Editing Advanced Installation (section)

===Fedora 25===
The following explains how to install madagascar on Fedora 25.

We use the following compiler: <code>gcc</code>, <code>g++</code> and <code>gfortran</code>.

* Install some packages
<syntaxhighlight lang="bash" inline style="white-space:wrap">sudo dnf install scons lapack-static lapack64-static atlas-static fftw-static gd gd-devel libtool-ltdl-devel \
libXaw-devel mesa-libGL-devel freeglut-devel netpbm-devel plplot-devel ffmpeg-devel swig openmpi openmpi-devel suitesparse-devel</syntaxhighlight>
This installed the following packages:
<pre>
scons-2.5.1-1.fc25.noarch
lapack-static-3.6.1-2.fc25.x86_64
lapack64-static-3.6.1-2.fc25.x86_64
atlas-static-3.10.2-14.fc25.x86_64
fftw-static-3.3.5-3.fc25.x86_64
gd-2.2.4-1.fc25.x86_64
gd-devel-2.2.4-1.fc25.x86_64
libtool-ltdl-devel-2.4.6-13.fc25.x86_64
libXaw-devel-1.0.13-4.fc25.x86_64
mesa-libGL-devel-17.0.5-3.fc25.x86_64
freeglut-devel-3.0.0-3.fc24.x86_64
netpbm-devel-10.78.00-1.fc25.x86_64
plplot-devel-5.11.1-13.fc25.x86_64
ffmpeg-devel-3.1.9-1.fc25.x86_64
swig-3.0.11-1.fc25.x86_64
openmpi-1.10.5-1.fc25.x86_64
openmpi-devel-1.10.5-1.fc25.x86_64
suitesparse-devel-4.4.6-7.fc25.x86_64
</pre>
and many other dependencies.

* Get the sources from the git repository
<syntaxhighlight lang="bash">git clone https://github.com/ahay/src</syntaxhighlight>

If you run now the <code>configure</code> script, you will get:

<syntaxhighlight lang="bash">
checking for Python ... /usr/bin/python
checking Python version ... 2.7.13
checking for RSFROOT ... /usr/local/rsf
checking for SCons ... /usr/bin/scons
checking SCons version ... v2.5.1.rel_2.5.1:3735:9dc6cee5c168[MODIFIED]
Running RSFROOT=/usr/local/rsf /usr/bin/scons  config ...
------------------------
scons: Reading SConscript files ...
checking platform ... (cached) linux [fedora]
checking for C compiler ... (cached) gcc
checking if gcc works ... yes
checking if gcc accepts '-x c -std=gnu99 -Wall -pedantic' ... yes
checking for ar ... (cached) ar
checking for libraries ... ['m']
checking complex support ... yes
checking for X11 headers ... /usr/include
checking for X11 libraries ... /usr/lib
checking for OpenGL ... yes
checking for sfpen ... (cached) xtpen
checking for ppm ... yes
checking for tiff ... yes
checking for GD (PNG) ... yes
checking for GD (GIF) ... yes
checking for plplot ... no

  Optional package: plplot-devel
checking for ffmpeg ... yes
checking for cairo (PNG) ... yes
checking for cairo (SVG) ... yes
checking for cairo (PDF) ... yes
checking for jpeg ... yes
checking for BLAS ... yes
checking for LAPACK ... no

  Optional package: blas + blas-devel + atlas + atlas-devel
checking for SWIG ... (cached) /usr/bin/swig
checking for numpy ... (cached) yes
checking API options ... (cached) []
checking for C++ compiler ... (cached) g++
checking if g++ works ... yes
checking if g++ accepts '-std=c++11 -U__STRICT_ANSI__ -Wall -pedantic' ... yes
checking for MPICC ... (cached) /usr/lib64/openmpi/bin/mpicc
checking if /usr/lib64/openmpi/bin/mpicc works ... yes
checking for MPICXX ... (cached) /usr/lib64/openmpi/bin/mpicxx
checking if /usr/lib64/openmpi/bin/mpicxx works ... yes
checking for MPIRUN ... (cached) /usr/lib64/openmpi/bin/mpirun
checking for Posix threads ... yes
checking for OpenMP ... yes
checking for CUDA ... (cached) no
checking for FFTW ... yes
checking if FFTW supports threads ... yes
checking for SuiteSparse ... yes
checking for pfft ... no
scons: done reading SConscript files.
scons: Building targets ...
shell_script(["env.sh"], [])
shell_script(["env.csh"], [])
scons: done building targets.
------------------------
Done with configuration.
</syntaxhighlight>

