Moved to Fedora-based base container images.

FROM lofarit_base_exstras:latest

MAINTAINER Giuliano Taffoni <giuliano.taffoni@inaf.it>

ENV CONTAINER_NAME='lofarit_base_astro'

USER root

ENV J=40

ENV INSTALLDIR=/opt/lofar

ENV PYTHON_VERSION=2.7

# Path to where the patch for python-casacore's setup is stored.

ENV PYTHON_CASACORE_PATCH=$INSTALLDIR/python-casacore/python_casacore_setup_patch.patch

ENV PATCH_LOFAR=$INSTALLDIR/lofar/lofar.patch

# Settings relevant to the installed software.

ENV AOFLAGGER_VERSION=v2.15.0

ENV ARMADILLO_VERSION=9.900.3

ENV BLAS_VERSION=3.8.0

ENV BOOST_VERSION=1.69.0

ENV CASACORE_VERSION=v2.4.1

ENV # Leave at latest, release versions crash for some reason.

ENV CASAREST_VERSION=latest

ENV CFITSIO_VERSION=7.3.47

ENV DPPP_VERSION=v4.2

ENV DYSCO_VERSION=v1.2

#export EVERYBEAM_VERSION=0cc64a81

ENV EVERYBEAM_VERSION=master

ENV FFTW_VERSION=3.5.8

ENV HDF5_VERSION=1.10.5

ENV IDG_VERSION=master

ENV LAPACK_VERSION=3.8.0

ENV LOFAR_VERSION=3_2_18

# Don't change LOSOTO2_VERSION. This is the last commit that plays nice with Python 2.

ENV LOSOTO2_VERSION=c8fbd61

ENV LOSOTO3_VERSION=latest

ENV LSMTOOL_VERSION=v1.4.2

ENV OPENBLAS_VERSION=3.8.0

ENV PYBDSF_VERSION=master

ENV PYTHON_CASACORE_VERSION=v2.2.1

ENV RMEXTRACT_VERSION=4c61232

ENV SUPERLU_VERSION=5.2.1

ENV WSCLEAN_VERSION=latest

ENV WCSLIB_VERSION=6.4

ENV HDF5_USE_FILE_LOCKING=FALSE

# Symlinks required for Fedora 31

RUN ln -s /usr/lib64/libboost_python37.so /usr/lib64/libboost_python3.so && \

    ln -s /usr/lib64/libboost_numpy37.so /usr/lib64/libboost_numpy3.so  && \

    ln -s /usr/lib64/libboost_python27.so /usr/lib64/libboost_python.so && \

    ln -s /usr/lib64/libboost_numpy27.so /usr/lib64/libboost_numpy.so && \

    ln -s /usr/lib64/libnsl.so.2.0.0 /usr/lib64/libnsl.so

#

# Setup the compiliong enviroment 

#

#ARG CFLAGS="-mno-avx512f -mno-avx512pf -mno-avx512er -mno-avx512cd -mno-avx512vl -mno-avx512bw -mno-avx512dq -mno-avx512ifma -mno-avx512vbmi"

#ARG CXXFLAGS="-std=c++11 -mno-avx512f -mno-avx512pf -mno-avx512er -mno-avx512cd -mno-avx512vl -mno-avx512bw -mno-avx512dq -mno-avx512ifma -mno-avx512vbmi"

# Use below to optimize for a specific architecture

#export CFLAGS="-march=skylake-avx512 -mtune=skylake-avx512"

#export CXXFLAGS="-march=skylake-avx512 -mtune=skylake-avx512"

ARG CPLUS_INCLUDE_PATH="/usr/include/openmpi-x86_64:/usr/include/c++/9:$CPLUS_INCLUDE_PATH:/usr/include/python2.7:$INSTALLDIR/casacore/include:/usr/include/boost:/usr/include/cfitsio:$INSTALLDIR/EveryBeam/include"

