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public:install_lofar_redhat5.8 [2013-10-10 09:55]
Jose Sabater Montes created
public:install_lofar_redhat5.8 [2017-03-08 15:27]
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-====== Intallation of LOFAR in Red Hat Enterprise 5.8 ====== 
  
-This is the description of the installation of LOFAR on the cluster of the [[http://​www.iaa.es/​|IAA]] in [[http://​es.wikipedia.org/​wiki/​Granada|Granada]]. It bundles an old version of Red Hat Enterprise Linux that does not contain many of the new libraries required by LOFAR. 
- 
-Description of the system: 
-  * Operating system: Red Hat Enterprise Linux Server release 5.8 (Tikanga) 
-  * PBS queue system: [[http://​www.adaptivecomputing.com/​products/​open-source/​torque/​|TORQUE]] 
-  * Libraries available: HDF5 and old versions of boost and fftw3. 
- 
-After some tests we determined that we needed to isntall, at least, the followin software and libraries: 
-  * scons 
-  * WCS 
-  * lapack 
-  * atlas 
-  * fftw3 
-  * Python 
-    * numpy 
-  * Boost 
-  * LOFAR related: 
-    * casacore 
-    * pyrap 
-    * casarest 
-    * LOFAR (LofIm) 
- 
- 
-===== Installation steps ===== 
- 
-The software was installed in the home of the use ''​jsm''​ (''/​home/​users/​dae/​jsm''​). You should change the scripts accordingly. 
- 
-Previous steps: 
-<code bash> 
-## Create the installation directory 
-mkdir -p /​home/​users/​dae/​jsm/​local/​src 
-cd /​home/​users/​dae/​jsm/​local/​src 
-</​code>​ 
- 
-Download and copy the data: 
-<code bash> 
-# scons 
-wget http://​prdownloads.sourceforge.net/​scons/​scons-2.3.0.tar.gz 
-# WCS 
-wget ftp://​ftp.atnf.csiro.au/​pub/​software/​wcslib/​wcslib.tar.bz2 
-# lapack 
-wget http://​www.netlib.org/​lapack/​lapack-3.4.2.tgz 
-# atlas 
-wget http://​prdownloads.sourceforge.net/​math-atlas/​Developer%20%28unstable%29/​3.11.11/​atlas3.11.11.tar.bz2 
-# FFTW3 
-wget http://​www.fftw.org/​fftw-3.3.3.tar.gz 
-# Boost 
-wget http://​prdownloads.sourceforge.net/​boost/​boost/​1.54.0/​boost_1_54_0.tar.gz 
-# LOFAR related software 
-# casacore 
-#svn co http://​casacore.googlecode.com/​svn/​tags/​casacore-1.5.0 
-cp -r /​home/​users/​dae/​jsm/​local-v0/​src/​casacore-1.5.0 . 
-rm -rf casacore-1.5.0/​build 
-# pyrap 
-#svn co http://​pyrap.googlecode.com/​svn/​tags/​pyrap-1.1.0 
-cp -r /​home/​users/​dae/​jsm/​local-v0/​src/​pyrap-1.1.0 . 
-# casarest 
-#svn co https://​svn.astron.nl/​casarest/​trunk/​casarest/​ 
-cp -r /​home/​users/​dae/​jsm/​local-v0/​src/​casarest . 
-rm -rf casarest/​build 
-</​code>​ 
- 
-We had already got a copy of the LOFAR software with SVN in ''/​home/​users/​dae/​jsm/​LOFAR'':​ 
-<code bash> 
-# LOFAR 
-cp -r /​home/​users/​dae/​jsm/​LOFAR . 
