install.tex 27.5 KB
 Klaus Mosthaf committed Oct 13, 2010 1 2 \section{Installation of \Dumux} \label{install} \subsection{Preliminary remarks}  Klaus Mosthaf committed Oct 12, 2010 3   Klaus Mosthaf committed Feb 16, 2011 4 5 6 7 8 In this section about the installation of \Dumux it is assumed that you work on a UNIX or Linux compatible operating system and that you are familiar with the use of a command line shell. Installation means that you unpack \Dune together with \Dumux in a certain directory. You than compile it in that directory tree and do you further working on there too. You also should know how to install new software packages or you should have a person aside which can give you assistance with the command line and package installation. In section \ref{sec:prerequisites} we list prerequisites for running \Dune and \Dumux. Please check this paragraph whether you can fulfill them. In addition, section \ref{sec:external-modules-libraries} provides some details on optional libraries and modules are given. \\  David Werner committed Jan 19, 2011 9   Klaus Mosthaf committed Oct 28, 2010 10 In a technical sense \Dumux is a module of \Dune.  David Werner committed Jan 17, 2011 11 That's why the installation procedure of \Dumux is the same as that of \Dune.  Klaus Mosthaf committed Feb 16, 2011 12 13 14 The details regarding the installation of \Dune are provided on the \Dune website \cite{DUNE-INST}. If you are interested in more details of the build system that is used, you can find them in the {\Dune}'s Build System Howto \cite{DUNE-BS}.\\  Klaus Mosthaf committed Oct 12, 2010 15   David Werner committed Jan 13, 2011 16   Klaus Mosthaf committed Feb 23, 2011 17 As in a \Dune installation, all \Dune modules including \Dumux get extracted into a common directory. We refer to that directory for purpose of documentation abstractly as {\Dune} root directory or shortly as {\Dune}-Root. If it is used as directory's path of a shell command it is typed as \texttt{\Dune-Root}. For the real {\Dune} root directory on your file system any valid directory name can be chosen.\\  David Werner committed Jan 13, 2011 18   David Werner committed Jan 19, 2011 19 Source code files for each \Dune module are contained in their own subdirectory within {\Dune}-Root.  Klaus Mosthaf committed Feb 16, 2011 20 21 22 We name this directory of a certain module module root directory" or \texttt{module-root-directory} if it is a directory path's, e.g. for module \texttt{dumux} these names are dumux root directory" respective \texttt{dumux-root-directory}. The real directory names for modules can be chosen arbitrarily, in this manual they are the same as the  David Werner committed Jan 19, 2011 23 module name or the module name extended by a version number suffix.  David Werner committed Jan 17, 2011 24 The name of a \Dune module itself is always defined via the content of file \texttt{dune.module} in its own root  David Werner committed Jan 19, 2011 25 directory, but this should not get changed by an user. The user is allowed to have own files and directories in \Dune-Root, which are not related to \Dune's need.  David Werner committed Jan 13, 2011 26   Klaus Mosthaf committed Feb 16, 2011 27 After installing source code for all relevant \Dune modules including \Dumux, \Dune is being built by the shell-command \texttt{dunecontrol} which is part of the \Dune build system. The \Dune build system is a front-end adapted to the needs of \Dune to the GNU build system.  David Werner committed Oct 25, 2010 28   David Werner committed Jan 17, 2011 29 \subsection{Prerequisites} \label{sec:prerequisites}  David Werner committed Jan 17, 2011 30 The GNU tool chain of \texttt{g++} and tools of GNU build system \cite{GNU-BS} also known as GNU autotools  David Werner committed Jan 19, 2011 31 (i.e. \texttt{autoconf}, \texttt{automake}, \texttt{autogen}, \texttt{libtool}) as well as GNU's variant of \texttt{make}  Klaus Mosthaf committed Feb 16, 2011 32 must be available in a recent version. For Ubuntu Linux, e.g., these are contained in the  David Werner committed Jan 17, 2011 33 34 packages \texttt{autoconf}, \texttt{automake}, \texttt{libtool} and the C++ compiler \texttt{g++} and \texttt{make} are contained in \texttt{build-essential}.  David Werner committed Jan 19, 2011 35   Klaus Mosthaf committed Feb 16, 2011 36 At the time of writing this manual, it is expected that \texttt{g++} of version $\geqslant$ 4.4.1, \texttt{automake} of version $\geqslant$ 1.11,  David Werner committed Jan 19, 2011 37 \texttt{autoconf} of version $\geqslant$ 2.65, \texttt{autogen} of version $\geqslant$ 5.9.7, \texttt{libtool} of version $\geqslant$ 2.2.6  David Werner committed Jan 17, 2011 38 and GNU \texttt{make} version $\geqslant$ 3.81 should do their job for building \Dumux.