FIX: Remove undistributable CHEMKIN files

[freefoam.git] / INSTALL

{project} Installation Instructions for Version {fullver}
=========================================================
Michael Wild <themiwi@users.sourceforge.net>
:Author Initials: MW
v{fullver}, {localdate}
{homepage}

:apidoc: {homepage}/doc/v{fullver}/API
:asciidoc: http://www.methods.co.nz/asciidoc[Asciidoc]
:bash: http://www.gnu.org/software/bash/[BASH]
:cd-adapco: http://www.cd-adapco.com[CD-adapco]
:cmake: http://cmake.org
:dblatex: http://dblatex.sourceforge.net[dblatex]
:debian: http://debian.org[Debian]
:dvipng: http://sourceforge.net/projects/dvipng[dvipng]
:emacs: http://www.gnu.org/software/emacs[Emacs]
:fop: http://xmlgraphics.apache.org/fop[Apache FOP]
:latex: http://www.latex-project.org[LaTeX]
:libccmio: http://freefoam.sf.net/nonfree/libccmio-2.6.1.tar.gz
:linuxcommand: http://linuxcommand.org
:mathjax: http://www.mathjax.org[MathJax]
:metis: http://freefoam.sf.net/nonfree/metis-5.0.1.tar.gz
:mgridgen: http://freefoam.sf.net/nonfree/ParMGridGen-1.0.tar.gz
:parmetis: http://freefoam.sf.net/nonfree/ParMetis-3.1.tar.gz
:scotch: http://sourceforge.net/projects/freefoam/files/ThirdParty/scotch/scotch_5.1.7.dfsg.orig.tar.gz
:tarball: http://sourceforge.net/projects/freefoam/files/FreeFOAM/{fullver}/freefoam-{fullver}.tar.bz2/download
:zlib: http://sourceforge.net/projects/freefoam/files/ThirdParty/zlib/zlib-1.2.5.tar.gz
:zsh: http://www.zsh.org/[ZSH]

Obtaining the Prerequisites
---------------------------
Some of the libraries {project} requires (or optionally can use) are often not
readily available as an installable package and are quite tricky to install
manually. {project} can automatically download and build these libraries for
you, refer to below instructions. However, if you are behind a firewall or
CMake is unable to download a source package, you can do so manually and place
the files in the 'ThirdParty' directory in the {project} source tree. When you
run CMake, it will detect the presence of the files and not try to download
them.

You can obtain the source packages from the following URLs:

'libccmio'::
  {libccmio}
'METIS'::
  {metis}
'MGRIDGEN'::
  {mgridgen}
'ParMetis'::
  {parmetis}
'scotch'::
  {scotch}
'zlib'::
  {zlib}

On a Ubuntu or Debian installation you can install the prerequisites as follows

---------------------------------------------------------------------------
$ apt-get install cmake-curses-gui build-essential flex bison zlib1g-dev \
    python paraview m4 libreadline-dev
---------------------------------------------------------------------------

Note that Debian Squeeze (the stable version at the time of this writing) and
Ubuntu 10.10 (Maverick Meerkat) contain too old versions of CMake. However, it
is very easy to download a binary distribution of CMake from {cmake} and use it
directly, no special installation required. Newer versions of these operating
systems contain more up-to-date versions of CMake.

The optional 'ParMetis' graph partitioning library and the
parallel-communications library can be installed with

---------------------------------------------------------------------------
$ apt-get install libparmetis-dev mpi-default-dev mpi-default-bin
---------------------------------------------------------------------------

Make sure that you have the 'multiverse' (Ubuntu) or 'non-free' (Debian)
repositories enabled if you want to install the 'libparmetis-dev' package.

The dependencies for the generation of the documentation can be installed with

---------------------------------------------------------------------------
$ apt-get install asciidoc docbook-xsl libxml2-utils asymptote graphviz \
    doxygen dblatex texlive-latex-extra texlive-fonts-recommended
---------------------------------------------------------------------------

