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Commit 4066791a authored by Giuliano Taffoni's avatar Giuliano Taffoni
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Build for inaf docker registry and optimized dockerfile

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vlbi/DigiCertCA.crt 0 → 100644
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vlbi/Dockerfile
+ 67
− 56
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FROM morgan1971/vlbi-base:0.0.1 FROM git.ia2.inaf.it:5050/lofarit/containers/vlbi-inaf-base:latest
MAINTAINER Giuliano Taffoni <giuliano.taffoni@inaf.it> MAINTAINER Giuliano Taffoni <giuliano.taffoni@inaf.it>
ENV CONTAINER_NAME='lovarVLBISoftware' ENV CONTAINER_NAME='lovarVLBISoftware'
USER root USER root
#
# Environmental variables
ENV J=40 #
ENV INSTALLDIR=/opt/lofar
ENV PYTHON_VERSION=2.7 ENV PYTHON_VERSION=2.7
# Path to where the patch for python-casacore's setup is stored. # Path to where the patch for python-casacore's setup is stored.
ENV PYTHON_CASACORE_PATCH=$INSTALLDIR/python-casacore/python_casacore_setup_patch.patch ENV PYTHON_CASACORE_PATCH=$INSTALLDIR/python-casacore/python_casacore_setup_patch.patch
...@@ -42,38 +41,53 @@ ENV WSCLEAN_VERSION=latest ...@@ -42,38 +41,53 @@ ENV WSCLEAN_VERSION=latest
ENV WCSLIB_VERSION=6.4 ENV WCSLIB_VERSION=6.4
ENV HDF5_USE_FILE_LOCKING=FALSE ENV HDF5_USE_FILE_LOCKING=FALSE
# Symlinks required for Fedora 31
RUN ln -s /usr/lib64/libboost_python37.so /usr/lib64/libboost_python3.so
RUN ln -s /usr/lib64/libboost_numpy37.so /usr/lib64/libboost_numpy3.so
RUN ln -s /usr/lib64/libboost_python27.so /usr/lib64/libboost_python.so
RUN ln -s /usr/lib64/libboost_numpy27.so /usr/lib64/libboost_numpy.so
RUN ln -s /usr/lib64/libnsl.so.2.0.0 /usr/lib64/libnsl.so
# #
# Setup the compiliong enviroment # Setup the compiling enviroment
# #
ARG CMAKE_C_COMPILER=/usr/bin/gcc
#ARG CFLAGS="-mno-avx512f -mno-avx512pf -mno-avx512er -mno-avx512cd -mno-avx512vl -mno-avx512bw -mno-avx512dq -mno-avx512ifma -mno-avx512vbmi" ARG CMAKE_CXX_COMPILER=/usr/bin/g++
#ARG CXXFLAGS="-std=c++11 -mno-avx512f -mno-avx512pf -mno-avx512er -mno-avx512cd -mno-avx512vl -mno-avx512bw -mno-avx512dq -mno-avx512ifma -mno-avx512vbmi" ARG CC_GLOBAL=/usr/bin/gcc
# Use below to optimize for a specific architecture ARG CXX_GLOBAL=/usr/bin/g++
#export CFLAGS="-march=skylake-avx512 -mtune=skylake-avx512" ARG MPICC=/usr/lib64/openmpi/bin/mpicc
#export CXXFLAGS="-march=skylake-avx512 -mtune=skylake-avx512" ARG MPICXX=/usr/lib64/openmpi/bin/mpic++
ARG CFLAGS_GLOBAL="-mno-avx512f -mno-avx512pf -mno-avx512er -mno-avx512cd -mno-avx512vl -mno-avx512bw -mno-avx512dq -mno-avx512ifma -mno-avx512vbmi"
ARG CXXFLAGS_GLOBAL="-std=c++11 -mno-avx512f -mno-avx512pf -mno-avx512er -mno-avx512cd -mno-avx512vl -mno-avx512bw -mno-avx512dq -mno-avx512ifma -mno-avx512vbmi"
ARG CASA_CXXFLAGS
ARG CASA_CFLAGS
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:$INSTALLDIR/EveryBeam/include" ARG CPLUS_INCLUDE_PATH="/usr/include/openmpi-x86_64:/usr/include/c++/9:$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 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:$INSTALLDIR/EveryBeam" ARG CMAKE_PREFIX_PATH="$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/:$INSTALLDIR/EveryBeam/lib:LD_LIBRARY_PATH" ARG LD_LIBRARY_PATH="$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:$PATH" ARG PATH="/usr/lib64/openmpi/bin:$PATH"