\\  David Werner committed Jan 17, 2011 39   Klaus Mosthaf committed Feb 16, 2011 40 \Dumux makes use of the \texttt{boost} library in the version $\geqslant$ 1.33.1 but optional external modules may require a more recent version.  David Werner committed Jan 17, 2011 41 It is thus necessary to install an appropriate developer package of \texttt{boost}  Klaus Mosthaf committed Feb 16, 2011 42 which is sometimes also named \texttt{libboost}. The matching Ubuntu Linux package is \texttt{libboost-dev}. \\  David Werner committed Jan 17, 2011 43   Klaus Mosthaf committed Feb 16, 2011 44 The building of included documentation like this handbook requires \LaTeX\ and auxiliary tools  David Werner committed Jan 17, 2011 45 like \texttt{dvipdf} and \texttt{bibtex}. One usually chooses a \LaTeX\ distribution like \texttt{texlive} for doing that.  Klaus Mosthaf committed Feb 16, 2011 46 It is possible to switch off the building of the documentation by setting the switch \texttt{--disable-documentation} in the \texttt{CONFIGURE\_FLAGS} of the building options as.  David Werner committed Jan 17, 2011 47 Additional parts of documentation are contained in source code files as special formatted comments.  David Werner committed Jan 19, 2011 48 Extracting them can be done by program \texttt{doxygen} (version $\geqslant$ 1.7.2 works). See for this optional step section \ref{sec:build-doxy-doc}.\\  David Werner committed Jan 17, 2011 49 50 51 52  Depending whether you are going to use external libraries and modules for additional \Dune features additional software packages may required. Some hints on that are given in section \ref{sec:external-modules-libraries}.\\  Klaus Mosthaf committed Feb 16, 2011 53 54 For the extraction of the content of tar-files, the GNU version of \texttt{tar} is used. The subversion (SVN) software repositories can be accessed with the help of a subversion client. We recommend the Apache Subversion command-line client \texttt{svn}  David Werner committed Jan 17, 2011 55 contained in Apache Subversion of version $\geqslant$ 1.6.0 \cite{APACHE-SUBVERSION-HP}.  Klaus Mosthaf committed Oct 12, 2010 56   David Werner committed Jan 13, 2011 57 \subsection{Obtaining source code for \Dune and \Dumux}  Klaus Mosthaf committed Feb 16, 2011 58 As written before the \Dumux release 2.0 is based on the \Dune release 2.0, comprising the core modules  David Werner committed Jan 17, 2011 59 \texttt{dune-common}, \texttt{dune-grid}, \texttt{dune-istl}, \texttt{dune-localfunctions} and the external dune  Klaus Mosthaf committed Feb 16, 2011 60 61 module \texttt{dune-pdelab}. Thus, for a proper \Dumux installation these modules are required. Naturally, the external \Dune module \texttt{dumux} is required, too.\\  David Werner committed Jan 13, 2011 62   Klaus Mosthaf committed Feb 16, 2011 63 64 Two possibilities exist to get the source code of \Dune and \Dumux. Firstly, \Dune and \Dumux can be downloaded as tar-files from the respective {\Dune} and {\Dumux} website. They have to be extracted as described in the next paragraph.  Klaus Mosthaf committed Feb 23, 2011 65 Secondly, a method to obtain the most recent source code (or more generally any of its the previous revisions) by direct access via Internet to the software repositories of the revision control system is described in the subsequent part. \Dune and \Dumux use Apache Subversion for their software repositories. However, if a user does not want to use the most recent version,  Klaus Mosthaf committed Feb 16, 2011 66 certain version tags (i.e. special names), version numbers and even software branches are means of the software revision control system to provide access to different versions of the software.  Klaus Mosthaf committed Oct 12, 2010 67   David Werner committed Jan 13, 2011 68 \paragraph{Obtaining the software by installing tar-files}  Klaus Mosthaf committed Feb 16, 2011 69 70 The slightly old-fashioned named tape-archive-file shortly named tar-file or tarball is a common file format for distributing collections of files contained in these archives. The extraction from the tar-files is done as follows:  Klaus Mosthaf committed Feb 23, 2011 71 72 Download the tarballs from the respective \Dune (version 2.0) and \Dumux websites to a certain folder in your file system. Create the {\Dune} root directory, named below in the example DUMUX, then extract the content of the tar-files by the command-line program tar there.  Klaus Mosthaf committed Feb 16, 2011 73 This can be achieved by the following shell commands. Replace \texttt{path\_to\_tarball} with the directory name where the downloaded files are actually located.  