ARG CPATH="/usr/include/openmpi-x86_64/:/opt/intel/mkl/include:${INSTALLDIR}/casacore/include:$INSTALLDIR/LOFARBeam/include:$INSTALLDIR/idg/include:$INSTALLDIR/aoflagger/include:$INSTALLDIR/EveryBeam/include:$CPATH"

ARG CMAKE_PREFIX_PATH="$INSTALLDIR/aoflagger:$INSTALLDIR/casacore:$INSTALLDIR/lofar:$INSTALLDIR/LOFARBeam:/usr/lib64/openmpi:$INSTALLDIR/EveryBeam"

ARG LD_LIBRARY_PATH="$INSTALLDIR/aoflagger/lib:$INSTALLDIR/casacore/lib:$INSTALLDIR/idg/lib:$INSTALLDIR/LOFARBeam/lib:/usr/lib64/openmpi/lib/:$INSTALLDIR/EveryBeam/lib:LD_LIBRARY_PATH"

ARG PATH="/usr/lib64/openmpi/bin:$PATH"

#ARG  make=`which make`

ARG OLD_PYTHONPATH=$PYTHONPATH

#

# Setup the Python environment.

#

COPY requirements3.txt $INSTALLDIR/requirements3.txt

RUN    pip --no-cache-dir install "virtualenv<20"

RUN    virtualenv $INSTALLDIR/pyenv-py3 --python=python3

RUN    source $INSTALLDIR/pyenv-py3/bin/activate && export HDF5_VERSION=1.10.5 && pip install numpy && pip install --no-binary h5py h5py && \

       pip install -r $INSTALLDIR/requirements3.txt && deactivate

COPY requirements.txt $INSTALLDIR/requirements.txt

RUN    virtualenv $INSTALLDIR/pyenv-py2 --python=python2

RUN    source $INSTALLDIR/pyenv-py2/bin/activate && export HDF5_VERSION=1.10.5 && pip install numpy && pip install --no-binary h5py h5py && \

       pip install -r $INSTALLDIR/requirements.txt && pip install --no-deps "reproject==0.5.1"

#

# Install Montage

#

RUN    mkdir -p /opt/montage && cd /opt/montage && wget https://github.com/Caltech-IPAC/Montage/archive/v6.0.tar.gz -O Montage_v6.0.tar.gz && \ 

    tar xf Montage_v6.0.tar.gz && cd Montage-6.0 && make -j $J

#

# Install difmap

#

RUN mkdir -p $INSTALLDIR/difmap && cd $INSTALLDIR/difmap && \

    wget https://github.com/tikk3r/lofar-grid-hpccloud/blob/master/misc/difmap2.5e.tar.gz?raw=true -O difmap2.5e.tar.gz && \

    tar zxf difmap2.5e.tar.gz && cd uvf_difmap && \

    wget https://raw.githubusercontent.com/nealjackson/loop3_difmap/master/corplt.c -O difmap_src/corplt.c && \

    sed -i.bak -e '97d' configure && \

    sed -i.bak -e '97 i PGPLOT_LIB=/usr/lib64/libpgplot.so.5' configure && \

    ./configure linux-i486-gcc && export PGPLOT_LIB=/usr/lib64/libpgplot.so.5 && export CFLAGS="-L/usr/lib64/libpgplot.so.5" && \

    ./makeall

RUN rm -rf $INSTALLDIR/difmap/*.tar.gz

#

# Install PyBDSF

#

#ARG CFLAGS="-mno-avx512f -mno-avx512pf -mno-avx512er -mno-avx512cd -mno-avx512vl -mno-avx512bw -mno-avx512dq -mno-avx512ifma -mno-avx512vbmi"

RUN  mkdir -p ${INSTALLDIR}/pybdsf && cd ${INSTALLDIR}/pybdsf && git clone https://github.com/lofar-astron/pybdsf pybdsf

RUN  if [ "${PYBDSF_VERSION}" != "latest" ]; then cd ${INSTALLDIR}/pybdsf/pybdsf && git checkout ${PYBDSF_VERSION}; fi