#ARG make=`which make`
ARG OLD_PYTHONPATH=$PYTHONPATH ARG OLD_PYTHONPATH=$PYTHONPATH
ARG NCORES=40
ARG INSTALLDIR=/opt/lofar
#
# Env to set at building
#
ENV CC=${CC_GLOBAL}
ENV CXX=${CXX_GLOBAL}
ENV CFLAGS=${CFLAGS_GLOBAL}
ENV CXXFLAGS=${CXXFLAGS_GLOBAL}
#
#
# Symlinks required for Fedora 31
#
RUN ln -s /usr/lib64/libboost_python37.so /usr/lib64/libboost_python3.so
RUN ln -s /usr/lib64/libboost_numpy37.so /usr/lib64/libboost_numpy3.so
RUN ln -s /usr/lib64/libboost_python27.so /usr/lib64/libboost_python.so
RUN ln -s /usr/lib64/libboost_numpy27.so /usr/lib64/libboost_numpy.so
RUN ln -s /usr/lib64/libnsl.so.2.0.0 /usr/lib64/libnsl.so
# #
# Setup the Python environment. # Setup the Python environment.
# #
RUN wget https://raw.githubusercontent.com/tikk3r/lofar-grid-hpccloud/fedora/requirements.txt -O $INSTALLDIR/requirements.txt RUN wget https://raw.githubusercontent.com/tikk3r/lofar-grid-hpccloud/fedora/requirements.txt -O $INSTALLDIR/requirements.txt
RUN wget https://raw.githubusercontent.com/tikk3r/lofar-grid-hpccloud/fedora/requirements3.txt -O $INSTALLDIR/requirements3.txt RUN wget https://raw.githubusercontent.com/tikk3r/lofar-grid-hpccloud/fedora/requirements3.txt -O $INSTALLDIR/requirements3.txt
RUN pip install xmlrunner RUN pip install xmlrunner && pip3 install xmlrunner
RUN pip3 install xmlrunner
RUN echo lofar-h5plot >> $INSTALLDIR/requirements3.txt RUN echo lofar-h5plot >> $INSTALLDIR/requirements3.txt
RUN pip --no-cache-dir install "virtualenv<20" RUN pip --no-cache-dir install "virtualenv<20"
RUN virtualenv $INSTALLDIR/pyenv-py3 --python=python3 RUN virtualenv $INSTALLDIR/pyenv-py3 --python=python3
...@@ -88,7 +102,7 @@ RUN source $INSTALLDIR/pyenv-py2/bin/activate && export HDF5_VERSION=1.10.5 & ...@@ -88,7 +102,7 @@ RUN source $INSTALLDIR/pyenv-py2/bin/activate && export HDF5_VERSION=1.10.5 &
# Install Montage # 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 && \ 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 tar xf Montage_v6.0.tar.gz && cd Montage-6.0 && make -j $NCORES
# #
# Install difmap # Install difmap
...@@ -105,43 +119,44 @@ RUN rm -rf $INSTALLDIR/difmap/*.tar.gz ...@@ -105,43 +119,44 @@ RUN rm -rf $INSTALLDIR/difmap/*.tar.gz
# #
# Install PyBDSF # Install PyBDSF
# #
#ARG CFLAGS="-mno-avx512f -mno-avx512pf -mno-avx512er -mno-avx512cd -mno-avx512vl -mno-avx512bw -mno-avx512dq -mno-avx512ifma -mno-avx512vbmi" ENV CFLAGS=${CFLAGS_GLOBAL}
RUN mkdir -p ${INSTALLDIR}/pybdsf && cd ${INSTALLDIR}/pybdsf && git clone https://github.com/lofar-astron/pybdsf pybdsf 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 ${PYBDSF_VERSION}; fi RUN if [ "${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}/pybdsf/pybdsf && python setup.py install && cd $INSTALLDIR && rm -rf $INSTALLDIR/pybdsf/pybdsf
RUN cd $INSTALLDIR && rm -rf $INSTALLDIR/pybdsf/pybdsf
# #
# Install CASAcore # Install CASAcore
# #
# Casacore 2.4.1 does not seem to deal well with AVX512 instructions, so disable them if needed # Casacore 2.4.1 does not seem to deal well with AVX512 instructions, so disable them if needed
#export CFLAGS="-march=skylake -mtune=skylake -mno-avx512f" ENV CFLAGS=$CASA_CFLAGS
#export CXXFLAGS="-march=skylake -mtune=skylake -mno-avx512f" ENV CXXFLAGS=$CASA_CXXFLAGS
RUN mkdir -p ${INSTALLDIR}/casacore/build && mkdir -p ${INSTALLDIR}/casacore/data RUN mkdir -p ${INSTALLDIR}/casacore/build && mkdir -p ${INSTALLDIR}/casacore/data && \