[[installation]]
Building {project}
------------------
- Install the prerequisites documented in the link:README.html[README] file. If
  your distribution does not have 'zlib', 'METIS', 'ParMetis', 'MGRIDGEN' or
  'libccmio' be not worried, {project} can handle those for you.
- Download the {project} source and unpack it somewhere convenient. For the
  further instructions we will use +$HOME/Source/+.
+
---------------------------------------------------------------------------
$ mkdir -p $HOME/Source
$ cd $HOME/Source
$ wget -O freefoam-{fullver}.tar.bz2 {tarball}
$ tar xjf freefoam-{fullver}.tar.bz2
---------------------------------------------------------------------------
- Create a build tree and _cd_ into it:
+
---------------
$ mkdir $HOME/Source/freefoam-{fullver}-build
$ cd $HOME/Source/freefoam-{fullver}-build
---------------
- Start the CMake-configuration:
+
---------------
$ ccmake $HOME/Source/freefoam-{fullver}
---------------
- Press the +c+ key. Use the arrow keys to navigate up and down and press
  +enter+ to edit a field. To commit the change, press +enter+ again, or +ESC+
  to abandon the change. ON/OFF fields are toggled by pressing +enter+.
  Advanced options can be displayed by hitting the +t+ key.
  * Set +CMAKE_BUILD_TYPE+ to 'Release' for an optimized build.
  * If CMake complains that it can't find MPI, and you don't want to install
    it, disable +FOAM_USE_MPI+.
  * Select the default Pstream implementation by setting +FOAM_DEFAULT_PSTREAM+
    to one of 'dummy' or 'mpi'. This setting will only influence the contents
    of the <<globalconfig,global 'controlDict' file>>.
  * If you want to use the 'metis' and 'parmetis' decomposition methods, make
    sure that +FOAM_ENABLE_METIS+ and +FOAM_ENABLE_PARMETIS+ are enabled,
    respectively. If you do not have 'METIS' or 'ParMetis' installed, enable
    +FOAM_BUILD_PRIVATE_METIS+ or +FOAM_BUILD_PRIVATE_PARMETIS+, respectively.
    CMake will then try to download and build the selected libraries for you.
    Conversely, if one of the libraries is provided by your system, you can
    turn the respective setting to 'OFF'. Please note that if your system
    provides only 'ParMetis', you do not have to install 'METIS', as the former
    also contains 'METIS' in an older version.
  * If you want to use the 'MGridGen' agglomeration method for the GAMG solver,
    you need to enable +FOAM_ENABLE_MGRIDGEN+ and if the library is not
    installed on your system ensure that +FOAM_BUILD_PRIVATE_MGRIDGEN+ is
    enabled. See <<enable-mgridgen,above>> regarding the unknown license status
    of this package.
  * In order to build 'ccm26ToFoam', a conversion utility for grids generated
    with 'ProStar/ccm' (C) version 2.6, enable the setting
    +FOAM_ENABLE_CCMIO+ and if 'libccmio' is not installed on your system,
    also +FOAM_BUILD_PRIVATE_CCMIO+. Refer to the <<enable-ccmio,above>>
    description of the 'libccmio' package for the license restrictions which
    apply to this package. If you decide to build a private version, please
    read the description of <<private-ccmio,+FOAM_BUILD_PRIVATE_CCMIO>>
    carefully.
  * If you plan on installing {project}, set +CMAKE_INSTALL_PREFIX+ to the base
    directory under which {project} should reside.
  * For more fine-grained control over what gets installed where, adjust
    +FOAM_INSTALL_<XXX>_PATH+, where +<XXX>+ is one of +BIN+, +CMAKE+,
    +CONFIG+, +DATA+, +DOC+, +FRAMEWORK+, +HEADER+, +LIBEXEC+, +LIBRARY+,
    +MAN+, +PLUGIN+, +PYTHON+, +TUTORIALS+ and +USERDFOAM+. Refer to the
    glossary for the detailed meaning of each of these variables. Paths
    not starting with a slash ('/') will be relative to +CMAKE_INSTALL_PREFIX+.
    If you include a leading slash, the paths are absolute.
  * If you want {project} to use 'float' as the floating point type instead of
    'double', change +FOAM_DOUBLE_PRECISION+ to 'OFF'.
- Hit +c+ again. You shouldn't get any errors anymore now. Keep pressing +c+
  until ccmake displays "++Press [g] to generate and exit++" in the legend at
  the bottom of the interface.
- Press +g+ to generate the Makefiles and exit the ccmake interface.
- Start the native build tool. If you used the 'Makefile' generator
  (which is the default for Unix-platforms), type
+
----------------
$ make
----------------
- If you have a multi-core/processor machine, you can speed things up
  significantly by telling Make to run independent jobs in parallel.
  A good choice for the number of parallel jobs to run is the
  number of CPU's/cores you have in your machine plus 1 (to compensate
  for disk-latency). For a typical dual-core machine, run
+
----------------
$ make -j3
----------------

Installing {project}
--------------------
If you want to, you can now install {project}. Depending on the
+CMAKE_INSTALL_PREFIX+ and the individual +FOAM_INSTALL_<XXX>_PATH+ it is
possible that you have to do this as root, i.e. use +su -c+ or +sudo+.
---------------
$ make install
---------------

Using {project}
---------------
If you didn't change +CMAKE_INSTALL_PREFIX+ and +FOAM_INSTALL_BIN_PATH+ chances
are that you can start using {project} right after you installed it without any
further steps being necessary.

