Changeset 854


Ignore:
Timestamp:
Dec 2, 2008, 12:33:39 AM (13 years ago)
Author:
Jari Häkkinen
Message:

Fixes #53

File:
1 edited

Legend:

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Added
Removed
  • plugins/base1/se.lu.thep.wenni/trunk/INSTALL

    r853 r854  
    4747General requirements to build the package are that you work in a
    4848decent computing environment where you have access to tools such as
    49 make and a standards comliant C++ compiler. Since parts of the
    50 algorthms in WeNNI depends on the GNU scientific library it is
     49make and a standards compliant C++ compiler. Since parts of the
     50algorithms in WeNNI depends on the GNU scientific library it is
    5151required. GSL can be downloaded from http://www.gnu.org/software/gsl/.
    5252
     
    7171 2. If you haven't access to a BASE2 installation or prefer to use the
    7272    standard compilation components, run the configure script with
    73 
    74     $ `./configure --with-plugindir=/path/to/base/plugin-directory/wenni`
    75     $ `make`
    76     $ `make check`
    77     $ `make install-plugin`
    78 
    79 If you have probems check the pre-requisites below.
     73    {{{
     74    $ ./configure --with-plugindir=/path/to/base/plugin-directory/wenni
     75    $ make
     76    $ make check
     77    $ make install-plugin
     78    }}}
     79
     80If you have problems check the pre-requisites below.
    8081
    8182== Pre-requisite ==
     
    8889    local libraries can be used.
    8990
    90  3. Version x of net.sf.basedb. .... package. Needed for creation of
    91     the Java wrapper. If the package is not available it will
    92     automatically be downloaded during the compilation process.
     91 3. Version 0.1 of !PluginUtilities (http://baseplugins.thep.lu.se)
     92    package. Needed for creation of the Java wrapper. If the package
     93    is not available it will automatically be downloaded during the
     94    compilation process.
    9395
    9496 4. BASE 2.9 or later for plug-in use. Earlier versions may work but
    9597    it is not tested.
    9698
    97  5. Optionally, for tetsing, Perl (http://www.cpan.org/). The test
     99 5. Optionally, for testing, Perl (http://www.cpan.org/). The test
    98100    programs can be run manually, see README for details.
    99101
     
    101103
    102104During the build process and depending on configuration options,
    103 required program libraries will be downloaded from the official base
    104 sites, http://base2.thep.lu.se and http://baseplugins.thep.lu.se. If
    105 you feel uncomfortable with this procedure you need to do some manual
    106 work.
     105required program libraries will be downloaded from the official BASE
     106sites, http://base2.thep.lu.se/base and
     107http://baseplugins.thep.lu.se. If you feel uncomfortable with this
     108procedure you need to do some manual work.
    107109
    108110 1. If you have no working BASE2 installation, download the latest
     
    112114    script below.
    113115
    114  2. Download the PluginsUtilites package from
    115     http://base.thep.lu.se/wiki/se.lu.thep.WeNNI and place the package
    116     file in directory `base/base2`. The install process will use this
    117     file automatically but beware, a `make distclean` will erase the
    118     file (but `make clean` will not). This WeNNI package is known to
    119     work with version 0.1 of the PluginUtilities package (only the
    120     latest known version will be given here), and the stated version
    121     is the one automatically downloaded in the build process.
     116 2. Download the !PluginUtilities package from
     117    http://base.thep.lu.se/wiki/net.sf.basedb.pluginutilities and
     118    place the package file in directory `base/base2`. The install
     119    process will use this file automatically but beware, a `make
     120    distclean` will erase the file (but `make clean` will not). This
     121    WeNNI package is known to work with version 0.1 of the
     122    !PluginUtilities package (only the latest known version will be
     123    given here), and the stated version is the one automatically
     124    downloaded in the build process.
    122125
    123126== Building and installing the plug-in (WeNNI and the Java wrapper) ==
     
    128131 2. If you haven't access to a BASE2 installation or prefer to use the
    129132    standard compilation components, run the configure script with
    130 
    131     $ `./configure`
    132 
     133    {{{
     134    $ ./configure
     135    }}}
    133136    This will automatically download required BASE related libraries
    134137    from the official BASE package repositories (see output from the
    135     configure scipt on details about the downloads).
    136 
    137     There is a possiblity to use the build tools to automatically
     138    configure script on details about the downloads).
     139    [[br]] [[br]]
     140    There is a possibility to use the build tools to automatically
    138141    install the package. In this case you may want to change the
    139142    default plug-in installation path.
    140 
    141     $ `./configure --with-plugindir=DIR`
    142 
     143    {{{
     144    $ ./configure --with-plugindir=DIR
     145    }}}
    143146    The default plug-in installation directory is the directory
    144147    plugins/se/lu/thep/wenni rooted in `basedir`.
    145 
     148    [[br]] [[br]]
    146149    If you prefer to compile WeNNI Java wrapper using your local BASE2
    147150    installation. This is only needed if you have made local changes
     
