Installation

Madagascar has been installed and is periodically tested on

• Different Linux distributions (Fedora, RedHat, SuSE, Debian, Ubuntu, Oracle, Mandriva, YellowDog)
• FreeBSD
• Solaris
• HP-UX
• SGI Irix
• MacOS X
• Windows under the Cygwin environment and under Microsoft's Services for UNIX environment.

Precompiled binary packages

A precompiled binary package of the latest Madagascar stable release exists for Mac OS X. See the Madagascar download page for details.

Installation from source

Development version installation

1. Configuration: Change to the top source directory and run <bash>./configure --prefix=/directory/where/you/want/madagascar/installed</bash> You can examine the config.py file that this command generates. Additional options are available. You can obtain a full list of customizable variables by running scons -h. For example, to install C++ and Fortran-90 API bindings in addition to the basic package, run <bash>./configure API=c++,f90 --prefix=/directory/where/you/want/madagascar/installed</bash>
2. Building and installing the package: Type <bash>make; make install</bash> If for some reason this does not work, an alternative procedure can be found in the Troubleshooting section .
3. User setup: If your shell is sh or bash, add to your $HOME/.bashrc file the line <bash>source RSFROOT/etc/madagascar/env.sh</bash> where RSFROOT is the install directory you specified in the --prefix option to ./configure . If your shell is (t)csh, edit your $HOME/.cshrc to source env.csh in the same directory as above. If you need "root" privileges for installing under $RSFROOT, you may need to run su; make install or sudo make install . Also, be aware that on some systems the default value for DATAPATH set in the script above gets automatically cleaned at some intervals, so if you want to keep your data binaries for a long time, set DATAPATH in your resource file to another location where you have write access and that allows large files. Do this after the line sourcing the other variables, and remember that the value of DATAPATH must always have a slash at the end.

Stable version (0.9.9) installation

Environment variables

Example configuration for bash: <bash> export RSFROOT=/usr/local/rsf # directory where Madagascar will be installed. if [ -n "$PYTHONPATH" ]; then export PYTHONPATH=${PYTHONPATH}:$RSFROOT/lib else export PYTHONPATH=$RSFROOT/lib fi export PATH=$RSFROOT/bin:$PATH export DATAPATH=/var/tmp/ export MANPATH=$RSFROOT/share/man:$(manpath) export LD_LIBRARY_PATH=$RSFROOT/lib:$LD_LIBRARY_PATH </bash> Notice the slash at the end of the DATAPATH variable.

Example configuration for csh and tcsh:

setenv RSFROOT /usr/local/rsf
if ($?PYTHONPATH) then
setenv PYTHONPATH ${PYTHONPATH}:$RSFROOT/lib
else
setenv PYTHONPATH $RSFROOT/lib
endif
set path = ($RSFROOT/bin $path)
setenv DATAPATH /var/tmp/
setenv MANPATH $RSFROOT/share/man:`manpath`
setenv LD_LIBRARY_PATH $RSFROOT/lib:$LD_LIBRARY_PATH

Notice the backticks surrounding the call to manpath.

Be aware that on some systems /var/tmp gets automatically cleaned at some intervals, so if you want to keep your data binaries for a long time, set DATAPATH to another location where you have write access and that allows large files.

Software construction

1. Configuration. Change to the top source directory and run

   ./configure

   You can examine the config.py file that this command generates. Additional options are available. You can obtain a full list of customizable variables by running scons -h. For example, to install C++ and Fortran-90 API bindings in addition to the basic package, run

   ./configure API=c++,fortran-90

2. Building and installing the package. Run scons install or the following two commands in succession:

   make; make install

   or

   scons; scons install

   If you need "root" privileges for installing under $RSFROOT, you may need to run

   su; scons install 

   or

   sudo scons install

3. Cleaning. To clean all intermediate files generated by SCons, run

   make clean

   or

   scons -c

Uninstall

To clean all intermediate files and all installed files, run

scons -c install

or

make distclean

in the source code directory.

