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%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% |
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% |
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% Copyright (c) 2003-2009 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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|
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\section{Installing from source for \linux} |
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\label{sec:srclinux} |
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|
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\subsection{Preliminaries} |
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|
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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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|
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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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% I suspect that these are only needed by VTK and if we aren't using it anymore they could be removed |
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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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|
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To compile matplotlib you will also need the following\footnote{For Debian and Ubuntu users, installing \filename{libfreetype6-dev} and \filename{libpng-dev} will be sufficient.} (if your distribution separates development files, |
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make sure to get the development packages): |
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\begin{itemize} |
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\item \filename{freetype2} |
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\item \filename{zlib} |
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\item \filename{libpng} |
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\end{itemize} |
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|
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|
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|
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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 visualization functionality see \Sec{sec:addfunc}. |
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|
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These instructions will produce the following directory 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{pkg} |
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\item[] \filename{pkg_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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|
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Before you start copy the \esfinley source into the \filename{escript.d} directory. |
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The following instructions refer to software versions in the \filename{escript-support-3-src} bundle. |
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If you download your own versions of those packages substitute their version numbers and names as appropriate. |
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There are a number of uses of the \filename{make} command in the following instructions. |
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If your computer has multiple cores/processors you can speed up the compilation process by adding -j 2 after the make command. |
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For example to use all processors on a computer with 4 cores: |
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\begin{shellCode} |
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make |
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\end{shellCode} |
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becomes |
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\begin{shellCode} |
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make -j 4 |
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\end{shellCode} |
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|
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\begin{shellCode} |
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mkdir stand |
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cd stand |
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mkdir build doc pkg pkg_src |
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export PKG_ROOT=$(pwd)/pkg |
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\end{shellCode} |
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|
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\subsection{Building the dependencies} |
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|
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Copy the compressed sources for the packages into \filename{stand/pkg_src}. |
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If you are using the support bundles, decompress them in the stand directory: |
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\begin{shellCode} |
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tar -xjf escript-support-3-src.tar.bz2 |
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\end{shellCode} |
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|
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Copy documentation files into \filename{doc} then unpack the archives: |
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|
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\begin{shellCode} |
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cd build |
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tar -jxf ../pkg_src/Python-2.6.2.tar.bz2 |
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tar -jxf ../pkg_src/boost_1_39_0.tar.bz2 |
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tar -zxf ../pkg_src/scons-1.2.0.tar.gz |
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tar -zxf ../pkg_src/numpy-1.3.0.tar.gz |
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tar -zxf ../pkg_src/netcdf-4.0.tar.gz |
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tar -zxf ../pkg_src/matplotlib-0.98.5.3.tar.gz |
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\end{shellCode} |
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|
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\begin{itemize} |
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|
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\item Build Python: |
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\begin{shellCode} |
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cd Python* |
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./configure --prefix=$PKG_ROOT/python-2.6.2 --enable-shared 2>&1 \ |
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| tee tt.configure.out |
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make |
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make install 2>&1 | tee tt.make.out |
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|
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cd .. |
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|
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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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|
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pushd ../pkg |
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ln -s python-2.6.2/ python |
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popd |
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\end{shellCode} |
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|
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Run the new python executable to make sure it works. |
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|
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\item Now build NumPy: |
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\begin{shellCode} |
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cd numpy-1.3.0 |
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python setup.py build |
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python setup.py install --prefix $PKG_ROOT/numpy-1.3.0 |
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cd .. |
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pushd ../pkg |
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ln -s numpy-1.3.0 numpy |
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popd |
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export PYTHONPATH=$PKG_ROOT/numpy/lib/python2.6/site-packages:$PYTHONPATH |
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\end{shellCode} |
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|
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% \begin{shellCode} |
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% cd numarray-1.5.2 |
