nektar/nektar.git nektar++  Chris Cantwell committed Aug 13, 2014 33  \end{lstlisting}  Chris Cantwell committed Sep 04, 2014 34 35 36 37  \begin{tipbox} You can easily switch to using the authenticated access from anonymous access at a later date. \end{tipbox}  Chris Cantwell committed Aug 13, 2014 38 39 40  \end{itemize} \end{itemize}  Chris Cantwell committed Aug 08, 2014 41 \subsection{Linux}  Chris Cantwell committed Aug 13, 2014 42 \subsubsection{Prerequisites}  Chris Cantwell committed Oct 22, 2014 43 44 45 46 47 48 49 50 51 52 53 \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  Dave Moxey committed Nov 04, 2014 54 55  & & \multicolumn{3}{c}{Installation} & \\ \cmidrule(r){3-5} Package & Req. & Sys. & User & Auto. & Note \\  Chris Cantwell committed Oct 22, 2014 56 \midrule  Dave Moxey committed Nov 04, 2014 57 58 C++ compiler & \cmark & \cmark & & & gcc, icc, etc \\ CMake $>2.8.7$ & \cmark & \cmark & \cmark & & Ncurses  Chris Cantwell committed Oct 22, 2014 59 60 GUI optional \\  Dave Moxey committed Nov 04, 2014 61 BLAS & \cmark & \cmark & \cmark & & Or MKL,  Chris Cantwell committed Oct 22, 2014 62 63 ACML, OpenBLAS \\  Dave Moxey committed Nov 04, 2014 64 LAPACK & \cmark & \cmark & \cmark & & \\  Chris Cantwell committed Apr 29, 2015 65 Boost $>=1.52$ & \cmark & \cmark & \cmark & \cmark & Compile  Chris Cantwell committed Oct 22, 2014 66 67 with iostreams \\  Dave Moxey committed Nov 04, 2014 68 69 ModMETIS & \cmark & & & \cmark & \\ FFTW $>3.0$ & & \cmark & \cmark & \cmark & For  Chris Cantwell committed Oct 22, 2014 70 high-performance FFTs\\  Dave Moxey committed Nov 04, 2014 71 ARPACK $>2.0$ & & \cmark & \cmark & & For  Chris Cantwell committed Oct 22, 2014 72 arnoldi algorithms\\  Dave Moxey committed Nov 04, 2014 73 OpenMPI & & \cmark & & & For  Chris Cantwell committed Oct 22, 2014 74 parallel execution\\  Dave Moxey committed Nov 04, 2014 75 GSMPI & & & & \cmark & For  Chris Cantwell committed Oct 22, 2014 76 parallel execution\\  Dave Moxey committed May 01, 2016 77 HDF5 & & \cmark & \cmark & \cmark & For  Dave Moxey committed Aug 12, 2016 78 large-scale parallel I/O (requires CMake >3.1)\\  Dave Moxey committed Nov 07, 2014 79 PETSc & & & \cmark & \cmark &  Chris Cantwell committed Oct 22, 2014 80 Alternative linear solvers\\  Dave Moxey committed Nov 04, 2014 81 Scotch & & \cmark & \cmark & \cmark &  Chris Cantwell committed Oct 22, 2014 82 Alternative mesh partitioning\\  Dave Moxey committed Nov 04, 2014 83 VTK $>5.8$ & & \cmark & \cmark & & Visualisation  Chris Cantwell committed Oct 22, 2014 84 85 86 87 88 89 90 91 92 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}  Chris Cantwell committed Aug 13, 2014 93 94 95 96 97 98 99  \subsubsection{Quick Start} Open a terminal. If you have downloaded the tarball, first unpack it: \begin{lstlisting}[style=BashInputStyle]  Chris Cantwell committed Jan 20, 2015 100 tar -zxvf nektar++-(*\nekver*).tar.gz  Chris Cantwell committed Aug 13, 2014 101 102 103 \end{lstlisting} Change into the \inlsh{nektar++} source code directory \begin{lstlisting}[style=BashInputStyle]  Michael Turner committed Jan 08, 2016 104  mkdir -p build && cd build  Chris Cantwell committed Aug 13, 2014 105 106 107 108 109 110 111 112 113  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]  Chris Cantwell committed Jan 20, 2015 114 tar -zxvf nektar++-(*\nekver*).tar.gz  Chris Cantwell committed Aug 13, 2014 115  \end{lstlisting}  Michael Turner committed Jan 08, 2016 116   Chris Cantwell committed Aug 13, 2014 117  \item Change into the source-code directory, create a \inltt{build}  Michael Turner committed Jan 08, 2016 118  subdirectory and enter it  Chris Cantwell committed Aug 13, 2014 119 120 121  \begin{lstlisting}[style=BashInputStyle] mkdir -p build && cd build \end{lstlisting}  Michael Turner committed Jan 08, 2016 122   Chris Cantwell committed Jan 20, 2015 123  \item Run the CMake GUI and configure the build by pressing \inltt{c}  Chris Cantwell committed Aug 13, 2014 124 125 126 127 128 129 130 131 132  \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.  