source.tex 25.8 KB
Newer Older
1
\section{Installing from Source}
2
\label{s:installation:source}
3

4
This section explains how to build Nektar++ from the source-code package.
5
6

Nektar++ uses a number of third-party libraries. Some of these are required,
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.
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
23
	credentials but any changes to the code cannot be pushed to the
Michael Turner's avatar
Michael Turner committed
24
	public repository. Use this initially if you would like to try using
25
	Nektar++ or make local changes to the code.
26
    \begin{lstlisting}[style=BashInputStyle]
Chris Cantwell's avatar
Chris Cantwell committed
27
        git clone https://gitlab.nektar.info/nektar/nektar.git nektar++
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]
32
        git clone git@gitlab.nektar.info:nektar/nektar.git nektar++
33
    \end{lstlisting}
34
35
36
37
    \begin{tipbox}
    You can easily switch to using the authenticated access from anonymous
    access at a later date.
    \end{tipbox}
38
39
40
	\end{itemize}
\end{itemize}

41
\subsection{Linux}
42
\subsubsection{Prerequisites}
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
54
55
        &      & \multicolumn{3}{c}{Installation} & \\ \cmidrule(r){3-5}
Package & Req. & Sys. & User & Auto.              & Note \\
56
\midrule
57
58
C++ compiler    & \cmark & \cmark & & & gcc, icc, etc \\
CMake  $>2.8.7$ & \cmark & \cmark & \cmark &        & Ncurses
59
60
GUI optional
\\
61
BLAS            & \cmark & \cmark & \cmark &        & Or MKL,
62
63
ACML, OpenBLAS
\\
64
LAPACK          & \cmark & \cmark & \cmark &        & \\
65
Boost $>=1.52$   & \cmark & \cmark & \cmark & \cmark & Compile
66
67
with iostreams
\\
68
69
ModMETIS        & \cmark &        &        & \cmark & \\
FFTW $>3.0$     &        & \cmark & \cmark & \cmark & For
70
high-performance FFTs\\
71
ARPACK $>2.0$   &        & \cmark & \cmark &        & For
72
arnoldi algorithms\\
73
OpenMPI         &        & \cmark &        &        & For
74
parallel execution\\
75
GSMPI           &        &        &        & \cmark & For
76
parallel execution\\
77
HDF5            &        & \cmark & \cmark & \cmark & For
78
large-scale parallel I/O (requires CMake >3.1)\\
79
PETSc           &        &        & \cmark & \cmark &
80
Alternative linear solvers\\
81
Scotch          &        & \cmark & \cmark & \cmark &
82
Alternative mesh partitioning\\
83
VTK $>5.8$      &        & \cmark & \cmark &        & Visualisation
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}
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]
100
tar -zxvf nektar++-(*\nekver*).tar.gz
101
102
103
\end{lstlisting}
Change into the \inlsh{nektar++} source code directory
\begin{lstlisting}[style=BashInputStyle]
Michael Turner's avatar
Michael Turner committed
104
    mkdir -p build && cd build
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]
114
tar -zxvf nektar++-(*\nekver*).tar.gz
115
    \end{lstlisting}
Michael Turner's avatar
Michael Turner committed
116

117
    \item Change into the source-code directory, create a \inltt{build}
Michael Turner's avatar
Michael Turner committed
118
    subdirectory and enter it
119
120
121
    \begin{lstlisting}[style=BashInputStyle]
    mkdir -p build && cd build
    \end{lstlisting}
Michael Turner's avatar
Michael Turner committed
122

123
    \item Run the CMake GUI and configure the build by pressing \inltt{c}
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.
133
        \item Select the libraries not already available on your system which
Michael Turner's avatar
Michael Turner committed
134
        you wish to be compiled automatically (prefixed with
135
        \inltt{THIRDPARTY\_BUILD\_})
136
137
138
    \end{itemize}
    A full list of configuration options can be found in
    Section~\ref{s:installation:source:cmake}.
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's avatar
Michael Turner committed
147
148


149
    \item Press \inltt{c} to configure the build. If errors arise relating to
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's avatar
Michael Turner committed
153

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's avatar
Michael Turner committed
157

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's avatar
Michael Turner committed
164

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's avatar
Michael Turner committed
173

