Difference between revisions of "Installation"

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==Troubleshooting==
 
==Troubleshooting==
 
===Alternative build/install procedure===
 
===Alternative build/install procedure===
# '''Set the environment variables:''' If your shell is <tt>sh</tt> or <tt>bash</tt>, type (or uncomment) <bash>source env.sh</bash> Else, if your shell is <tt>csh</tt> or <tt>tcsh</tt>, type <bash>source env.csh</bash>
+
# '''Set the environment variables:''' If your shell is <tt>sh</tt> or <tt>bash</tt>, type (or uncomment) <syntaxhighlight lang="bash">source env.sh</syntaxhighlight> Else, if your shell is <tt>csh</tt> or <tt>tcsh</tt>, type <syntaxhighlight lang="bash">source env.csh</syntaxhighlight>
 
# '''Build:''' Type <tt>scons</tt>
 
# '''Build:''' Type <tt>scons</tt>
# '''Install:'''  Run <tt>scons install</tt> . If you need "root" privileges for installing under <tt>&#36;RSFROOT</tt>, you may need to run <bash>su; scons install </bash> or <bash>sudo scons install</bash>
+
# '''Install:'''  Run <tt>scons install</tt> . If you need "root" privileges for installing under <tt>&#36;RSFROOT</tt>, you may need to run <syntaxhighlight lang="bash">su; scons install </syntaxhighlight> or <syntaxhighlight lang="bash">sudo scons install</syntaxhighlight>
 +
 
 
===Other issues===
 
===Other issues===
 
Note that <tt>scons</tt> does not inherit your environmental variables including <tt>PATH</tt>.  
 
Note that <tt>scons</tt> does not inherit your environmental variables including <tt>PATH</tt>.  

Revision as of 13:14, 8 April 2014

Fotolia 4727725 XS.jpg

Madagascar has been installed and is periodically tested on

  • Different Linux distributions (Fedora, RedHat, Ubuntu, etc.)
  • Solaris
  • MacOS X
  • Windows under the Cygwin environment.

It was previously tested on

  • FreeBSD
  • HP-UX
  • SGI Irix
  • Windows under Microsoft's Services for UNIX environment.

Precompiled binary packages

See the Madagascar download page for availability of binary packages.

Installation from source

Platform-specific instructions

Specific instructions are provided for Windows users.

For other platform-specific instructions, 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 not common, but if you experience problems and you have an earlier version you should probably upgrade.
  3. 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. Alternatively you can get it through yum with "yum install scons" in a terminal window. For more information see the Advanced Installation guide.

Each API option has its own prerequisites.

Prerequisites for optional add-on functionality are platform-specific.

Building under cygwin on Windows requires several preparatory steps.

General instructions

  1. Configuration: Open a terminal window and change to the top source directory (sometimes called "RSFSRC"). Next, you'll have to make some changes to your .bashrc file, so open it in you're favorite editor, e.g.
     vim ~/.bashrc </bash> or <bash> gedit ~/.bashrc
    
    Now simply append these lines to the bottom of the .bashrc file:
      export DATAPATH=$HOME/scratch/
      export EDITOR=nedit
      export OMP_NUM_THREADS=2
      export LATEX2HTML=$HOME/texmf/latex2html
      export RSFROOT=~/madagascar
      #source $HOME/Desktop/RSFSRC/env.sh
      
      Notice that the "source" line of this file is commented out for now. After this directory is created during the install, we'll come back here to fix this. Another tweak you make elect to implement is changing the OMP_NUM_THREADS line to a number greater than 2 but less than or equal to the number of cores on your machine (2 is the max for a dual-core processor). Incrementing this environment variable will have benefits when running parallelized code. I also assume that you want Madagascar installed to a directory called "madagascar". Feel free to adjust the second to last line accordingly. To have the changes you just made to the file take effect, type
      bash
      into your terminal window. Now you're ready to 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> Oftentimes after running "./configure ..." you'll see a list of things that your system may not have installed (the items that have "no" next to them). Usually they are optional, but for the best experience with Madagascar, it is strongly recommended that you install these packages using a package manager such as yum. Example syntax is used here. Just change the name from "python-devel" to whatever you might be missing.<bash>yum install python-devel</bash>After installing this dependency, rerun the .configure command above and repeat this step until you have all of the desired packages installed.
    1. Building and installing the package: Run
      make install
      
      If you need "root" privileges for installing under $RSFROOT, you may need to run
      make; su; make install
      
      or
      make; sudo make install
      
      If make does not exist on your system, an alternative procedure can be found in the Troubleshooting section.
    2. User setup: If your shell is sh or bash, add to your $HOME/.bashrc and $HOME/.bash_profile files the line
      source $RSFROOT/share/madagascar/etc/env.sh
      
      where RSFROOT is the install directory you specified in the --prefix option to ./configure. If your shell is (t)csh, add to your $HOME/.cshrc file the line
      source $RSFROOT/share/madagascar/etc/env.csh
      
      Please be aware that, on some systems, the default value for DATAPATH set in the script above may get 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. Remember that the value of DATAPATH should have a slash at the end.

    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

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

    Other issues

    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.

    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=y < 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=y | \
    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>

    1. Setting up

    from rsf.proj import *

    1. Make filter.rsf

    Flow('filter',None,'spike n1=1000 k1=300 | bandpass fhi=2 phase=y')

    1. 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.