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2     %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
3     %
4     % Copyright (c) 2003-2008 by University of Queensland
5     % Earth Systems Science Computational Center (ESSCC)
6     % http://www.uq.edu.au/esscc
7     %
8     % Primary Business: Queensland, Australia
9     % Licensed under the Open Software License version 3.0
10     % http://www.opensource.org/licenses/osl-3.0.php
11     %
12     %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
13    
14     \section{Installing from source for \linux}
15 jfenwick 2317 \label{sec:srclinux}
16     The following instructions assume you are running the \filename{bash} shell.
17     Comments are indicated with \# characters.
18    
19     Make sure you have the following installed:
20     \begin{itemize}
21     \item \filename{g++} and associated tools.
22     \item \filename{make}
23     \item \filename{libXext.so}\footnote{In Debian this is in the libXext-dev package.}
24     \item \filename{libxt.so}\footnote{In Debian this is in the libxt-dev package.}
25     \end{itemize}
26    
27     You will also need a copy of the \esfinley source code.
28     If you retrieved the source using subversion, don't forget that one can use the export command instead of checkout to get a smaller copy.
29     For additional visualisation functionality see Section~\ref{sec:linaddfunc}.
30    
31     These instructions will produce the following structure:
32     \begin{itemize}
33     \item \filename{stand}: \begin{itemize}
34     \item \filename{escript.d}
35     \item \filename{packages}
36     \item \filename{package_src}
37     \item \filename{build}
38     \item \filename{doc}
39     \end{itemize}
40     \end{itemize}
41    
42     The build directory can be removed when you are finished.
43    
44     \begin{shellCode}
45     mkdir stand
46     cd stand
47     export PKG_ROOT=`pwd`/packages
48     \end{shellCode}
49    
50     Copy compressed source bundles into \filename{stand/package_src}.
51     Copy documentation files into \filename{doc}.
52    
53     \begin{shellCode}
54     mkdir packages
55     mkdir build
56     cd build
57     tar -jxf ../package_src/Python-2.6.1.tar.bz2
58     tar -jxf ../package_src/boost_1_37_0.tar.bz2
59     tar -jxf ../package_src/MesaLib-7.2.tar.bz2
60     tar -zxf ../package_src/netcdf-4.0.tar.gz
61     tar -zxf ../package_src/vtk-5.2.1.tar.gz
62     tar -zxf ../package_src/vtkdata-5.2.1.tar.gz
63     tar -zxf ../package_src/numarray-1.5.2.tar.gz
64     tar -zxf ../package_src/cmake-2.6.3.tar.gz
65     tar -zxf ../package_src/scons-1.2.0.tar.gz
66     \end{shellCode}
67    
68     Build python.
69     \begin{shellCode}
70     cd Python*
71     ./configure --prefix=\$PKG_ROOT/python-2.6.1 --enable-shared 2>&1 \
72     | tee tt.configure.out
73     make install 2>&1 | tee tt.make.out
74    
75     cd ..
76    
77     export PATH=\$PKG_ROOT/python/bin:\$PATH
78     export PYTHONHOME=\$PKG_ROOT/python
79     export LD_LIBRARY_PATH=\$PKG_ROOT/python/lib:\$LD_LIBRARY_PATH
80    
81     pushd ../packages
82     ln -s python-2.6.1/ python
83     popd
84    
85     \end{shellCode}
86    
87     Run python to make sure it works.
88     Now build numarray.
89    
90     \begin{shellCode}
91     cd numarray-1.5.2
92    
93     python setup.py install \
94     --gencode --install-lib=\$PKG_ROOT/numarray-1.5.2/lib \
95     --install-headers=\$PKG_ROOT=\$PKG_ROOT/numarray-1.5.2/include/numarray \
96     2>&1 | tee tt.install.out
97    
98    
99     export PYTHONPATH=\$PKG_ROOT/numarray/lib:\$PYTHONPATH
100     cd ..
