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public:install_lofar_centos6.5 [2017-01-03 19:28] – [3. Installation the LOFAR software] Frank Breitlingpublic:install_lofar_centos6.5 [2017-03-08 15:27] (current) – external edit 127.0.0.1
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-====== Installing LOFAR Software on a CentOS 6.5 (Final) system (cluster Newton of the AIP Potsdam) ======+====== 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
  --- //[[fbreitling@aip.de|Frank Breitling]] 2015/06/26 18:47//  --- //[[fbreitling@aip.de|Frank Breitling]] 2015/06/26 18:47//
  
  
-I was mainly following the previous installation notes provided by others: \\+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:lofar \\
 http://www.lofar.org/operations/doku.php?id=public:user_software:ubuntu_12_4 http://www.lofar.org/operations/doku.php?id=public:user_software:ubuntu_12_4
  
-However a few problems occured and had to be solved as described below. \\+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. \\ Ideas and support by **Arno Schoenmakers**, **Ger van Diepen** and **Marcel Loose** were very helpful and highly appreciated. \\
-===== 1. Setup of the environment =====+ 
 + 
 +===== 1. Setup of build environment =====
  
 The following packages are already provided on the cluster: The following packages are already provided on the cluster:
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 The cluster also provides a //module system// to load newer versions of the installed software. \\ The cluster also provides a //module system// to load newer versions of the installed software. \\
-We will activate it and replace the default version of gcc 4.4.7 with gcc 4.8.3 for C++11 support.+Its used below to replace the default version of gcc 4.4.7 with gcc 4.8.3 for C++11 support.
  
  
-=== 1.1 Pathes === +=== 1.1 Paths === 
-This instruction will install all packages in $HOME/local/. \\ + 
-And for the installation of Pyrap (python-casacore) we need a Python path with write access. \\ +The following changes are required: 
-So I added the following lines to $HOME/.bashrc:+ 
 +  * 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> <file>
-source /usr/share/Modules/init/sh  # activate module system, needs to be done first +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> 
-module load gcc  # use gcc 4.8.3 (instead of 4.4.7) for C++11 support+    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) 
 +</file>
  
 +  * The packages will be installed in $HOME/local/. \\
 +  * Pyrap (python-casacore) needs a writable Python path. \\
 +
 +This adds the following lines to $HOME/.bashrc:
 +<file>
 +source /usr/share/Modules/init/sh  # activate module system, needs to be done first
 +module load gcc/4.8.3  # use gcc 4.8.3 (instead of 4.4.7) for C++11 support
 +export LD_LIBRARY_PATH=/opt/gcc-4.8.3/lib64:$HOME/local/lib:$LD_LIBRARY_PATH
 export PYTHONPATH=$HOME/local/lib64/python2.6/site-packages:$PYTHONPATH export PYTHONPATH=$HOME/local/lib64/python2.6/site-packages:$PYTHONPATH
-export LD_LIBRARY_PATH=$HOME/local/lib:$LD_LIBRARY_PATH 
 export PATH=$HOME/local:$PATH export PATH=$HOME/local:$PATH
 </file> </file>
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 === 1.2 CMake === === 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 [[https://en.wikipedia.org/wiki/Environment_Modules_%28software%29|Environment Modules]] (see also http://modules.sourceforge.net/).\\ 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 [[https://en.wikipedia.org/wiki/Environment_Modules_%28software%29|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. \\ The environment modules also provide more recent HDF5 libraries. Both could be loaded by adding ''module load cmake hdf5'' to $HOME/.bashrc. \\
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-=== 1.3 Boost === +=== 1.3 Python === 
-Also a newer version of Boost is required since AOFlagger v2.8.0 and later:+To use matplotlib 2 one also needs Python 2.7 or later. 
 + 
 +<file> 
 +V_PY=2.7.13 
 +cd ~/local/src/ 
 +wget https://www.python.org/ftp/python/$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 
 +</file> 
 + 
 + 
 + 
 +=== 1.4 Boost === 
 +Also a newer version of [[http://www.boost.org/build/doc/html/bbv2/installation.html | Boost]] is required since AOFlagger v2.8.0 and later:
  
 <file> <file>
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 time ./b2 install --prefix=${HOME}/local time ./b2 install --prefix=${HOME}/local
 </file> </file>
-===== 2. Installation of required packages =====+ 
 + 
 +===== 2. Installation of dependencies ===== 
 Next we need to build and install these other packages as follows: Next we need to build and install these other packages as follows:
 +
 +=== 2.1 WCSLIB ===
 +The [[http://www.atnf.csiro.au/people/mcalabre/WCS/ | WCSLIB]]:
 +
 <file> <file>
 cd $HOME/local/src/ cd $HOME/local/src/
 wget ftp://ftp.atnf.csiro.au/pub/software/wcslib/wcslib.tar.bz2 wget ftp://ftp.atnf.csiro.au/pub/software/wcslib/wcslib.tar.bz2
 tar xf packages/wcslib.tar.bz2 tar xf packages/wcslib.tar.bz2
-cd wcslib-5.6/+cd wcslib-5.15  # (-5.6)
 ./configure --prefix=$HOME/local/ ./configure --prefix=$HOME/local/
-make install+time make -j install 
 +</file>
  