Chris Cantwell committed Oct 22, 2014 133  \item Select the libraries not already available on your system which  Michael Turner committed Jan 08, 2016 134  you wish to be compiled automatically (prefixed with  Chris Cantwell committed Oct 22, 2014 135  \inltt{THIRDPARTY\_BUILD\_})  Chris Cantwell committed Aug 13, 2014 136 137 138  \end{itemize} A full list of configuration options can be found in Section~\ref{s:installation:source:cmake}.  Chris Cantwell committed Oct 22, 2014 139 140 141 142 143 144 145 146  \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}  Michael Turner committed Jan 08, 2016 147 148   Chris Cantwell committed Aug 13, 2014 149  \item Press \inltt{c} to configure the build. If errors arise relating to  Chris Cantwell committed Oct 22, 2014 150 151 152  missing libraries, review the \inltt{THIRDPARTY\_BUILD\_} selections in the configuration step above or install the missing libraries manually or from system packages.  Michael Turner committed Jan 08, 2016 153   Chris Cantwell committed Aug 13, 2014 154 155 156  \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.  Michael Turner committed Jan 08, 2016 157   Chris Cantwell committed Aug 13, 2014 158 159 160 161 162 163  \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.  Michael Turner committed Jan 08, 2016 164   Chris Cantwell committed Aug 13, 2014 165 166 167 168 169 170 171 172  % 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}  Michael Turner committed Jan 08, 2016 173   Chris Cantwell committed Aug 13, 2014 174 175 176  \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  Chris Cantwell committed Oct 22, 2014 177  the number of simultaneous jobs to spawn. For example, use  Michael Turner committed Jan 08, 2016 178   Chris Cantwell committed Aug 13, 2014 179  \noindent\usebox\installationLinuxTip  Michael Turner committed Jan 08, 2016 180   Chris Cantwell committed Oct 22, 2014 181  on a quad-core system.  Chris Cantwell committed Aug 13, 2014 182  \end{tipbox}  Michael Turner committed Jan 08, 2016 183   Chris Cantwell committed Aug 13, 2014 184 185 186 187 188  \item Test the build by running unit and regression tests. \begin{lstlisting}[style=BashInputStyle] ctest \end{lstlisting} \end{enumerate}  Chris Cantwell committed Aug 08, 2014 189   Dave Moxey committed Nov 04, 2014 190 \subsection{OS X}  Chris Cantwell committed Aug 13, 2014 191 192  \subsubsection{Prerequisites}  Chris Cantwell committed Oct 22, 2014 193 194 195 196 \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  Michael Turner committed Jan 08, 2016 197 optional and required only for specific features, or can be downloaded and  Chris Cantwell committed Oct 22, 2014 198 199 200 201 compiled for use with Nektar++ \emph{automatically} (but not installed system-wide). \begin{notebox}  Dave Moxey committed Nov 04, 2014 202 203 204 205 206 207  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).  