RUN cd $INSTALLDIR/casacore && git clone https://github.com/casacore/casacore.git src 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 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 # 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 # 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 # 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 && 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 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/ 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}/casacore/build && make -s -j ${NCORES} && make install && cd $INSTALLDIR && rm -rf $INSTALLDIR/casacore/build && rm -rf $INSTALLDIR/casacore/src
RUN cd $INSTALLDIR && rm -rf $INSTALLDIR/casacore/build && rm -rf $INSTALLDIR/casacore/src
# #
# Install Python-CASAcore # Install Python-CASAcore
# #
RUN mkdir ${INSTALLDIR}/python-casacore && cd ${INSTALLDIR}/python-casacore && git clone https://github.com/casacore/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 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 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 RUN cd $INSTALLDIR && rm -rf $INSTALLDIR/python-casacore/python-casacore
# and then reset the flags again if needed
#export CFLAGS="-march=skylake-avx512 -mtune=skylake-avx512" #
#export CXXFLAGS="-march=skylake-avx512 -mtune=skylake-avx512" # reset to global
#
ENV CFLAGS=${CFLAGS_GLOBAL}
ENV CXXFLAGS=${CXXFLAGS_GLOBAL}
# #
# Install Dysco # Install Dysco
...@@ -149,7 +164,7 @@ RUN cd $INSTALLDIR && rm -rf $INSTALLDIR/python-casacore/python-casacore ...@@ -149,7 +164,7 @@ RUN cd $INSTALLDIR && rm -rf $INSTALLDIR/python-casacore/python-casacore
RUN mkdir -p $INSTALLDIR/dysco/build RUN mkdir -p $INSTALLDIR/dysco/build
RUN cd $INSTALLDIR/dysco && git clone https://github.com/aroffringa/dysco.git src && cd src 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 $DYSCO_VERSION; fi RUN if [ "$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 $INSTALLDIR/dysco/build && cmake -DCMAKE_INSTALL_PREFIX=$INSTALLDIR/dysco -DCASACORE_ROOT_DIR=$INSTALLDIR/casacore -DPORTABLE=True ../src && make -s -j ${NCORES} && make install
RUN cd $INSTALLDIR && rm -rf $INSTALLDIR/dysco/build && rm -rf $INSTALLDIR/dysco/src RUN cd $INSTALLDIR && rm -rf $INSTALLDIR/dysco/build && rm -rf $INSTALLDIR/dysco/src
# #
...@@ -158,7 +173,7 @@ RUN cd $INSTALLDIR && rm -rf $INSTALLDIR/dysco/build && rm -rf $INSTALLDIR/dysco ...@@ -158,7 +173,7 @@ RUN cd $INSTALLDIR && rm -rf $INSTALLDIR/dysco/build && rm -rf $INSTALLDIR/dysco
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 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 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 ${INSTALLDIR}/aoflagger/build && cmake -DCMAKE_INSTALL_PREFIX=${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 source $INSTALLDIR/pyenv-py2/bin/activate && cd ${INSTALLDIR}/aoflagger/build && make -s -j ${NCORES} && make install
RUN cd $INSTALLDIR && rm -rf $INSTALLDIR/aoflagger/aoflagger && rm -rf $INSTALLDIR/aoflagger/build && rm -rf $INSTALLDIR/aoflagger/src RUN cd $INSTALLDIR && rm -rf $INSTALLDIR/aoflagger/aoflagger && rm -rf $INSTALLDIR/aoflagger/build && rm -rf $INSTALLDIR/aoflagger/src
# #
...@@ -172,11 +187,7 @@ RUN cd $INSTALLDIR/lofar/ && wget https://raw.githubusercontent.com/tikk3r/lofar ...@@ -172,11 +187,7 @@ RUN cd $INSTALLDIR/lofar/ && wget https://raw.githubusercontent.com/tikk3r/lofar
patch $INSTALLDIR/lofar/src/CMake/variants/GNUCXX11.cmake $PATCH_LOFAR && \ patch $INSTALLDIR/lofar/src/CMake/variants/GNUCXX11.cmake $PATCH_LOFAR && \