Troubleshooting

Alternative build/install procedure for the development version

1. Set the environment variables: If your shell is sh or bash, type <bash>source env.sh</bash> Else, if your shell is csh or tcsh, type <bash>source env.csh</bash>
2. Build: Type scons
3. Install: Run scons install . If you need "root" privileges for installing under $RSFROOT, you may need to run <bash>su; scons install </bash> or <bash>sudo scons install</bash>

Other

Note that scons does not inherit your environmental variables including PATH. If the configuration part ends with the message like

checking if cc works ... failed

the problem may be that your compiler is in unusual place. Try

./configure CC=/full/path/to/cc

or

./configure CC=`which cc`

On Windows under SFU, use the gcc compiler

./configure CC=/opt/gcc.3.3/bin/gcc

For more information, please consult the Advanced Installation guide.

Prerequisites

1. C compiler. Any ANSI-compliant compiler such as GCC should work. GCC usually comes pre-installed on Linux machines.
2. Python interpreter. Python is an interpretable programming language. It is used in Madagascar installation scripts and project management scripts. Python comes pre-installed on some platforms. Madagascar currently attempts to support Python versions 2.2 through 2.6. Versions before 2.2 are probably not common, but if you experience problems and you have an earlier version you should probably upgrade.

SCons is also required, but it is included with Madagascar and the configure scripts will attempt to install it for you if you don't have it already. For more information see the Advanced Installation guide.

Each API option has its own prerequisites.

Note that building under cygwin on Windows requires several preparatory steps .

Testing and quick start

Here are a few simple tests and and a brief introduction to Madagascar:

Typing any Madagascar command in a terminal window without parameters should generate a brief documentation on that command. Try one of the following:

sfin
sfattr
sfspike
sfbandpass
sfwiggle

If you get an error like "Command not found", you may not have your $PATH environment variable set correctly, or you may need to issue the rehash command.

Now try making a simple Madagascar data file:

sfspike n1=1000 k1=300 > spike.rsf

This command generates a one dimensional list of 1000 numbers, all zero except for a spike equal to one at position 300. If this generates an error like

Cannot write to data file /path/spike.rsf@: Bad file descriptor

you may need to create the directory pointed to by your $DATAPATH environment variable.

The file spike.rsf is a text header. The actual data are stored in the binary file pointed to by the in= parameter in the header. You can look at the header file directly with more, or better, examine the file properties with

sfin spike.rsf

You can learn more about the contents of spike.rsf with

sfattr < spike.rsf

The following command applies a bandpass filter to spike.rsf and puts the result in filter.rsf:

sfbandpass fhi=2 phase=1 < spike.rsf > filter.rsf

The following command makes a graphics file from filter.rsf:

sfwiggle clip=0.02 title="Welcome to Madagascar" < filter.rsf > filter.vpl

If you have an X11 display program running, and your $DISPLAY environment variable is set correctly, you can display the graphics file with:

sfpen < filter.vpl

You can pipe Madagascar commands together and do the whole thing at once like this:

sfspike n1=1000 k1=300 | sfbandpass fhi=2 phase=1 | \
sfwiggle clip=0.02 title="Welcome to Madagascar" | sfpen

If you have SCons installed, you can use it to automate Madagascar processing. Here is a simple SConstruct file to make filter.rsf and filter.vpl:

<python>

2. Setting up

from rsfproj import *

2. Make filter.rsf

Flow('filter',None,

    'spike n1=1000 k1=300 | bandpass fhi=2 phase=1')

2. Make filter.vpl

Result('filter',

      'wiggle clip=0.02 title="Welcome to Madagascar"')

End() </python>

Put the file in an empty directory, give it the name SConstruct, cd to that directory, and issue the command:

scons

The graphics file is now stored in the Fig subdirectory. You can view it manually with:

sfpen Fig/filter.vpl

... or you can use:

scons view

When an SConstruct file makes more than one graphics file, the scons view command will display all of them in sequence.

Welcome to Madagascar.

Now edit the SConstruct file: change the title string on the Result line to "Hello World!", save the file, and rerun the scons command. You will see that scons has figured out that the file filter.rsf does not need to be rebuilt because nothing that affects it has changed. Only the file filter.vpl is rebuilt.