NAME
    INSTALL Installation instructions for SenseClusters

SYNOPSIS
    If you have su or sudo access, you should be able to install and test
    the installation of SenseClusters via automatic download from CPAN as
    follows:

      # install SenseClusters and all dependent CPAN modules
      perl -MCPAN -e 'install Bundle::Text::SenseClusters';

      # install cluto and SVDPACKC (included in SenseClusters)
      cd ~/.cpan/build/Text-SenseClusters-[insert_version]
      cd External
      csh ./install.sh /usr/local/bin
      cd ~

      # run SC test cases (note that location of cpan build 
      # directory might vary on your system. 

      cd ~/.cpan/build/Text-SenseClusters-[insert_version]
      cd Testing
      csh ./ALL-TESTS.sh
      cd ~

    This assumes that /usr/local/bin is in your PATH and is your preferred
    location for user installed executable scripts. If it is not, substitute
    your perferred directory here.

INSTALLATION OVERVIEW
    SenseClusters consists of the core SenseClusters programs (primarily .pl
    programs found in this distribution), Perl modules available from CPAN,
    and two external programs (SVDPACKC and Cluto).

    You can download the core and external programs from CPAN
    <http://search.cpan.org/dist/Text-SenseClusters> or Sourceforge
    <http://senseclusters.sourceforge.net>.

    You may be able to download and install the SenseClusters core,
    dependent CPAN modules, and External programs via a single command using
    the CPAN module.

    If you have sudo or su access, then installation of the CPAN modules and
    the core SenseClusters programs can be achieved as follows:

      perl -MCPAN -e 'install Bundle::Text::SenseClusters';

    If you do not have su or sudo access, then you will need to install
    manually, as described below.

    You may be able to install the external programs Cluto and SVDPACKC via
    the following script we provide :

      cd Text-SenseClusters-[insert_version]
      cd External
      csh ./install.sh INSTALLDIR
      cd ~

    If you have sudo or su access, INSTALLDIR should be a directory in your
    PATH, such as /usr/local/bin. If you do not, you will need to install
    into a directory you have read and write access to, and then include in
    your path. If install.sh fails for some reason, you will need to install
    Cluto and SVDPATH manually, as described below.

    At present SenseClusters does not utilize 'make test', so testing must
    be done via scripts found in the /Testing directory. Please make certain
    to run these tests after the installation of the External programs, CPAN
    modules, and SenseClusters core has concluded.

      cd ~/.cpan/build/Text-SenseClusters-[insert_version]
      cd Testing
      csh ./ALL-TESTS.sh
      cd ~

DESCRIPTION OF PACKAGE COMPONENTS
    SenseClusters has been developed and tested on Linux and Solaris,
    primarily using Perl and the C shell (csh). It is based primarily on
    Perl command line programs distributed with the package and Perl modules
    that are available from CPAN. However, it does include two external
    programs, one distributed as C source code (SVDPACKC) and one
    distributed in binary form (CLUTO) for Linux and Solaris. This
    dependence on CLUTO limits SenseClusters to running on Linux or Solaris.
    There is a Windows version of CLUTO available, but we have not tested
    how well this integrates into SenseClusters.

  DEPENDENCIES
    SenseClusters requires version 5.6.0 (or better) of Perl. You can check
    with version of perl you have via :

            perl -v

    If you need a more recent version, you can find that at
    <http://perl.org>.

   CPAN Modules
    SenseClusters uses a number of different CPAN modules. These are all
    included in the Bundle above, and can be installed via the Bundle
    (recommended) or individually (described below).