cd ${INSTALLDIR}/lofar/build/gnucxx11_opt 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 ${INSTALLDIR}/lofar/src/ #cmake -DCMAKE_PREFIX_PATH=$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 RUN source $INSTALLDIR/pyenv-py2/bin/activate && cd ${INSTALLDIR}/lofar/build/gnucxx11_opt && cmake -DCMAKE_PREFIX_PATH=$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 ${NCORES} && make install
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 RUN cd $INSTALLDIR && rm -rf $INSTALLDIR/lofar/build && rm -rf $INSTALLDIR/lofar/src
# #
...@@ -192,7 +203,7 @@ RUN cd $INSTALLDIR && rm -rf $INSTALLDIR/msoverview ...@@ -192,7 +203,7 @@ RUN cd $INSTALLDIR && rm -rf $INSTALLDIR/msoverview
# Install the standalone StationResponse libraries. # 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 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 source $INSTALLDIR/pyenv-py2/bin/activate && cd $INSTALLDIR/LOFARBeam/build && cmake -DCMAKE_INSTALL_PREFIX=$INSTALLDIR/lofar ../src && make -j ${NCORES} && make install
RUN touch /opt/lofar/lofar/lib64/python2.7/site-packages/lofar/__init__.py 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 RUN cd $INSTALLDIR && rm -rf $INSTALLDIR/LOFARBeam/build && rm -rf $INSTALLDIR/LOFARBeam/src
...@@ -203,14 +214,14 @@ RUN mkdir -p $INSTALLDIR/EveryBeam/build && cd $INSTALLDIR/EveryBeam && git clon ...@@ -203,14 +214,14 @@ RUN mkdir -p $INSTALLDIR/EveryBeam/build && cd $INSTALLDIR/EveryBeam && git clon
cd src && git checkout $EVERYBEAM_VERSION && \ cd src && git checkout $EVERYBEAM_VERSION && \
cd $INSTALLDIR/EveryBeam/build && \ cd $INSTALLDIR/EveryBeam/build && \
cmake -DCMAKE_INSTALL_PREFIX=$INSTALLDIR/EveryBeam ../src && \ cmake -DCMAKE_INSTALL_PREFIX=$INSTALLDIR/EveryBeam ../src && \
make -j $J && make install make -j ${NCORES} && make install
# #
# Install DPPP # Install DPPP
# #
RUN mkdir -p $INSTALLDIR/DPPP/build && git clone https://github.com/lofar-astron/DP3.git $INSTALLDIR/DPPP/src && \ 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} 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 $INSTALLDIR/DPPP/build && cmake3 -DCMAKE_CXX_FLAGS="-D_GLIB_USE_CXX_ABI=1 -DBOOST_NO_CXX11_SCOPED_ENUMS" -DCMAKE_INSTALL_PREFIX:PATH=$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 ${NCORES} && make install
RUN cd $INSTALLDIR && rm -rf $INSTALLDIR/DPPP/build && rm -rf $INSTALLDIR/DPPP/src RUN cd $INSTALLDIR && rm -rf $INSTALLDIR/DPPP/build && rm -rf $INSTALLDIR/DPPP/src
############################################ ############################################
...@@ -266,16 +277,16 @@ RUN cd $INSTALLDIR && rm -rf $INSTALLDIR/losoto ...@@ -266,16 +277,16 @@ RUN cd $INSTALLDIR && rm -rf $INSTALLDIR/losoto
RUN mkdir $INSTALLDIR/wsclean && cd ${INSTALLDIR}/wsclean && git clone https://gitlab.com/aroffringa/wsclean.git && \ 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 $WSCLEAN_VERSION; fi if [ "$WSCLEAN_VERSION" != "latest" ]; then cd ${INSTALLDIR}/wsclean/wsclean && git checkout $WSCLEAN_VERSION; fi
RUN cd ${INSTALLDIR}/wsclean/wsclean && mkdir build && cd build RUN cd ${INSTALLDIR}/wsclean/wsclean && mkdir build && cd build
ARG CC=/usr/lib64/openmpi/bin/mpicc ENV CC=${MPICC}
ARG CXX=/usr/lib64/openmpi/bin/mpic++ ENV CXX=${MPICXX}
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 .. && \ 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 -j ${NCORES} && \
make install && \ make install && \
cd $INSTALLDIR && rm -rf $INSTALLDIR/wsclean/wsclean cd $INSTALLDIR && rm -rf $INSTALLDIR/wsclean/wsclean
# #
# Switch back to normal compilers # Switch back to normal compilers
ARG CC=/usr/bin/gcc ENV CC=${CC_GLOBAL}
ARG CXX=/usr/bin/g++ ENV CXX=${CXX_GLOBAL}
# #
# #
# Install DS9 # Install DS9
......