David Werner committed Jan 14, 2011 74 75 76 77 78 79 80 81 82 83 84  \begin{lstlisting}[style=Bash] $mkdir DUMUX$ cd DUMUX $tar xzvf path_to_tarball_of/dune-common-2.0.tar.gz$ tar xzvf path_to_tarball_of/dune-grid-2.0.tar.gz $tar xzvf path_to_tarball_of/dune-istl-2.0.tar.gz$ tar xzvf path_to_tarball_of/dune-localfunctions-2.0.tar.gz $tar xzvf path_to_tarball_of/dumux-2.0.tar.gz \end{lstlisting}  Klaus Mosthaf committed Feb 23, 2011 85 After extraction, the actual name of the dumux root directory is \texttt{dumux-2.0}.\\  David Werner committed Jan 19, 2011 86   Klaus Mosthaf committed Feb 16, 2011 87 Furthermore, if you with to install the optional \Dune Grid-Howto:  David Werner committed Jan 14, 2011 88 89 90 91 92  \begin{lstlisting}[style=Bash]$ tar xzvf path_to_tarball_of/dune-grid-howto-2.0.tar.gz \end{lstlisting}  David Werner committed Jan 19, 2011 93 94 However, the required \Dune-module \texttt{dune-pdelab} is not available as tar-file. That's why one has to install it from a software repository by the second method.  Klaus Mosthaf committed Feb 16, 2011 95 If the svn command is available in the command line, it can done as follows:  David Werner committed Jan 19, 2011 96   David Werner committed Jan 14, 2011 97 98 99 \begin{lstlisting}[style=Bash] $svn co https://svn.dune-project.org/svn/dune-pdelab/branches/2.0snapshot dune-pdelab \end{lstlisting}  Klaus Mosthaf committed Oct 12, 2010 100   David Werner committed Jan 13, 2011 101 102 \paragraph{Obtaining \Dune and \Dumux from software repositories}  Klaus Mosthaf committed Feb 23, 2011 103 104 Direct access to a software revision control system for downloading code can be of later advantage for the user. It can be easier for him to keep up with code changes and to receive important bug fixes using the update command of the revision control system. \Dune and \Dumux use Apache Subversion. \\  Bernd Flemisch committed Jul 16, 2010 105   Klaus Mosthaf committed Feb 23, 2011 106 107 To access the software repositories a certain program is needed which is referred here shortly as subversion client. In our description, we use the subversion client of the Apache Subversion software itself, which is a command-line tool named \texttt{svn}. The Apache Subversion client \texttt{svn} is available for most Linux and UNIX distributions as software package.  David Werner committed Jan 13, 2011 108   Klaus Mosthaf committed Feb 23, 2011 109 110 111 In the technical speech of Apache Subversion checking out a certain software version" means nothing more then fetching a local copy from the software repository and laying it out in the file system. Additionally to the software some more files for the use of the software revision control system itself are created. They are kept in directories named \texttt{.svn} and can be found in each subfolder that is under version control. If you have developer access to \Dumux, it is also possible to do the opposite, i.e. loading up a modified revision of software into the software repository. This is usually termed as software commit".\\  David Werner committed Jan 13, 2011 112   David Werner committed Jan 19, 2011 113 The installation procedure is done as follows:  Klaus Mosthaf committed Feb 23, 2011 114 115 116 117 Create a {\Dune} root directory, named DUMUX in the lines below. Then, enter the previously created directory and check out the desired modules. As you see below, the check-out uses two different servers for getting the sources, one for \Dune and one for {\Dumux}. The \Dune modules of the stable 2.0 release are checked out as described on the \Dune website \cite{DUNE-DOWNLOAD-SVN}:  David Werner committed Jan 14, 2011 118 119  \begin{lstlisting}[style=Bash]  David Werner committed Jan 17, 2011 120 121 $ mkdir DUMUX $cd DUMUX  David Werner committed Jan 14, 2011 122 123 124 125 126 127 $ svn co https://svn.dune-project.org/svn/dune-common/releases/2.0 dune-common $svn co https://svn.dune-project.org/svn/dune-grid/releases/2.0 dune-grid$ svn co https://svn.dune-project.org/svn/dune-istl/releases/2.0 dune-istl $svn co https://svn.dune-project.org/svn/dune-localfunctions/releases/2.0 dune-localfunctions$ svn co https://svn.dune-project.org/svn/dune-pdelab/branches/2.0snapshot dune-pdelab \end{lstlisting}  Bernd Flemisch committed Jul 16, 2010 128   Klaus Mosthaf committed Feb 23, 2011 129 130 131 132 133 The newest (unstable) developments are also provided in these repositories (usually in a folder called trunk''). Please check the \Dune website \cite{DUNE-DOWNLOAD-SVN} for further information. However, the current \Dumux release is based on the stable 2.0 release and it will not compile without further adaptations using the the newest versions of \Dune.