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
177
    the number of simultaneous jobs to spawn. For example, use
Michael Turner's avatar
Michael Turner committed
178

179
    \noindent\usebox\installationLinuxTip
Michael Turner's avatar
Michael Turner committed
180

181
    on a quad-core system.
182
    \end{tipbox}
Michael Turner's avatar
Michael Turner committed
183

184
185
186
187
188
    \item Test the build by running unit and regression tests.
    \begin{lstlisting}[style=BashInputStyle]
    ctest
    \end{lstlisting}
\end{enumerate}
189

Dave Moxey's avatar
Dave Moxey committed
190
\subsection{OS X}
191
192

\subsubsection{Prerequisites}
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's avatar
Michael Turner committed
197
optional and required only for specific features, or can be downloaded and
198
199
200
201
compiled for use with Nektar++ \emph{automatically} (but not installed
system-wide).

\begin{notebox}
Dave Moxey's avatar
Dave Moxey committed
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).
208
\end{notebox}
209

210
211
212
\begin{center}
\begin{tabular}{lccccl}
\toprule
213
214
        &      & \multicolumn{3}{c}{Installation} & \\ \cmidrule(r){3-5}
Package & Req. & MacPorts & User & Auto.          & Note \\
215
\midrule
216
217
Xcode           & \cmark &        & & & Provides developer tools \\
CMake  $>2.8.7$ & \cmark & \texttt{cmake}   & \cmark &        & Ncurses
218
GUI optional \\
219
BLAS            & \cmark &                  &        &        & Part of
220
Xcode \\
221
LAPACK          & \cmark &                  &        &        & Part of
222
Xcode \\
223
Boost $>=1.52$   & \cmark & \texttt{boost}   & \cmark & \cmark & Compile
224
225
226
227
with iostreams \\
TinyXML         & \cmark & \texttt{tinyxml} & \cmark & \cmark & \\
ModMETIS        & \cmark &                  &        & \cmark & \\
FFTW $>3.0$     &        & \texttt{fftw-3}  & \cmark & \cmark & For
228
high-performance FFTs\\
229
ARPACK $>2.0$   &        & \texttt{arpack}  & \cmark &        & For
230
arnoldi algorithms\\
231
OpenMPI         &        & \texttt{openmpi} &        &        & For
232
parallel execution\\
233
GSMPI           &        &                  &        & \cmark & For
234
parallel execution\\
235
HDF5            &        & \cmark & \cmark & \cmark & For
Dave Moxey's avatar
Dave Moxey committed
236
large-scale parallel I/O (requires CMake >3.1)\\
237
PETSc           &        & \texttt{petsc}   & \cmark & \cmark &
238
Alternative linear solvers\\
239
Scotch          &        & \texttt{scotch}  & \cmark & \cmark &
240
Alternative mesh partitioning\\
241
VTK $>5.8$      &        & \texttt{vtk}     & \cmark &        &
242
243
244
245
246
247
248
Visualisation utilities\\
\bottomrule
\end{tabular}
\end{center}

\newsavebox\installationOSXMacPortsTip
\begin{lrbox}{\installationOSXMacPortsTip}\begin{minipage}{0.8\linewidth}
249
250
251
\begin{lstlisting}[style=BashInputStyle]
sudo port install cmake
\end{lstlisting}
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
260
261
262

Package names are given in the table above. Similar packages also exist in other
package managers such as Homebrew.
263
\end{tipbox}
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]
271
tar -zxvf nektar++-(*\nekver*).tar.gz
272
273
274
\end{lstlisting}
Change into the \inlsh{nektar++} source code directory
\begin{lstlisting}[style=BashInputStyle]
Michael Turner's avatar
Michael Turner committed
275
    mkdir -p build && cd build
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]
285
tar -zxvf nektar++-(*\nekver*).tar.gz
286
287
288
    \end{lstlisting}

    \item Change into the source-code directory, create a \inltt{build}
Michael Turner's avatar
Michael Turner committed
289
    subdirectory and enter it
290
291
292
    \begin{lstlisting}[style=BashInputStyle]
    mkdir -p build && cd build
    \end{lstlisting}
Michael Turner's avatar
Michael Turner committed
293