vlbi/build-base.sh
+ 6
− 2
View file @ 4066791a
#!/bin/bash #!/bin/bash
if [ 'xxx${VERSION}' == 'xxx' ]; then export SSL_CERT_FILE=${PWD}/DigiCertCA.crt
docker login git.ia2.inaf.it:5050
if [ "xxx${VERSION}" = "xxx" ]; then
VERSION='latest' VERSION='latest'
fi fi
docker build -t morgan1971/vlbi-base:${VERSION} -f Dockerfile.base . docker build -t git.ia2.inaf.it:5050/lofarit/containers/vlbi-inaf-base:${VERSION} -f Dockerfile.base .
vlbi/build-sw.sh
+ 21
− 2
View file @ 4066791a
#!/bin/bash #!/bin/bash
if [ 'xxx${VERSION}' == 'xxx' ]; then if [ "xxx${VERSION}" = "xxx" ]; then
VERSION='latest' VERSION='latest'
fi fi
export SSL_CERT_FILE=${PWD}/DigiCertCA.crt
docker login git.ia2.inaf.it:5050
docker build -t morgan1971/skadc-software:${VERSION} -f Dockerfile . # Use below to optimize for a specific architecture
# docker build -t git.ia2.inaf.it:5050/lofarit/containers/vlbi-inaf-sw:${VERSION} --build-arg CFLAGS_GLOBAL="-march=skylake-avx512 -mtune=skylake-avx512" \
# --build-arg CXXFLAGS_GLOBAL="-march=skylake-avx512 -mtune=skylake-avx512" -f Dockerfile .
#
# Default values
#
# CMAKE_C_COMPILER=/usr/bin/gcc
# CMAKE_CXX_COMPILER=/usr/bin/g++
# CC_GLOBAL=/usr/bin/gcc
# CXX_GLOBAL=/usr/bin/g++
# MPICC=/usr/lib64/openmpi/bin/mpicc
# MPICXX=/usr/lib64/openmpi/bin/mpic++
# CFLAGS_GLOBAL="-mno-avx512f -mno-avx512pf -mno-avx512er -mno-avx512cd -mno-avx512vl -mno-avx512bw -mno-avx512dq -mno-avx512ifma -mno-avx512vbmi"
# CXXFLAGS_GLOBAL="-std=c++11 -mno-avx512f -mno-avx512pf -mno-avx512er -mno-avx512cd -mno-avx512vl -mno-avx512bw -mno-avx512dq -mno-avx512ifma -mno-avx512vbmi"
# CASA_CXXFLAGS
# CASA_CFLAGS
docker build -t git.ia2.inaf.it:5050/lofarit/containers/vlbi-inaf-sw:${VERSION} -f Dockerfile .
vlbi/run_singularity.sh 0 → 100644
+ 26
− 0
View file @ 4066791a
#!/bin/bash
#
# This Script allows to execute the container using singularity
# in an isolated enviroment, home directory and tmp are not
# shared directly and removed at the end of the run, persistent data
# is saved in /data
#
# author <giuliano.taffoni@inaf.it>
#
export CONTAINER_NAME=git.ia2.inaf.it:5050/lofarit/containers/vlbi-inaf-sw
export CONTAINER_VERSION=0.1.0
export BASE_PORT=
if [ 'XXX'$1 = 'XXX' ]; then
COMMAND=
else
COMMAND=$1
fi
export SINGULARITYENV_AUTH_USER=testpass
HOMEDIR=`mktemp -d -t singularity_XXXXXXX`
mkdir $HOMEDIR/tmp
mkdir $HOMEDIR/home
singularity run --pid --no-home --home=/home/skauser --workdir ${HOMEDIR}/tmp -B${HOMEDIR}:/home/ -B`pwd`:/data --containall --cleanenv docker://${CONTAINER_NAME}:${CONTAINER_VERSION} $COMMAND
rm -fr ${HOMEDIR}
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