\\ The additional module \texttt{dune-grid-howto} is a tutorial which provides information about the \Dune grid interface. It may give you an idea how some abstractions in \Dune are done. The \texttt{dune-grid-howto} is not required by \Dumux, the installation is optional. It is done by:  David Werner committed Jan 14, 2011 134 135 136 137  \begin{lstlisting}[style=Bash] $svn co https://svn.dune-project.org/svn/dune-grid-howto/releases/2.0 dune-grid-howto \end{lstlisting}  Klaus Mosthaf committed Oct 08, 2010 138   Klaus Mosthaf committed Feb 23, 2011 139 140 141 The \texttt{dumux} module is then checked out as described below (see also the \Dumux website \cite{DUMUX-HP}). Its file tree has to be created in the \Dune-Root directory, where the \Dune modules are also have been checked out to. That's why the next command is executed there, too:  David Werner committed Jan 13, 2011 142   David Werner committed Jan 14, 2011 143 144 145 \begin{lstlisting}[style=Bash]$ svn co --username=anonymous --password='' svn://svn.iws.uni-stuttgart.de/DUMUX/dumux/trunk dumux \end{lstlisting}  Klaus Mosthaf committed Oct 12, 2010 146   Klaus Mosthaf committed Feb 23, 2011 147 We call the dumux root directory just \texttt{dumux} here.  David Werner committed Jan 19, 2011 148   David Werner committed Jan 13, 2011 149 \paragraph{Hints for \Dumux-Developers}  Klaus Mosthaf committed Feb 23, 2011 150 If you also want to actively participate in the development of \Dumux, you can apply either for full developer  David Werner committed Jan 19, 2011 151 access or for developer access on certain parts of \Dumux. Granted developer access means that  Klaus Mosthaf committed Feb 23, 2011 152 153 154 you are allowed to commit own code and that you can access the \texttt{dumux-devel} module. This enhances \texttt{dumux} by providing code from the developer group, which is currently being developed. A developer usually checks out non-anonymously the modules \texttt{dumux} and \texttt{dumux-devel}.  David Werner committed Jan 19, 2011 155 This is done by the commands below. But \texttt{joeuser} needs to replaced by  Klaus Mosthaf committed Feb 23, 2011 156 the actual user name of the developer for accessing the software repository:  David Werner committed Jan 14, 2011 157 158 159 160 161 162  \begin{lstlisting}[style=Bash] $svn co --username=joeuser svn://svn.iws.uni-stuttgart.de/DUMUX/dumux/trunk dumux$ svn co --username=joeuser svn://svn.iws.uni-stuttgart.de/DUMUX/dune-mux/trunk dumux-devel \end{lstlisting}  Klaus Mosthaf committed Feb 23, 2011 163 164 \texttt{Dumux-devel} itself makes use of the stable part \texttt{dumux}. Hence, the two parts have to be checked out together. One can omit the \texttt{--username} option in the commands above, if the user name for the repository access is  David Werner committed Jan 19, 2011 165 identical to the one for the system account.\\  David Werner committed Jan 14, 2011 166   David Werner committed Jan 19, 2011 167 Please choose either not to store the password by subversion in an insecure way or  Klaus Mosthaf committed Feb 23, 2011 168 169 choose to store it by subversion in a secure way, e.g. together with \texttt{kwallet} or \texttt{gnomekeyring}. Check the documentation of subversion, how this is being done.  David Werner committed Jan 19, 2011 170 A leaked out password can be used by evil persons to abuse a software repository.  Klaus Mosthaf committed Oct 12, 2010 171   David Werner committed Jan 24, 2011 172 173 \paragraph{checkout-dumux script} The shell-script \texttt{checkout-dumux} facilitates setting up a {\Dune}/{\Dumux} directory tree.  Klaus Mosthaf committed Feb 23, 2011 174 175 It is contained in the download section of \Dumux' web page \cite{DUMUX-HP}. For example the second line below will check out the required \Dune modules and \texttt{dumux}, \texttt{dumux-devel} and the \texttt{external} folder, which contains some useful external software and libraries.  David Werner committed Jan 24, 2011 176 177 178 179 180 181  \begin{lstlisting}[style=Bash] $checkout-dumux -h # show help,$ checkout-dumux -gme -u joeuser -p password -d DUMUX \end{lstlisting}  David Werner committed Feb 03, 2011 182 183 \subsection{Patching \Dune or external libraries} Patching of \Dune modules in order to work together with \Dumux  Klaus Mosthaf committed Feb 23, 2011 184 can be necessary for several reasons.  David Werner committed Feb 03, 2011 185 Software like a compiler or even a standard library  Klaus Mosthaf committed Feb 23, 2011 186 187 188 changes at times. But, for example, a certain release of a software-component that we depend on, does not reflect that change. In the dynamic developing process of software that depends on other modules it is not always feasible to adapt everything to the most recent version of each module. That's why patches exist or they are be brought into existence, which fix problems with a certain module  David Werner committed Feb 03, 2011 189 of a certain release but do not introduce to much structural change. It can also happen  Klaus Mosthaf committed Feb 23, 2011 190 that a release gets amendments (updates) and a formerly useful patch becomes obsolete.