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% |
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% python setup.py install \ |
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% --gencode --install-lib=$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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% |
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% |
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% export PYTHONPATH=$PKG_ROOT/numarray/lib:$PYTHONPATH |
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% cd .. |
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% pushd ../pkg |
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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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|
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\item Next 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=$PKG_ROOT/scons-1.2.0 |
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|
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export PATH=$PKG_ROOT/scons/bin:$PATH |
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cd .. |
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pushd ../pkg |
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ln -s scons-1.2.0 scons |
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popd |
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\end{shellCode} |
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|
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\item The Boost libraries...: |
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\begin{shellCode} |
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pushd ../pkg |
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mkdir boost_1_39_0 |
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ln -s boost_1_39_0 boost |
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popd |
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cd boost_1_39_0 |
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./bootstrap.sh --with-libraries=python --prefix=$PKG_ROOT/boost |
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./bjam |
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./bjam install --prefix=$PKG_ROOT/boost --libdir=$PKG_ROOT/boost/lib |
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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 ../pkg/boost/lib/ |
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ln *.so.* libboost_python.so |
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popd |
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\end{shellCode} |
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|
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\item ...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=$PKG_ROOT/netcdf-4.0 |
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|
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make |
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make install |
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|
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export LD_LIBRARY_PATH=$PKG_ROOT/netcdf/lib:$LD_LIBRARY_PATH |
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cd .. |
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pushd ../pkg |
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ln -s netcdf-4.0 netcdf |
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popd |
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\end{shellCode} |
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|
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\item Finally matplotlib: |
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\begin{shellCode} |
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cd matplotlib-0.98.5.3 |
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python setup.py build |
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python setup.py install --prefix=$PKG_ROOT/matplotlib-0.98.5.3 |
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cd .. |
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pushd ../pkg |
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ln -s matplotlib-0.98.5.3 matplotlib |
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popd |
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cd .. |
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\end{shellCode} |
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|
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\end{itemize} |
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|
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% \subsection{VTK support} |
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% VTK is only required for pyvisi. To build it you need CMake and Mesa. |
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% The packages can be downloaded independently or in the \filename{escript-support-visi-3-src}. |
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% If you will not be using pyvisi, then skip to \Sec{sec:compileescriptlinux} |
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% |
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% Copy the compressed sources for the packages into \filename{stand/pkg_src}. |
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% If you are using the support bundles, decompress them in the stand directory. |
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% \begin{shellCode} |
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% tar -xjf escript-support-visi-3-src.tar.bz2 |
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% \end{shellCode} |
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% |
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% \begin{shellCode} |
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% cd build |
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% tar -jxf ../pkg_src/MesaLib-7.2.tar.bz2 |
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% tar -zxf ../pkg_src/vtk-5.2.1.tar.gz |
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% tar -zxf ../pkg_src/vtkdata-5.2.1.tar.gz |
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% tar -zxf ../pkg_src/cmake-2.6.3.tar.gz |
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% \end{shellCode} |
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% |
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% \begin{itemize} |
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% |
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% \item Build CMake: |
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% \begin{shellCode} |
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% cd cmake-2.6.3 |
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% ./configure --prefix=$PKG_ROOT/cmake-2.6.3 2>&1 | tee tt.configure |
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% make |
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% make install |
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% |
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% export PATH=$PKG_ROOT/cmake/bin:$PATH |
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% cd .. |
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% pushd ../pkg |
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% ln -s cmake-2.6.3 cmake |
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% popd |
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% \end{shellCode} |
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% |
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% \item Build Mesa: |
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% \begin{shellCode} |
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% cd Mesa-7.2 |
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% ./configure --prefix=$PKG_ROOT/mesa-7.2 --enable-gl-osmesa --with-driver=xlib |
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% |
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% make |
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% make install |
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% |
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% export LD_LIBRARY_PATH=$PKG_ROOT/mesa/lib:$LD_LIBRARY_PATH |
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% cd .. |
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% pushd ../pkg |
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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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% 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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% |
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% \item Finally, build VTK: |
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% \begin{shellCode} |
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% cd VTK |
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% cmake . |
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% \end{shellCode} |
