Commit 7ab3e3bc authored by Chris Cantwell's avatar Chris Cantwell
Browse files

Updates to user-guide following feedback from CPC journal.

parent 74ce6ecd
......@@ -40,17 +40,54 @@ There are two ways to obtain the source code for \nekpp:
\subsection{Linux}
\subsubsection{Prerequisites}
\nekpp requires the following to be pre-installed on your system
\begin{itemize}
\item CMake
\item BLAS and LAPACK
\item A 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}
\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}
......@@ -75,20 +112,6 @@ From a terminal:
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. Note that FFTW version 3 or later is required.
\end{notebox}
\item Change into the source-code directory, create a \inltt{build}
subdirectory and enter it
\begin{lstlisting}[style=BashInputStyle]
......@@ -105,13 +128,26 @@ From a terminal:
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 previous
step or install the missing libraries from system packages.
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}
......@@ -136,8 +172,11 @@ From a terminal:
\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,
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.
......@@ -149,26 +188,74 @@ From a terminal:
\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}
\nekpp also requires the following to be pre-installed on your system
\begin{itemize}
\item CMake
\item BLAS and LAPACK
\end{itemize}
CMake is available from MacPorts (\url{http://macports.org}) and can be
installed using
\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}
\begin{notebox}
CMake 2.8.7 or later is required.
\end{notebox}
\subsubsection{Quick Start}
Open a terminal (Applications->Utilities->Terminal).
......@@ -191,23 +278,6 @@ From a terminal (Applications->Utilities->Terminal):
\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 so they are available system-wide:
\begin{lstlisting}[style=BashInputStyle]
sudo port install boost 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
......@@ -227,14 +297,14 @@ From a terminal (Applications->Utilities->Terminal):
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}.
\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 from system packages.
\begin{notebox}
Selecting \inltt{THIRDPARTY\_BUILD\_} options will request CMake to
automatically download thirdparty libraries and compile them within the
......@@ -242,6 +312,11 @@ From a terminal (Applications->Utilities->Terminal):
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.
......@@ -298,18 +373,22 @@ The following software must be pre-installed on your system:
\begin{itemize}
\item Unpack the \inlsh{nektar++-\nekver.tar.gz} file using
WinRAR
\item Unpack the \inlsh{ThirdParty-\nekver.tar.gz} file using WinRAR
\item Rename the resulting directory to \inlsh{ThirdParty} and put it in
\inlsh{nektar++-\nekver}. (This will mean \inlsh{library} and
\inlsh{ThirdParty} are both sub-directories of the original
\inlsh{nektar++-\nekver}.) Note: Some windows version do not
\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}
......@@ -456,6 +535,13 @@ Components of the \nekpp package can be selected using the following options:
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
......
......@@ -33,6 +33,7 @@ openany, % A chapter may start on either a recto or verso page.
\usepackage{graphicx} % Include figures
\usepackage{makeidx}
\usepackage{import}
\usepackage{amssymb}
%%% PAGE LAYOUT
%%%-----------------------------------------------------------------------------
......
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