File: INSTALL

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1 Installing rheolef
********************

(Source file: 'configure.ac')

1.1 Reading the documentation
=============================

Rheolef comes with three documentations:

   * an users guide with a set of complete examples (two volumes)
   * a reference manual for unix commands an C++ classes
   * the full browsable source code in html format

All these documentations are downloadable in various formats from the
Rheolef home page.  These files are also locally installed during the
'make install' stage.  See
             rheolef-config --docdir
The users guide is generated in 'pdf' format:

       evince http://ljk.imag.fr/membres/Pierre.Saramito/rheolef/rheolef.pdf
       evince http://ljk.imag.fr/membres/Pierre.Saramito/rheolef/rheolef2-dg.pdf

The reference manual is generated in 'html' format:

       firefox http://ljk.imag.fr/membres/Pierre.Saramito/rheolef/rheolef-refman.html

and you could add it to your bookmarks.  Moreover, after performing
'make install', unix manuals are available for commands and classes:

       man field
       man 2 field

The browsable source code is generated in 'html' format:

       firefox http://ljk.imag.fr/membres/Pierre.Saramito/rheolef/source_html/files.html

1.2 Installing from source as root user
=======================================

       ./configure
       make
       sudo make install

By default, the installation directory is '/usr/local'.  Commands are in
'/usr/local/bin', libraries in '/usr/local/lib', header files in
'/usr/local/include' and others file in '/usr/local/share'.

1.3 Using and alternative installation directory
================================================

The default install prefix is '/usr/local'.  If you are not the root
user, or do not have its password, you could prefer an alternative
directory, e.g.  'HOME/sys'.  You should enter:

       ./configure --prefix=$HOME/sys

In that case, you have to add the following lines at the end of your
'.profile' or '.bash_profile' file:

       export PATH="$HOME/sys/bin:$PATH"
       export LD_LIBRARY_PATH="$HOME/sys/lib:$LD_LIBRARY_PATH"
       export MANPATH="$HOME/sys/man:$MANPATH"

Assuming you are using the 'sh' or the 'bash' unix interpreter.
Conversely, if you are using 'csh' or 'tcsh', add at the bottom of your
'.cshrc' file:

       set path = ($HOME/sys/bin $path)
       setenv LD_LIBRARY_PATH "$HOME/sys/lib:$LD_LIBRARY_PATH"
       setenv MANPATH "$HOME/sys/man:$MANPATH"

If you are unsure about unix interpreter, get the SHELL value:
       echo $SHELL

Then, you have to 'source' the modified file, e.g.:

       source ~/.bashrc

hpux users should replace 'LD_LIBRARY_PATH' by 'SHLIB_PATH'.  If you are
unsure, get the shared library path variable:

       rheolef-config --shlibpath-var

Check also your installation by compiling a sample program with the
installed library:

       make installcheck

Since it is a common mistake, you can later, at each time, test your
run-time environment sanity with:

       rheolef-config --check

1.4 Requiered libraries
=======================

The following required libraries are available as precompiled packages
under Debian GNU/Linux and Ubuntu systems.

'a)'
     The 'boost' library.  It provides useful extensions of the c++
     standard template library.  See <http://www.boost.org>.

'b)'
     The 'armadillo' library.  It provides efficient c++ linear algebra
     subroutines.  See <http://arma.sourceforge.net>.

1.5 Optional highly recommended libraries
=========================================

'a)'
     The 'umfpack' library provides a multifrontal sparse direct solver.
     Rheolef solvers run faster when using this library.  See
     <http://faculty.cse.tamu.edu/davis/suitesparse.html>.

'b)'
     The 'cgal' library provide an easy access to efficient and reliable
     geometric algorithms.  With it, Rheolef implements the
     characteristic method and interpolation from one mesh to another.
     This library is optional, but allows, when available, extended
     Rheolef features.  See <http://www.cgal.org>.

1.6 Optional distributed and parallel libraries
===============================================

With the optional following libraries, Rheolef is able to run in
parallel and and with distributed memory.  By default, the Rheolef
'configure' script tries to autodetect these libraries and be able to
run in parallel.  When these libraries are not found, the distributed
features are turned off.  If your libraries are installed in a
non-standard location, you should indicate it by a suitable 'configure'
option.  See below for these options.