-</​code>​ 
- 
-We used the following paths: 
-<code bash> 
-# PATH 
-export PATH=/​home/​users/​dae/​jsm/​local/​bin:/​home/​users/​dae/​jsm/​python/​bin:/​usr/​local/​casapy-stable-42.0.25430-001-64b:/​usr/​local/​iraf/​bin:/​usr/​local/​mpich-install/​bin:/​usr/​local/​bin:/​bin:/​usr/​bin 
-# LD_LIBRARY_PATH 
-export LD_LIBRARY_PATH=/​home/​users/​dae/​jsm/​local/​lib:/​home/​users/​dae/​jsm/​local/​atlas/​lib:/​home/​users/​dae/​jsm/​python/​lib:/​usr/​local/​hdf5-1.8.11-linux-x86_64-shared/​lib:/​usr/​local/​mpich-install/​lib:/​usr/​local/​lib 
-</​code>​ 
- 
-Install Python and their important libraries: 
-<code bash> 
-# Compile 
-mkdir -p /​home/​users/​dae/​jsm/​python/​src 
-cd /​home/​users/​dae/​jsm/​python/​src 
-# Download Python **** CHANGE 
-# Extract Python **** CHANGE 
-cd Python-2.7.5 ​ 
-./configure --prefix=/​home/​users/​dae/​jsm/​python --enable-shared 
-make  
-make install 
- 
-# Install zeromq (used by IPython parallel) 
-cd /​home/​users/​dae/​jsm/​python/​src 
-wget http://​download.zeromq.org/​zeromq-3.2.4.tar.gz 
-tar xzf zeromq-3.2.4.tar.gz 
-cd zeromq-3.2.4 
-./configure --prefix=/​home/​users/​dae/​jsm/​local 
-make  
-make install 
- 
-# Install easy install and pip 
-cd /​home/​users/​dae/​jsm/​python/​src 
-wget https://​bitbucket.org/​pypa/​setuptools/​raw/​bootstrap/​ez_setup.py 
-python ez_setup.py 
-wget https://​raw.github.com/​pypa/​pip/​master/​contrib/​get-pip.py 
-# rm -r /​tmp/​pip-build-jsm/​pip 
-python get-pip.py 
- 
-# Install packages 
-pip install virtualenv 
-pip install numpy 
-pip install h5py 
-pip install scipy 
-pip install matplotlib 
-pip install pandas 
-pip install pyfits 
-pip install pywcs 
-pip install astropy 
-pip install cython 
- 
-# Install pyzmq 
-cd /​home/​users/​dae/​jsm/​python/​src 
-wget https://​pypi.python.org/​packages/​source/​p/​pyzmq/​pyzmq-13.0.2.tar.gz --no-check-certificate 
-tar xzf pyzmq-13.0.2.tar.gz 
-cd pyzmq-13.0.2 
-python setup.py configure --zmq=/​home/​users/​dae/​jsm/​local/​ 
-python setup.py install 
- 
-# Install IPython 
-cd /​home/​users/​dae/​jsm/​python/​src 
-pip install ipython[all] 
-</​code>​ 
- 
-From now on we need to enter an interactive PBS job to avoid our jobs to be killed after certain amount of time (the maximum allowed lenght for a job without using PBS is 10 minutes). The nodes do not have direct access to the Internet (that is why they were previously downloaded):​ 
- 
-<​code>​ 
-### Enter interactive qsub session 
-qsub -I -X -N LOFAR_soft 
- 
-## Update the PATH and the LD_LIBRARY_PATH 
-# PATH 