Libraries <code>plplot</code> and <code>lapack</code> are not found. File <code>config.log</code> says
<pre>
/bin/ld: cannot find -lplplotd
</pre>

and

<pre>
gcc -o .sconf_temp/sfconftest_21 .sconf_temp/conftest_21.o -L/usr/lib64/atlas -lm -lf77blas -lcblas -latlas -llapack -lcblas
/usr/lib64/atlas/liblapack.a(dgesv.o): In function `dgesv_':
(.text+0x69): undefined reference to `xerbla_'
/usr/lib64/atlas/liblapack.a(ATL_f77wrap_dgesv.o): In function `atl_f77wrap_dgesv_':
(.text+0x10d): undefined reference to `ATL_xerbla'
/usr/lib64/atlas/liblapack.a(ATL_dgetf2.o): In function `ATL_dgetf2':
(.text+0x184): undefined reference to `ATL_dger'
...
</pre>

So library <code>plplotd</code> doesn't exist on Fedora 25 and the <code>configure</code> script is looking for the wrong <code>lapack</code> library.

If compiling now, 2 other libraries won't be found: <code>gfortran</code> and <code>quadmath</code>

* Regarding the <code>plplotd</code> library, edit file <code>framework/configure.py</code> and change the line 724:
<syntaxhighlight lang="python" line start="724">plplot = context.env.get('PLPLOT','plplotd')</syntaxhighlight>
to
<syntaxhighlight lang="python" line start="724">plplot = context.env.get('PLPLOT','plplot')</syntaxhighlight>

* As for the libraries
** <code>lapack</code>
** <code>gfortran</code>
** <code>quadmath</code>
We must use the <code>lapack</code> library installed in <code>/usr/lib64</code>, not the one installed in <code>/usr/lib64/atlas</code>. And libraries <code>gfortran</code> and <code>quadmath</code> are installed in <code>/usr/lib/gcc/x86_64-redhat-linux/6.3.1/</code>.
Edit file <code>framework/configure.py</code> and add the following 4 lines:
<pre>
['/usr/lib/gcc/x86_64-redhat-linux/6.3.1/',
 '/usr/lib64/',
</pre>
and
<pre>
LIBS.append('gfortran')
LIBS.append('quadmath')
</pre>

so that we end up with the following <code>blas</code> function: 
<syntaxhighlight lang="python" line start="971">def blas(context):
    context.Message("checking for BLAS ... ")
    text = '''
    #ifdef __APPLE__
    #include <Accelerate/Accelerate.h>
    #else
    #ifdef HAVE_MKL
    #include <mkl.h>
    #else
    #include <cblas.h>
    #endif
    #endif
    int main(int argc,char* argv[]) {
    float d, x[]={1.,2.,3.}, y[]={3.,2.,1.};
    d = cblas_sdot(3,x,1,y,1);
    return 0;
    }\n'''

    if plat['OS'] == 'cygwin':
        context.env['ENV']['PATH'] = context.env['ENV']['PATH'] + \
                                         ':/lib/lapack'

