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jfenwick |
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%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% |
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% |
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% Copyright (c) 2003-2008 by University of Queensland |
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% Earth Systems Science Computational Center (ESSCC) |
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% http://www.uq.edu.au/esscc |
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% |
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% Primary Business: Queensland, Australia |
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% Licensed under the Open Software License version 3.0 |
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% http://www.opensource.org/licenses/osl-3.0.php |
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% |
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%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% |
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\section{Installing from source for \linux} |
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jfenwick |
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\label{sec:srclinux} |
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The following instructions assume you are running the \filename{bash} shell. |
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Comments are indicated with \# characters. |
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Make sure you have the following installed: |
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\begin{itemize} |
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\item \filename{g++} and associated tools. |
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\item \filename{make} |
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\item \filename{libXext.so}\footnote{In Debian this is in the libXext-dev package.} |
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\item \filename{libxt.so}\footnote{In Debian this is in the libxt-dev package.} |
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\end{itemize} |
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You will also need a copy of the \esfinley source code. |
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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. |
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For additional visualisation functionality see Section~\ref{sec:linaddfunc}. |
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These instructions will produce the following structure: |
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\begin{itemize} |
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\item \filename{stand}: \begin{itemize} |
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\item \filename{escript.d} |
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\item \filename{packages} |
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\item \filename{package_src} |
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\item \filename{build} |
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\item \filename{doc} |
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\end{itemize} |
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\end{itemize} |
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The build directory can be removed when you are finished. |
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\begin{shellCode} |
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mkdir stand |
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cd stand |
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export PKG_ROOT=`pwd`/packages |
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\end{shellCode} |
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Copy compressed source bundles into \filename{stand/package_src}. |
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Copy documentation files into \filename{doc}. |
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\begin{shellCode} |
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mkdir packages |
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mkdir build |
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cd build |
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tar -jxf ../package_src/Python-2.6.1.tar.bz2 |
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tar -jxf ../package_src/boost_1_37_0.tar.bz2 |
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tar -jxf ../package_src/MesaLib-7.2.tar.bz2 |
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tar -zxf ../package_src/netcdf-4.0.tar.gz |
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tar -zxf ../package_src/vtk-5.2.1.tar.gz |
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tar -zxf ../package_src/vtkdata-5.2.1.tar.gz |
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tar -zxf ../package_src/numarray-1.5.2.tar.gz |
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tar -zxf ../package_src/cmake-2.6.3.tar.gz |
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tar -zxf ../package_src/scons-1.2.0.tar.gz |
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\end{shellCode} |
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Build python. |
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\begin{shellCode} |
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cd Python* |
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./configure --prefix=\$PKG_ROOT/python-2.6.1 --enable-shared 2>&1 \ |
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| tee tt.configure.out |
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make install 2>&1 | tee tt.make.out |
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cd .. |
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export PATH=\$PKG_ROOT/python/bin:\$PATH |
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export PYTHONHOME=\$PKG_ROOT/python |
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export LD_LIBRARY_PATH=\$PKG_ROOT/python/lib:\$LD_LIBRARY_PATH |
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pushd ../packages |
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ln -s python-2.6.1/ python |
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popd |
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\end{shellCode} |
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Run python to make sure it works. |
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Now build numarray. |
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\begin{shellCode} |
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cd numarray-1.5.2 |
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python setup.py install \ |
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--gencode --install-lib=\$PKG_ROOT/numarray-1.5.2/lib \ |
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--install-headers=\$PKG_ROOT=\$PKG_ROOT/numarray-1.5.2/include/numarray \ |
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2>&1 | tee tt.install.out |
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export PYTHONPATH=\$PKG_ROOT/numarray/lib:\$PYTHONPATH |
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cd .. |
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pushd ../packages |
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ln -s numarray-1.5.2 numarray |
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popd |
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\end{shellCode} |
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Now we build scons. |
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\begin{shellCode} |
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cd scons-1.2.0 |
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python setup.py install --prefix=\$PKG_ROOT/scons-1.2.0 |
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export PATH=\$PKG_ROOT/scons/bin:\$PATH |
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cd .. |
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pushd ../packages |
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ln -s scons-1.2.0 scons |
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popd |
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\end{shellCode} |
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...Boost libraries ... |
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\begin{shellCode} |
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cd boost_1_37_0 |
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./configure --prefix=\$PKG_ROOT/boost_1_37_0 --with-python-root=\$PKG_ROOT/python \ |
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--with-python-version=2.6 --with-libraries=python |
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make |
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make install |
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ln -s \$PKG_ROOT/boost_1_37_0 \$PKG_ROOT/boost |
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export LD_LIBRARY_PATH=\$PKG_ROOT/boost/lib:\$LD_LIBRARY_PATH |
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cd .. |
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pushd ../packages |
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ln -s boost_1_37_0 boost |
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popd |
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\end{shellCode} |
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... and netcdf. |
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\begin{shellCode} |
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cd netcdf-4.0 |
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CFLAGS="-O2 fPIC -Df2cFortran" CXXFLAGS="-O2 fPIC -Df2cFortran" \ |
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FFLAGS="-O2 fPIC -Df2cFortran" FCFLAGS="-O2 fPIC -Df2cFortran" \ |
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./configure --prefix=\$PKG_ROOT/netcdf-4.0 |
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make -j2 |
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make install |
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export LD_LIBRARY_PATH=\$PKG_ROOT/netcdf/lib:\$LD_LIBRARY_PATH |
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cd .. |
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pushd ../packages |
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ln -s netcdf-4.0 netcdf |
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popd |
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\end{shellCode} |
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CMake and Mesa are required for VTK. |
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\begin{shellCode} |
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cd cmake-2.6.3 |
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./configure --prefix=\$PKG_ROOT/cmake-2.6.3 2>&1 | tee tt.configure |