Chris Cantwell committed Oct 22, 2014 208 \end{notebox}  Chris Cantwell committed Aug 13, 2014 209   Chris Cantwell committed Oct 22, 2014 210 211 212 \begin{center} \begin{tabular}{lccccl} \toprule  Dave Moxey committed Nov 04, 2014 213 214  & & \multicolumn{3}{c}{Installation} & \\ \cmidrule(r){3-5} Package & Req. & MacPorts & User & Auto. & Note \\  Chris Cantwell committed Oct 22, 2014 215 \midrule  Dave Moxey committed Nov 07, 2014 216 217 Xcode & \cmark & & & & Provides developer tools \\ CMake $>2.8.7$ & \cmark & \texttt{cmake} & \cmark & & Ncurses  Chris Cantwell committed Oct 22, 2014 218 GUI optional \\  Dave Moxey committed Nov 07, 2014 219 BLAS & \cmark & & & & Part of  Chris Cantwell committed Oct 22, 2014 220 Xcode \\  Dave Moxey committed Nov 07, 2014 221 LAPACK & \cmark & & & & Part of  Chris Cantwell committed Oct 22, 2014 222 Xcode \\  Chris Cantwell committed Apr 29, 2015 223 Boost $>=1.52$ & \cmark & \texttt{boost} & \cmark & \cmark & Compile  Dave Moxey committed Nov 07, 2014 224 225 226 227 with iostreams \\ TinyXML & \cmark & \texttt{tinyxml} & \cmark & \cmark & \\ ModMETIS & \cmark & & & \cmark & \\ FFTW $>3.0$ & & \texttt{fftw-3} & \cmark & \cmark & For  Chris Cantwell committed Oct 22, 2014 228 high-performance FFTs\\  Dave Moxey committed Nov 07, 2014 229 ARPACK $>2.0$ & & \texttt{arpack} & \cmark & & For  Chris Cantwell committed Oct 22, 2014 230 arnoldi algorithms\\  Dave Moxey committed Nov 07, 2014 231 OpenMPI & & \texttt{openmpi} & & & For  Chris Cantwell committed Oct 22, 2014 232 parallel execution\\  Dave Moxey committed Nov 07, 2014 233 GSMPI & & & & \cmark & For  Chris Cantwell committed Oct 22, 2014 234 parallel execution\\  Dave Moxey committed May 01, 2016 235 HDF5 & & \cmark & \cmark & \cmark & For  Dave Moxey committed Aug 12, 2016 236 large-scale parallel I/O (requires CMake >3.1)\\  Dave Moxey committed Nov 07, 2014 237 PETSc & & \texttt{petsc} & \cmark & \cmark &  Chris Cantwell committed Oct 22, 2014 238 Alternative linear solvers\\  Dave Moxey committed Nov 07, 2014 239 Scotch & & \texttt{scotch} & \cmark & \cmark &  Chris Cantwell committed Oct 22, 2014 240 Alternative mesh partitioning\\  Dave Moxey committed Nov 07, 2014 241 VTK $>5.8$ & & \texttt{vtk} & \cmark & &  Chris Cantwell committed Oct 22, 2014 242 243 244 245 246 247 248 Visualisation utilities\\ \bottomrule \end{tabular} \end{center} \newsavebox\installationOSXMacPortsTip \begin{lrbox}{\installationOSXMacPortsTip}\begin{minipage}{0.8\linewidth}  Chris Cantwell committed Sep 24, 2014 249 250 251 \begin{lstlisting}[style=BashInputStyle] sudo port install cmake \end{lstlisting}  Chris Cantwell committed Oct 22, 2014 252 253 254 255 256 257 258 259 \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  Dave Moxey committed Nov 07, 2014 260 261 262  Package names are given in the table above. Similar packages also exist in other package managers such as Homebrew.  Chris Cantwell committed Oct 22, 2014 263 \end{tipbox}  Chris Cantwell committed Aug 13, 2014 264 265 266 267 268 269 270  \subsubsection{Quick Start} Open a terminal (Applications->Utilities->Terminal). If you have downloaded the tarball, first unpack it: \begin{lstlisting}[style=BashInputStyle]  Chris Cantwell committed Jan 20, 2015 271 tar -zxvf nektar++-(*\nekver*).tar.gz  Chris Cantwell committed Aug 13, 2014 272 273 274 \end{lstlisting} Change into the \inlsh{nektar++} source code directory \begin{lstlisting}[style=BashInputStyle]  Michael Turner committed Jan 08, 2016 275  mkdir -p build && cd build  Chris Cantwell committed Aug 13, 2014 276 277 278 279 280 281 282 283 284  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]  Chris Cantwell committed