RUN cd ${INSTALLDIR}/pybdsf/pybdsf && python setup.py install

RUN cd $INSTALLDIR && rm -rf $INSTALLDIR/pybdsf/pybdsf

#

# Install CASAcore

#

# Casacore 2.4.1 does not seem to deal well with AVX512 instructions, so disable them if needed

#export CFLAGS="-march=skylake -mtune=skylake -mno-avx512f"

#export CXXFLAGS="-march=skylake -mtune=skylake -mno-avx512f"

RUN mkdir -p ${INSTALLDIR}/casacore/build && mkdir -p ${INSTALLDIR}/casacore/data

RUN cd $INSTALLDIR/casacore && git clone https://github.com/casacore/casacore.git src

RUN if [ "${CASACORE_VERSION}" != "latest" ]; then cd ${INSTALLDIR}/casacore/src && git checkout tags/${CASACORE_VERSION}; fi

# Backport patch UVFITS for LOFAR. This is fixed in recent versions > May 26 2020

# wget https://patch-diff.githubusercontent.com/raw/casacore/casacore/pull/1033.patch -O $INSTALLDIR/casacore/1033.patch

# cd $INSTALLDIR/casacore/src && patch --fuzz 3 -p1 < $INSTALLDIR/casacore/1033.patch

RUN cd ${INSTALLDIR}/casacore/data && wget --retry-connrefused ftp://anonymous@ftp.astron.nl/outgoing/Measures/WSRT_Measures.ztar

RUN cd ${INSTALLDIR}/casacore/data && tar xf WSRT_Measures.ztar && rm WSRT_Measures.ztar

RUN cd ${INSTALLDIR}/casacore/build && cmake -DCMAKE_INSTALL_PREFIX=${INSTALLDIR}/casacore/ -DDATA_DIR=${INSTALLDIR}/casacore/data -DBUILD_PYTHON=True -DUSE_OPENMP=True -DUSE_FFTW3=TRUE -DUSE_HDF5=True -DBUILD_PYTHON3=False ../src/ 

RUN cd ${INSTALLDIR}/casacore/build && make -s -j ${J} && make install

RUN cd $INSTALLDIR && rm -rf $INSTALLDIR/casacore/build && rm -rf $INSTALLDIR/casacore/src

#

# Install Python-CASAcore

#

RUN mkdir ${INSTALLDIR}/python-casacore && cd ${INSTALLDIR}/python-casacore && git clone https://github.com/casacore/python-casacore

RUN if [ "$PYTHON_CASACORE_VERSION" != "latest" ]; then cd ${INSTALLDIR}/python-casacore/python-casacore && git checkout tags/${PYTHON_CASACORE_VERSION}; fi

RUN source $INSTALLDIR/pyenv-py2/bin/activate && cd ${INSTALLDIR}/python-casacore/python-casacore && python setup.py build_ext -I${INSTALLDIR}/casacore/include/:/usr/include/python2.7:/usr/include/cfitsio -L${INSTALLDIR}/casacore/lib/:/usr/lib64/ && python setup.py install #--prefix=${INSTALLDIR}/python-casacore/

RUN cd $INSTALLDIR && rm -rf $INSTALLDIR/python-casacore/python-casacore 

# and then reset the flags again if needed

#export CFLAGS="-march=skylake-avx512 -mtune=skylake-avx512"

#export CXXFLAGS="-march=skylake-avx512 -mtune=skylake-avx512"

#

# Install Dysco

#

RUN mkdir -p $INSTALLDIR/dysco/build

RUN cd $INSTALLDIR/dysco && git clone https://github.com/aroffringa/dysco.git src && cd src

RUN if [ "$DYSCO_VERSION" != "latest" ]; then cd $INSTALLDIR/dysco/src && git checkout $DYSCO_VERSION; fi