[[globalconfig]]
Global Configuration Files
~~~~~~~~~~~~~~~~~~~~~~~~~~
Unfortunately the OpenFOAM library (on which {project} builds) and some
applications require some files to be present for start-up. It finds those
in the following places (in the specified order, picking the first hit):

1. Under the directory specified in the +$FREEFOAM_CONFIG_DIR+ environment
   variable
2. In '$HOME/.{project}/{shortver}'
3. In '$HOME/.{project}'
4. In the installation directory of the configuration files. There are
   two possible places for this:
+
   '<CMAKE_INSTALL_PREFIX>/<FOAM_INSTALL_CONFIG_PATH>':: if you specified
     +<FOAM_INSTALL_CONFIG_PATH>+ as a relative path.
   '<FOAM_INSTALL_CONFIG_PATH>':: if you specified +<FOAM_INSTALL_CONFIG_PATH>+
     as an absolute path.
+
The default location is '/usr/local/etc/{project}-{ver}'.

Selecting the Parallel Communications Library
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Both, {project} and OpenFOAM abstract the parallel operations into the
'Pstream' library, making it rather simple to firstly switch between parallel
implementations and secondly port the software to a new communications library.
However, {project} uses a much more flexible mechanism of determining which
'Pstream' implementation library to use than OpenFOAM. The latter does this by
adjusting the +LD_LIBRARY_PATH+ environment variable. As {project} wants to be
a well behaved Linux citizen, this is not an option. Instead, {project}
dynamically loads the desired 'Pstream' library at startup (i.e. as a plug-in).
The following list details how {project} determines what library to load (if at
all):

1. If the environment variable +FREEFOAM_PSTREAM_LIBRARY+ is set,
   {project} will try to load the library specified by it.
2. If the sub-dictionary +PstreamImplementation+ exists in the global
   'controlDict' file (see <<globalconfig,'Global Configuration Files'>>), it
   reads the value of the entry +configName+ therein. It then expects that a
   sub-dictionary of +PstreamImplementation+ with the name specified in
   +configName+ exists. If that sub-dictionary contains the entry +library+, it
   will try to load a library specified by the value of that entry.

After {project} (possibly) loaded the library, it will try to instantiate
concrete implementations of the abstract base classes +PstreamImpl+,
+IPstreamImpl+ and +OPstreamImpl+. Which classes are to be instantiated
is determined as follows:

1. {project} queries the environment variables +FREEFOAM_PSTREAM_CLASS+,
   +FREEFOAM_IPSTREAM_CLASS+ and +FREEFOAM_OPSTREAM_CLASS+ for the class
   names to be instantiated.
2. For any of the variables not set, it requires the sub-dictionary
   +PstreamImplementation+ to be present in the global 'controlDict', reads the
   value of +configName+ and similarly to the library loading, loads the
   sub-dictionary specified by that value. It then expects to find the entries
   +Pstream+, +IPstream+ and +OPstream+ which specify the names of the classes
   to load.

This means that one can create a global 'controlDict' file containing
(among other things) something like the following:
=========
---------
PstreamImplementation
{
    //configName dummy;
    configName mpi;

    dummy
    {
        library libdummyPstream.so;
        Pstream dummyPstreamImpl;
        OPstream dummyOPstreamImpl;
        IPstream dummyIPstreamImpl;
    }

    mpi
    {
        library libmpiPstream.so;
        Pstream mpiPstreamImpl;
        OPstream mpiOPstreamImpl;
        IPstream mpiIPstreamImpl;
    }
}
---------
=========

This way the administrator can provide a global 'controlDict' in the {project}
installation. Every user can then override that 'controlDict' by supplying her
own file in her home directory as detailed in <<globalconfig,'Global
Configuration Files'>>. In order to select a particular 'Pstream'
implementation for a specific communications library, the user can then either
adjust the +PstreamImplementation::configName+ entry in the global
'controlDict' file, set the +FREEFOAM_PSTREAM_CONFIG+ variable or for full
control, set the variables +FREEFOAM_PSTREAM_LIBRARY+,
+FREEFOAM_PSTREAM_CLASS+, +FREEFOAM_IPSTREAM_CLASS+ and
+FREEFOAM_OPSTREAM_CLASS+.

Running {project} From the Build Tree
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
You can use {project} without installing it first, directly from the build
tree. However, this might take a little bit more effort to set up because most
likely you will have to adjust the following environment variables:

`PATH`::
  Must contain '$HOME/Source/freefoam-{fullver}-build/bin'
`LD_LIBRARY_PATH`::
  Must contain '$HOME/Source/freefoam-{fullver}-build/lib/{project}-{ver}'
`FREEFOAM_CONFIG_DIR`::
 Should point to '$HOME/Source/freefoam-{fullver}-build/etc'