  
 +=== 2.2 FFTW ===
 +The [[http://www.fftw.org/ | FFTW lib]]:
 +
 +<file>
 +V_FFTW=3.3.5  # 3.3.4
 cd $HOME/local/src/ cd $HOME/local/src/
-wget http://www.fftw.org/fftw-3.3.4.tar.gz +wget http://www.fftw.org/fftw-$V_FFTW.tar.gz 
-cd fftw-3.3.4 +cd fftw-$V_FFTW 
-configure --prefix=$HOME/local --enable-threads --enable-shared --enable-float +./configure --prefix=$HOME/local --enable-threads --enable-shared --enable-float --enable-sse --enable-sse2 --enable-avx 
-make -j12 install+time make -j install
 </file> </file>
 +
  
  
 ===== 3. Installation the LOFAR software ===== ===== 3. Installation the LOFAR software =====
-Now we can continue building the LOFAR software. \\+Now we can build the LOFAR software. \\
  
 +We will need the following CMake switches:
  
-=== 3.1 Essential CMake switches === +   1. -DCMAKE_INSTALL_PREFIX:PATH=$HOME/local 
-We will need these essential CMake switches:+   2. -DBOOST_ROOT=$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. -DUSE_OPENMP=YES +1.) Sets the installation path to $HOME/local.
-   2. -DCMAKE_INSTALL_PREFIX:PATH=$HOME/local +
-   3. -DBoost_NO_BOOST_CMAKE=YES +
-   4. -DENABLE_TABLELOCKING=NO (only for Casacore) +
-   5. -DUSE_LOG4CPLUS=NO (only for the LOFAR packages) +
-   6. -DUSE_BACKTRACE=NO+
  
-1.) OpenMP makes use of multi-core CPUs. We want to use this since it speeds up our processing.+2.) Necessary to find the new Boost installation
  
-2.) Sets the installation path to $HOME/local/.+3.) Necessary to link against the new Boost installation
  
-3.) Is necessary when using some older versions of boost with cmake-2.8.6-rc2 or later, where the boost finding has changed. \\ +# 4.) Was required by some older versions of boost e.g. 1.41 with cmake-2.8.6-rc2, producing this problem: \\ 
-(See https://stackoverflow.com/questions/9948375/cmake-find-package-succeeds-but-returns-wrong-path.)\\ +https://stackoverflow.com/questions/9948375/cmake-find-package-succeeds-but-returns-wrong-path resulting in\\
-Otherwise make will show this error later:+
 <file> <file>
 make[2]: *** No rule to make target `/usr/lib64/lib64/libboost_program_options-mt.so.5', needed by `segment'.  Stop. make[2]: *** No rule to make target `/usr/lib64/lib64/libboost_program_options-mt.so.5', needed by `segment'.  Stop.
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 make: *** [all] Error 2 make: *** [all] Error 2
 </file> </file>
 +It is not necessary any more with the new boost installation.
 +
 +
 +=== 3.2 Casacore ===
 +[[https://github.com/casacore/casacore | Casacore]] also requires the CASA data. 
 +This is for example provided with [[http://casa.nrao.edu/casa_obtaining.shtml | 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'' .\\
  
-4.) On the AIP Lustre file system Casacore cannot acquire read locks leading to errors like:+''-DENABLE_TABLELOCKING=NO'' switches off table locking, since read locks could not be acquired from the AIP Lustre file system leading to errors like:
 <file> <file>
 msoverview: Version 20110407GvD msoverview: Version 20110407GvD
Line 123: Line 173:
 /lustre/fkbreitl/data/L206894/L206894.cal/L206894_SAP000_SB200_uv.MS.dppp_00001~00040/table.lock /lustre/fkbreitl/data/L206894/L206894.cal/L206894_SAP000_SB200_uv.MS.dppp_00001~00040/table.lock
 </file> </file>
-With table locking switched off these errors are avoided. For practical work there is no disadvantage in disabling table locking. \\ +For practical work there is no disadvantage in disabling table locking. \\
-This switch is only needed for Casacore! +
- +
-5.) Is necessary for the LOFAR packages if the Log4cplus libs are not installed. +
- +
-6.) 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). +
- +
-So we can build the rest of the packages as follows. +
- +
-=== 3.2 Casacore === +
-[[https://github.com/casacore/casacore | Casacore]] also requires the CASA data.  +
-This is for example provided with [[http://casa.nrao.edu/casa_obtaining.shtml | CASA]]. \\ +
-Here we assume CASA is already installed and $HOME/local/casa is a link to the CASA folder. Then the data is in $HOME/local/casa. \\ +
-We will specify this via -DDATA_DIR, otherwise we need a ~/.casarc file with the line: ''measures.directory: $HOME/local/casa/data'' .\\+
  