    * PDL (Perl Data Language, version 2.4.1 or better)
    * Algorithm::Munkres (version 0.07 or better)
    * Algorithm::RandomMatrixGeneration (version 0.06 or better)
    * Bit::Vector (version 6.3 or better)
    * Math::SparseMatrix (version 0.02 or better)
    * Math::SparseVector (version 0.04 or better)
    * Set::Scalar (version 1.19 or better)
    * Text::NSP (version 1.09 or better)

   External Packages (/External)
    The following packages are not written in Perl and are developed outside
    of the SenseClusters project. SVDPACKC is distributed as C source code,
    and Cluto is distributed as pre-complied binaries for Linux and Solaris.

    Please note that SVDPACK is optional - SenseClusters will run without it
    (just don't use the --svd option). However, Cluto is mandatory,
    SenseClusters will not be able to perform clustering without it.

    * CLUTO (version 2.1.1 or better)
    * SVDPACKC (Feb 2004 version or better, compiled with gcc 3.2.2, 3.2.3,
    or 3.3.0)

MANUAL INSTALLATION OF CPAN MODULES
    You can install all of the modules described below and the Core of
    SenseClusters by using the Bundle described above. However, if you have
    problems with that or prefer to install modules individually, you can
    proceed as follows.

    You may want to check to see which Perl modules are installed on your
    system already via :

    "perldoc perllocal"

        The following modules must be installed for proper use of
        SenseClusters:

    Perl Data Language (version 2.4.1 or better)
        SenseClusters uses the Perl Data Language (PDL) for efficient
        computations and storage of high dimensional data structures.

        It is available at: <http://search.cpan.org/dist/PDL/>

        Note that if you have supervisor access on your machine, and have
        the MCPAN Perl module available, you can install PDL automatically
        via:

        "perl -MCPAN -e 'install PDL';"

        If you do not have supervisor access, you will need to install this
        module locally. Note that you can configure the CPAN module to
        install locally by setting PREFIX and LIB options to directories you
        have read write authority over.

        Note that PDL has quite a few dependencies, and can be tricky to
        install. You may want to check with your system administrator and
        see if they can install on your behalf before you tackle the local
        install of PDL. All the other code mentioned here can be locally
        installed quite routinely.

        This is a good description of how to do local installs of Perl
        modules: <http://www.perl.com/pub/a/2002/04/10/mod_perl.html>

    Bit::Vector (version 6.3 or better)
        The Bit::Vector module is used with binary context vectors (via
        --binary option in wrappers or program bitsimat.pl). This can be
        downloaded from:

        <http://search.cpan.org/dist/Bit-Vector/>

         Note that the following installation instructions apply to all of the
         CPAN modules, and will not be repeated in detail for each module.

        If you have supervisor access, or have configured MCPAN for local
        install, you can install via:

        "perl -MCPAN -e 'install Bit::Vector';"

        If not, you can, "manually" install by downloading the *.tar.gz
        file, unpacking, and executing the following commands.

         perl Makefile.PL PREFIX=/space/kulka020/Bit-Vector LIB=/space/kulka020/MyPerlLib
         make
         make test
         make install

        Note that the PREFIX and LIB settings are just examples to help you
        create a local install, if you do not have supervisor (su) access.

        You must include /space/kulka020/MyPerlLib in your PERL5LIB
        environment variable to access this module when running.

    Ngram Statistics Package (version 1.05 or better)
        SenseClusters uses Text-NSP to select a variety of lexical features.
        Text-NSP is freely available at
        <http://search.cpan.org/dist/Text-NSP/>

        "perl -MCPAN -e 'install Text::NSP';"

        or manual installation.

    Set::Scalar (version 1.19 or better)
        The Set::Scalar module is used by the program bitsimat.pl.

        It is available at: <http://search.cpan.org/dist/Set-Scalar/>

        "perl -MCPAN -e 'install Set::Scalar';"

        or manual installation.

    Math::SparseVector (version 0.04 or better)
        This is a Perl module that implements sparse vector operations.

        It is available at: <http://search.cpan.org/dist/Math-SparseVector/>

        "perl -MCPAN -e 'install Math::SparseVector';"

        or manual installation.