Where it is assumed that you followed the <<installation,installation
instructions>>. If you used different paths for downloading and compiling
{project}, you will have to adjust these names. Refer to
<<environment,'Extending Search Paths And Setting Environment Variables
Permanently'>> if you need help setting these variables.

Running the tutorials
---------------------
Now you should be able to run the tutorial cases. For this copy the +tutorials+
directory to some convenient place:
---------------
$ mkdir -p $HOME/{project}/$LOGNAME-{shortver}/run
$ cp -r $HOME/Source/freefoam-{fullver}-build/tutorials \
  $HOME/{project}/$LOGNAME-{shortver}/run/
$ cd $HOME/{project}/$LOGNAME-{shortver}/run/tutorials
---------------
And try to run e.g. the 'cavity' tutorial case:
---------------
$ cd incompressible/icoFoam
$ freefoam blockMesh -case cavity
$ freefoam checkMesh -case cavity
$ freefoam ico -case cavity
---------------
Things should run smoothly and finish without an error.

All the tutorials contain a script for automatic execution since some of the
cases are quite intricate and it is not obvious how to run them. Also, these
scripts are used for automated testing. The scripts are called 'Allrun', where
the one located in the 'tutorials' directory is a driver script to run all the
other tutorials.

Obtaining the Source Code from the GIT repository
-------------------------------------------------
- Clone the {project} repository (here the clone is placed in
  +$HOME/Source/{project}+):
+
---------------------------------------------------------------------------
$ mkdir -p $HOME/Source
$ git clone git://repo.or.cz/freefoam.git $HOME/Source/{project}
---------------------------------------------------------------------------
- Proceed in the same way (replacing the path names appropriately) as in the
  above build instructions.

Shell completion scripts
------------------------
{project} comes with completions scripts for the {bash} and {zsh} shells. The
former is quite simplistic and only offers very basic completion of the
available application names. The ZSH completion, however, is quite complete and
also completes options and arguments for all applications. These completion
functions are not installed by +make install+, because no two systems have the
same locations for these kinds of scripts. You find them for manual
installation in the {project} sources in the directory
'data/shellFunctions/bashCompletion' and 'data/shellFunctions/zshCompletion'
respectively. Please refer to the documentation of your system/shell on where
to place them.

Emacs mode
----------
{project} includes a rudimentary major mode for the {emacs} programming editor.
If you want to use this mode, place the file
'data/editor-modes/foamdict-mode.el' in a directory where your Emacs
installation finds it. Please refer to the Emacs documentation for further
instructions.

Build Configuration Reference
-----------------------------
All installation paths below, if not absolute, are relative to
'CMAKE_INSTALL_PREFIX'.

///////////////////////////
KEEP ALPHABETICALLY SORTED!
///////////////////////////

[glossary]
+CMAKE_BUILD_TYPE+::
  One of '<empty>', 'Debug', 'Release', 'RelWithDebInfo' and 'MinSizeRel'.
  Refer to the CMake documentation for more detail.
+CMAKE_INSTALL_PREFIX+::
  Installation prefix under which to install {project}.
+FOAM_DOUBLE_PRECISION+::
  If set to 'ON' {project} will be compiled using 'double' as the
  floating point type. If set to 'OFF' it will use 'float'.
+FOAM_BUILD_FRAMEWORKS+::
  If this is enabled, the libraries are built as frameworks. Only available on
  Mac OS X.
+FOAM_BUILD_PRIVATE_CCMIO+::
  [[private-ccmio]]
  Automatically download and build libccmio. Unfortunately this process may
  fail in the download step if CMake cannot find either 'wget' or 'curl' on
  your system, since CMake itself currently does not support 'https' URLs. If
  this happens, the build process will abort. To fix the issue, Download the
  file {libccmio} manually and place it in +ThirdParty/ccmio/src+ (relative to
  the build directory). It is important that you re-run CMake *before*
  restarting the build in order to notify the build system that the file is now
  there.
+FOAM_BUILD_PRIVATE_METIS+::
  Automatically download and build 'METIS'.
+FOAM_BUILD_PRIVATE_MGRIDGEN+::
  Automatically download and build 'MGRIDGEN'.
+FOAM_BUILD_PRIVATE_PARMETIS+::
  Automatically download and build 'ParMetis'.
+FOAM_BUILD_PRIVATE_SCOTCH+::
  [[private-scotch]]
  Automatically download and build 'SCOTCH'.
+FOAM_BUILD_PRIVATE_ZLIB+::
  Automatically download and build the 'ZLIB' compression library.
+FOAM_DEFAULT_PSTREAM+::
  The default Pstream selection in the global 'controlDict' file.
+FOAM_DOXYDOCS_FOR_SF+::
  This setting is for the maintainers of the {project} and indicates whether