Jan 20, 2015 285 tar -zxvf nektar++-(*\nekver*).tar.gz  Chris Cantwell committed Aug 13, 2014 286 287 288  \end{lstlisting} \item Change into the source-code directory, create a \inltt{build}  Michael Turner committed Jan 08, 2016 289  subdirectory and enter it  Chris Cantwell committed Aug 13, 2014 290 291 292  \begin{lstlisting}[style=BashInputStyle] mkdir -p build && cd build \end{lstlisting}  Michael Turner committed Jan 08, 2016 293   Chris Cantwell committed Aug 13, 2014 294 295 296 297  \item Run the CMake GUI and configure the build \begin{lstlisting}[style=BashInputStyle] ccmake ../ \end{lstlisting}  Chris Cantwell committed Sep 24, 2014 298 299  Use the arrow keys to navigate the options and \inlsh{ENTER} to select/edit an option.  Chris Cantwell committed Aug 13, 2014 300 301 302 303 304 305  \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.  Chris Cantwell committed Oct 22, 2014 306  \item Select the libraries not already available on your system which  Michael Turner committed Jan 08, 2016 307  you wish to be compiled automatically (prefixed with  Chris Cantwell committed Oct 22, 2014 308  \inltt{THIRDPARTY\_BUILD\_})  Michael Turner committed Jan 08, 2016 309  \item  Chris Cantwell committed Aug 13, 2014 310 311 312  \end{itemize} A full list of configuration options can be found in Section~\ref{s:installation:source:cmake}.  Chris Cantwell committed Oct 22, 2014 313   Chris Cantwell committed Sep 24, 2014 314 315 316 317 318 319  \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}  Michael Turner committed Jan 08, 2016 320   Chris Cantwell committed Oct 22, 2014 321  \item Press \inltt{c} to configure the build. If errors arise relating to  Michael Turner committed Jan 08, 2016 322  missing libraries (variables set to \inlsh{NOTFOUND}), review the  Chris Cantwell committed Oct 22, 2014 323  \inltt{THIRDPARTY\_BUILD\_} selections in the previous  Michael Turner committed Jan 08, 2016 324 325  step or install the missing libraries manually or through MacPorts.  Chris Cantwell committed Aug 13, 2014 326 327 328  \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.  Michael Turner committed Jan 08, 2016 329   Chris Cantwell committed Aug 13, 2014 330 331 332 333 334 335  \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.  Michael Turner committed Jan 08, 2016 336   Chris Cantwell committed Aug 13, 2014 337 338 339 340 341 342 343 344  % 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}  Michael Turner committed Jan 08, 2016 345   Chris Cantwell committed Aug 13, 2014 346 347 348 349 350 351  \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}  Michael Turner committed Jan 08, 2016 352   Chris Cantwell committed Aug 13, 2014 353 354 355 356 357 358  \item Test the build by running unit and regression tests. \begin{lstlisting}[style=BashInputStyle] ctest \end{lstlisting} \end{enumerate}  Dave Moxey committed Oct 28, 2014 359 \subsection{Windows}  Chris Cantwell committed Aug 13, 2014 360   Dave Moxey committed Nov 04, 2014 361 362 363 364 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.  