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Installing LOFAR Software on a CentOS 6.5 (Final) System - The Newton Cluster of the AIP Potsdam
This document is evolving and was created by — Frank Breitling 2015/06/26 18:47
A useful starting point were previous installation notes such as:
http://www.lofar.org/operations/doku.php?id=public:user_software:lofar
http://www.lofar.org/operations/doku.php?id=public:user_software:ubuntu_12_4
However some additional issues occurred at the Newton cluster 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.
1. Setup of build environment
The following packages are already provided on the cluster:
- BLAS
- LAPACK
- Boost 1.41.0 (but too old for AOFlagger v2.8.0 and later)
- cfitsio 3.240
- HDF5
- OpenMP
The cluster also provides a module system to load newer versions of the installed software.
Its used below to replace the default version of gcc 4.4.7 with gcc 4.8.3 for C++11 support.
1.1 Paths
The following changes are required:
- A more recent version of GCC with C++11 required by Casacore is activated through the module system. This also requires adding /opt/gcc-4.8.3/lib64 to the LD_LIBRARY_PATH since otherwise Pyrap will not find it and complain with
File "/home/fkbreitl/local/lib64/python2.6/site-packages/python_casacore-2.1.2-py2.6-linux-x86_64.egg/casacore/tables/table.py", line 43, in <module>
from ._tables import Table
ImportError: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.15' not found (required by /home/fkbreitl/local/lib/libboost_python.so.1.63.0)
- The packages will be installed in $HOME/local/.
- Pyrap (python-casacore) needs a writable Python path.
This adds the following lines to $HOME/.bashrc:
source /usr/share/Modules/init/sh # activate module system, needs to be done first module load gcc/4.8.3 # use gcc 4.8.3 (instead of 4.4.7) for C++11 support export LD_LIBRARY_PATH=/opt/gcc-4.8.3/lib64:$HOME/local/lib:$LD_LIBRARY_PATH export PYTHONPATH=$HOME/local/lib64/python2.6/site-packages:$PYTHONPATH export PATH=$HOME/local:$PATH
1.2 CMake
The 4 Newton head nodes provide CMake 2.6 by default, but the LOFAR Software requires at least 2.6.6. A sufficiently recent version of CMake 3.0.0 is provided via Environment Modules (see also http://modules.sourceforge.net/).
The environment modules also provide more recent HDF5 libraries. Both could be loaded by adding module load cmake hdf5 to $HOME/.bashrc.
But unfortunately the CMake 3.0.0 loaded on the head node newl1 is broken. Furthermore loading the HDF5 libs has no effect on the libs found by CMake, which are still the system's default. So we don't load any module and don't add this line to the .bashrc. Instead we 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 $HOME/local make -j12 make install
1.3 Python
To use matplotlib 2 one also needs Python 2.7 or later.
V_PY=2.7.13 cd ~/local/src/ wget https://www.python.org/ftp/python/$V_PY/Python-$V_PY.tgz tar xf Python-$V_PY.tgz cd Python-$V_PY ./configure --prefix=$HOME/local --enable-shared time make -j make install
1.4 Boost
Also a newer version of Boost is required since AOFlagger v2.8.0 and later:
cd $HOME/local/src
V_BOOST=1_63_0
wget wget https://sourceforge.net/projects/boost/files/boost/$V_BOOST/boost_$V_BOOST.tar.bz2
tar xf boost_$V_BOOST.tar.bz2
cd boost_$V_BOOST
./bootstrap.sh
time ./b2 install --prefix=${HOME}/local
2. Installation of dependencies
Next we need to build and install these other packages as follows:
2.1 WCSLIB
The WCSLIB:
cd $HOME/local/src/ wget ftp://ftp.atnf.csiro.au/pub/software/wcslib/wcslib.tar.bz2 tar xf packages/wcslib.tar.bz2 cd wcslib-5.15 # (-5.6) ./configure --prefix=$HOME/local/ time make -j install
2.2 FFTW
The FFTW lib:
V_FFTW=3.3.5 # 3.3.4 cd $HOME/local/src/ wget http://www.fftw.org/fftw-$V_FFTW.tar.gz cd fftw-$V_FFTW ./configure --prefix=$HOME/local --enable-threads --enable-shared --enable-float --enable-sse --enable-sse2 --enable-avx time make -j install
3. Installation the LOFAR software
Now we can build the LOFAR software.
We will need the following CMake switches:
1. -DCMAKE_INSTALL_PREFIX:PATH=$HOME/local 2. -DBOOST_ROOT=$HOME/local/src/boost_1_63_0 3. -DCMAKE_CXX_FLAGS="-lboost_thread -lboost_filesystem -L$HOME/local/lib" # 4. -DBoost_NO_BOOST_CMAKE=YES (not necessary with new installed Boost)
1.) Sets the installation path to $HOME/local.
2.) Necessary to find the new Boost installation
3.) Necessary to link against the new Boost installation
# 4.) Was required by some older versions of boost e.g. 1.41 with cmake-2.8.6-rc2, producing this problem:
https://stackoverflow.com/questions/9948375/cmake-find-package-succeeds-but-returns-wrong-path resulting in
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
It is not necessary any more with the new boost installation.
