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Installation on Redhat
======================
This page describes installing AOFlagger 2.14 on RHEL 7.6
(Thanks to Leonardo Saavedra from NRAO)
aoflagger depends on many packages, most of then are provided by RHEL 7.6, but you will need to install the modern version of them. In particular: **fftw** and **boost**
* https://gitlab.com/aroffringa/aoflagger
* http://www.fftw.org
* https://github.com/casacore/casacore
* https://www.boost.org/
Install RPMs
------------
You need install hdf from epel (or install from the sources as detailed below), so you need to set EPEL repo.
.. code-block :: bash
yum install hdf hdf-devel
yum install gtkmm30 gtkmm30-devel
Set environment
---------------
.. code-block :: bash
mkdir ~/Downloads2/aoflagger
cd ~/Downloads2/aoflagger
wget -c http://www.fftw.org/fftw-3.3.8.tar.gz
wget -c https://github.com/casacore/casacore/archive/v3.1.1.tar.gz
wget -c https://sourceforge.net/projects/aoflagger/files/aoflagger-2.14.0/aoflagger-2.14.0.tar.bz2
wget -c https://dl.bintray.com/boostorg/release/1.68.0/source/boost_1_68_0.tar.gz
LOCAL5=/opt/local5
Install FFTW 3.3.8
------------------
.. code-block :: bash
tar xzvf fftw-3.3.8.tar.gz
cd fftw-3.3.8/
./configure --prefix=${LOCAL5} --enable-threads --enable-openmp --enable-shared
make -j `nproc`
make install
cd ..
Install Casacore 3.3.1
----------------------
Set new environment
^^^^^^^^^^^^^^^^^^^
.. code-block :: bash
export LD_LIBRARY_PATH=${LOCAL5}/lib:$LD_LIBRARY_PATH
export PATH=$PATH:${LOCAL5}/bin
.. code-block :: bash
tar xzvf v3.1.1.tar.gz
cd casacore-3.1.1/
mkdir build
cd build
cmake ../ -DCMAKE_PREFIX_PATH=${LOCAL5}
make -j `nproc`
make install
vim cmake_install.cmake <-- modified CMAKE_INSTALL_PREFIX to point to ${LOCAL5}
make install
Install boost 1.68
------------------
Previous to compile boost, you have to make sure that your python installation uses a 4-byte representation for Unicode characters.
To check that, you can run the following script, if it reports 'UCS2 Build', you have to either install a new python or use other python version.
https://docs.python.org/2/faq/extending.html#can-i-create-an-object-class-with-some-methods-implemented-in-c-and-others-in-python-e-g-through-inheritance
.. code-block :: bash
python
cat CheckUnide.py
import sys
if sys.maxunicode > 65535:
print ('UCS4 Build')
else:
print ('UCS2 Build')
.. code-block :: bash
python CheckUnide.py
UCS4 Build
.. code-block :: bash
tar xzvf boost_1_68_0.tar.gz
cd boost_1_68_0
./bootstrap.sh --with-python=python --prefix=${LOCAL5} --with-icu
./b2
./b2 link=shared install --prefix=${LOCAL5}
(cd ${LOCAL5}/lib ; ln -s libboost_python27.so libboost_python.so)
cd ..
Install HDF5
------------
This is optional, you can skip if you have hdf5 from Epel.
Download hdf-1.10.5.tar from https://www.hdfgroup.org/downloads/hdf5/source-code/
.. code-block :: bash
./configure --enable-cxx --with-szlib --enable-shared --enable-hl --disable-silent-rules --enable-fortran --enable-fortran2003 --prefix=${LOCAL5}
make -j `nproc`
make check
make install
make installcheck
Install AOFlagger 2.14
----------------------
.. code-block :: bash
tar xjvf aoflagger-2.14.0.tar.bz2
cd aoflagger-2.14.0
mkdir build
cd build
cmake ../ -DCMAKE_PREFIX_PATH=${LOCAL5} -DCMAKE_INSTALL_PREFIX={LOCAL5}
make -j `nproc`
vim cmake_install.cmake <-- modified (or make sure) CMAKE_INSTALL_PREFIX point to ${LOCAL5}
make install
Check aoflagger version
-----------------------
.. code-block :: bash
which python
/opt/local5/bin/python
aoflagger --version
AOFlagger 2.14.0 (2019-02-14)
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