'a)'
     Rheolef bases on 'mpi', the message passing interface standard.

'b)'
     'mumps' is a massively distributed sparse direct solver.  The use
     of implicit numerical schemes leads to the resolution of large
     sparse linear systems.  Rheolef installation optionally requires
     'mumps' is available at <http://graal.ens-lyon.fr/MUMPS> .

'c)'
     Rheolef bases either on 'scotch' or 'metis' for distributed mesh
     partitioning.  'scotch' is available at
     <http://www.labri.fr/perso/pelegrin/scotch>.  'metis' is available
     at <http://www.cs.umn.edu/~metis>.

'd)'
     Rheolef installation optionally uses 'trilinos/ifpack' as a library
     of preconditioner used for iterative solvers.  'trilinos' is
     available at <http://trilinos.sandia.gov> .  When 'trilinos' is not
     available, a less efficient builtin IC0 preconditioner is used.

1.7 Run-time optional tools
===========================

Using Rheolef suggests the use of the following optional tools for pre-
and post-processing purpose:

       gmsh
       gnuplot
       paraview
       mayavi2

None of these tools are required when building and installing Rheolef.

1.8 Build-time extra tools for rheolef developers
=================================================

These tools are required if you build from the development version
(under CVS). Re-generating some source files, as initiated with the
"bootstrap" command, requires autotools 'autoconf', 'automake' and
'libtool' and also 'flex' and 'bison'.  It requires also 'ginac' for
polynomial basis management.  'ginac' is available at
<http://www.ginac.de> .  It requiers finaly latex figure management
tools to.  Here is the 'apt-get' commands to install these tools under
Debian GNU/Linux and Ubuntu:

       apt-get install cvs autoconf automake libtool
       apt-get install flex bison
       apt-get install pkg-config libginac-dev ginac-tools
       apt-get install ghostscript gnuplot xfig transfig imagemagick graphviz

1.9 Portability issues
======================

Rheolef is based on STL and its extensions, the BOOST library.
Therefore you need a compiler that supports the ANSI C++ standards.  STL
and Rheolef especially depend heavily on the template support of the
compiler.  The C++ 2011 standard features are recommanded but still
optional: when available, it allows extended features, e.g.  an elegant
matrix concatenation syntax via the 'std::initializer_list' class.

Current distributed version of Rheolef has been heavily tested with GNU
C++, CLANG C++ and INTEL C++ on debian, ubuntu, mint, suse and redhat
GNU/Linux systems for various 32 and 64 bits architectures, up to 200
distributed memories and processes.  Successful installation from
sources on MAC-OS-X systems has been also repported.

The GNU C++ compiler is a free software available at
<http://www.gnu.org>.  The CLANG C++ compiler is also a free software
available at <http://clang.llvm.org>.  The Intel C++ compiler is a
privative software.

So, the Rheolef library is expected to compile without problems with one
of these compilers.  Otherwise, please send a bug report to
<mailto:rheolef@grenet.fr>.

Older Rheolef 5.x versions was tested also on the KAI C++ compiler
(KCC-3.2b) and the CRAY C++ compiler (CC-3.0.2.0) on the following
operating systems:

       mac os x (i386-apple-darwin9.8.0), using GNU C++
       sun solaris 2.8, ultrasparc, using GNU C++
       compacq OSF1 alpha (V5.1, V4.0), using Compacq C++
       aix 4.1 ibm sp2, multiprocessor based on rs6000
       cray unicos t3e, multiprocessor based on 64 bits dec alpha
       cray unicos c94
       hpux 9.05 and 10.20, hppa
       sgi irix 6.3, mips
       sun solaris 2.5.1, sparc

The KAI C++ is available at <http://www.kai.com>.  The CRAY C++ is
available on CRAY platforms.  Nevertheless, the current version has no
more been tested on these compilers and systems.