3.2 Casacore
Casacore also requires the CASA data.
This is for example provided with CASA.
Here we assume CASA is already installed and can be found in the $CASAPATH given below. For convenience this is a link to the CASA folder.
Then the data is in $CASAPATH/data.
We will specify this via -DDATA_DIR, otherwise we need a ~/.casarc file with the line: measures.directory: $HOME/local/casa/casa/data .
-DENABLE_TABLELOCKING=NO switches off table locking, since read locks could not be acquired from the AIP Lustre file system leading to errors like:
msoverview: Version 20110407GvD 2015-06-30 19:32:19 INFO Process 13592: waiting for read-lock on file /lustre/fkbreitl/data/L206894/L206894.cal/L206894_SAP000_SB200_uv.MS.dppp_00001~00040/table.lock Error: Error (Function not implemented) when acquiring lock on /lustre/fkbreitl/data/L206894/L206894.cal/L206894_SAP000_SB200_uv.MS.dppp_00001~00040/table.lock
For practical work there is no disadvantage in disabling table locking.
# 2.1, 2.2 cd ~/local/src/ git clone https://github.com/casacore/casacore mkdir build/casacore cd build/casacore CASAPATH=$HOME/local/casa/casa time cmake ../../casacore -DBUILD_PYTHON=YES -DCMAKE_INSTALL_PREFIX=~/local -DUSE_FFTW3=YES -DENABLE_TABLELOCKING=NO \ -DUSE_OPENMP=YES -DDATA_DIR=$CASAPATH/data -DUSE_HDF5=YES -DCMAKE_PREFIX_PATH=$HOME/local time make -j make install
3.3 Pyrap
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=$HOME/local
3.3.1 Alternative Pyrap installation
Alternatively we can install Pyrap with pip if we install pip before:
wget https://bootstrap.pypa.io/get-pip.py python get-pip.py --user ~/.local/bin/pip install python-casacore --global-option=build_ext --global-option=-I/usr/include/cfitsio:$HOME/local/include \ --global-option=-L$HOME/local/lib --install-option=--prefix=$HOME/local
3.4 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 ../../casarest -DCMAKE_INSTALL_PREFIX:PATH=$HOME/local -DCASACORE_ROOT_DIR=$HOME/local -DCMAKE_PREFIX_PATH=/usr/include/cfitsio -DBUILD_ALL=1 \ -DBOOST_ROOT=$HOME/local/src/boost_1_63_0 -DCMAKE_CXX_FLAGS="-lboost_thread -lboost_filesystem -L$HOME/local/lib" # not necessary any more -DBoost_NO_BOOST_CMAKE=YES time make -j make install
3.5 AOFlagger
The AOFlagger is also required since the
LOFAR Offline release 2.15.0.
For further details see the LOFAR release link or the
installation instructions.
The AOFlagger v2.8.0 and later requires a version of Boost later than 1.41.0.
V_AOF=2.9.0 # 2.7.1, 2.8.0 cd ~/local/src/ wget http://downloads.sourceforge.net/project/aoflagger/aoflagger-$AOVER/aoflagger-$V_AOF.tar.bz2 tar xf aoflagger-$V_AOF.tar.bz2 mkdir aoflagger-$V_AOF/build/ cd aoflagger-$V_AOF/build/ time cmake ../ -DCMAKE_INSTALL_PREFIX:PATH=$HOME/local -DBUILD_SHARED_LIBS=YES -DBOOST_ROOT=$HOME/local/src/boost_1_63_0 \ -DCMAKE_CXX_FLAGS="-lboost_thread -lboost_filesystem -L$HOME/local/lib" time make -j make install
3.6 The LOFAR packages
Finally we can build the LOFAR packages. We can chose between a release,
an offline release
or the latest version in trunk/ by commenting in and out the corresponding RELEASE lines.
-DUSE_BACKTRACE=NO is necessary for building shared libraries (the default), but libiberty.so is not installed.
(See https://support.astron.nl/lofar_issuetracker/issues/8046).
cd ~/local/src/ RELEASE=LOFAR-Release-2_19 && svn checkout --ignore-externals -N https://svn.astron.nl/LOFAR/branches/$RELEASE # 2_16_4, 2_16, 2_12 #RELEASE=LOFAR && svn checkout --ignore-externals -N https://svn.astron.nl/LOFAR/trunk $RELEASE svn update $RELEASE/CMake mkdir -p build/gnu_opt cd build/gnu_opt time cmake ../../$RELEASE -DCASACORE_ROOT_DIR=$HOME/local -DBUILD_PACKAGES="DP3 Calibration" -DCMAKE_INSTALL_PREFIX:PATH=$HOME/local -DUSE_BACKTRACE=NO # -DUSE_LOG4CPLUS=NO was required in absence of the Log4cplus lib time make -j make install
Done!
Now the commands NDPPP and calibrate-stand-alone should be available on this system.
Enjoy!