    Math::SparseMatrix (version 0.02 or better)
        This is a Perl module that implements sparse matrix operations, in
        particular the sparse matrix transpose operation.

        It is available at: <http://search.cpan.org/dist/Math-SparseMatrix/>

        "perl -MCPAN -e 'install Math::SparseMatrix'";

        or manual installation.

    Algorithm::Munkres (version 0.07 or better)
        This is a Perl module that implements Munkres' solution to classical
        Assignment Problem. This is used when carrying out evaluation of
        discovered clusters with a provided gold standard.

        It is available at: <http://search.cpan.org/dist/Algorithm-Munkres/>

        "perl -MCPAN -e 'install Algorithm::Munkres';"

        or manual installation.

    Algorithm::RandomMatrixGeneration (version 0.06 or better)
        This is a Perl module that generates random matrix given the row and
        column marginals. This is required for SenseClusters to run the
        Adapted Gap Statistic in clusterstopping.pl.

        It is available at:
        <http://search.cpan.org/dist/Algorithm-RandomMatrixGeneration/>

        "perl -MCPAN -e 'install Algorithm::RandomMatrixGeneration';"

        or manual installation.

  External Packages
        Please note that we provide a modified version of SVDPACK in
        /External/SVDPACKC that makes all the changes described below. You
        should be able to compile and install this code via the
        External/install.sh script. If that fails you can follow the steps
        described in the install script manually. If for some reason you
        would prefer to start with a fresh copy of SVDPACKC, you can follow
        the directions below (which also explain the changes we have made
        and included in SenseClusters /External/SVDPACKC).

    SVDPACKC (Feb 2004 version or better)
        SVDPACKC is a C program that performs SVD. It is available for
        download from <http://www.netlib.org/svdpack>. SVDPACKC does not
        have a version number associated with it, but check the files in
        your download to make sure they are dated from at least Feb 2004.
        The version we include and modify in /External/SVDPACKC is the Feb
        2004 version.

        Please note that you should use version 3.2.2, 3.2.3, or 3.3.0 of
        the gcc compiler. Segmentation faults results if you use version 4
        or better. We are currently investigating the use of SVDLIDC as an
        alternative for our SVD processing.

        While installing SVDPACKC, make sure to -

           1.   In las2.c, uncomment the following line 

                /*      #define  UNIX_CREAT     */

                if you are running on a Unix or Linux platform.

           2.   In las2.h, modify the default values of constants LMTNW, NMAX and  
                NZMAX to some larger numbers such that -

                NMAX    = Maximum size of the feature space before reduction 
                          (we set this to 30,000)
                NZMAX   = Maximum possible number of Non-zero entries 
                          (we assume our 30,000 x 30,000 matrix is at most 1% dense
                          and hence NZMAX = 30,000 x 30,000 / 100 = 9,000,000)
                LMTNW   = Maximum Work Space Area required 
                        = 6*NMAX + 4*NMAX + 1 + NMAX*NMAX
                          (we set LMTNW = 900300001 for a 
                          1% dense 30,000 x 30,000 matrix)

           3.   Modify the file makefile so that ANSI C is used. 

                CC = gcc -ansi

                [Please use gcc version 3.2.2, 3.2.3, or 3.3.0 when compiling SVDPACKC.
                gcc versions 4.0.0 and above appear to result in segmentation faults.] 

           4.   Run 'make las2' after the above modifications are done in las2.h,
                las2.c, and makefile.

        *   QUICK TEST of SVDPACKC

        The following will will help you check that SVDPACKC is installed
        correctly.

         # unzip the sample belladit.gz data file that comes with SVDPACKC
         gunzip belladit.gz

         # copy this as the input matrix to SVDPACKC
         cp belladit matrix

         # run las2 to test if everything is ok
         las2

         # this will not produce any output to STDOUT, but it should create 2  
         # output files - lav2 (binary) and lao2 (text)

    CLUTO (version 2.1.1 or better)
        The script External/install.sh will attempt to retrieve and install
        Cluto automatically. If that fails, you can follow the steps outline
        in the install script, or the instructions below.

