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Prosa2003

Installation of Prosa2003
  1. Fill out License form and download Prosa2003 from http://www.came.sbg.ac.at/typo3/index.php?id=home

  2. Unpack it and run installation script:

    mkdir prosatemp
    mv prosa2003.linux.tar.gz prosatemp
    cd prosatemp
    tar xvf prosa2003.linux.tar.gz
    sudo ./prosa2003.install
    

    Provide fresh target folder, PDB folder and PDB binary folder (anything works, neither is used by Biskit). We choose to install prosa into /usr/local/lib/prosa2003.

  3. Link the prosa binary into your favourite bin folder

    This requires a trick because the default prosa2003 script only works in the prosa2003/bin folder. Instead of a link create the following file in, e.g., /usr/local/bin:

    #!/bin/sh
    /usr/local/lib/prosa2003/bin/prosa2003 $*
    

    This assumes you installed Prosa into /usr/local/lib/prosa2003. Adapt the line accordingly!

    Make the file executable, for example:

    sudo chmod 755 /usr/local/bin/prosa2003
    

    Note:

    If you use a binary name different than prosa2003 or a location that is not in the $PATH, you will need to adapt the Biskit configuration file exe_prosa2003.dat -- Copy it from biskit/external/defaults to ~/.biskit/ and adjust the bin parameter. See also below!

  4. Activate license

    The file LicenseDB should arrive via e-mail. Copy it into the ProSaData folder of your prosa installation.

    Note:

    For a larger number of computers (cluster nodes) you should send an e-mail with a list of hardware addresses to prosa__AT__came.sbg.ac.at rather than filling out the license form 100 times. The LicenseDB file can hold many license keys for different machines (one license per line).

  5. Set $PROSA_BASE

    Point the PROSA_BASE environment variable to the location of the Prosa potential files, e.g.:

    export PROSA_BASE=/usr/local/shared/Prosa2003/ProSaData
    

    (for bash and zsh) Add this line to your shell configuration file (.bashrc, .zshenv, etc.).

    Alternatively, you can also copy the exe_Prosa2003.dat from biskit/external/defaults to ~/.biskit/ and assign the PROSA_BASE value in this file. Biskit will then create the PROSA_BASE variable on the fly before calling Prosa. By default, Biskit only checks that PROSA_BASE exists (this is the effect of an empty variable in the environment section of the settings file).

  6. Test Prosa installation

    Run Prosa2003.py test code:

    python biskit/Biskit/Prosa2003.py
    

    This should yield:

    Result:  [ -94.568  -64.903 -159.463]
    

    Problems? See Prosa troubleshooting!


Usage:
see Prosa2003
Custom configuration:
see biskit/external/defaults/exe_prosa2003.dat