-export PATH=/​home/​users/​dae/​jsm/​local/​bin:/​home/​users/​dae/​jsm/​python/​bin:/​usr/​local/​hdf5-1.8.11-linux-x86_64-shared/​bin:/​usr/​local/​casapy-stable-42.0.25430-001-64b:/​usr/​local/​iraf/​bin:/​usr/​local/​mpich-install/​bin:/​usr/​local/​bin:/​bin:/​usr/​bin 
-# LD_LIBRARY_PATH 
-export LD_LIBRARY_PATH=/​home/​users/​dae/​jsm/​local/​lib:/​home/​users/​dae/​jsm/​local/​atlas/​lib:/​home/​users/​dae/​jsm/​python/​lib:/​usr/​local/​hdf5-1.8.11-linux-x86_64-shared/​lib:/​usr/​local/​mpich-install/​lib:/​usr/​local/​lib 
-</​code>​ 
- 
-Compile the libraries and tools: 
-<code bash> 
-## scons 
-cd /​home/​users/​dae/​jsm/​local/​src 
-tar xfz scons-2.3.0.tar.gz 
-cd scons-2.3.0 
-python setup.py install --prefix=/​home/​users/​dae/​jsm/​local 
- 
- 
-## ATLAS + LAPACK + BLAS 
-cd /​home/​users/​dae/​jsm/​local/​src 
-tar xfj atlas3.11.11.tar.bz2 
-mkdir -p ATLAS/build 
-cd ATLAS/build 
-../​configure -b 64 -D c -DPentiumCPS=2932 --shared \ 
-  --prefix=/​home/​users/​dae/​jsm/​local/​atlas \ 
-  --with-netlib-lapack-tarfile=/​home/​users/​dae/​jsm/​local/​src/​lapack-3.4.2.tgz 
-make build 
-make check 
-make ptcheck 
-make time 
-make install 
-ln -s /​home/​users/​dae/​jsm/​local/​atlas/​lib/​libcblas.a \ 
-  /​home/​users/​dae/​jsm/​local/​atlas/​lib/​libblas.a 
- 
- 
-## WCS 
-cd /​home/​users/​dae/​jsm/​local/​src 
-tar xfj wcslib.tar.bz2 
-cd wcslib-4.19 
-./configure --prefix=/​home/​users/​dae/​jsm/​local/​ 
-make 
-make install 
- 
- 
-## FFTW3 
-cd /​home/​users/​dae/​jsm/​local/​src 
-tar xfz fftw-3.3.3.tar.gz 
-cd fftw-3.3.3 
-./configure --enable-threads --enable-shared \ 
-  --prefix=/​home/​users/​dae/​jsm/​local/​ 
-make 
-make install 
-make clean 
-./configure --enable-threads --enable-shared ​ --enable-float \ 
-  --prefix=/​home/​users/​dae/​jsm/​local/​ 
-make  
-make install 
- 
- 
-## Boost  
-cd /​home/​users/​dae/​jsm/​local/​src 
-tar xfz boost_1_54_0.tar.gz 
-cd boost_1_54_0 
-./​bootstrap.sh --prefix=/​home/​users/​dae/​jsm/​local \ 
-  --with-python=/​home/​users/​dae/​jsm/​python/​bin/​python 
-./b2  
-./b2 install 
-</​code>​ 
- 
-Compile casacore 
-<code bash> 
-## casacore 
-cd /​home/​users/​dae/​jsm/​local/​src 
-cd casacore-1.5.0 
-mkdir build; cd build 
-cmake .. -DWCSLIB_LIBRARY=/​home/​users/​dae/​jsm/​local/​lib/​libwcs.so \ 
-         ​-DWCSLIB_INCLUDE_DIR=/​home/​users/​dae/​jsm/​local/​include/​ \ 
-         ​-DCMAKE_INSTALL_PREFIX=/​home/​users/​dae/​jsm/​local/​casacore \ 
-         ​-DUSE_HDF5=ON -DUSE_FFTW3=ON \ 
-         ​-DHDF5_ROOT_DIR=/​usr/​local/​hdf5-1.8.11-linux-x86_64-shared \ 
-         ​-DLAPACK_LIBRARIES=/​home/​users/​dae/​jsm/​local/​atlas/​lib/​liblapack.a \ 