  the Doxygen documentation should be built for deployment on {homepage}
[[enable-ccmio]]
+FOAM_ENABLE_CCMIO+::
  Enable the use of 'libccmio'. This is required to build the grid conversion
  utility 'ccm26ToFoam'.
+
[WARNING]
The license of 'libccmio' (C) is proprietary and requires the consent of the
copyright holders ({cd-adapco}) to download and use the
library. Further it is not allowed to redistribute it in any form. The request
for permission of inclusion with {debian} was answered as
follows by mailto:geoffrey.prewett@us.cd-adapco.com[Geoffrey Prewett]:
+
-------------------------------------------------------------------------------
Gerber,

Sorry for the delay in response.  I checked back with our development director,
and he felt that it would be best to not include libccmio with Debian.
Instead, we would prefer to continue our current policy and keep it on our
web/FTP and have people ask for it.  There are three reasons for this:

1) We don't support STAR on Debian, and don't want to give the impression that
   we do.
2) We would like to keep a list of people that we give the library to.
3) This is not a general purpose library;  its sole purpose is to communicate
between our products.  Accepting outside changes risks committing a change that
would break our own software in possibly subtle ways.

So I regret to tell you that my company has declined to permit libccmio to be
distributed as part of Debian.

Regards,
Geoff Prewett
-------------------------------------------------------------------------------
+
+FOAM_ENABLE_DOXYGEN_DOCS+::
  Enable building of the 'Doxygen API documentation'. The documentation will
  only be built once and is not updated automatically. This is because it
  depends on a huge number of files and would make dependency tracking very
  slow and difficult to maintain. To force the re-generation of the API
  documentation execute +make apidoc+.
+FOAM_ENABLE_METIS+::
  Enable the use of the 'METIS' graph partitioning library which is required to
  implement the 'metis' decomposition method.
[[enable-mgridgen]]
+FOAM_ENABLE_MGRIDGEN+::
  Enable the use of 'MGRIDGEN' which is required to build
  'MGridGenGamgAgglomeration' providing the 'MGridGen' agglomeration method for
  the GAMG solver.
+
[WARNING]
The license of 'MGRIDGEN' is unknown and the upstream authors so far have not
answered any inquiries to resolve the issue. If you enable the use of
'MGRIDGEN' you alone are responsible for ensuring that you don't violate any
license conditions applying to these libraries. The authors of {project} will
and cannot take any responsibility for your actions.
+
+FOAM_ENABLE_MANPAGE_HELP+::
  [[foam_enable_manpage_help]]
  Build (and install) the help-pages in manpage format. This requires a
  complete {asciidoc} toolchain to be present.
+FOAM_ENABLE_MATHJAX+::
  When 'FOAM_ENABLE_XHTML_GUIDES' is enabled, use {mathjax} for the math
  rendering.
+FOAM_ENABLE_PARMETIS+::
  Enable the use of the 'ParMetis' graph partitioning library which is required
  to implement the 'parMetis' decomposition method.
+FOAM_ENABLE_PDF_GUIDES+::
  Build a PDF version of the user guide. In addition to a complete {asciidoc}
  toolchain, this requires either {dblatex} (for better results) or {fop} to be
  installed. If FOP is used, {latex} and {dvipng} are required.
+FOAM_ENABLE_XHTML_GUIDES+::
  Build a XHTML version of the user guide. This requires a complete {asciidoc}
  toolchain. If +FOAM_ENABLE_MATHJAX+ is disabled, this also requires {latex}
  and {dvipng} to be available.
+FOAM_ENABLE_XHTML_HELP+::
  Build (and install) the help-pages in XHTML format for the display in a web
  browser. The requirements are the same as for
  <<foam_enable_manpage_help,+FOAM_ENABLE_MANPAGE_HELP+>>.
+FOAM_EXE_PREFIX+::
  Prefix used to mangle application names. Normally this shouldn't be changed.
+FOAM_ENABLE_FULL_TUTORIAL_TESTS+::
  Run the full tutorials as tests, don't limit their run-time to a single time
  step.
+FOAM_INSTALL_BIN_PATH+::
  Installation path of the binaries.
+FOAM_INSTALL_CMAKE_PATH+::
  Installation path of the CMake development files.
+FOAM_INSTALL_CONFIG_PATH+::
  Installation path of the configuration files.
+FOAM_INSTALL_DATA_PATH+::
  Installation path of the architecture-independent files.
+FOAM_INSTALL_DOC_PATH+::
  Installation path of the documentation files.
+FOAM_INSTALL_FRAMEWORK_PATH+::
  Installation path of the Mac OS X frameworks. This is only available and
  takes effect if {project} is compiled on Mac OS X, and if
  'FOAM_BUILD_FRAMEWORKS' is enabled.
+FOAM_INSTALL_HEADER_PATH+::
  Installation path of the header files. On Mac OS X, and if
  'FOAM_BUILD_FRAMEWORKS' is enabled, this setting is ignored.
+FOAM_INSTALL_LIBEXEC_PATH+::
  Installation path of the binaries which should not be on the +PATH+.