RUN cd $INSTALLDIR/dysco/build && cmake -DCMAKE_INSTALL_PREFIX=$INSTALLDIR/dysco -DCASACORE_ROOT_DIR=$INSTALLDIR/casacore -DPORTABLE=True ../src && make -s -j $J && make install

RUN cd $INSTALLDIR && rm -rf $INSTALLDIR/dysco/build && rm -rf $INSTALLDIR/dysco/src

#

# Install AOFlagger

#

RUN mkdir -p ${INSTALLDIR}/aoflagger/build &&  cd ${INSTALLDIR}/aoflagger && git clone git://git.code.sf.net/p/aoflagger/code aoflagger && cd ${INSTALLDIR}/aoflagger/aoflagger

RUN if [ "${AOFLAGGER_VERSION}" != "latest" ]; then cd ${INSTALLDIR}/aoflagger/aoflagger &&  git checkout tags/${AOFLAGGER_VERSION}; fi

RUN source $INSTALLDIR/pyenv-py2/bin/activate && cd ${INSTALLDIR}/aoflagger/build && cmake -DCMAKE_INSTALL_PREFIX=${INSTALLDIR}/aoflagger/ -DCASACORE_ROOT_DIR=${INSTALLDIR}/casacore -DBUILD_SHARED_LIBS=ON -DPORTABLE=True ../aoflagger

RUN source $INSTALLDIR/pyenv-py2/bin/activate && cd ${INSTALLDIR}/aoflagger/build && make -s -j ${J}  && make install

RUN cd $INSTALLDIR && rm -rf $INSTALLDIR/aoflagger/aoflagger && rm -rf $INSTALLDIR/aoflagger/build &&  rm -rf $INSTALLDIR/aoflagger/src

#

# Install LOFAR

#

RUN mkdir -p ${INSTALLDIR}/lofar/build/gnucxx11_opt 

RUN if [ "${LOFAR_VERSION}" = "latest" ]; then cd ${INSTALLDIR}/lofar && svn checkout https://svn.astron.nl/LOFAR/trunk src; fi

RUN if [ "${LOFAR_VERSION}" != "latest" ]; then cd ${INSTALLDIR}/lofar && svn checkout https://svn.astron.nl/LOFAR/tags/LOFAR-Release-${LOFAR_VERSION} src; fi

RUN cd $INSTALLDIR/lofar && svn update --depth=infinity $INSTALLDIR/lofar/src/CMake

RUN cd $INSTALLDIR/lofar/ && wget https://raw.githubusercontent.com/tikk3r/lofar-grid-hpccloud/master/patches/lofar.patch && \

    patch $INSTALLDIR/lofar/src/CMake/variants/GNUCXX11.cmake $PATCH_LOFAR && \

    cd ${INSTALLDIR}/lofar/build/gnucxx11_opt

    #cmake -DCMAKE_PREFIX_PATH=$INSTALLDIR/aoflagger:$INSTALLDIR/casacore:$INSTALLDIR/dysco -DBUILD_PACKAGES="StationResponse pystationresponse ParmDB pyparmdb Pipeline MS" -DCMAKE_INSTALL_PREFIX=$INSTALLDIR/lofar/ -DUSE_LOG4CPLUS=OFF -DUSE_OPENMP=True ${INSTALLDIR}/lofar/src/

ARG CMAKE_C_COMPILER=/usr/bin/gcc

ARG CMAKE_CXX_COMPILER=/usr/bin/g++

ARG CC=/usr/bin/gcc

ARG CXX=/usr/bin/g++

RUN source $INSTALLDIR/pyenv-py2/bin/activate && cd ${INSTALLDIR}/lofar/build/gnucxx11_opt && CC=/usr/bin/gcc && CXX=/usr/bin/g++ && cmake -DCMAKE_PREFIX_PATH=$INSTALLDIR/aoflagger:$INSTALLDIR/casacore:$INSTALLDIR/dysco -DBUILD_PACKAGES="Pipeline" -DCMAKE_INSTALL_PREFIX=$INSTALLDIR/lofar/ -DUSE_LOG4CPLUS=OFF -DUSE_OPENMP=True -DBUILD_PYTHON3=OFF ${INSTALLDIR}/lofar/src/ && make -s -j $J && make install