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make -j 4 |
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make install |
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export PATH=\$PKG_ROOT/cmake/bin:\$PATH |
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cd .. |
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pushd ../packages |
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ln -s cmake-2.6.3 cmake |
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popd |
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\end{shellCode} |
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These instructions do not compile MesaDemos or GLUT. |
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If you need to check if Mesa compiled correctly, then the demos are a good test. |
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\begin{shellCode} |
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cd Mesa-7.2 |
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./configure --prefix=\$PKG_ROOT/mesa-7.2 --enable-gl-osmesa --with-driver=xlib |
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make -j 4 |
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make install |
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export LD_LIBRARY_PATH=\$PKG_ROOT/mesa:\$LD_LIBRARY_PATH |
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cd .. |
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pushd ../packages |
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ln -s mesa-7.2 mesa |
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popd |
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\end{shellCode} |
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\begin{shellCode} |
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cd VTK |
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cmake . |
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#Edit the CMakeCache and make the following changes: |
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#(Please replace .... with an absolute path to the stand directory) |
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#----------------- |
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BUILD_EXAMPLES should be OFF |
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BUILD_SHARED_LIBS should be ON |
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CMAKE_INSTALL_PREFIX ..../stand/packages/vtk-5.2.1 |
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CMAKE_VERBOSE_MAKEFILE TRUE |
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#check PYTHON_EXECUTABLE is correct. |
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#but it seems to be when I went through these steps |
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VTK_OPENGL_HAS_OSMESA TRUE |
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VTK_USE_64BIT_IDS ON |
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# That last one is marked as "May cause some bugs" in the original instructions |
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VTK_WRAP_PYTHON ON |
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VTK_USE_MANGLED_MESA OFF |
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#-------------------- |
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cmake . |
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#It won't work but it will put some variables in that you need. |
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#Edit CMakeCache again and make the following changes |
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#---------------- |
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VTK_USE_TK OFF |
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OSMESA_INCLUDE_DIR ..../stand/packages/mesa/include |
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OSMESA_LIBRARY ..../stand/packages/mesa/lib/libOSMesa.so |
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PYTHON_INCLUDE_PATH ..../stand/packages/python/include/python2.6 |
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PYTHON_LIBRARY ..../stand/packages/python/lib/libpython2.6.so |
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OPENGL_INCLUDE_DIR ..../stand/packages/mesa/include |
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OPENGL_gl_LIBRARY ..../stand/packages/mesa/lib/libGL.so |
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#---------------- |
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cmake . |
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make |
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make install |
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cd ../../packages |
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ln -s vtk-5.2.1 vtk |
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cd .. |
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\end{shellCode} |
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Now copy the \esfinley source into an \filename{escript.d} directory in \filename{stand}. |
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\begin{shellCode} |
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cd scons |
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cp linux_options_example.py YourMachineName_options.py |
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#edit the options file and make the following changes: |
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#----------------------------------------------------------------- |
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declare a PKG_ROOT variable at the top of the file eg: |
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PKG_ROOT='/home/jfenwick/stand/packages' |
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python_path = PKG_ROOT+'python/include/python2.6' |
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python_lib_path = PKG_ROOT+'python/lib' |
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python_libs = 'python2.6' |
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boost_path = PKG_ROOT+'boost/include/boost-1_37' |
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boost_lib_path = PKG_ROOT+'boost/lib' |
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boost_libs = ['boost_python-gcc43-mt'] |
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# You could simlink the boost python library to give a shorter |
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# name but it's not worth it |
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usevtk = 'yes' |
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#------------------------------------------------------------------- |
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ln -s \$PKG_ROOT/vtk-5.2.1 \$PKG_ROOT/vtk |
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Modify /scripts/finley_wrapper_template |
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STANDALONE=1 |
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#Check to make sure the paths in the if [ \$STANDALONE == 1 ] |
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# Section are correct |
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#----------------------------------------------------------------- |
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scons bin/escript |
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#start a new terminal |
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cd stand |
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export PATH=`pwd`/packages/scons/bin:\$PATH |
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cd escript.d |
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eval `bin/escript -e` |
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scons |
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\end{shellCode} |
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If you wish to test your build, then you can do the following. |
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Note this may take a while if you have a slow processor and/or less than 1Gb of RAM. |
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\begin{shellCode} |
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scons all_tests |
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\end{shellCode} |
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Once you are satisfied, the \filename{build} and \filename{\$PKG_ROOT/build} directories can be removed. |
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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. |
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If you are not redistributing this bundle you can remove \filename{\$PKG_ROOT/package_src}. |
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If you do not plan to edit or recompile the source you can remove it. |
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The only entries which are required in \filename{escript.d} are: |
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\begin{itemize} |
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\item \filename{bin} |
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\item \filename{esys} |
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\item \filename{include} |
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\item \filename{lib} |
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\item \filename{README_LICENSE} |
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\end{itemize} |
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Hidden files can be removed with |
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\begin{shellCode} |
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find . -name .?* | xargs rm -rf |
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\end{shellCode} |
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\section{Additional Functionality}\label{sec:linaddfunc} |
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To perform visualisations you will need some additional tools. |
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Since these do not need to be linked with any of the packages above, you can install versions available for your |
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system, or build them from source. |
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\begin{itemize} |
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\item \filename{ppmtompeg} and \filename{jpegtopnm} from the \filename{netpbm} suite. - To build from source |
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you would also need \filename{libjpeg} and its headers as well as \filename{libpng}\footnote{libpng requires zlib to build} and its headers. |
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\item A tool to visualise VTK files. For example Mayavi or Visit. |
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\end{itemize} |
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