Dave Moxey committed Nov 03, 2014 365 366  \begin{center}  Dave Moxey committed Nov 04, 2014 367 \begin{tabular}{lcccl}  Dave Moxey committed Nov 03, 2014 368 \toprule  Dave Moxey committed Nov 04, 2014 369 370  & & \multicolumn{2}{c}{Installation} & \\ \cmidrule(r){3-4} Package & Req. & User & Auto. & Note \\  Dave Moxey committed Nov 03, 2014 371 \midrule  Julian Marcon committed Sep 22, 2016 372 MS Visual Studio & \cmark & \cmark & & 2012, 2013 and 2015 known working\\  Dave Moxey committed Nov 04, 2014 373 374 375 376 377 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 & \\  Dave Moxey committed Nov 03, 2014 378 379 380 \bottomrule \end{tabular} \end{center}  Chris Cantwell committed Aug 08, 2014 381   Dave Moxey committed Nov 04, 2014 382 383 384 \subsubsection{Detailed instructions} \begin{enumerate}  Julian Marcon committed Sep 22, 2016 385  \item Install Microsoft Visual Studio 2015 (preferred), 2013 or 2012 (known to  Dave Moxey committed Nov 04, 2014 386  work). This can be obtained from Microsoft free of charge by using their  Julian Marcon committed Sep 22, 2016 387 388  Community developer tools from \url{https://www.visualstudio.com/en-us/products/visual-studio-community-vs.aspx}.  Dave Moxey committed Nov 04, 2014 389 390 391 392 393 394 395 396 397  \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  Julian Marcon committed Sep 22, 2016 398  \url{http://sourceforge.net/projects/boost/files/boost-binaries/1.61.0/}. By  Dave Moxey committed Nov 04, 2014 399  default these install into \inlsh{C:\textbackslash local\textbackslash  Julian Marcon committed Sep 22, 2016 400  boost\_1\_61\_0}. If you use these libraries, you will need to:  Dave Moxey committed Oct 28, 2014 401  \begin{itemize}  Julian Marcon committed Sep 22, 2016 402  \item Rename \texttt{libs-msvc14.0} to \texttt{lib}  Dave Moxey committed Nov 04, 2014 403 404  \item Inside the \texttt{lib} directory, create duplicates of \texttt{boost\_zlib.dll} and \texttt{boost\_bzip2.dll} called  Julian Marcon committed Sep 22, 2016 405 406 407 408 409 410 411  \texttt{zlib.dll} and \texttt{libbz2.dll} \item Add a \inlsh{BOOST\_HOME} environment variable. To do so, 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, click \emph{New}. In the \emph{New System Variable} window, type \inlsh{BOOST\_HOME} next to \emph{Variable name} and \inlsh{C:\textbackslash local\textbackslash  Julian Marcon committed Sep 22, 2016 412  boost\_1\_61\_0} next to\emph{Variable value}.  Dave Moxey committed Oct 28, 2014 413  \end{itemize}  Dave Moxey committed Nov 04, 2014 414 415 416 417 418 419 420 421 422 423 424  \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  Julian Marcon committed Sep 22, 2016 425 426  \emph{All Programs > Visual Studio 2015 > Visual Studio Tools > Developer Command Prompt for VS2015}.  Dave Moxey committed Nov 04, 2014 427 428 429 430 431 432 433  \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  Julian Marcon committed Sep 22, 2016 434 435  that \emph{Visual Studio 2015} is listed as \emph{Visual Studio 14} in the drop-down list. If you have a 64-bit installation of Windows, you should  Dave Moxey committed Nov 04, 2014 436 437  select the \emph{Win64} variant, otherwise 32-bit executables will be generated. Select the option to use the native compilers.  Dave Moxey committed Jan 16, 2015 438  \item Click the \emph{Configure} button, then the \emph{Generate} button.  Dave Moxey committed Nov 04, 2014 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456  \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}  Dave Moxey committed Jan 16, 2015 457  \item \inlsh{builds\textbackslash dist\textbackslash lib\textbackslash nektar++-\nekver}  Dave Moxey committed Nov 04, 2014 458 459  \item \inlsh{builds\textbackslash dist\textbackslash bin} \item Optionally, if you installed Boost from the binary packages,  Julian Marcon committed Sep 22, 2016 460  \inlsh{C:\textbackslash local\textbackslash boost\_1\_61\_0 \textbackslash lib}  Dave Moxey committed Nov 04, 2014 461  \end{itemize}  