\\  David Werner committed Feb 03, 2011 191   Klaus Mosthaf committed Feb 23, 2011 192 193 194 \Dumux contains within the directory \texttt{dumux/patches} patches and documentation about their usage and application. Please check the README file in that directory for recent information. In general, a patch can be applied as follows (but the exact command or the used parameters may be slightly different).  David Werner committed Jan 24, 2011 195   David Werner committed Feb 03, 2011 196 197 \begin{lstlisting}[style=Bash] $# make sure you are in DUNE-Root  David Werner committed Feb 03, 2011 198 $ cd dune-istl  David Werner committed Feb 03, 2011 199 200 201 $patch -p1 < ../dumux/patches/dune-istl-2.0.patch \end{lstlisting}  Klaus Mosthaf committed Feb 23, 2011 202 The \texttt{checkout-dumux} script also applies patches, if not explicitly requested to do not so.  David Werner committed Jan 24, 2011 203   David Werner committed Jan 14, 2011 204 205 \subsection{Build of \Dune and \Dumux} \label{buildIt}  Klaus Mosthaf committed Feb 23, 2011 206 207 208 209 Building of \Dune and \Dumux is done by the command-line script \texttt{dunecontrol} as described in \Dune Installation Notes \cite{DUNE-INST} and in much more comprehensive form in the \Dune Buildsystem Howto \cite{DUNE-BS}. If something fails during the execution of \texttt{dunecontrol} feel free to report it to the \Dune or \Dumux developer mailing list, but also try to include error details.\\  David Werner committed Jan 14, 2011 210   Klaus Mosthaf committed Feb 23, 2011 211 212 213 214 215 216 217 218 It is possible to compile \Dumux with nearly no explicit options to the build system. %, but experience showed that the code quality through all parts of \Dune is not yet high enough to give the compiler full %freedom for allowing certain kind optimizations. However, for the successful compilation of \Dune and \Dumux, it is currently necessary to pass the %As options, switches for the optimization can be set in parts %build system for code by default, it is safer to pass the option \texttt{-fno-strict-aliasing} to the C++-compiler \cite{WIKIPED-ALIASING}, which is done here via a command-line argument to \texttt{dunecontrol}:  David Werner committed Jan 14, 2011 219 220 221  \begin{lstlisting}[style=Bash]  David Werner committed Jan 17, 2011 222 $ # make sure you are in the directory DUNE-Root  David Werner committed Jan 14, 2011 223 224 225 $./dune-common/bin/dunecontrol --configure-opts="CXXFLAGS=-fno-strict-aliasing" all \end{lstlisting}  Klaus Mosthaf committed Feb 23, 2011 226 Too many options can make life hard, that's why usually option-files are being used together with dunecontrol and its sub-tools.  David Werner committed Jan 19, 2011 227 228 Larger sets of options are kept in them. \\  Benjamin Faigle committed Feb 04, 2011 229 If you are going to compile with options suited for debugging of the code, the following  David Werner committed Jan 14, 2011 230 231 can be a starting point:  David Werner committed Jan 19, 2011 232 %Below in command-line make sure to insert the right name of dumux' root directory, which is in case of installation from tar-files \texttt{dumux-2.0} or in case of installation from subversion just \texttt{dumux}. For a developer it is also possible to take options file from \texttt{dumux-devel}.  David Werner committed Jan 14, 2011 233 234  \begin{lstlisting}[style=Bash]  David Werner committed Jan 17, 2011 235 $ # make sure you are in the directory DUNE-Root  David Werner committed Jan 19, 2011 236 237 $cp dumux/debug.opts my-debug.opts # create a personal version$ gedit my-debug.opts # optional editing the options file  David Werner committed Jan 17, 2011 238 $./dune-common/bin/dunecontrol --opts=my-debug.opts all  David Werner committed Jan 14, 2011 239 240 \end{lstlisting}  Klaus Mosthaf committed Feb 23, 2011 241 More optimized code, which is typically not usable for standard debugging tasks, can produced by  David Werner committed Jan 14, 2011 242 243  \begin{lstlisting}[style=Bash]  David Werner committed Jan 17, 2011 244 245 $ cp dumux/optim.opts my-optim.opts $./dune-common/bin/dunecontrol --opts=my-optim.opts all  David Werner committed Jan 14, 2011 246 247 \end{lstlisting}  David Werner committed Jan 19, 2011 248 249 250 251 Sometimes it is necessary to have additional options which are specific to a package set of an operating system or sometimes you have your own preferences. Feel free to work with your own set of options, which may evolve over time.  