+FOAM_INSTALL_LIBRARY_PATH+::
  Installation path of the libraries.
+FOAM_INSTALL_MAN_PATH+::
  Installation path of the manpage files.
+FOAM_INSTALL_PLUGIN_PATH+::
  Installation base-path of plugins.
+FOAM_INSTALL_PYTHON_PATH+::
  Installation path for Python modules.
+FOAM_INSTALL_USERDFOAM_PATH+::
  Installation path of the Ensight plug-in.
+FOAM_INSTALL_TUTORIALS_PATH+::
  Installation path of the tutorials.
+FOAM_USE_FOP+::
  Use {fop} instead of {dblatex} when building the PDF of the user guide.
+FOAM_USE_MPI+::
  If enabled, {project} will use the MPI parallel communications library.
  This is required in order to build some of the libraries and utilities.
+FOAM_USE_LOCAL_DOXYGEN_DOCS+::
  This setting influences the location in which the Doxygen source
  code documentation is looked for if any of the {project} applications
  is invoked with the '-doc' or '-srcDoc' options. If it is disabled,
  the documentation will be loaded over the network from
  {apidoc}. If you enable it, the
  documentation will be loaded locally. This requires that you either
  build and install the documentation by enabling +FOAM_ENABLE_DOXYGEN_DOCS+,
  or provide the required HTML files otherwise.
+HTML_DOC_BROWSER+::
  This is the program used to display the Doxygen source code documentation
  if any of the {project} applications is invoked with the '-doc' or '-srcDoc'
  options. The special value of 'ECHO' changes the behaviour to just write
  the location of the HTML file to the output. This is a good setting if
  you're system doesn't have any kind of HTML browser installed (such
  as on a cluster).
+FOAM_HTML_DOC_BROWSER_COMMAND+::
  This is the command with which to invoke the HTML browser. By default
  it calls the program named in +HTML_DOC_BROWSER+ and passes it the
  name/URL of the documentation file to be displayed. You shouldn't
  have to change this unless your HTML browser requires some unusual
  options or arguments.

Troubleshooting
---------------

The {project} Executables Are Not Found By The Shell
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
There are three possible reasons for this:

1. Your shell (notably 'csh', 'tcsh' and 'zsh') requires you to refresh the
   cache of available executables. You can do so by entering the command:
+
--------------
$ rehash
--------------
+
2. If 'rehashing' didn't solve the problem, the problem most likely is that you
   installed {project} into a non-standard location by changing the
   configuration variables +CMAKE_INSTALL_PREFIX+ or +FOAM_INSTALL_BIN_PATH+ in
   which case the executables where installed into a directory not searched by
   the shell. In this case you have to add the installation directory of the
   executables to the +PATH+ variable. There are two possible locations:
+
--
'<CMAKE_INSTALL_PREFIX>/<FOAM_INSTALL_BIN_PATH>':: if you specified
  +FOAM_INSTALL_BIN_PATH+ as a relative path
'<FOAM_INSTALL_BIN_PATH>':: if you specified +FOAM_INSTALL_BIN_PATH+ as an
  absolute path
--
+
After extending the +PATH+ variable with the installation directory of the
executables, you should be able to run all {project} applications as any other
binary available on the system. See <<environment,'Extending Search Paths And
Setting Environment Variables Permanently'>> for
instructions on how to extend the search path.

3. This option is similar to the previous solution and applies if you want to
   run {project} from the build tree (i.e. without running +make install+). In
   this case you again have to make sure that your shell finds the executables
   built by CMake by extending the +PATH+ variable. Further, you have to tell
   {project} where to find the global configuration files (see
   <<globalconfig,'Global Configuration Files'>>). Here, you have the option to
   place the files under your home directory or set an environment variable.
   The former can be achieved by:
+
--------------
$ mkdir -p $HOME/.{project}/{shortver}
$ cp $HOME/Source/freefoam-{fullver}-build/etc/controlDict \
    $HOME/.{project}/{shortver}
$ cp $HOME/Source/freefoam-{fullver}-build/etc/cellModels \
    $HOME/.{project}/{shortver}
$ cp -r $HOME/Source/freefoam-{fullver}-build/etc/thermoData \
    $HOME/.{project}/{shortver}
--------------
+
The latter (and recommended) method is to set the environment variable
+FREEFOAM_CONFIG_DIR+ to '$HOME/Source/freefoam-{fullver}-build/etc'. Adjust
the paths to match the build tree to your actual setup.

Starting Any {project} Application Fails Because Some Libraries Cannot Be Found
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Although CMake should have taken care of this by using +RPATH+ on Linux and
+install_name+ on Mac OS X, it might be necessary on some systems to adjust the
library search paths:

+LD_LIBRARY_PATH+:: This variable is used by all Unix like systems (e.g. Linux,
  Mac OS X, etc.)
+DYLD_LIBRARY_PATH+:: This variable is used by Mac OS X.

If you installed {project}, there are (as with the executables), two possible
installation directories:

'<CMAKE_INSTALL_PREFIX>/<FOAM_INSTALL_LIBRARY_PATH>':: if you specified
  +FOAM_INSTALL_LIBRARY_PATH+ as a relative path.
'<FOAM_INSTALL_LIBRARY_PATH>':: if you specified +FOAM_INSTALL_LIBRARY_PATH+ as
  an absolute path.

If you are trying to run from the build tree, you have to include
'$HOME/Source/freefoam-{fullver}-build/lib/{project}-{ver}' in the above
mentioned search paths (where you have to adjust the location of the build tree
to your actual setup).

A Running {project} Application Aborts Because It Can't 'dlopen' A Library
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{project} (and OpenFOAM) often dynamically load libraries at run-time (a.k.a
plug-ins) to add features the user requested without requiring that the whole
application be recompiled. This makes it very simple to add new boundary
conditions, turbulence and combustion models etc. However, it also requires
that {project} must be able to find these libraries at run-time. The operating
system function which does the loading of the libraries ('dlopen') usually
tries to find the library with the given name in several places; namely a
default search path and a search path configured by one or multiple environment
variables such as +LD_LIBRARY_PATH+ or +DYLD_LIBRARY_PATH+ (on Mac OS X). The
details vary from platform to platform, so you best consult the documentation
of 'dlopen' for the details.

Additionally {project} allows you to configure a custom search path for
plug-ins in the <<globalconfig,global 'controlDict'>> file by listing the
directories to be searched in the list +LibrarySearchPaths+. By default
{project} is configured to search for plug-ins in the location where CMake
installed them.

If you want to add your own plug-in libraries (e.g. you want to add your own
boundary conditions class), you most probably will want to extend this search
path.

{project} Aborts When Trying To Instantiate a Plugin Class
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
If you get a warning message similar to the following

 --> FOAM Warning :
     From function dlLibraryTable::open(const dictionary& dict, const word& libsEntry, const TablePtr tablePtr)
     in file XXX/src/OpenFOAM/db/dlLibraryTable/dlLibraryTableTemplates.C at line 68
     library "libfieldFunctionObjects.so" did not introduce any new entries

(where +XXX+ is the path to the {project} source code and the actual library
name can be different), followed by a fatal error stating that {project} does
not know a class or type, e.g.

 --> FOAM FATAL ERROR:
 Unknown function type fieldAverage

 Table of functionObjects is empty


     From function functionObject::New(const word& name, const Time&, const dictionary&)
     in file XXX/src/OpenFOAM/db/functionObjects/functionObject/functionObject.C at line 74.

 FOAM exiting

and you are absolutely sure that the named type actually exists in the library
mentioned in the preceding warning message, the issue is very likely that
{project} is loading the plugin library from a different binary tree than the
executable belongs to.

[IMPORTANT]
Always make sure that you never load plugins from different binary trees (where
the build tree and the install tree count as such). If you want to run a binary
from the build tree but already have a corresponding installation tree, use the
+FREEFOAM_CONFIG_DIR+ environment variable to point {project} to the directory
'<path to build tree>/etc/' containing the global 'controlDict' file in the
**build tree**. Otherwise the binaries are likely to be incompatible with each
other.

[[environment]]
Extending Search Paths And Setting Environment Variables Permanently
--------------------------------------------------------------------
The way one sets environment variables and extends the executable and library
search paths permanently strongly depends on the shell used. Usually one has to
create or change an initialization file in the users home directory. In the
following this will be discussed very briefly for the popular shells 'BASH' and
'tcsh'. However, if you need more help or want information on using the shell,
there is an excellent tutorial available at {linuxcommand}.

BASH
~~~~
The BASH shell is the default shell for most Linux/Unix distributions. Most
systems configure the BASH shell such that it reads the text file
'$HOME/.bashrc' when starting up, so this is the place where one appends
customizations of the environment variables. On some systems this file is not
processed by default (notably Mac OS X). In this case you can use
'$HOME/.bash_profile'.