        SenseClusters uses CLUTO to support extensive clustering options,
        analysis and visualization. CLUTO is freely available from
        <http://www-users.cs.umn.edu/~karypis/cluto/>

        If you run on both Linux and Solaris platforms, you will need to set
        your path slightly differently each time to allow SenseClusters to
        run. The following code in your .cshrc file will take care of this.

         set OSNAME=`uname -s`

         if ($OSNAME == "SunOS") then
                set path = (PATH_2_CLUTO/Sun $path)
         else if ($OSNAME == "Linux") then
                set path = (PATH_2_CLUTO/Linux $path)
         else echo "lost"
         endif

        where, PATH_2_CLUTO is a complete path to the directory where CLUTO
        is downloaded and unpacked. If you only run on Solaris or Linux,
        then of course you can just set the path with the appropriate
        statement from above.

    GCLUTO [optional]
        Users interested in graphical visualization of clusters are
        encouraged to try GCLUTO which is also freely down-loadable from
        <http://www-users.cs.umn.edu/~karypis/cluto/gcluto/index.html>

        To use GCLUTO, you will require the libglut.so.3 library installed
        on your system. These can be downloaded from -
        <http://at.rpmfind.net/opsys/linux/RPM/libglut.so.3.html>

CORE SENSECLUSTERS INSTALLATION
        Note that SenseClusters can be installed via the Bundle command
        described in the SYNOPSIS. If for some reason that fails, you can
        proceed as follows:

        To install the core of SenseClusters, if you have su or sudo access
        (root user), then you can install via :

        "perl -MCPAN -e 'install Text::SenseClusters';"

        Or you can install manually as follows:

            perl Makefile.PL
            make
            cd Testing
            csh testall.sh
            cd ..
            make install 

        Note that the testall.sh scripts will not be run via automatic
        installation. If you do not install manually, you should go back and
        run the test scripts just to verify that everything is working as
        expected.

        The exact location where SenseClusters will be installed depends on
        your system configuration. A message will be printed out after 'make
        install' telling you exactly where it was installed.

  Local Installation of Core SenseClusters programs
        If you are not able to log in as su or sudo (to be the root user),
        then you may need to install SenseClusters in a local directory that
        you own and have permissions to read and write into. You can proceed
        as above, except that you will need to provide PREFIX and LIB
        options for your Makefile.PL command, as in:

        "perl Makefile.PL PREFIX = /YOUR/DIR LIB=/YOUR/DIR/lib"

        This will set up a Makefile that will install the core SenseClusters
        programs (*.pl) into :

                        /YOUR/DIR/bin/

        The Sensecluster.pm module will be installed into :

                        /YOUR/DIR/lib

        man pages will be installed into :

                        /YOUR/DIR/share/man/ (Linux)
                        /YOUR/DIR/man/       (Solaris)

        You will have to explicitly set your $PATH to include :

                        /YOUR/DIR/bin/

        You will have to explicitly set your $PERL5LIB to include :

                        /YOUR/DIR/lib/

        and your $MANPATH to include:

                        /YOUR/DIR/share/man/ (Linux)
                        /YOUR/DIR/man/       (Solaris)

        Note that the exact locations will be shown after executing 'make
        install' command. Please double check the recommended settings for
        PATH and MANPATH there as those will be tailored to your system.

C SHELL (csh) SETUP
        If you install without root or superuser access, you will need to
        set the paths of the dependent packages mentioned previously. The
        following is an example of how you might set your paths before using
        SenseClusters if you are using the C shell (csh). If you use another
        shell then you will need to modify this accordingly.

        This assumes that Perl and PDL have been installed by your system
        administrator and you do not need to set paths to find them. In
        general we would recommend that Perl and PDL be installed with root
        access as it's more simple that way.