    res = context.TryLink(text,'.c')
    if res: 
        context.Result(res)
        context.env['BLAS'] = True 
    else:
        # first try blas
        LIBS = path_get(context,'LIBS')
        blas = context.env.get('BLAS','blas')
        LIBS.append(blas)
        res = context.TryLink(text,'.c')
        if res: 
            context.Result(res)
            context.env['LIBS'] = LIBS 
            context.env['BLAS'] = blas 
        else:
            # some systems require cblas and atlas
            for atlas_dir in filter(os.path.isdir,
                                    ['/usr/lib/gcc/x86_64-redhat-linux/6.3.1/',  # <--- add this line
                                     '/usr/lib64/',                              # <--- add this line
                                     '/usr/lib64/atlas/',
                                     '/usr/lib/atlas/']):
                context.env['LIBPATH'].append(atlas_dir)
            LIBS.pop()
            LIBS.append('f77blas')
            LIBS.append('cblas')
            LIBS.append('atlas')
            LIBS.append('gfortran')  # <----------------------------------------------- add this line
            LIBS.append('quadmath')  # <----------------------------------------------- add this line
            res = context.TryLink(text,'.c')
            if res: 
                context.Result(res)
                context.env['LIBS'] = LIBS 
                context.env['BLAS'] = 'cblas'
            else:
                context.Result(context_failure)
                context.env['CPPDEFINES'] = \
                    path_get(context,'CPPDEFINES','NO_BLAS')
                LIBS.pop()
                LIBS.pop()
                LIBS.pop()
                context.env['BLAS'] = None 
                need_pkg('blas', fatal=False)
</syntaxhighlight>
* Run the <code>configure</code> script, for example:
<syntaxhighlight lang="bash">./configure --prefix=/usr/local/rsf</syntaxhighlight>
Output should give:
<syntaxhighlight lang="bash">
checking for Python ... /usr/bin/python
checking Python version ... 2.7.13
checking for RSFROOT ... /usr/local/rsf
checking for SCons ... /usr/bin/scons
checking SCons version ... v2.5.1.rel_2.5.1:3735:9dc6cee5c168[MODIFIED]
Running RSFROOT=/usr/local/rsf /usr/bin/scons  config ...
------------------------
scons: Reading SConscript files ...
checking platform ... (cached) linux [fedora]
checking for C compiler ... (cached) gcc
checking if gcc works ... yes
checking if gcc accepts '-x c -std=gnu99 -Wall -pedantic' ... yes
checking for ar ... (cached) ar
checking for libraries ... ['m']
checking complex support ... yes
checking for X11 headers ... /usr/include
checking for X11 libraries ... /usr/lib
checking for OpenGL ... yes
checking for sfpen ... (cached) xtpen
checking for ppm ... yes
checking for tiff ... yes
checking for GD (PNG) ... yes
checking for GD (GIF) ... yes
checking for plplot ... yes
checking for ffmpeg ... yes
checking for cairo (PNG) ... yes
checking for cairo (SVG) ... yes
checking for cairo (PDF) ... yes
checking for jpeg ... yes
checking for BLAS ... yes
checking for LAPACK ... yes
checking for SWIG ... (cached) /usr/bin/swig
checking for numpy ... (cached) yes
checking API options ... (cached) []
checking for C++ compiler ... (cached) g++
checking if g++ works ... yes
checking if g++ accepts '-std=c++11 -U__STRICT_ANSI__ -Wall -pedantic' ... yes
checking for MPICC ... (cached) /usr/lib64/openmpi/bin/mpicc
checking if /usr/lib64/openmpi/bin/mpicc works ... yes
checking for MPICXX ... (cached) /usr/lib64/openmpi/bin/mpicxx
checking if /usr/lib64/openmpi/bin/mpicxx works ... yes
checking for MPIRUN ... (cached) /usr/lib64/openmpi/bin/mpirun
checking for Posix threads ... yes
checking for OpenMP ... yes
checking for CUDA ... (cached) no
checking for FFTW ... yes
checking if FFTW supports threads ... yes
checking for SuiteSparse ... yes
checking for pfft ... no
scons: done reading SConscript files.
scons: Building targets ...
shell_script(["env.sh"], [])
shell_script(["env.csh"], [])
scons: done building targets.
------------------------
Done with configuration.
</syntaxhighlight>
* Then run the compilation:
<syntaxhighlight lang="bash">make</syntaxhighlight>

* and finally the installation
<syntaxhighlight lang="bash">sudo make install</syntaxhighlight>