Klaus Mosthaf committed Feb 23, 2011 252 253 The option files above are more to be understood as a starting point for setting up an own customization than as something which is fixed.  David Werner committed Jan 19, 2011 254 255 The use of external libraries can make it necessary to add quite many options in an option-file. It can be helpful to give your customized option file its own name, as done above.  Klaus Mosthaf committed Feb 23, 2011 256 257 One avoids to be confused with option files that came out of the distribution and that can be possible updated by subversion later on.  David Werner committed Jan 17, 2011 258 259 260  \subsection{Building doxygen documentation} \label{sec:build-doxy-doc}  David Werner committed Jan 19, 2011 261 262 Doxygen documentation is done by especially formatted comments in source code, which can get extracted by the program \texttt{doxygen}. Beside extracting these comments, \texttt{doxygen} builds up web-browsable code structure documentation  David Werner committed Jan 17, 2011 263 264 like class hierarchy of code displayed as graphs, see \cite{DOXYGEN-HP}.\\  David Werner committed Jan 19, 2011 265 266 Building a modules doxygen documentation is done as follows provided the program \texttt{doxygen} is installed: Set in building options the \texttt{--enable-doxygen} switch.  David Werner committed Jan 17, 2011 267 This is either accomplished by adding it in \texttt{dunecontrol} options-file to \texttt{CONFIGURE\_FLAGS}, or by adding  David Werner committed Jan 19, 2011 268 269 it to \texttt{dunecontrol}'s command-line-argument \texttt{--configure-opts}. After running \texttt{dunecontrol} enter in module's root directory the subdirectory \texttt{doc/doxygen}.  Klaus Mosthaf committed Feb 23, 2011 270 271 272 273 You then run the command \texttt{doxygen} within that directory. Point your web browser to the file \texttt{module-root-directory/doc/doxygen/html/index.html} to read the generated documentation. All \Dune-modules that are used here except \texttt{dune-grid-howto} including also \texttt{dumux} contain some doxygen documentation, which can be extracted as described in the following lines. The external library UG has also a \texttt{doc/doxygen} directory for building its doxygen documentation.  David Werner committed Jan 17, 2011 274   David Werner committed Jan 17, 2011 275 276 277 278 279 280 281 \begin{lstlisting}[style=Bash]$ # change before next command your directory to DUNE-Root $cd dumux/doc/doxygen$ doxygen $firefox html/index.html \end{lstlisting}  David Werner committed Jan 17, 2011 282 283 \subsection{Building documentation of other \Dune modules}  Klaus Mosthaf committed Feb 23, 2011 284 285 286 287 288 If the \texttt{--enable-documentation} switch has been set to configure flags of \texttt{dunecontrol}, this does not necessarily mean that for every \Dune module the documentation is being build. However, at least Makefiles for building the documentation are generated. Provided you run \texttt{dunecontrol} with the option above,  David Werner committed Jan 19, 2011 289 it should be possible to build documentation if available.  Klaus Mosthaf committed Feb 23, 2011 290 291 Check in \texttt{module-root-directory/doc/Makefile.am} which targets you can build. E.g., for the module \texttt{dune-istl} you can build the documentation \texttt{istl.pdf} by typing the following into the console, when you are in the \Dune-Root:  David Werner committed Jan 17, 2011 292 293  \begin{lstlisting}[style=Bash]  David Werner committed Jan 17, 2011 294 $ # change before next command your directory to DUNE-Root  David Werner committed Jan 17, 2011 295 296 297 298 $cd dune-istl/doc$ make istl.pdf \end{lstlisting}  Klaus Mosthaf committed Feb 23, 2011 299 Or for module \texttt{dune-grid-howto} the documentation can be build by:  David Werner committed Jan 19, 2011 300 301 302 303 304 305 306  \begin{lstlisting}[style=Bash] $# change before next command your directory to DUNE-Root$ cd dune-grid-howto/doc $make grid-howto.pdf \end{lstlisting}  Klaus Mosthaf committed Feb 23, 2011 307 This applies for \Dumux too. Rebuilding the handbook can be done as follows:  David Werner committed Jan 19, 2011 308 309 310 311 312 313 314  \begin{lstlisting}[style=Bash]$ cd dumux/doc/handbook $make dumux-handbook.pdf \end{lstlisting}  Klaus Mosthaf committed Feb 23, 2011 315 %At the time writing this to the author no general method of building documentation contained in \Dune's modules is known.  David Werner committed Jan 14, 2011 316 317  %Alternatively, the tool CMake can be used to build \Dumux. Please check the file \texttt{INSTALL.cmake} for details.  