Referencing A Variable
^^^^^^^^^^^^^^^^^^^^^^
To retrieve the value stored in a shell variable or environment variable, one
prefixes its name with the dollar (+$+) character.

Setting A Variable
^^^^^^^^^^^^^^^^^^
The syntax for setting a variable and making it available to child-processes of
the shell is the following:
-------
$ export variable_name=variable_value
-------
Note that no white-space characters are allowed surrounding the +=+ sign.

Extending A Search Path
^^^^^^^^^^^^^^^^^^^^^^^
The shell and other Unix system facilities use environment variables to locate
executables and dynamically linked libraries. These search paths consist of
strings naming directories in which the executables and libraries should be
searched for. The individual paths are separated by a colon (+:+) character. To
add the e.g. the directory '$HOME/bin' to the search path for executables, one
would do the following:
-------
$ export PATH=$PATH:$HOME/bin
-------
which appends '$HOME/bin' to the end of the +PATH+ variable.

TCSH
~~~~
Some users and administrators prefer to use a 'C-Shell', such as the TCSH. Here
you can use e.g. the file '$HOME/.tcshrc' to customize the environment.

Referencing A Variable
^^^^^^^^^^^^^^^^^^^^^^
As with the BASH, one retrieves the value stored in a shell variable or
environment variable by prefixing its name with the dollar (+$+) character.
Sometimes it is also necessary to protect the variable name by surrounding it
with curly braces (+{+ and +}+).

Setting A Variable
^^^^^^^^^^^^^^^^^^
The syntax for setting a variable and making it available to child-processes of
the shell is the following:
-------
$ setenv variable_name variable_value
-------

Extending A Search Path
^^^^^^^^^^^^^^^^^^^^^^^
The shell and other Unix system facilities use environment variables to locate
executables and dynamically linked libraries. These search paths consist of
strings naming directories in which the executables and libraries should be
searched for. The individual paths are separated by a colon (+:+) character. To
add the e.g. the directory '$HOME/bin' to the search path for executables, one
would do the following:
[subs="verbatim"]
-------
$ setenv PATH ${PATH}:${HOME}/bin
-------
which appends '$HOME/bin' to the end of the +PATH+ variable. Note that
'C-shells' usually require the user to type 'rehash' after changing the +PATH+
variable to update the cache of available programs.

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