 <file> <file>
 +# 2.1, 2.2
 cd ~/local/src/ cd ~/local/src/
 git clone https://github.com/casacore/casacore git clone https://github.com/casacore/casacore
 mkdir build/casacore mkdir build/casacore
 cd build/casacore cd build/casacore
-time cmake -DBUILD_PYTHON=YES -DCMAKE_INSTALL_PREFIX=~/local -DUSE_FFTW3=YES -DENABLE_TABLELOCKING=NO \ +CASAPATH=$HOME/local/casa/casa 
-  -DUSE_OPENMP=YES -DDATA_DIR=~/local/casa/data -DUSE_HDF5=YES -DCMAKE_PREFIX_PATH=$HOME/local ../../casacore+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 time make -j
 make install make install
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    --global-option=-L$HOME/local/lib --install-option=--prefix=$HOME/local    --global-option=-L$HOME/local/lib --install-option=--prefix=$HOME/local
 </file> </file>
 +
  
 === 3.4 Casarest === === 3.4 Casarest ===
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 mkdir build/casarest mkdir build/casarest
 cd build/casarest cd build/casarest
-cmake -DCASACORE_ROOT_DIR=$HOME/local -DBUILD_ALL=1 -DCMAKE_INSTALL_PREFIX:PATH=$HOME/local \ +cmake ../../casarest -DCMAKE_INSTALL_PREFIX:PATH=$HOME/local -DCASACORE_ROOT_DIR=$HOME/local -DCMAKE_PREFIX_PATH=/usr/include/cfitsio -DBUILD_ALL=1 \ 
-  -DCMAKE_PREFIX_PATH=/usr/include/cfitsio -DBoost_NO_BOOST_CMAKE=YES ../../casarest+  -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 time make -j
 make install make install
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 <file> <file>
-V_AOF=2.9.0+V_AOF=2.9.0  # 2.7.1, 2.8.0
 cd ~/local/src/ cd ~/local/src/
 wget http://downloads.sourceforge.net/project/aoflagger/aoflagger-$AOVER/aoflagger-$V_AOF.tar.bz2 wget http://downloads.sourceforge.net/project/aoflagger/aoflagger-$AOVER/aoflagger-$V_AOF.tar.bz2
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 mkdir aoflagger-$V_AOF/build/ mkdir aoflagger-$V_AOF/build/
 cd 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/ \+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$HOME/local/lib"   -DCMAKE_CXX_FLAGS="-lboost_thread -lboost_filesystem -L$HOME/local/lib"
 time make -j time make -j
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 [[http://www.lofar.org/operations/doku.php?id=public:lofar_offline_releases | an offline release]]  [[http://www.lofar.org/operations/doku.php?id=public:lofar_offline_releases | an offline release]] 
 or the latest version in [[https://svn.astron.nl/LOFAR/ | trunk/]] by commenting in and out the corresponding RELEASE lines. \\ or the latest version in [[https://svn.astron.nl/LOFAR/ | 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).
  
 <file> <file>
 cd ~/local/src/ cd ~/local/src/
 RELEASE=LOFAR-Release-2_19 && svn checkout --ignore-externals -N https://svn.astron.nl/LOFAR/branches/$RELEASE RELEASE=LOFAR-Release-2_19 && svn checkout --ignore-externals -N https://svn.astron.nl/LOFAR/branches/$RELEASE
 +# 2_16_4, 2_16, 2_12
 #RELEASE=LOFAR && svn checkout --ignore-externals -N https://svn.astron.nl/LOFAR/trunk $RELEASE #RELEASE=LOFAR && svn checkout --ignore-externals -N https://svn.astron.nl/LOFAR/trunk $RELEASE
 svn update $RELEASE/CMake svn update $RELEASE/CMake
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 cd build/gnu_opt cd build/gnu_opt
 time cmake ../../$RELEASE -DCASACORE_ROOT_DIR=$HOME/local -DBUILD_PACKAGES="DP3 Calibration" -DCMAKE_INSTALL_PREFIX:PATH=$HOME/local -DUSE_BACKTRACE=NO time cmake ../../$RELEASE -DCASACORE_ROOT_DIR=$HOME/local -DBUILD_PACKAGES="DP3 Calibration" -DCMAKE_INSTALL_PREFIX:PATH=$HOME/local -DUSE_BACKTRACE=NO
-# apparently no longer required: -DUSE_OPENMP=YES -DUSE_LOG4CPLUS=NO -DBoost_NO_BOOST_CMAKE=YES+# -DUSE_LOG4CPLUS=NO was required in absence of the Log4cplus lib
 time make -j time make -j
 make install make install
  • Last modified: 2017-01-03 19:28
  • by Frank Breitling