-         ​-DBLAS_LIBRARIES=/​home/​users/​dae/​jsm/​local/​atlas/​lib/​libf77blas.a\;/​home/​users/​dae/​jsm/​local/​atlas/​lib/​libcblas.a\;/​home/​users/​dae/​jsm/​local/​atlas/​lib/​libatlas.a \ 
-         ​-DBLA_VENDOR=ATLAS \ 
-         ​-DFFTW3_LIBRARY=/​home/​users/​dae/​jsm/​local/​lib/​libfftw3.so \ 
-         ​-DFFTW3_THREADS_LIBRARY=/​home/​users/​dae/​jsm/​local/​lib/​libfftw3_threads.so \ 
-         ​-DFFTW3F_LIBRARY=/​home/​users/​dae/​jsm/​local/​lib/​libfftw3f.so \ 
-         ​-DFFTW3F_THREADS_LIBRARY=/​home/​users/​dae/​jsm/​local/​lib/​libfftw3f_threads.so \ 
-         ​-DFFTW3_INCLUDE=/​home/​users/​dae/​jsm/​local/​include/​ \ 
-         ​-DCMAKE_Fortran_COMPILER:​FILEPATH=/​usr/​bin/​gfortran 
-make 
-make install 
-</​code>​ 
- 
-Install pyrap (scons needed): 
-<code bash> 
-## pyrap 
-cd /​home/​users/​dae/​jsm/​local/​src 
-cd pyrap-1.1.0 
-## PATCH pyrap ******* 
-python batchbuild.py --boost-root=/​home/​users/​dae/​jsm/​local \ 
-  --casacore-root=/​home/​users/​dae/​jsm/​local/​casacore \ 
-  --enable-hdf5 --hdf5-root=/​usr/​local/​hdf5-1.8.11-linux-x86_64-shared \ 
-  --lapack-root=/​home/​users/​dae/​jsm/​local/​atlas \ 
-  --wcs-root=/​home/​users/​dae/​jsm/​local \ 
-  --prefix=/​home/​users/​dae/​jsm/​local ​ 
-</​code>​ 
- 
-Install casarest 
-<code bash> 
-## casarest 
-cd /​home/​users/​dae/​jsm/​local/​src 
-cd casarest 
-mkdir build; cd build 
-cmake .. -DBOOST_ROOT=/​home/​users/​dae/​jsm/​local \ 
-         ​-DLAPACK_LIBRARIES=/​home/​users/​dae/​jsm/​local/​atlas/​lib/​liblapack.a \ 
-         ​-DLAPACK_INCLUDE=/​home/​users/​dae/​jsm/​local/​atlas/​include/​ \ 
-         ​-DBLAS_LIBRARIES=/​home/​users/​dae/​jsm/​local/​atlas/​lib/​libf77blas.a\;/​home/​users/​dae/​jsm/​local/​atlas/​lib/​libcblas.a\;/​home/​users/​dae/​jsm/​local/​atlas/​lib/​libatlas.a \ 
-         ​-DBLAS_INCLUDE=/​home/​users/​dae/​jsm/​local/​atlas/​include/​ \ 
-         ​-DWCSLIB_LIBRARY=/​home/​users/​dae/​jsm/​local/​lib/​libwcs.so \ 
-         ​-DWCSLIB_INCLUDE_DIR=/​home/​users/​dae/​jsm/​local/​include/​ \ 
-         ​-DCASACORE_ROOT_DIR=/​home/​users/​dae/​jsm/​local/​casacore \ 
-         ​-DCMAKE_INSTALL_PREFIX=/​home/​users/​dae/​jsm/​local/​casarest \ 
-         ​-DHDF5_ROOT_DIR=/​usr/​local/​hdf5-1.8.11-linux-x86_64-shared \ 
-         ​-DLIB_EXTRA_SYNTHESIS=/​home/​users/​dae/​jsm/​local/​atlas/​lib/​libcblas.a\;/​home/​users/​dae/​jsm/​local/​atlas/​lib/​libatlas.a \ 
-         ​-DBUILD_ALL=1 
-make 
-make install 
-</​code>​ 
- 
-Install LOFAR: 
-<code bash> 
-cd /​home/​users/​dae/​jsm/​local/​src 
-#cp -r ~/LOFAR . 