1.10 Configure command line options
===================================

If the required libraries are located in a non-standard directory,
please use the configure options:

       ./configure --help

and also consider the CXX, CXXFLAGS and LIBS variables, as in the
following more complex configure command:

       CXX=clang++ CXXFLAGS=-I/misc/include LIBS="-L/misc/lib" ./configure

Finaly, if troubles still persist after the configure step, you can also
edit directly the config/config.mk and config/config.h files.  In these
cases please also post to the mailling list <mailto:rheolef@grenet.fr>
for any portability problem.

If you are running a another compiler and operating system combination,
please run the non-regression test suite:

       make check

Please, send mails and bug reports to the mailing list
<mailto:rheolef@grenet.fr>.

1.11 Configure command line options
===================================


'--with-float=OPTION'
     Turns on/off the extended arithmetic feature.  The OPTION could be
     either 'float128' (quadruple precision, 32 digits), or the default
     'double' (double precision, 16 digits).

'--enable-permissive'
     The compiler do not turns all warnings into errors and becomes
     permissive.  This feature is for code developers and is off by
     default.

'--with-bigfloat=DIGITS10'
     Turn on Bruno Haible's 'cln' arbitrary precision float library with
     DIGITS10 precision,

     See <http://clisp.cons.org/~haible/packages-cln.html>.  Default is
     off.  The DIGITS10 value is optional and default DIGITS10 value is
     60.  This feature is still under development.

'--with-cln=DIR_CLN'
     Set the home directory for the 'cln' library.  Default DIR_CLN is
     '/usr/local/math'.

'--enable-debian-packaging=DEBIAN_PACKAGING'
     Generate files the debian way by respecting the 'Debian Policy
     Manual'.

'--with-boost-incdir=INCDIR_BOOST'
'--with-boost-libdir=LIBDIR_BOOST'
     Specifies the 'boost' library.  This library is required by
     rheolef.

'--with-armadillo-incdir=INCDIR_ARMADILLO'
'--with-armadillo-libdir=LIBDIR_ARMADILLO'
     Specifies the 'armadillo' library.  This library is required by
     rheolef.

'--enable-debug'
     Produce a 'c++ -g' like code.
'--enable-dmalloc'
     With debugging, also uses dynamic allocation runtime checking with
     'dmalloc' when available.

'--enable-old-code'
     Turns on/off the old code branch (before distributed computation
     features).  Default is off.

'--enable-mpi'
     Turns on/off the distributed computation features.  Default is on
     when distributed is on.  This feature is currently in development.
     When on, configure try to detect either the scotch or the parmetis
     libraries.

'--with-scotch-incdir=INCDIR_SCOTCH'
'--with-scotch-libdir=LIBDIR_SCOTCH'
'--with-scotch-libs=LIBS_SCOTCH'
     Turns on/off the 'scotch' distributed mesh partitioner.  Check in
     LIBDIR_SCOTCH for 'libptscotchparmetis.so', 'libptscotch.so' and
     'libptscotcherrexit.so' or corresponding '.a' libraries.  Default
     is to auto-detect when mpi is available.

'--with-parmetis-incdir=INCDIR_PARMETIS'
'--with-parmetis-libdir=LIBDIR_PARMETIS'
     Turns on/off the 'parmetis' distributed mesh partitioner.  Check in
     LIBDIR_PARMETIS for 'libparmetis.so', 'libparmetis.a' and also
     'libmetis.a' 'libmetis.so'.  Default is to autodetect when mpi is
     available and scotch unavailable.

'--with-blas-libdidr=RHEO_LIBDIR_BLAS'
'--with-blas-libs=RHEO_LIBS_BLAS'
     Turns on/off the 'blas' libraries.  Check in RHEO_LIBS_BLAS for
     'libblas.so', or the corresponding '.a' libraries.  Default is to
     auto-detect.  This librariy is required for the pastix library.

'--with-scalapack-libdidr=RHEO_LIBDIR_SCALAPACK'
'--with-scalapack-libs=RHEO_LIBS_SCALAPACK'
     Turns on/off the 'scalapack' libraries.  Check in
     RHEO_LIBS_SCALAPACK for 'libscalapack.so', or the corresponding
     '.a' libraries.  Default is to auto-detect.  This librariy is
     required for the pastix library.