RUN cd $INSTALLDIR && rm -rf $INSTALLDIR/lofar/build && rm -rf $INSTALLDIR/lofar/src

#

# Install msoverview separately

#

RUN    mkdir -p $INSTALLDIR/msoverview/src

RUN    cd $INSTALLDIR/msoverview/src && svn export https://svn.astron.nl/LOFAR/tags/LOFAR-Release-3_2_18/CEP/MS/src/msoverview.cc && \

       source $INSTALLDIR/pyenv-py2/bin/activate && gcc -I/opt/lofar/casacore/include/casacore/ -L/opt/lofar/casacore/lib msoverview.cc \

        -o $INSTALLDIR/lofar/bin/msoverview -lcasa_casa -lcasa_ms -lcasa_tables -lstdc++

RUN cd $INSTALLDIR && rm -rf $INSTALLDIR/msoverview

#

# Install the standalone StationResponse libraries.

#   

RUN mkdir -p $INSTALLDIR/LOFARBeam/build && cd $INSTALLDIR/LOFARBeam && git clone https://github.com/lofar-astron/LOFARBeam.git src

RUN source $INSTALLDIR/pyenv-py2/bin/activate && cd $INSTALLDIR/LOFARBeam/build && cmake -DCMAKE_INSTALL_PREFIX=$INSTALLDIR/lofar ../src && make -j $J && make install

RUN touch /opt/lofar/lofar/lib64/python2.7/site-packages/lofar/__init__.py

RUN cd $INSTALLDIR && rm -rf $INSTALLDIR/LOFARBeam/build && rm -rf $INSTALLDIR/LOFARBeam/src

#

# Install EveryBeam library

#

RUN mkdir -p $INSTALLDIR/EveryBeam/build && cd $INSTALLDIR/EveryBeam && git clone https://git.astron.nl/RD/EveryBeam.git src && \ 

    cd src && git checkout $EVERYBEAM_VERSION && \

    cd $INSTALLDIR/EveryBeam/build && \

    cmake -DCMAKE_INSTALL_PREFIX=$INSTALLDIR/EveryBeam ../src && \

    make -j $J && make install

#

# Install DPPP

#

RUN mkdir -p $INSTALLDIR/DPPP/build && git clone https://github.com/lofar-astron/DP3.git $INSTALLDIR/DPPP/src && \ 

    cd $INSTALLDIR/DPPP/src && git checkout tags/${DPPP_VERSION}

RUN cd $INSTALLDIR/DPPP/build && cmake3 -DCMAKE_CXX_FLAGS="-D_GLIB_USE_CXX_ABI=1 -DBOOST_NO_CXX11_SCOPED_ENUMS" -DCMAKE_INSTALL_PREFIX:PATH=$INSTALLDIR/DPPP -DLOFAR_STATION_RESPONSE_DIR:PATH=$INSTALLDIR/lofar/include -DLOFAR_STATION_RESPONSE_LIB:FILEPATH=$INSTALLDIR/lofar/lib/libstationresponse.so -DIDGAPI_LIBRARIES=$INSTALLDIR/idg/lib/libidg-api.so -DIDGAPI_INCLUDE_DIRS=$INSTALLDIR/idg/include -DAOFLAGGER_INCLUDE_DIR=$INSTALLDIR/aoflagger/include -DAOFLAGGER_LIB=$INSTALLDIR/aoflagger/lib/libaoflagger.so ../src && make -s -j $J && make install

RUN cd $INSTALLDIR && rm -rf $INSTALLDIR/DPPP/build && rm -rf $INSTALLDIR/DPPP/src