Dave Moxey committed Jan 16, 2015 462 463  \item To run the test suite, open a \textbf{new} command line window, change to the \inlsh{builds} directory, and then issue the command  Dave Moxey committed Nov 04, 2014 464 465 466 467  \begin{lstlisting}[style=BashInputStyle] ctest -C Release \end{lstlisting} \end{enumerate}  Chris Cantwell committed Aug 08, 2014 468 469  \subsection{CMake Option Reference}  Chris Cantwell committed Aug 12, 2014 470 \label{s:installation:source:cmake}  Chris Cantwell committed Aug 13, 2014 471 472 473 474 475 476 477 478 479 480 481 482 483 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)  Michael Turner committed Jan 08, 2016 484   Chris Cantwell committed Aug 13, 2014 485 486 487 488  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.  Chris Cantwell committed Oct 22, 2014 489 490 491 492 493 494 495  \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}  Chris Cantwell committed Aug 13, 2014 496  \item \inlsh{NEKTAR\_BUILD\_LIBRARY} (Required)  Michael Turner committed Jan 08, 2016 497   Chris Cantwell committed Aug 13, 2014 498 499 500 501  Compiles the Nektar++ framework libraries. This is required for all other options. \item \inlsh{NEKTAR\_BUILD\_SOLVERS} (Recommended)  Michael Turner committed Jan 08, 2016 502   Chris Cantwell committed Aug 13, 2014 503 504 505  Compiles the solvers distributed with the \nekpp framework. If enabling \inlsh{NEKTAR\_BUILD\_SOLVERS}, individual solvers can be  Chris Cantwell committed Jan 20, 2015 506  enabled or disabled. See Part~\ref{p:applications} for the list of available  Chris Cantwell committed Aug 13, 2014 507 508 509 510 511 512 513 514 515 516 517 518 519 520 521 522 523 524  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.  Michael Turner committed Jan 08, 2016 525   Chris Cantwell committed Aug 13, 2014 526  \item \inlsh{NEKTAR\_SOLVER\_X}  Michael Turner committed Jan 08, 2016 527   Chris Cantwell committed Aug 13, 2014 528 529 530  Enabled compilation of the 'X' solver. \end{itemize}  Spencer Sherwin committed Jun 11, 2015 531 532 533 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:  Chris Cantwell committed Aug 13, 2014 534 \begin{itemize}  Chris Cantwell committed Jul 14, 2015 535 536 537 538  \item \inlsh{NEKTAR\_USE\_ACML} Use the optimised BLAS library for AMD processors.  Spencer Sherwin committed Jun 11, 2015 539  \item \inlsh{NEKTAR\_USE\_ACCELERATE\_FRAMEWORK}  Michael Turner committed Jan 08, 2016 540   Spencer Sherwin committed Jun 11, 2015 541 542 543 544 545  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}  Michael Turner committed Jan 08, 2016 546   Spencer Sherwin committed Jun 11, 2015 547 548 549  Build \nekpp with support for ARPACK. This provides routines used for linear stability analyses. Alternative Arnoldi algorithms are also implemented directly in \nekpp.  Michael Turner committed Jan 08, 2016 550   Chris Cantwell committed Aug 13, 2014 551  \item \inlsh{NEKTAR\_USE\_BLAS\_LAPACK} (Required)  Michael Turner committed Jan 08, 2016 552   Chris Cantwell committed Aug 13, 2014 553 554 555 556  Enables the use of Basic Linear Algebra Subroutines libraries for linear algebra operations. \item \inlsh{NEKTAR\_USE\_SYSTEM\_BLAS\_LAPACK} (Recommended)  Michael Turner committed Jan 08, 2016 557   Chris Cantwell committed Aug 13, 2014 558 559 560  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.  