        Assume that all of the external C packages (SVDPACKC, Cluto) have
        been installed in directories beneath /space/kulka020 (our home
        directory for this example). It also assumes that all of the CPAN
        modules have been installed in /space/kulka020/MyPerlLib. In other
        words, it is assumed that all CPAN modules were installed via the
        following command:

        "perl Makefile.PL PREFIX=/space/kulka020/Text-SenseClusters-1.00
        LIB=/space/kulka020/MyPerlLib"

         #######################################################################
         #    insert the following into ~/.cshrc and modify HOMEDIR and LIBHOME
         #######################################################################
 
         # local directory where we are installing everything
 
         setenv HOMEDIR /space/kulka020
 
         # library name extension used by Perl on our system

         setenv LIBDIR /space/kulka020/MyPerlLib
 
         # UMD developed code, we need to set their /bin directories in the PATH
 
         setenv SENSECLUSTERS $HOMEDIR/Text-SenseClusters-1.00
         setenv NSP $HOMEDIR/Text-NSP-1.09

         # externally developed C code, directories contain executable code so must 
         # be included in PATH
 
         setenv SVDPACK $HOMEDIR/SVDPACKC
         setenv CLUTO $HOMEDIR/cluto-2.1.1
 
         # pick the right version of Cluto (Solaris or Linux)
 
         set OSNAME=`uname -s`
 
         if ($OSNAME == "SunOS") then
                setenv MYCLUTO $CLUTO/Sun
         else if ($OSNAME == "Linux") then
                setenv MYCLUTO $CLUTO/Linux
         else echo "lost"
         endif
 
         # set the path that Perl searches for CPAN modules
 
         setenv PERL5LIB $LIBDIR

         # set the path that is searched for executables
 
         set AKPATH = ($SVDPACK $NSP/bin $MYCLUTO $SENSECLUSTERS/bin .)
 
         set path = ($AKPATH $path)

INSTALLING SenseClusters' Web-interface:
        If you would like to setup the SenseClusters' web-interface locally
        please refer to README.Web.pod for installation instructions.

AUTHORS
         Ted Pedersen, University of Minnesota, Duluth
         tpederse at d.umn.edu

         Anagha Kulkarni, Carnegie Mellon University

         Amruta Purandare, University of Pittsburgh

        This document last modified by : $Id: INSTALL.pod,v 1.13 2008/03/29
        15:16:30 tpederse Exp $

SEE ALSO
        The main SenseClusters web page provides links to downloads, the web
        interface, documentation, and CVS directories:

         L<http://senseclusters.sourceforge.net>

        We have three mailing lists available for SenseClusters:

         L<http://lists.sourceforge.net/lists/listinfo/senseclusters-news>
         L<http://lists.sourceforge.net/lists/listinfo/senseclusters-users>
         L<http://lists.sourceforge.net/lists/listinfo/senseclusters-developers>

        senseclusters-news will provide announcements of new versions, while
        users is intended to provide a way for users to post questions or
        bug reports. senseclusters-developers is where detailed discussion
        of ongoing coding efforts will take place. You are welcome to
        subscribe to any of these!

        If you have any trouble installing and using SenseClusters, please
        contact us via the users mailing list :

        <https://lists.sourceforge.net/lists/listinfo/senseclusters-users>

COPYRIGHT AND LICENSE
        Copyright (c) 2004-2008, Ted Pedersen

        Permission is granted to copy, distribute and/or modify this
        document under the terms of the GNU Free Documentation License,
        Version 1.2 or any later version published by the Free Software
        Foundation; with no Invariant Sections, no Front-Cover Texts, and no
        Back-Cover Texts.

        Note: a copy of the GNU Free Documentation License is available on
        the web at <http://www.gnu.org/copyleft/fdl.html> and is included in
        this distribution as FDL.txt.