    149152    the WeNNI Java wrapper. You should know if this is required, if
    150153    you do not know simply go for the above option. So, if you know do
    151 
    152     $ `./configure --with-basedir=/path/to/base`
    153 
     154    {{{
     155    $ ./configure --with-basedir=/path/to/base
     156    }}}
    154157    where `/path/to/base` should point to the directory containing
    155158    directory `www`.
    156 
    157     Some notes on configure options:
    158 
    159     The configure script accepts a few options that may be of
    160     interest. You can provide `./configure` with BASE2 location
    161     information with `--with-basedir=BASEDIR`. This information is
    162     used to find jar files such as `BASE2Core.jar` needed for
    163     compilation. The plug-in installation directory can be changed
    164     using `./configure` option `--with-plugindir=DIR`. Files will be
    165     installed in `<DIR>`. Default `DIR` is set to
     159    [[br]] [[br]]
     160    ''Some notes on configure options:'' The configure script accepts
     161    a few options that may be of interest. You can provide
     162    `./configure` with BASE2 location information with
     163    `--with-basedir=BASEDIR`. This information is used to find jar
     164    files such as `BASE2Core.jar` needed for compilation. The plug-in
     165    installation directory can be changed using `./configure` option
     166    `--with-plugindir=DIR`. Files will be installed in
     167    `<DIR>`. Default `DIR` is set to
    166168    `<BASEDIR>/plugins/se/lu/thep/wenni/`. You may use `with-gsl=DIR`
    167169    to provide information on GSL location. The option `enable-debug`
     
    170172
    171173 3. Now build using
    172 
    173     $ `make`
    174 
     174    {{{
     175    $ make
     176    }}}
    175177    If all went well `nni` was created in directory `bin/nni` as well
    176178    as `WeNNI.jar` in directory `base/base2/`.
    177179
    178180 4. Optionally, run the test programs
    179 
    180     $ `make check`
     181    {{{
     182    $ make check
     183    }}}
    181184
    182185 5. Install files using
    183 
    184     $ `make install-plugin`
    185 
     186    {{{
     187    $ make install-plugin
     188    }}}
    186189    Note! `make install` will install in location `${exec_prefix}/bin`
    187190    which maybe something else than the BASE plugin directory.
     
    214217
    215218 1. Download and unpack WeNNI. `cd` to the root directory of the
    216     distribution.
     219    distribution.
    217220
    218221 2. If you do not have access to a working BASE1 installation do the
     
    223226    download, issue the following sequence of commands in to prepare
    224227    the devkit for WeNNI:
    225 
     228    {{{
    226229    $ tar zxpf BASE-plugindevkit-1.2.17.tar.gz
    227230    $ cd BASE-plugindevkit-1.2.17/bogus_base
     
    231234    $ cd ../..
    232235    $ ln -s BASE-plugindevkit-1.2.17 BASE-plugindevkit
     236    }}}
    233237
    234238== Building and installing the plug-in (WeNNI with support) ==
    235239
    236240 1. You should already have downloaded WeNNI above if not please
    237     return to the previous section. `cd` to the root directory of the
    238     distribution.
     241    return to the previous section. `cd` to the root directory of the
     242    distribution.
    239243
    240244 2. Run configure script with
    241 
    242     $ `./configure --enable-state=base1 --with-basedir=BASEDIR`
    243 
    244     where <BASEDIR> is the absolute path to the root direcotry of your
    245     working BASE1 installation, or if you are using the developer kit,
    246     the absolute path to the bogus_base direcotry created above:
    247     `/path/to/wenni/BASE-plugindevkit/bogus-base`
    248 
    249     Some notes on configure options:
    250 
    251     The configure script accepts a few options that may be of
    252     interest. You generally must provide `./configure` with BASE1
    253     location information with `--with-basedir=BASEDIR`. This
    254     information is used to find BASE1 API (program libraries and
    255     header files). Header file `basefile.h` is expected to reside in
    256     `<BASEDIR>/include/cxx/`. `<BASEDIR>` must be an absolute
    257     path. The plug-in installation directory can be changed using
    258     `./configure` option `with-plugindir=DIR`. Default `DIR` is set to
     245    {{{
     246    $ ./configure --enable-state=base1 --with-basedir=BASEDIR
     247    }}}
     248    where <BASEDIR> is the absolute path to the root directory of your
     249    working BASE1 installation, or if you are using the developer kit,
     250    the absolute path to the bogus_base directory created above:
     251    `/path/to/wenni/BASE-plugindevkit/bogus-base`
     252    [[br]] [[br]]
     253    ''Some notes on configure options:'' The configure script accepts
     254    a few options that may be of interest. You generally must provide
     255    `./configure` with BASE1 location information with
     256    `--with-basedir=BASEDIR`. This information is used to find BASE1
     257    API (program libraries and header files). Header file `basefile.h`
     258    is expected to reside in `<BASEDIR>/include/cxx/`. `<BASEDIR>`
     259    must be an absolute path. The plug-in installation directory can
     260    be changed using `./configure` option
     261    `with-plugindir=DIR`. Default `DIR` is set to
    259262    `<BASEDIR>/plugins/bin/wenni/`. You may use `with-gsl=DIR` to
    260263    provide information on GSL location. The option `enable-debug`
     