############################################

# Install Python packages for Python 2 now #

############################################

#

# Install RMextract

#

RUN mkdir -p $INSTALLDIR/RMextract/build && cd $INSTALLDIR/RMextract/build && git clone https://github.com/lofar-astron/RMextract.git src && \

    cd src && if [ "$RMEXTRACT_VERSION" != "latest" ]; then git checkout $RMEXTRACT_VERSION; fi

RUN source $INSTALLDIR/pyenv-py2/bin/activate &&  cd $INSTALLDIR/RMextract/build/src &&  python setup.py build --add-lofar-utils && \

    python setup.py install --add-lofar-utils && deactivate

RUN cd $INSTALLDIR && rm -rf $INSTALLDIR/RMextract

#

# Install LoSoTo

#

RUN mkdir -p $INSTALLDIR/losoto/build && cd ${INSTALLDIR}/losoto/build && \

    git clone https://github.com/revoltek/losoto.git src && \

    cd src && if [ "$LOSOTO2_VERSION" != "latest" ]; then git checkout $LOSOTO2_VERSION; fi

RUN source $INSTALLDIR/pyenv-py2/bin/activate &&  cd ${INSTALLDIR}/losoto/build/src &&  python setup.py build && \

    python setup.py install  && deactivate

RUN cd $INSTALLDIR && rm -rf $INSTALLDIR/losoto

#

# Install LSMTool.

#

RUN mkdir -p $INSTALLDIR/lsmtool && cd $INSTALLDIR/lsmtool && \

    git clone https://github.com/darafferty/LSMTool.git lsmtool && \ 

    cd $INSTALLDIR/lsmtool/lsmtool && \

    if [ "$LSMTOOL_VERSION" != "latest" ]; then git checkout $LSMTOOL_VERSION; fi

RUN source $INSTALLDIR/pyenv-py2/bin/activate && cd $INSTALLDIR/lsmtool/lsmtool &&  python setup.py install  && deactivate

RUN cd $INSTALLDIR && rm -rf $INSTALLDIR/lsmtool

############################################

# Install Python packages for Python 3 now #

############################################

#

# Install LoSoTo

#

RUN mkdir -p $INSTALLDIR/losoto/build && \

    cd $INSTALLDIR/losoto/build && \

    git clone https://github.com/revoltek/losoto.git src 

RUN cd $INSTALLDIR/losoto/build/src && source $INSTALLDIR/pyenv-py3/bin/activate && \

    python setup.py build && \

    python setup.py install && deactivate

RUN cd $INSTALLDIR && rm -rf $INSTALLDIR/losoto

# Switch back to py2 to wrap up installation

#

# Install-WSClean

#

RUN mkdir $INSTALLDIR/wsclean && cd ${INSTALLDIR}/wsclean && git clone https://gitlab.com/aroffringa/wsclean.git && \ 

    if [ "$WSCLEAN_VERSION" != "latest" ]; then cd ${INSTALLDIR}/wsclean/wsclean && git checkout $WSCLEAN_VERSION; fi

RUN cd ${INSTALLDIR}/wsclean/wsclean &&  mkdir build && cd build

ARG CC=/usr/lib64/openmpi/bin/mpicc

ARG CXX=/usr/lib64/openmpi/bin/mpic++

RUN source $INSTALLDIR/pyenv-py2/bin/activate  && cd ${INSTALLDIR}/wsclean/wsclean/build &&  cmake -DCMAKE_INSTALL_PREFIX=$INSTALLDIR/wsclean -DPORTABLE=True -DIDGAPI_LIBRARIES=$INSTALLDIR/idg/lib/libidg-api.so -DIDGAPI_INCLUDE_DIRS=$INSTALLDIR/idg/include .. && \