294
295
296
297
    \item Run the CMake GUI and configure the build
    \begin{lstlisting}[style=BashInputStyle]
    ccmake ../
    \end{lstlisting}
298
299
    Use the arrow keys to navigate the options and \inlsh{ENTER} to select/edit
    an option.
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.
306
        \item Select the libraries not already available on your system which
Michael Turner's avatar
Michael Turner committed
307
        you wish to be compiled automatically (prefixed with
308
        \inltt{THIRDPARTY\_BUILD\_})
Michael Turner's avatar
Michael Turner committed
309
        \item
310
311
312
    \end{itemize}
    A full list of configuration options can be found in
    Section~\ref{s:installation:source:cmake}.
313

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's avatar
Michael Turner committed
320

321
    \item Press \inltt{c} to configure the build. If errors arise relating to
Michael Turner's avatar
Michael Turner committed
322
        missing libraries (variables set to \inlsh{NOTFOUND}), review the
323
        \inltt{THIRDPARTY\_BUILD\_} selections in the previous
Michael Turner's avatar
Michael Turner committed
324
325
    step or install the missing libraries manually or through MacPorts.

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's avatar
Michael Turner committed
329

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's avatar
Michael Turner committed
336

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's avatar
Michael Turner committed
345

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's avatar
Michael Turner committed
352

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}

359
\subsection{Windows}
360

Dave Moxey's avatar
Dave Moxey committed
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's avatar
Dave Moxey committed
365
366

\begin{center}
Dave Moxey's avatar
Dave Moxey committed
367
\begin{tabular}{lcccl}
Dave Moxey's avatar
Dave Moxey committed
368
\toprule
Dave Moxey's avatar
Dave Moxey committed
369
370
                  &        & \multicolumn{2}{c}{Installation} & \\ \cmidrule(r){3-4}
Package           & Req.   & User   & Auto.        & Note \\
Dave Moxey's avatar
Dave Moxey committed
371
\midrule
372
MS Visual Studio  & \cmark & \cmark &              & 2012, 2013 and 2015 known working\\
Dave Moxey's avatar
Dave Moxey committed
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's avatar
Dave Moxey committed
378
379
380
\bottomrule
\end{tabular}
\end{center}
381

Dave Moxey's avatar
Dave Moxey committed
382
383
384
\subsubsection{Detailed instructions}

\begin{enumerate}
385
  \item Install Microsoft Visual Studio 2015 (preferred), 2013 or 2012 (known to
Dave Moxey's avatar
Dave Moxey committed
386
  work). This can be obtained from Microsoft free of charge by using their
387
388
  Community developer tools from
  \url{https://www.visualstudio.com/en-us/products/visual-studio-community-vs.aspx}.
Dave Moxey's avatar
Dave Moxey committed
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
398
  \url{http://sourceforge.net/projects/boost/files/boost-binaries/1.61.0/}. By
Dave Moxey's avatar
Dave Moxey committed
399
  default these install into \inlsh{C:\textbackslash local\textbackslash
400
    boost\_1\_61\_0}. If you use these libraries, you will need to:
401
  \begin{itemize}
402
    \item Rename \texttt{libs-msvc14.0} to \texttt{lib}
Dave Moxey's avatar
Dave Moxey committed
403
404
    \item Inside the \texttt{lib} directory, create duplicates of
    \texttt{boost\_zlib.dll} and \texttt{boost\_bzip2.dll} called
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
412
	boost\_1\_61\_0} next to\emph{Variable value}.
413
  \end{itemize}
Dave Moxey's avatar
Dave Moxey committed
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
425
426
  \emph{All Programs > Visual Studio 2015 > Visual Studio Tools > Developer
    Command Prompt for VS2015}.
Dave Moxey's avatar
Dave Moxey committed
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
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's avatar
Dave Moxey committed
436
437
  select the \emph{Win64} variant, otherwise 32-bit executables will be
  generated. Select the option to use the native compilers.
438
  \item Click the \emph{Configure} button, then the \emph{Generate} button.
Dave Moxey's avatar
Dave Moxey committed
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}
457
    \item \inlsh{builds\textbackslash dist\textbackslash lib\textbackslash nektar++-\nekver}
Dave Moxey's avatar
Dave Moxey committed
458
459
    \item \inlsh{builds\textbackslash dist\textbackslash bin}
    \item Optionally, if you installed Boost from the binary packages,
460
    \inlsh{C:\textbackslash local\textbackslash boost\_1\_61\_0 \textbackslash lib}
Dave Moxey's avatar
Dave Moxey committed
461
  \end{itemize}
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's avatar
Dave Moxey committed
464
465
466
467
  \begin{lstlisting}[style=BashInputStyle]
    ctest -C Release
  \end{lstlisting}
\end{enumerate}
468
469

\subsection{CMake Option Reference}
470
\label{s:installation:source:cmake}
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's avatar
Michael Turner committed
484

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.