'--with-mumps-incdir=INCDIR_MUMPS'
'--with-mumps-libdir=LIBDIR_MUMPS'
'--with-mumps-libs=LIBS_MUMPS'
     Turns on/off the 'mumps' distributed solver.  Check in LIBDIR_MUMPS
     for 'libmumps.so', or the corresponding '.a' libraries.  Default is
     to auto-detect when mpi is available.

'--with-trilinos'
'--with-trilinos=LIBDIR_TRILINOS'
     Turns on/off the 'trilinos' distributed preconditioner library.
     Check in LIBDIR_TRILINOS for 'libtrilinos_ifpack.so', or the
     corresponding '.a' libraries.  Default is to auto-detect when mpi
     is available.

'--with-pastix'
'--with-pastix=LIBDIR_PASTIX'
     Turns on/off the 'pastix' distributed solver.  Check in
     LIBDIR_PASTIX for 'libpastix.so', or the corresponding '.a'
     libraries.  Default is to auto-detect when mpi is available.

'--with-cholmod-incdir=INCDIR_CHOLMOD'
'--with-cholmod-libdir=LIBDIR_CHOLMOD'
'--with-cholmod-libs=LIBS_CHOLMOD'
     Turns on/off the 'cholmod' multifrontal direct solver.  Default
     INCDIR_CHOLMOD is LIBDIR_CHOLMOD.  Check in LIBDIR_CHOLMOD for
     'libcholmod.so' or 'libcholmod.a' and for header
     INCDIR_CHOLMOD/cholmod.h or INCDIR_CHOLMOD/cholmod/cholmod.h.

'--with-umfpack-incdir=INCDIR_UMFPACK'
'--with-umfpack-libdir=LIBDIR_UMFPACK'
'--with-umfpack-libs=LIBS_UMFPACK'
     Turns on/off the 'umfpack' version 4.3 multifrontal direct solver.
     Default INCDIR_UMFPACK is LIBDIR_UMFPACK.  Check in LIBDIR_UMFPACK
     for 'libumfpack.so' or 'libumfpack.a' and for header
     INCDIR_UMFPACK/umfpack.h or INCDIR_UMFPACK/umfpack/umfpack.h.

'--with-taucs-ldadd=TAUCS_LDADD'
'--with-taucs-incdir=TAUCS_INCDIR'
     Turns on/off the 'taucs' version 2.0 out-of-core sparse direct
     solver.  When this library is not available, the configure script
     check for the spooles multifrontal (see below).

'--with-spooles-libdir=LIBDIR_SPOOLES'
'--with-spooles-incdir=INCDIR_SPOOLES'
     Turns on/off the 'spooles' version 2.2 multifrontal direct solver.
     Default INCDIR_SPOOLES is LIBDIR_SPOOLES.  Check in LIBDIR_SPOOLES
     for 'libspooles.so', 'libspooles.a' or 'spooles.a' and for header
     INCDIR_SPOOLES/FrontMtx.h.  When this library is not available, the
     direct solver bases upon a traditionnal skyline Choleski
     factorisation combined with a reverse Cuthill-Mc Kee reordering.

'--with-cgal-incdir=INCDIR_CGAL'
'--with-cgal-libdir=LIBDIR_CGAL'
     Turns on/off the 'cgal' distributed solver.  Check in LIBDIR_CGAL
     for 'libcgal.so', or the corresponding '.a' libraries.  Default is
     to auto-detect.  Generic or hardware-dependant optimization

'--enable-optim'
     Turns compile-time optimization to maximum available.  Include
     architecture-dependent compilation (e.g.  on intel, executable are
     less portable accross intel variants).  Default is on.  optimize or
     not ?  architecture-dependent optim architecture-independent optim,
     when no debug rpath issue for debian package: seems to be buggy
     with DESTDIR!=""

1.12 The directory structure
============================

'config'
     portability related files and documentation extractors
'util'
     a collection of useful C++ classes and functions for smart
     pointers, handling files and directories, using strings, timing.
'skit'
     sparse matrix library, linear solvers.
'nfem'
     finite element library, mesh, spaces and forms.
'doc'
     reference manual, user's guide and examples.