101     pushd ../packages
102     ln -s numarray-1.5.2 numarray
103     popd
104     \end{shellCode}
105    
106     Now we build scons.
107     \begin{shellCode}
108     cd scons-1.2.0
109     python setup.py install --prefix=\$PKG_ROOT/scons-1.2.0
110    
111     export PATH=\$PKG_ROOT/scons/bin:\$PATH
112     cd ..
113     pushd ../packages
114     ln -s scons-1.2.0 scons
115     popd
116     \end{shellCode}
117    
118     ...Boost libraries ...
119     \begin{shellCode}
120     cd boost_1_37_0
121    
122     ./configure --prefix=\$PKG_ROOT/boost_1_37_0 --with-python-root=\$PKG_ROOT/python \
123     --with-python-version=2.6 --with-libraries=python
124    
125     make
126     make install
127     ln -s \$PKG_ROOT/boost_1_37_0 \$PKG_ROOT/boost
128     export LD_LIBRARY_PATH=\$PKG_ROOT/boost/lib:\$LD_LIBRARY_PATH
129     cd ..
130     pushd ../packages
131     ln -s boost_1_37_0 boost
132     popd
133     \end{shellCode}
134    
135     ... and netcdf.
136     \begin{shellCode}
137     cd netcdf-4.0
138     CFLAGS="-O2 fPIC -Df2cFortran" CXXFLAGS="-O2 fPIC -Df2cFortran" \
139     FFLAGS="-O2 fPIC -Df2cFortran" FCFLAGS="-O2 fPIC -Df2cFortran" \
140     ./configure --prefix=\$PKG_ROOT/netcdf-4.0
141    
142     make -j2
143     make install
144    
145     export LD_LIBRARY_PATH=\$PKG_ROOT/netcdf/lib:\$LD_LIBRARY_PATH
146     cd ..
147     pushd ../packages
148     ln -s netcdf-4.0 netcdf
149     popd
150     \end{shellCode}
151    
152     CMake and Mesa are required for VTK.
153     \begin{shellCode}
154     cd cmake-2.6.3
155     ./configure --prefix=\$PKG_ROOT/cmake-2.6.3 2>&1 | tee tt.configure
156     make -j 4
157     make install
158    
159     export PATH=\$PKG_ROOT/cmake/bin:\$PATH
160     cd ..
161     pushd ../packages
162     ln -s cmake-2.6.3 cmake
163     popd
164     \end{shellCode}
165    
166     These instructions do not compile MesaDemos or GLUT.
167     If you need to check if Mesa compiled correctly, then the demos are a good test.
168     \begin{shellCode}
169     cd Mesa-7.2
170     ./configure --prefix=\$PKG_ROOT/mesa-7.2 --enable-gl-osmesa --with-driver=xlib
171    
172     make -j 4
173     make install
174    
175     export LD_LIBRARY_PATH=\$PKG_ROOT/mesa:\$LD_LIBRARY_PATH
176     cd ..
177     pushd ../packages
178     ln -s mesa-7.2 mesa
179     popd
180     \end{shellCode}
181    
182     \begin{shellCode}
183     cd VTK
184     cmake .
185    
186     #Edit the CMakeCache and make the following changes:
187     #(Please replace .... with an absolute path to the stand directory)
188    
189     #-----------------
190    
191     BUILD_EXAMPLES should be OFF
192     BUILD_SHARED_LIBS should be ON
193    
194     CMAKE_INSTALL_PREFIX ..../stand/packages/vtk-5.2.1
195     CMAKE_VERBOSE_MAKEFILE TRUE
196    
197     #check PYTHON_EXECUTABLE is correct.
198     #but it seems to be when I went through these steps
199    
200     VTK_OPENGL_HAS_OSMESA TRUE
201     VTK_USE_64BIT_IDS ON
202     # That last one is marked as "May cause some bugs" in the original instructions
203    
204     VTK_WRAP_PYTHON ON
205     VTK_USE_MANGLED_MESA OFF
206    
207     #--------------------
208    
209     cmake .
210     #It won't work but it will put some variables in that you need.