David Werner committed Jan 17, 2011 318 319  \subsection{External libraries and modules} \label{sec:external-modules-libraries}  David Werner committed Oct 25, 2010 320   Klaus Mosthaf committed Feb 23, 2011 321 The libraries described in the sequel of this paragraph provide additional functionality but are not generally required to run \Dumux.  David Werner committed Jan 19, 2011 322 323 If you are going to use an external library check the information provided on the \Dune website \cite{DUNE-EXT-LIB}. If you are going to use an external \Dune module the website on external modules \cite{DUNE-EXT-MOD} can be helpful.\\  David Werner committed Jan 17, 2011 324 %Further information on external modules and libraries seemed to be contained in {\Dune}s Wiki \cite{DUNE-MAIN-WIKI}.  David Werner committed Jan 19, 2011 325 326   Klaus Mosthaf committed Feb 23, 2011 327 328 329 Installing an external library can require additional libraries which are also used by \Dune. For some libraries, such as BLAS or MPI, multiple versions can be installed on system. Make sure that it uses the same library as \Dune when configuring the external library.\\  David Werner committed Jan 19, 2011 330   Klaus Mosthaf committed Feb 23, 2011 331 In the following list, you can find some external modules and external libraries, and some more libraries and tools which are prerequisites for their use.  David Werner committed Oct 25, 2010 332   Philipp Nuske committed Sep 27, 2010 333 \begin{itemize}  Klaus Mosthaf committed Feb 23, 2011 334 \item \textbf{ALBERTA}: External library for use as GRID. Adaptive multi Level finite element toolbox using Bisectioning refinement and Error control by Residual Techniques for scientific Applications. Building it requires a FORTRAN compiler \texttt{gfortran}. Download: \texttt{\url{http://www.alberta-fem.de}}.  David Werner committed Jan 14, 2011 335   Klaus Mosthaf committed Feb 23, 2011 336 337 \item \textbf{ALUGrid}: External library for use as GRID. ALUGrid is build by a C++-compiler like \texttt{g++}. If you want to build a parallel version, you will need \texttt{MPI}. It was successfully run with \texttt{openmpi}. The parallel version needs also a graph partitioner, such as \texttt{METIS}. It was run successfully in combination with \Dune using \texttt{METIS}. \\ Download: \texttt{\url{http://aam.mathematik.uni-freiburg.de/IAM/Research/alugrid}}  Philipp Nuske committed Sep 27, 2010 338   Klaus Mosthaf committed Feb 23, 2011 339 340 341 \item \textbf{\Dune-multidomaingrid}: External module. If you going to run on the same grid different domains or subdomains, this can be the package of choice. This is done by providing a meta grid. It can be useful for multi-physics approaches or domain decomposition methods. Download: \texttt{\url{http://gitorious.org/dune-multidomaingrid}}. %Furthermore, the external module \textbf{\Dune-multidomain} can be useful for solving heterogenous problems on spatial subdomains. These subdomains are managed using another DUNE module called dune-multidomaingrid.  Philipp Nuske committed Sep 27, 2010 342   David Werner committed Jan 19, 2011 343 \item \textbf{PARDISO}: External library for solving linear equations. The package PARDISO is a thread-safe, high-performance, robust, memory efficient and easy to use software for solving large sparse symmetric and asymmetric linear systems of equations on shared memory multiprocessors. The precompiled binary can be downloaded after personal registration from the PARDISO website (\texttt{\url{http://www.pardiso-project.org}}).  Philipp Nuske committed Sep 27, 2010 344   Klaus Mosthaf committed Feb 23, 2011 345 346 347 \item \textbf{SuperLU}: External library for solving linear equations. SuperLU is a general purpose library for the direct solution of large, sparse, non-symmetric systems of linear equations. \\ (\texttt{\url{http://crd.lbl.gov/~xiaoye/SuperLU}}). \item \textbf{UG}: External library for use as GRID. UG is a toolbox for Unstructured Grids: For \Dumux it has to be build by GNU buildsystem and a C++-compiler. That's why \Dune specific patches need applied before use. Building it makes use of the tools \texttt{lex}/\texttt{yacc} or the GNU variants \texttt{flex}/\texttt{bison}.  Philipp Nuske committed Sep 27, 2010 348   David Werner committed Oct 25, 2010 349 350 \end{itemize}  Klaus Mosthaf committed Oct 28, 2010 351 The following are dependencies of some of the used libraries. You will need them depending on which modules of \Dune and which external libraries you use.  