source.tex 14.4 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 Aug 13, 2014 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 This section explains how to build Nektar++ from the source-code package. We recommend using pre-built binaries for your distribution, if available. See Sections~\ref{s:installation:debian}-\ref{s:installation:osx}. 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. % \begin{custombox}{Warning}{\bcdanger}{red} % Don't do this. % \end{custombox} \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 repository. Use this if you would like to try using Nektar++ and do not intend to be an active developer. \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} \end{itemize} \end{itemize}  Chris Cantwell committed Aug 08, 2014 43 \subsection{Linux}  Chris Cantwell committed Aug 13, 2014 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 \subsubsection{Prerequisites} \nekpp requires the following to be pre-installed on your system \begin{itemize} \item CMake \item BLAS and LAPACK \item Modern C++ compiler: g++, icpc, etc \end{itemize} This software should be available through your Linux distribution. \begin{notebox} CMake 2.8.7 or later is required. \end{notebox} \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 (Optional) If you have administrative access, install the third-party libraries supplied with your Linux distribution. \begin{warningbox} Boost version 1.51 has a bug which prevents \nekpp working correctly. Please use a newer version. \end{warningbox} \begin{notebox} FFTW and Arpack are optional. They provide additional or optimised functionality, but alternative implementations are included as part of \nekpp. \end{notebox} \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. \end{itemize} A full list of configuration options can be found in Section~\ref{s:installation:source:cmake}. \item Press \inltt{c} to configure the build. If errors arise relating to missing libraries, review the \inltt{THIRDPARTY\_BUILD\_} selections in the previous step or install the missing libraries 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, \noindent\usebox\installationLinuxTip \end{tipbox} \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 150 151  \subsection{OSX}  Chris Cantwell committed Aug 13, 2014 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267  \subsubsection{Prerequisites} 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). \nekpp also requires the following to be pre-installed on your system \begin{itemize} \item CMake \item BLAS and LAPACK \end{itemize} This software should be available through your Linux distribution. \begin{notebox} CMake 2.8.7 or later is required. \end{notebox} \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 (Optional) If you have administrative access, install the third-party libraries from MacPorts: \begin{lstlisting}[style=BashInputStyle] sudo port install cmake zlib fftw-3 arpack \end{lstlisting} \begin{warningbox} Boost version 1.51 has a bug which prevents \nekpp working correctly. Please use a newer version. \end{warningbox} \begin{notebox} FFTW and Arpack are optional. They provide additional or optimised functionality, but alternative implementations are included as part of \nekpp. \end{notebox} \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. \end{itemize} A full list of configuration options can be found in Section~\ref{s:installation:source:cmake}. \item Press \inltt{c} to configure the build. If errors arise relating to missing libraries, review the \inltt{THIRDPARTY\_BUILD\_} selections in the previous step or install the missing libraries 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\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}  Chris Cantwell committed Aug 08, 2014 268 269 270 271 272  \subsection{Windows} 3.4/UserGuide/Compile/Windows \subsection{CMake Option Reference}  Chris Cantwell committed Aug 12, 2014 273 \label{s:installation:source:cmake}  Chris Cantwell committed Aug 13, 2014 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 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\_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}