-cd LOFAR 
-### PATCH LOFAR ******** 
-mkdir -p build/​gnu_opt;​ cd build/​gnu_opt 
-mkdir /​home/​users/​dae/​jsm/​local/​LofIm 
-cmake ../.. -DBUILD_SHARED_LIBS=ON \ 
-  -DCMAKE_INSTALL_PREFIX=/​home/​users/​dae/​jsm/​local/​LofIm \ 
-  -DUSE_LOG4CPLUS=OFF \ 
-  -DBOOST_ROOT=/​home/​users/​dae/​jsm/​local \ 
-  -DHDF5_ROOT_DIR=/​usr/​local/​hdf5-1.8.11-linux-x86_64-shared \ 
-  -DWCSLIB_LIBRARY=/​home/​users/​dae/​jsm/​local/​lib/​libwcs.so \ 
-  -DWCSLIB_INCLUDE_DIR=/​home/​users/​dae/​jsm/​local/​include/​ \ 
-  -DLAPACK_LIBRARIES=/​home/​users/​dae/​jsm/​local/​atlas/​lib/​libf77blas.a\;/​home/​users/​dae/​jsm/​local/​atlas/​lib/​libcblas.a\;/​home/​users/​dae/​jsm/​local/​atlas/​lib/​libatlas.a\;/​home/​users/​dae/​jsm/​local/​atlas/​lib/​liblapack.a \ 
-  -DBLAS_LIBRARIES=/​home/​users/​dae/​jsm/​local/​atlas/​lib/​libf77blas.a\;/​home/​users/​dae/​jsm/​local/​atlas/​lib/​libcblas.a\;/​home/​users/​dae/​jsm/​local/​atlas/​lib/​libatlas.a\;/​home/​users/​dae/​jsm/​local/​atlas/​lib/​liblapack.a ​ \ 
-  -DFFTW3_LIBRARY=/​home/​users/​dae/​jsm/​local/​lib/​libfftw3.so \ 
-  -DFFTW3_THREADS_LIBRARY=/​home/​users/​dae/​jsm/​local/​lib/​libfftw3_threads.so \ 
-  -DFFTW3F_LIBRARY=/​home/​users/​dae/​jsm/​local/​lib/​libfftw3f.so \ 
-  -DFFTW3F_THREADS_LIBRARY=/​home/​users/​dae/​jsm/​local/​lib/​libfftw3f_threads.so \ 
-  -DFFTW3_INCLUDE=/​home/​users/​dae/​jsm/​local/​include/​ \ 
-  -DCASACORE_ROOT_DIR=/​home/​users/​dae/​jsm/​local/​casacore \ 
-  -DCASA_CASA_LIBRARY=/​home/​users/​dae/​jsm/​local/​casacore/​lib/​libcasa_casa.so\;/​home/​users/​dae/​jsm/​local/​atlas/​lib/​libf77blas.a\;/​home/​users/​dae/​jsm/​local/​atlas/​lib/​libcblas.a\;/​home/​users/​dae/​jsm/​local/​atlas/​lib/​libatlas.a\;/​home/​users/​dae/​jsm/​local/​atlas/​lib/​liblapack.a \ 
-  -DUSE_OPENMP=ON \ 
-  -DBUILD_PACKAGES=Offline\;​LofarFT\;​StaticMetaData\;​SPW_Combine \ 
-  -DCASAREST_ROOT_DIR=/​home/​users/​dae/​jsm/​local/​casarest/​ \ 
-  -DPYTHON_LIBRARY=/​home/​users/​dae/​jsm/​python/​lib/​libpython2.7.so \ 
-  -DPYTHON_EXECUTABLE:​FILEPATH=/​home/​users/​dae/​jsm/​python/​bin/​python \ 
-  -DPYTHON_INCLUDE_DIR:​PATH=/​home/​users/​dae/​jsm/​python/​include \ 
-  -DPYRAP_INCLUDE_DIR=/​home/​users/​dae/​jsm/​local/​include/​pyrap \ 
-  -DPYRAP_LIBRARY=/​home/​users/​dae/​jsm/​local/​lib/​libpyrap.so \ 
-  -DCMAKE_Fortran_COMPILER:​FILEPATH=/​usr/​bin/​gfortran \ 
-  -DF2PY_FCOMPILER=gnu95 2>&1 | tee log.txt 
-make 
-make install 
-</​code>​ 
- 
-Finish the installation (FIXME): 
-  * Configure .bashrc 
-  * Configure .casarc 
- 
-==== Patches needed ==== 
- 
-pyrap and LOFAR need to be patched to allow them to compile in this old system. 
- 
-===== Problems ===== 
  • Last modified: 2017-03-08 15:27
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