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Installing LOFAR Software on a CentOS 6.5 (Final) system (cluster Newton of the AIP Potsdam)
— Frank Breitling 2015/06/26 18:47
I was mainly following the previous installation notes provided by others:
http://www.lofar.org/operations/doku.php?id=public:user_software:lofar
http://www.lofar.org/operations/doku.php?id=engineering:user_software:ubuntu_12_4
However a few problems occured and had to be solved as described below.
Ideas and support by Arno Schoenmakers, Ger van Diepen and Marcel Loose were very helpful and highly appreciated.
This instruction will install all packages in $HOME/local/.
1. Setup of the environment
The 4 Newton head nodes provide some necessary libraries via Environment Modules (see also http://modules.sourceforge.net/).
We need its HDF5 libs and its more recent CMake version 3, since the systems version 2.6 is too old.
Moreover, for the installation of Pyrap we need a Python path with write access.
So I added the following two lines to my $HOME/.bashrc:
module load cmake hdf5 export PYTHONPATH=$HOME/local/lib64/python2.6/site-packages:$PYTHONPATH export PATH=$HOME/local:$PATH
1.1 Optional CMake installation - only necessary if using newl1
Unfortunately CMake is broken on newl1. To build the LOFAR software on this head node, we need to build our own CMake as follows:
mkdir -p $HOME/local/src cd $HOME/local/src wget http://www.cmake.org/files/v3.2/cmake-3.2.3.tar.gz tar xf cmake-3.2.3.tar.gz cd cmake-3.2.3 .bootstrap --prefix $HOME/local make -j12 make install
If working on the other head nodes newl2 to newl4 this step is not necessary.
2. Installation of required packages
Next we need to build and install these other packages as follows:
cd $HOME/local/src/ wget ftp://ftp.atnf.csiro.au/pub/software/wcslib/wcslib.tar.bz2 tar xf packages/wcslib.tar.bz2 cd wcslib-5.6/ ./configure --prefix=$HOME/local/ make install cd $HOME/local/src/ wget http://www.fftw.org/fftw-3.3.4.tar.gz cd fftw-3.3.4 configure --prefix=$HOME/local --enable-threads --enable-shared --enable-float make -j12 install
3. Installation the LOFAR software
Now we can continue building the LOFAR software.
3.1 Essential CMake switches
We will need these essential CMake switches:
1. -DBoost_NO_BOOST_CMAKE=ON 2. -DUSE_LOG4CPLUS=NO 3. -DUSE_BACKTRACE=OFF 4. -DCMAKE_INSTALL_PREFIX:PATH=$HOME/local
1.) Is necessary when using some older versions of boost with cmake-2.8.6-rc2 or later, where the boost finding has changed.
(See https://stackoverflow.com/questions/9948375/cmake-find-package-succeeds-but-returns-wrong-path.)
Otherwise make will show this error later:
make[2]: *** No rule to make target `/usr/lib64/lib64/libboost_program_options-mt.so.5', needed by `segment'. Stop. make[1]: *** [CMakeFiles/segment.dir/all] Error 2 make: *** [all] Error 2
2.) Is necessary if the Log4cplus libs are not installed.
3.) Is necessary if building shared libraries (the default with LOFAR), but libiberty.so is not installed on your system, only libiberty.a.
(See https://support.astron.nl/lofar_issuetracker/issues/8046).
4.) Sets the install path to $HOME/local/.
3.2 Casacore
So we can build the rest of the packages as follows:
cd ~local/src/ git clone https://github.com/casacore/casacore mkdir build/casacore cd build/casacore time cmake -DBUILD_PYTHON=yes -DBUILD_TESTING=NO -DCMAKE_INSTALL_PREFIX=~/local -DUSE_FFTW3=yes -DUSE_THREADS=YES \ -DUSE_OPENMP=yes -DDATA_DIR=~/local/data -DUSE_HDF5=yes -DCMAKE_PREFIX_PATH="$HOME/local;" ../../casacore time make -j12 make install
3.3 Pyrap
make install pip install python-casacore --global-option=build_ext --global-option=-I/usr/include/cfitsio:$HOME/local/include \ --global-option=-L$HOME/local/lib --install-option=--prefix=$HOME/local
3.3.1 Alternative Pyrap installation
Or alternatively if we don't want to install Pyrap with pip we can do:
cd ~/local/src/ git clone https://github.com/casacore/python-casacore.git cd python-casacore python setup.py build_ext -I/usr/include/cfitsio:$HOME/local/include -L$HOME/local/lib python setup.py install --prefix=$HOME/local
3.4 Casarest
Now we continue with the rest:
cd ~local/src/ svn co https://svn.astron.nl/casarest/trunk/casarest mkdir build/casarest cd build/casarest cmake -DCASACORE_ROOT_DIR=$HOME/local -DBUILD_ALL=1 -DCMAKE_INSTALL_PREFIX:PATH=$HOME/local \ -DCMAKE_PREFIX_PATH=/usr/include/cfitsio -DBoost_NO_BOOST_CMAKE=ON ../../casarest time make -j12 make install
3.4 DP3 and Calibration
cd ~local/src/ svn checkout --ignore-externals https://svn.astron.nl/LOFAR/trunk LOFAR mkdir -p build/gnu_opt cd build/gnu_opt cmake -DCASACORE_ROOT_DIR=$HOME/local -DBUILD_SHARED_LIBS=ON -DUSE_OPENMP=ON -DBUILD_PACKAGES="DP3 Calibration" \ -DCMAKE_INSTALL_PREFIX:PATH=$HOME/local -DUSE_LOG4CPLUS=NO -DUSE_BACKTRACE=OFF -DBoost_NO_BOOST_CMAKE=ON ../../LOFAR time make -j12 make install
Done!
Now the commands NDPPP
and calibrate-stand-alone
should be available on this system.
Enjoy!