    make -j ${J} && \

    make install && \

    cd $INSTALLDIR && rm -rf $INSTALLDIR/wsclean/wsclean

#

# Switch back to normal compilers

ARG CC=/usr/bin/gcc

ARG CXX=/usr/bin/g++

#

# Finaly cleanup of unnecessary stuff

# 

ENV  PYTHONPATH=$OLD_PYTHONPATH

RUN rm -rf /var/cache/dnf/* && \

    rm -rf /var/cache/yum/* && \

    rm -rf /var/log/* && \

    dnf -y clean all 

#

# init-lofar

#

RUN    ln -s /opt/lofar/DPPP/bin/DPPP /opt/lofar/lofar/bin/NDPPP && \

       ln -s /opt/lofar/DPPP/bin/makesourcedb /opt/lofar/lofar/bin/makesourcedb &&\

       ln -s $INSTALLDIR/pyenv-py3/bin/h5plot /usr/bin/h5plot

COPY files/post_init /tmp/post_init

RUN  cat /tmp/post_init >> $INSTALLDIR/init.sh

RUN  sed -e 's/\\\$/\$/g' /opt/lofar/init.sh

USER metauser

 No newline at end of file

#!/bin/bash

docker build ./ -t lofarit_base_astro

export INSTALLDIR=$INSTALLDIR

export HDF5_USE_FILE_LOCKING=FALSE

source $INSTALLDIR/lofar/lofarinit.sh

export PYTHONPATH=$INSTALLDIR/dppp:$INSTALLDIR/lofar/lib64/python2.7/site-packages

export PATH=/opt/montage/Montage-6.0/bin:$PATH

export PATH=$INSTALLDIR/aoflagger/bin:$PATH

export PATH=$INSTALLDIR/casacore/bin:$PATH

export PATH=$INSTALLDIR/ds9/bin:$PATH

export PATH=$INSTALLDIR/DPPP/bin:$PATH

export PATH=$INSTALLDIR/difmap/uvf_difmap:$PATH

export PATH=$INSTALLDIR/dysco/bin:$PATH

export PATH=$INSTALLDIR/lofar/bin:$PATH

export PATH=$INSTALLDIR/wsclean/bin:$PATH

export PATH=/usr/lib64/openmpi/bin:$PATH

export LD_LIBRARY_PATH=$INSTALLDIR/aoflagger/lib:$INSTALLDIR/casacore/lib:$INSTALLDIR/DPPP/lib:$INSTALLDIR/dysco/lib:$INSTALLDIR/EveryBeam/lib:$INSTALLDIR/idg/lib:$INSTALLDIR/lofar/lib:$INSTALLDIR/lofar/lib64:$INSTALLDIR/LOFARBeam/lib:$LD_LIBRARY_PATH

export LD_LIBRARY_PATH=/opt/intel/mkl/lib/intel64:$LD_LIBRARY_PATH

export LD_LIBRARY_PATH=/usr/lib64/openmpi/lib/:$LD_LIBRARY_PATH

export OPENBLAS_NUM_THREADS=64

export OPENBLAS_MAX_THREADS=64

export OMP_NUM_THREADS=64

export OMP_MAX_THREADS=64

export PYTHONPATH=$INSTALLDIR/dppp:$INSTALLDIR/lofar/lib64/python2.7/site-packages:$PYTHONPATH

source $INSTALLDIR/pyenv-py2/bin/activate

measures.directory: $INSTALLDIR/casacore/data

export CASARCFILES=$INSTALLDIR/.casarc

#

# This file MUST be edited with the 'visudo' command as root.

#

# Please consider adding local content in /etc/sudoers.d/ instead of

# directly modifying this file.

#

# See the man page for details on how to write a sudoers file.

#

Defaults        env_reset

Defaults        mail_badpass

Defaults        secure_path="/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin"