David Werner committed Jan 19, 2011 352   David Werner committed Oct 25, 2010 353 \begin{itemize}  David Werner committed Jan 19, 2011 354 \item \textbf{MPI}: The parallel version of \Dune and also some of the external dependencies need MPI when they are going to be built for parallel computing. \texttt{Openmpi} version$\geqslant$1.4.2 and \texttt{MPICH} in a recent version have been reported to work.  Philipp Nuske committed Sep 27, 2010 355   Klaus Mosthaf committed Oct 28, 2010 356 \item \textbf{lex/yacc} or \textbf{flex/bison}: These are quite common developing tools, code generators for lexical analyzers and parsers. This is a prerequisite for UG.  Philipp Nuske committed Sep 27, 2010 357   David Werner committed Jan 17, 2011 358 \item \textbf{BLAS}: Alberta makes use of BLAS. Thus install GotoBLAS2, ATLAS, non-optimized BLAS or BLAS provided by a chip manufacturer. Take care that the installation scripts select the intended version of BLAS. See \texttt{\url{http://en.wikipedia.org/wiki/Basic_Linear_Algebra_Subprograms}}.  Philipp Nuske committed Oct 18, 2010 359   Klaus Mosthaf committed Feb 23, 2011 360 \item \textbf{GotoBLAS2}: This is an optimized version of BLAS. It covers not always available all processors of the day, but quite a broad range. Its license is now very open. A FORTRAN compiler like \texttt{gfortran} is needed to compile it.\\  David Werner committed Jan 17, 2011 361 Available by \texttt{\url{http://www.tacc.utexas.edu/tacc-projects/gotoblas2/}}.  David Werner committed Oct 25, 2010 362   Klaus Mosthaf committed Feb 23, 2011 363 364 \item \textbf{METIS}: This is a dependency of ALUGrid, if you are going to run it parallel.  David Werner committed Jan 17, 2011 365 \item \textbf{Compilers}: Beside \texttt{g++} it has been reported that \Dune was successfully build with the Intel C++ compiler.  David Werner committed Jan 17, 2011 366 C and FORTRAN compiler is needed for a some external libraries. As code of different compilers is linked together they have to be be compatible with each other. A good choice is the GNU compiler suite \texttt{gcc},\texttt{g++} and \texttt{gfortran}.  David Werner committed Oct 25, 2010 367   Klaus Mosthaf committed Feb 23, 2011 368 \item \textbf{libgomp}: External libraries, such as ALUGrid, can make use of OpenMP when used together with METIS. For that purpose it can be necessary to install the \texttt{libgomp} library.  David Werner committed Oct 25, 2010 369 370 % http://openmp.org/  David Werner committed Jan 17, 2011 371 %\item \textbf{libgmp}: The Gnu Multiple Precision Arithmetic Library (GMP) is also a prerequisite for \Dune. It may be necessary to install it.  David Werner committed Oct 25, 2010 372 % http://gmplib.org/  David Werner committed Oct 25, 2010 373 \end{itemize}  Klaus Mosthaf committed Oct 21, 2010 374   David Werner committed Jan 19, 2011 375 376 377 378 379 \subsection{Hints for Users from IWS} We provide some features to make life a little bit easier for users from the Institute of Hydraulic Engineering, University of Stuttgart. There exists internally a svn repository made for several external libraries.  Klaus Mosthaf committed Feb 23, 2011 380 If you are allowed to access it, go to the {\Dune}-Root, then do:  David Werner committed Jan 19, 2011 381 \paragraph{prepared external directory}  382   David Werner committed Jan 14, 2011 383 \begin{lstlisting}[style=Bash]  David Werner committed Jan 19, 2011 384 $ # Make sure you are in DUNE-Root  David Werner committed Jan 14, 2011 385 386 $svn checkout svn://svn.iws.uni-stuttgart.de/DUMUX/external/trunk external \end{lstlisting}  387   Klaus Mosthaf committed Oct 27, 2010 388 This directory \texttt{external} contains a script to install external libraries, such as  David Werner committed Jan 19, 2011 389 390 ALBERTA, ALUGrid, UG, METIS and GotoBLAS2:  David Werner committed Jan 14, 2011 391 \begin{lstlisting}[style=Bash]  David Werner committed Jan 19, 2011 392 $ cd external  David Werner committed Jan 14, 2011 393 394 $./installExternal.sh all \end{lstlisting}  David Werner committed Jan 19, 2011 395   Klaus Mosthaf committed Feb 23, 2011 396 It is also possible to install only the actual needed external libraries:  David Werner committed Jan 19, 2011 397   David Werner committed Jan 14, 2011 398 \begin{lstlisting}[style=Bash]  David Werner committed Jan 19, 2011 399 400 $ ./installExternal.sh -h # show, what options this script provide \$ ./installExternal.sh --parallel alu  David Werner committed Jan 14, 2011 401 \end{lstlisting}  402   David Werner committed Jan 19, 2011 403 The libraries are then compiled within that directory and are not installed in a different place.  Klaus Mosthaf committed Feb 23, 2011 404 A \Dune build may need to know their location. That's why one may have to refer to them as options for \texttt{dunecontrol}, for example via options file \texttt{my-debug.opts}.  David Werner committed Jan 19, 2011 405