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% |
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% Now edit the \filename{CMakeCache.txt} file and make the following changes. |
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% Where .... appears please replace it with the absolute path to the pkg directory. |
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% For example, replace \filename{CMAKE_INSTALL_PREFIX:PATH=..../vtk-5.2.1} with |
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% \filename{CMAKE_INSTALL_PREFIX:PATH=/home/bob/stand/pkg/vtk-5.2.1} |
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% (Search for the text before the =). |
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% \begin{shellCode} |
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% BUILD_EXAMPLES:BOOL=OFF |
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% BUILD_SHARED_LIBS:BOOL=ON |
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% CMAKE_INSTALL_PREFIX:PATH=..../vtk-5.2.1 |
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% CMAKE_VERBOSE_MAKEFILE:BOOL=TRUE |
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% VTK_OPENGL_HAS_OSMESA:BOOL=TRUE |
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% VTK_USE_64BIT_IDS:BOOL=ON |
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% VTK_WRAP_PYTHON:BOOL=ON |
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% VTK_USE_MANGLED_MESA:BOOL=OFF |
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% \end{shellCode} |
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% |
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% Now rerun cmake (it won't work but it adds some variables you need). |
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% |
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% \begin{shellCode} |
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% cmake . |
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% \end{shellCode} |
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% |
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% Edit \filename{CMakeCache.txt} and change the following variables: |
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% |
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% \begin{shellCode} |
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% VTK_USE_OFFSCREEN:BOOL=ON |
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% VTK_USE_TK:BOOL=OFF |
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% OSMESA_INCLUDE_DIR:PATH=..../mesa/include |
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% OSMESA_LIBRARY:FILEPATH=..../mesa/lib/libOSMesa.so |
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% PYTHON_INCLUDE_PATH:PATH=..../python/include/python2.6 |
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% PYTHON_LIBRARY:FILEPATH=..../python/lib/libpython2.6.so |
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% OPENGL_INCLUDE_DIR:PATH=..../mesa/include |
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% OPENGL_gl_LIBRARY:FILEPATH=..../mesa/lib/libGL.so |
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% \end{shellCode} |
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% |
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% The following steps will take a while so grab a coffee while it compiles. |
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% \begin{shellCode} |
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% cmake . |
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% make |
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% chmod +w Utilities/vtktiff/tif_fax3sm.c |
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% make install |
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% |
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% cd ../../pkg |
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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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% |
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% \end{itemize} |
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|
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\subsection{Compiling escript}\label{sec:compileescriptlinux} |
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Change to the directory containing your escript source (\filename{stand/escript.d}), then: |
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\begin{shellCode} |
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cd escript.d/scons |
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cp linux_standalone_options_example.py YourMachineName_options.py |
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|
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echo $PKG_ROOT |
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\end{shellCode} |
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Where \texttt{YourMachineName} is the name of your computer as returned by the hostname command. |
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If the name contains non-alphanumeric characters, then you will need to replace them with underscores. |
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For example the options file for \texttt{bob-desktop} would be named \filename{bob_desktop_options.py}. |
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|
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Edit the options file and put the value of PKG_ROOT between the quotes in the PKG_ROOT= line. |
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For example: |
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\begin{shellCode} |
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PKG_ROOT="/home/bob/stand/pkg" |
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\end{shellCode} |
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|
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\begin{shellCode} |
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cd ../bin |
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\end{shellCode} |
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Modify the STANDALONE line of \filename{escript} to read: |
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STANDALONE=1 |
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Start a new terminal and go to the \filename{stand} directory. |
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|
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\begin{shellCode} |
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export PATH=$(pwd)/pkg/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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|
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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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|
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\subsection{Cleaning up} |
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Once you are satisfied, the \filename{escript.d/build} and \filename{\$PKG_ROOT/build} directories can be removed. |
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|
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If you \emph{really} want to save space and do not wish to be able to edit or recompile \esfinley, you can remove the following: |
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\begin{itemize} |
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\item From the \filename{escript.d} directory:\begin{itemize} |
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\item Everything except: \filename{bin}, \filename{include}, \filename{lib}, \filename{esys}, |
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\filename{README_LICENSE}. |
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\item Hidden files, which can be removed using |
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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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in the \filename{escript.d} directory. |
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\end{itemize} |
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\item from the \filename{pkg} directory: |
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\begin{itemize} |
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\item \filename{scons}, \filename{scons-1.2.0}, \filename{cmake-2.6.3} and \filename{cmake} |
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\end{itemize} |
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\item \filename{package\_src}\footnote{Do not remove this if you intend to redistribute.}. |
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\end{itemize} |
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|
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Please note that removing all these files may make it more difficult for us to diagnose problems. |
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