# Host alias specification

# User alias specification

# Cmnd alias specification

# User privilege specification

root    ALL=(ALL:ALL) ALL

# Members of the admin group may gain root privileges

%admin ALL=(ALL) ALL

# Allow members of group sudo to execute any command

%sudo   ALL=(ALL:ALL) NOPASSWD:ALL

# See sudoers(5) for more information on "#include" directives:

#includedir /etc/sudoers.d

APLpy==1.1.1

asn1crypto==0.24.0

astLib==0.11.4

astro-kittens==1.4.3

astro-pyxis==1.6.1

astropy==2.0.11

astropy-healpix==0.2

astropy-helpers==2.0.11

astroquery==0.4.1

atomicwrites==1.3.0

attrs==19.3.0

backports.functools-lru-cache==1.6.1

backports.shutil-get-terminal-size==1.0.0

backports.ssl-match-hostname==3.5.0.1

bcrypt==3.1.7

beautifulsoup4==4.9.3

blurhash==1.1.4

boost==0.1

cachetools==3.1.1

certifi==2019.11.28

cffi==1.14.4

chardet==3.0.4

configparser==4.0.2

cryptography==3.2.1

cycler==0.10.0

Cython==0.29.14

deap==1.3.1

decorator==4.4.1

emcee==3.0.2

entrypoints==0.3

enum34==1.1.10

ephem==3.7.7.0

funcsigs==1.0.2

future==0.18.2

google-api-python-client==1.7.11

google-auth==1.10.1

google-auth-httplib2==0.0.3

google-auth-oauthlib==0.4.1

h5py==2.10.0

html5lib==1.1

httplib2==0.18.0

idna==2.8

iniparse==0.4

ipaddress==1.0.16

ipdb==0.13.4

IPy==0.75

ipython==5.10.0

ipython-genutils==0.2.0

keyring==18.0.1

kitchen==1.1.1

kittens==0.1.2

kiwisolver==1.1.0

linecache2==1.0.0

git+https://github.com/revoltek/losoto.git@990900edbc2ea228013557936806a8578ac9a709

lsmtool==1.4.3

lxml==4.6.1

Mastodon.py==1.5.0

matplotlib==2.2.4

meqtrees-cattery==1.7.0

mimeparse==0.1.3

mock==3.0.5

montage-wrapper==0.9.9

more-itertools==5.0.0

mysqlclient==1.4.6

nose==1.3.7

numexpr==2.7.0

numpy==1.16.5

oauthlib==3.1.0

owlcat==1.6.3

paramiko==2.7.2

pathlib2==2.3.5

pexpect==4.8.0

pickleshare==0.7.5

Pillow==6.2.2

pluggy==0.7.1

Polygon2==2.0.8

pp==1.6.5

prettytable==1.0.1

progressbar==2.5

prompt-toolkit==1.0.18

psutil==5.7.3

ptyprocess==0.6.0

purr==1.5.0

py==1.8.0

py-cpuinfo==3.3.0

pyasn1==0.4.8

pyasn1-modules==0.2.8

pybind11==2.6.1

pycparser==2.20

pyephem==3.7.7.0

pyFFTW==0.12.0

pyfits==3.5

Pygments==2.5.2

pyliblzma==0.5.3

PyMySQL==0.10.1

PyNaCl==1.4.0

pyparsing==2.4.5

pyregion==2.0

pytest==3.6.4

python-casacore==3.3.1

python-dateutil==2.8.1

python-magic==0.4.15

python-monetdb==11.19.3.2

pytz==2019.3

pyvo==0.9.3

regions==0.4

reproject==0.5.1

requests==2.22.0

requests-oauthlib==1.3.0

RMextract==0.4.1

rsa==4.0

scandir==1.10.0

scikit-learn==0.20.0

scipy==1.2.2

SecretStorage==2.3.1

SharedArray==3.2.1

simplegeneric==0.8.1

six==1.13.0

soupsieve==1.9.6

SQLAlchemy==1.3.11

sshtunnel==0.3.1

subprocess32==3.5.4

tables==3.4.4

tqdm==4.52.0

traceback2==1.4.0

traitlets==4.3.3

unittest2==1.1.0

uritemplate==3.0.1

urllib3==1.25.7

wcwidth==0.2.5

webencodings==0.5.1

xmlrunner==1.7.7