Changeset 854
- Timestamp:
- Dec 2, 2008, 12:33:39 AM (13 years ago)
- File:
-
- 1 edited
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plugins/base1/se.lu.thep.wenni/trunk/INSTALL (modified) (14 diffs)
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plugins/base1/se.lu.thep.wenni/trunk/INSTALL
r853 r854 47 47 General requirements to build the package are that you work in a 48 48 decent computing environment where you have access to tools such as 49 make and a standards com liant C++ compiler. Since parts of the50 algor thms in WeNNI depends on the GNU scientific library it is49 make and a standards compliant C++ compiler. Since parts of the 50 algorithms in WeNNI depends on the GNU scientific library it is 51 51 required. GSL can be downloaded from http://www.gnu.org/software/gsl/. 52 52 … … 71 71 2. If you haven't access to a BASE2 installation or prefer to use the 72 72 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 80 If you have problems check the pre-requisites below. 80 81 81 82 == Pre-requisite == … … 88 89 local libraries can be used. 89 90 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. 93 95 94 96 4. BASE 2.9 or later for plug-in use. Earlier versions may work but 95 97 it is not tested. 96 98 97 5. Optionally, for te tsing, Perl (http://www.cpan.org/). The test99 5. Optionally, for testing, Perl (http://www.cpan.org/). The test 98 100 programs can be run manually, see README for details. 99 101 … … 101 103 102 104 During the build process and depending on configuration options, 103 required program libraries will be downloaded from the official base104 sites, http://base2.thep.lu.se and http://baseplugins.thep.lu.se. If105 you feel uncomfortable with this procedure you need to do some manual 106 work.105 required program libraries will be downloaded from the official BASE 106 sites, http://base2.thep.lu.se/base and 107 http://baseplugins.thep.lu.se. If you feel uncomfortable with this 108 procedure you need to do some manual work. 107 109 108 110 1. If you have no working BASE2 installation, download the latest … … 112 114 script below. 113 115 114 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. 122 125 123 126 == Building and installing the plug-in (WeNNI and the Java wrapper) == … … 128 131 2. If you haven't access to a BASE2 installation or prefer to use the 129 132 standard compilation components, run the configure script with 130 131 $ `./configure`132 133 {{{ 134 $ ./configure 135 }}} 133 136 This will automatically download required BASE related libraries 134 137 from the official BASE package repositories (see output from the 135 configure sc ipt on details about the downloads).136 137 There is a possib lity to use the build tools to automatically138 configure script on details about the downloads). 139 [[br]] [[br]] 140 There is a possibility to use the build tools to automatically 138 141 install the package. In this case you may want to change the 139 142 default plug-in installation path. 140 141 $ `./configure --with-plugindir=DIR`142 143 {{{ 144 $ ./configure --with-plugindir=DIR 145 }}} 143 146 The default plug-in installation directory is the directory 144 147 plugins/se/lu/thep/wenni rooted in `basedir`. 145 148 [[br]] [[br]] 146 149 If you prefer to compile WeNNI Java wrapper using your local BASE2 147 150 installation. This is only needed if you have made local changes … … 149 152 the WeNNI Java wrapper. You should know if this is required, if 150 153 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 }}} 154 157 where `/path/to/base` should point to the directory containing 155 158 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 166 168 `<BASEDIR>/plugins/se/lu/thep/wenni/`. You may use `with-gsl=DIR` 167 169 to provide information on GSL location. The option `enable-debug` … … 170 172 171 173 3. Now build using 172 173 $ `make`174 174 {{{ 175 $ make 176 }}} 175 177 If all went well `nni` was created in directory `bin/nni` as well 176 178 as `WeNNI.jar` in directory `base/base2/`. 177 179 178 180 4. Optionally, run the test programs 179 180 $ `make check` 181 {{{ 182 $ make check 183 }}} 181 184 182 185 5. Install files using 183 184 $ `make install-plugin`185 186 {{{ 187 $ make install-plugin 188 }}} 186 189 Note! `make install` will install in location `${exec_prefix}/bin` 187 190 which maybe something else than the BASE plugin directory. … … 214 217 215 218 1. Download and unpack WeNNI. `cd` to the root directory of the 216 219 distribution. 217 220 218 221 2. If you do not have access to a working BASE1 installation do the … … 223 226 download, issue the following sequence of commands in to prepare 224 227 the devkit for WeNNI: 225 228 {{{ 226 229 $ tar zxpf BASE-plugindevkit-1.2.17.tar.gz 227 230 $ cd BASE-plugindevkit-1.2.17/bogus_base … … 231 234 $ cd ../.. 232 235 $ ln -s BASE-plugindevkit-1.2.17 BASE-plugindevkit 236 }}} 233 237 234 238 == Building and installing the plug-in (WeNNI with support) == 235 239 236 240 1. You should already have downloaded WeNNI above if not please 237 238 241 return to the previous section. `cd` to the root directory of the 242 distribution. 239 243 240 244 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 259 262 `<BASEDIR>/plugins/bin/wenni/`. You may use `with-gsl=DIR` to 260 263 provide information on GSL location. The option `enable-debug` … … 263 266 264 267 3. Now build using 265 266 $ `make` 268 {{{ 269 $ make 270 }}} 267 271 268 272 4. Optionally, run the test programs 269 270 $ `make check` 273 {{{ 274 $ make check 275 }}} 271 276 272 277 5. Install files using 273 274 $ `make install-plugin`275 278 {{{ 279 $ make install-plugin 280 }}} 276 281 Note! `make install` will install in location `${exec_prefix}/bin` 277 282 which maybe something else than the BASE plugin directory. 278 283 279 6. Make BASE1 aware of the plugin.280 281 Make sure that the settings in the plug-in definitions file are set282 appropriately when importing the plug-in definitions file283 (base/base1/base_plugin_script/plugin_WeNNI.base) into BASE1. More284 explicitly make sure that the entry in the web GUI: 'Name of285 executable' is set according to the wenni.pl install location. If286 you prefer to make the change in the file you should manipulate the287 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 the291 WeNNIParams section of the plug-in definition file. Change the 5th292 column of parameters 4 through 7 appropriately, i.e., if the293 standard deviation is defined in another column than the default294 change lines 6 and 7:295 296 6 h BCh1SD 30 _xc_BCh1SD 0297 7 h BCh2SD 30 _xc_BCh2SD 0284 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 }}} 298 303 299 304 … … 312 317 313 318 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 }}} 319 325 320 326 == Pre-requisite == … … 330 336 2. If you haven't access to a BASE installation or prefer to use the 331 337 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). 341 346 342 347 3. Now build using 343 344 $ `make`345 348 {{{ 349 $ make 350 }}} 346 351 If the package was successfully compiled two binaries are created; 347 352 `NNIFileConverter` and `nni`. 348 353 349 354 4. Optionally, run the test programs 350 351 $ `make check` 355 {{{ 356 $ make check 357 }}} 352 358 353 359 5. Install with 354 355 $ `make install`356 357 Note! `make install-plugin` will do the same thing as `make install`.358 359 360 = Test program s fail=361 362 The numerical checks are very res itrictive, if 'make check' fails this360 {{{ 361 $ make install 362 }}} 363 Note! `make install-plugin` will do the same thing as `make install`. 364 365 366 = Test program fails = 367 368 The numerical checks are very restrictive, if 'make check' fails this 363 369 may be due to rounding errors. You can loosen the error bound in the 364 370 tests by changing the default value in test/wenni_test.cc. Search for:
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