211    
212     #Edit CMakeCache again and make the following changes
213    
214     #----------------
215    
216     VTK_USE_TK OFF
217    
218     OSMESA_INCLUDE_DIR ..../stand/packages/mesa/include
219    
220     OSMESA_LIBRARY ..../stand/packages/mesa/lib/libOSMesa.so
221    
222     PYTHON_INCLUDE_PATH ..../stand/packages/python/include/python2.6
223    
224     PYTHON_LIBRARY ..../stand/packages/python/lib/libpython2.6.so
225    
226     OPENGL_INCLUDE_DIR ..../stand/packages/mesa/include
227    
228     OPENGL_gl_LIBRARY ..../stand/packages/mesa/lib/libGL.so
229    
230     #----------------
231    
232     cmake .
233     make
234     make install
235    
236    
237     cd ../../packages
238     ln -s vtk-5.2.1 vtk
239     cd ..
240     \end{shellCode}
241    
242     Now copy the \esfinley source into an \filename{escript.d} directory in \filename{stand}.
243    
244     \begin{shellCode}
245     cd scons
246     cp linux_options_example.py YourMachineName_options.py
247    
248     #edit the options file and make the following changes:
249     #-----------------------------------------------------------------
250     declare a PKG_ROOT variable at the top of the file eg:
251     PKG_ROOT='/home/jfenwick/stand/packages'
252    
253     python_path = PKG_ROOT+'python/include/python2.6'
254     python_lib_path = PKG_ROOT+'python/lib'
255     python_libs = 'python2.6'
256    
257     boost_path = PKG_ROOT+'boost/include/boost-1_37'
258     boost_lib_path = PKG_ROOT+'boost/lib'
259     boost_libs = ['boost_python-gcc43-mt']
260     # You could simlink the boost python library to give a shorter
261     # name but it's not worth it
262    
263     usevtk = 'yes'
264     #-------------------------------------------------------------------
265    
266     ln -s \$PKG_ROOT/vtk-5.2.1 \$PKG_ROOT/vtk
267    
268     Modify /scripts/finley_wrapper_template
269    
270     STANDALONE=1
271    
272     #Check to make sure the paths in the if [ \$STANDALONE == 1 ]
273     # Section are correct
274    
275     #-----------------------------------------------------------------
276    
277     scons bin/escript
278    
279     #start a new terminal
280     cd stand
281     export PATH=`pwd`/packages/scons/bin:\$PATH
282     cd escript.d
283     eval `bin/escript -e`
284     scons
285     \end{shellCode}
286    
287     If you wish to test your build, then you can do the following.
288     Note this may take a while if you have a slow processor and/or less than 1Gb of RAM.
289     \begin{shellCode}
290     scons all_tests
291     \end{shellCode}
292    
293     Once you are satisfied, the \filename{build} and \filename{\$PKG_ROOT/build} directories can be removed.
294     Within the \filename{packages} directory, the \filename{scons}, \filename{scons-1.2.0}, \filename{cmake-2.6.3} and \filename{cmake} entries can also be removed.
295     If you are not redistributing this bundle you can remove \filename{\$PKG_ROOT/package_src}.
296    
297     If you do not plan to edit or recompile the source you can remove it.
298     The only entries which are required in \filename{escript.d} are:
299     \begin{itemize}
300     \item \filename{bin}
301     \item \filename{esys}
302     \item \filename{include}
303     \item \filename{lib}
304     \item \filename{README_LICENSE}
305     \end{itemize}
306    
307     Hidden files can be removed with
308     \begin{shellCode}
309     find . -name .?* | xargs rm -rf
310     \end{shellCode}
311    
312     \section{Additional Functionality}\label{sec:linaddfunc}
313     To perform visualisations you will need some additional tools.
314     Since these do not need to be linked with any of the packages above, you can install versions available for your
315     system, or build them from source.
316     \begin{itemize}
317     \item \filename{ppmtompeg} and \filename{jpegtopnm} from the \filename{netpbm} suite. - To build from source
318     you would also need \filename{libjpeg} and its headers as well as \filename{libpng}\footnote{libpng requires zlib to build} and its headers.
319     \item A tool to visualise VTK files. For example Mayavi or Visit.
320     \end{itemize}

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