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}

496
    \item \inlsh{NEKTAR\_BUILD\_LIBRARY} (Required)
Michael Turner's avatar
Michael Turner committed
497

498
499
500
501
    Compiles the Nektar++ framework libraries. This is required for all other
    options.

    \item \inlsh{NEKTAR\_BUILD\_SOLVERS} (Recommended)
Michael Turner's avatar
Michael Turner committed
502

503
504
505
    Compiles the solvers distributed with the \nekpp framework.

    If enabling \inlsh{NEKTAR\_BUILD\_SOLVERS}, individual solvers can be
506
    enabled or disabled. See Part~\ref{p:applications} for the list of available
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's avatar
Michael Turner committed
525

526
    \item \inlsh{NEKTAR\_SOLVER\_X}
Michael Turner's avatar
Michael Turner committed
527

528
529
530
    Enabled compilation of the 'X' solver.
\end{itemize}

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:
534
\begin{itemize}
535
536
537
538
    \item \inlsh{NEKTAR\_USE\_ACML}

    Use the optimised BLAS library for AMD processors.

539
    \item \inlsh{NEKTAR\_USE\_ACCELERATE\_FRAMEWORK}
Michael Turner's avatar
Michael Turner committed
540

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's avatar
Michael Turner committed
546

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's avatar
Michael Turner committed
550

551
    \item \inlsh{NEKTAR\_USE\_BLAS\_LAPACK} (Required)
Michael Turner's avatar
Michael Turner committed
552

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's avatar
Michael Turner committed
557

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's avatar
Michael Turner committed
561

562
    \item \inlsh{NEKTAR\_USE\_CCM}
Michael Turner's avatar
Michael Turner committed
563

564
    Use the ccmio library provided with the Star-CCM package for
Michael Turner's avatar
Michael Turner committed
565
    reading ccm files. This option is required as part of NekMesh
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's avatar
Michael Turner committed
572

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's avatar
Michael Turner committed
576

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's avatar
Chris Cantwell committed
581
    processes. HDF5 output can be enabled by using a command-line option or
582
    in the \inlsh{SOLVERINFO} section of the XML file. This option requires 
Dave Moxey's avatar
Dave Moxey committed
583
584
    that \nekpp be built with MPI support with \inlsh{NEKTAR\_USE\_MPI} enabled
    and that HDF5 is compiled with MPI support.
585

586
    \item \inlsh{NEKTAR\_USE\_MKL}
Michael Turner's avatar
Michael Turner committed
587

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.
591

592
    \item \inlsh{NEKTAR\_USE\_MPI} (Recommended)
Michael Turner's avatar
Michael Turner committed
593

594
595
    Build Nektar++ with MPI parallelisation. This allows solvers to be run in
    serial or parallel.
Michael Turner's avatar
Michael Turner committed
596

597
    \item \inlsh{NEKTAR\_USE\_OPENBLAS}
Michael Turner's avatar
Michael Turner committed
598

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's avatar
Michael Turner committed
602

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.

618
    \item \inlsh{NEKTAR\_USE\_VTK}
Michael Turner's avatar
Michael Turner committed
619

620
    Build \nekpp with support for VTK libraries. This is only needed for
621
    specialist utilities and is not needed for general use.
Michael Turner's avatar
Michael Turner committed
622

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's avatar
Michael Turner committed
640

641
    (MPI-only) Parallel communication library.
Michael Turner's avatar
Michael Turner committed
642

643
    \item \inlsh{METIS}
Michael Turner's avatar
Michael Turner committed
644

645
    A graph partitioning library used for substructuring of matrices and mesh
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.

657
    \item \inlsh{TINYXML}
Michael Turner's avatar
Michael Turner committed
658

659
660
    Library for reading and writing XML files.
\end{itemize}