Michael Turner committed Jan 08, 2016 561   Spencer Sherwin committed Jun 11, 2015 562  \item \inlsh{NEKTAR\_USE\_CCM}  Michael Turner committed Jan 08, 2016 563   Spencer Sherwin committed Jun 11, 2015 564  Use the ccmio library provided with the Star-CCM package for  Michael Turner committed Jan 08, 2016 565  reading ccm files. This option is required as part of NekMesh  Spencer Sherwin committed Jun 11, 2015 566 567 568 569 570 571  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}  Michael Turner committed Jan 08, 2016 572   Spencer Sherwin committed Jun 11, 2015 573 574 575  Build \nekpp with support for FFTW for performing Fast Fourier Transforms (FFTs). This is used only when using domains with homogeneous coordinate directions.  Michael Turner committed Jan 08, 2016 576   Dave Moxey committed May 01, 2016 577 578 579 580  \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  Chris Cantwell committed Aug 11, 2016 581  processes. HDF5 output can be enabled by using a command-line option or  Dave Moxey committed May 01, 2016 582  in the \inlsh{SOLVERINFO} section of the XML file. This option requires  Dave Moxey committed Aug 12, 2016 583 584  that \nekpp be built with MPI support with \inlsh{NEKTAR\_USE\_MPI} enabled and that HDF5 is compiled with MPI support.  Dave Moxey committed May 01, 2016 585   Chris Cantwell committed Aug 13, 2014 586  \item \inlsh{NEKTAR\_USE\_MKL}  Michael Turner committed Jan 08, 2016 587   Chris Cantwell committed Aug 13, 2014 588 589 590  Use the Intel MKL library. This is typically available on cluster environments and should offer performance tuned for the specific cluster environment.  Spencer Sherwin committed Jun 11, 2015 591   Chris Cantwell committed Aug 13, 2014 592  \item \inlsh{NEKTAR\_USE\_MPI} (Recommended)  Michael Turner committed Jan 08, 2016 593   Chris Cantwell committed Aug 13, 2014 594 595  Build Nektar++ with MPI parallelisation. This allows solvers to be run in serial or parallel.  Michael Turner committed Jan 08, 2016 596   Spencer Sherwin committed Jun 11, 2015 597  \item \inlsh{NEKTAR\_USE\_OPENBLAS}  Michael Turner committed Jan 08, 2016 598   Spencer Sherwin committed Jun 11, 2015 599 600 601  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.  Michael Turner committed Jan 08, 2016 602   Chris Cantwell committed Jul 14, 2015 603 604 605 606 607 608 609 610 611 612 613 614 615 616 617  \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.  Chris Cantwell committed Aug 13, 2014 618  \item \inlsh{NEKTAR\_USE\_VTK}  Michael Turner committed Jan 08, 2016 619   Chris Cantwell committed Jan 20, 2015 620  Build \nekpp with support for VTK libraries. This is only needed for  Chris Cantwell committed Aug 13, 2014 621  specialist utilities and is not needed for general use.  Michael Turner committed Jan 08, 2016 622   Chris Cantwell committed Aug 13, 2014 623 624 625 626 627 628 629 630 631 632 633 634 635 636 637 638 639  \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}  Michael Turner committed Jan 08, 2016 640   Chris Cantwell committed Aug 13, 2014 641  (MPI-only) Parallel communication library.  Michael Turner committed Jan 08, 2016 642   Chris Cantwell committed Aug 13, 2014 643  \item \inlsh{METIS}  Michael Turner committed Jan 08, 2016 644   Chris Cantwell committed Aug 13, 2014 645  A graph partitioning library used for substructuring of matrices and mesh  Chris Cantwell committed Jan 20, 2015 646 647 648 649 650 651 652 653 654 655 656  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.  Chris Cantwell committed Aug 13, 2014 657  \item \inlsh{TINYXML}  Michael Turner committed Jan 08, 2016 658   Chris Cantwell committed Aug 13, 2014 659 660  Library for reading and writing XML files. \end{itemize}