    263266
    264267 3. Now build using
    265 
    266     $ `make`
     268    {{{
     269    $ make
     270    }}}
    267271
    268272 4. Optionally, run the test programs
    269 
    270     $ `make check`
     273    {{{
     274    $ make check
     275    }}}
    271276
    272277 5. Install files using
    273 
    274     $ `make install-plugin`
    275 
     278    {{{
     279    $ make install-plugin
     280    }}}
    276281    Note! `make install` will install in location `${exec_prefix}/bin`
    277282    which maybe something else than the BASE plugin directory.
    278283
    279  6. Make BASE1 aware of the plugin.
    280 
    281    Make sure that the settings in the plug-in definitions file are set
    282    appropriately when importing the plug-in definitions file
    283    (base/base1/base_plugin_script/plugin_WeNNI.base) into BASE1. More
    284    explicitly make sure that the entry in the web GUI: 'Name of
    285    executable' is set according to the wenni.pl install location. If
    286    you prefer to make the change in the file you should manipulate the
    287    line starting with `execName`.
    288 
    289    If you want use other than the default fields for intensity1,
    290    intensity2, BCh1SD, and BCh2SD, you need to indicate this in the
    291    WeNNIParams section of the plug-in definition file. Change the 5th
    292    column of parameters 4 through 7 appropriately, i.e., if the
    293    standard deviation is defined in another column than the default
    294    change lines 6 and 7:
    295 
    296       6 h BCh1SD    30  _xc_BCh1SD    0
    297       7 h BCh2SD    30  _xc_BCh2SD    0
     284 6. ''Make BASE1 aware of the plugin.''  Make sure that the settings
     285    in the plug-in definitions file are set appropriately when
     286    importing the plug-in definitions file
     287    (`base/base1/base_plugin_script/plugin_WeNNI.base`) into
     288    BASE1. More explicitly make sure that the entry in the web GUI:
     289    'Name of executable' is set according to the wenni.pl install
     290    location. If you prefer to make the change in the file you should
     291    manipulate the line starting with `execName`.
     292    [[br]] [[br]]
     293    If you want use other than the default fields for intensity1,
     294    intensity2, BCh1SD, and BCh2SD, you need to indicate this in the
     295    WeNNIParams section of the plug-in definition file. Change the 5th
     296    column of parameters 4 through 7 appropriately, i.e., if the
     297    standard deviation is defined in another column than the default
     298    change lines 6 and 7:
     299    ≈ß©{{{
     300    6 h BCh1SD    30  _xc_BCh1SD    0
     301    7 h BCh2SD    30  _xc_BCh2SD    0
     302    }}}
    298303
    299304
     
    312317
    313318 2. Do
    314 
    315     $ `./configure --enable-state=stand-alone`
    316     $ `make`
    317     $ `make check`
    318     $ `make install`
     319    {{{
     320    $ ./configure --enable-state=stand-alone
     321    $ make
     322    $ make check
     323    $ make install
     324    }}}
    319325
    320326== Pre-requisite ==
     
    330336 2. If you haven't access to a BASE installation or prefer to use the
    331337    standard compilation components, run the configure script with
    332 
    333     $ `./configure  --enable-state=stand-alone`
    334 
    335     Some notes on configure options:
    336 
    337     Do `./configure --help` for details in available options. You may
    338     use `with-gsl=DIR` to provide information on GSL location. The
    339     option `enable-debug` turns on debug options on the compilation of
    340     binary `nni` (e.g. enables assertions).
     338    {{{
     339    $ ./configure  --enable-state=stand-alone
     340    }}}
     341    ''Some notes on configure options:'' Do `./configure --help` for
     342    details in available options. You may use `with-gsl=DIR` to
     343    provide information on GSL location. The option `enable-debug`
     344    turns on debug options on the compilation of binary `nni`
     345    (e.g. enables assertions).
    341346
    342347 3. Now build using
    343 
    344     $ `make`
    345 
     348    {{{
     349    $ make
     350    }}}
    346351    If the package was successfully compiled two binaries are created;
    347352    `NNIFileConverter` and `nni`.
    348353
    349354 4. Optionally, run the test programs
    350 
    351     $ `make check`
     355    {{{
     356    $ make check
     357    }}}
    352358
    353359 5. Install with
    354 
    355     $ `make install`
    356 
    357     Note! `make install-plugin` will do the samething as `make install`.
    358 
    359 
    360 = Test programs fail =
    361 
    362 The numerical checks are very resitrictive, if 'make check' fails this
     360    {{{
     361    $ make install
     362    }}}
     363    Note! `make install-plugin` will do the same thing as `make install`.
     364
     365
     366= Test program fails =
     367
     368The numerical checks are very restrictive, if 'make check' fails this
    363369may be due to rounding errors. You can loosen the error bound in the
    364370tests by changing the default value in test/wenni_test.cc. Search for:
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