public:install_lofar_centos6.5

Differences

This shows you the differences between two versions of the page.

Link to this comparison view

Both sides previous revision Previous revision
Next revision		 Previous revision
public:install_lofar_centos6.5 [2017-01-04 15:41] – [3. Installation the LOFAR software] Frank Breitlingpublic:install_lofar_centos6.5 [2017-03-08 15:27] (current) – external edit 127.0.0.1
Line 1: Line 1:
-====== 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. \\
  
Line 25: Line 26:
  
 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 Paths === === 1.1 Paths ===
  
-This instruction will install all packages in $HOME/local/. \\ +The following changes are required: 
-And for the installation of Pyrap (python-casacore) we need a Python path with write access. \\ + 
-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>
Line 61: Line 71:
  
  
-=== 1.3 Boost ===+=== 1.3 Python === 
 +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: 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:
  
Line 73: Line 99:
 time ./b2 install --prefix=${HOME}/local time ./b2 install --prefix=${HOME}/local
 </file> </file>
- 
  
  
Line 87: Line 112:
 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-5.15/+cd wcslib-5.15  # (-5.6)
 ./configure --prefix=$HOME/local/ ./configure --prefix=$HOME/local/
 time make -j install time make -j install
Line 97: Line 122:
  
 <file> <file>
-V_FFTW=3.3.5+V_FFTW=3.3.5  # 3.3.4
 cd $HOME/local/src/ cd $HOME/local/src/
 wget http://www.fftw.org/fftw-$V_FFTW.tar.gz wget http://www.fftw.org/fftw-$V_FFTW.tar.gz
Line 136: Line 161:
 [[https://github.com/casacore/casacore | Casacore]] also requires the CASA data.  [[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]]. \\ 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. \\ +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. 
-We will specify this via -DDATA_DIR, otherwise we need a ~/.casarc file with the line: ''measures.directory: $HOME/local/casa/data'' .\\+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: ''-DENABLE_TABLELOCKING=NO'' switches off table locking, since read locks could not be acquired from the AIP Lustre file system leading to errors like:
Line 150: Line 176:
  
 <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
 +CASAPATH=$HOME/local/casa/casa
 time cmake ../../casacore -DBUILD_PYTHON=YES -DCMAKE_INSTALL_PREFIX=~/local -DUSE_FFTW3=YES -DENABLE_TABLELOCKING=NO \ time cmake ../../casacore -DBUILD_PYTHON=YES -DCMAKE_INSTALL_PREFIX=~/local -DUSE_FFTW3=YES -DENABLE_TABLELOCKING=NO \
-  -DUSE_OPENMP=YES -DDATA_DIR=~/local/casa/data -DUSE_HDF5=YES -DCMAKE_PREFIX_PATH=$HOME/local+  -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
Line 179: Line 207:
    --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 ===
Line 203: Line 232:
  
 <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
Line 227: Line 256:
 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
  • Last modified: 2017-01-04 15:41
  • by Frank Breitling