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Dockerfile-first_part
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#
FROM centos:7
MAINTAINER Dave Gill <[email protected]>
ENV NML_VERSION 4.2
# Set up base OS environment
RUN yum -y update
# Install SCL release package and python SCL
RUN yum -y install centos-release-scl \
&& yum -y install --setopt=tsflags=nodocs rh-python36
# Enable rh-python scl binary
COPY entrypoint.sh /usr/bin/entrypoint.sh
RUN chmod +x /usr/bin/entrypoint.sh
ENTRYPOINT [ "/usr/bin/entrypoint.sh" ]
RUN yum -y install file gcc gcc-gfortran gcc-c++ glibc.i686 libgcc.i686 libpng-devel jasper \
jasper-devel hostname m4 make perl tar bash tcsh time wget which zlib zlib-devel \
openssh-clients openssh-server net-tools fontconfig libgfortran libXext libXrender \
sudo epel-release git flex flex-devel byacc
# Newer version 9 of GNU compiler, required to fix WRF RRTMG-derivative builds
RUN yum -y install centos-release-scl \
&& yum -y install devtoolset-9 \
&& yum -y install devtoolset-9-gcc devtoolset-9-gcc-gfortran devtoolset-9-gcc-c++ \
&& scl enable devtoolset-9 bash \
&& scl enable devtoolset-9 tcsh
RUN yum -y install php-devel php-pear
RUN yum -y install ImageMagick ImageMagick-devel
RUN groupadd wrf -g 9999
RUN useradd -u 9999 -g wrf -G wheel -M -d /wrf wrfuser
RUN mkdir /wrf \
&& chown -R wrfuser:wrf /wrf \
&& chmod 6755 /wrf
# Build the libraries with a parallel Make
ENV J 4
# Build OpenMPI
RUN mkdir -p /wrf/libs/openmpi/BUILD_DIR
RUN source /opt/rh/devtoolset-9/enable \
&& cd /wrf/libs/openmpi/BUILD_DIR \
&& curl -L -O https://download.open-mpi.org/release/open-mpi/v4.0/openmpi-4.0.0.tar.gz \
&& tar -xf openmpi-4.0.0.tar.gz \
&& cd openmpi-4.0.0 \
&& ./configure --prefix=/usr/local &> /wrf/libs/build_log_openmpi_config \
&& echo dummy printout to keep travis happy openmpi config \
&& make all install \
&& echo "make all install | awk 'NR % 1000 == 0'" \
&& echo "make all install &> /wrf/libs/build_log_openmpi_make" \
&& echo dummy printout to keep travis happy openmpi make \
&& cd / \
&& rm -rf /wrf/libs/openmpi/BUILD_DIR
# Build HDF5 libraries
RUN mkdir -p /wrf/libs/hdf5/BUILD_DIR
RUN source /opt/rh/devtoolset-9/enable \
&& cd /wrf/libs/hdf5/BUILD_DIR \
&& git clone https://bitbucket.hdfgroup.org/scm/hdffv/hdf5.git \
&& cd hdf5 \
&& git checkout hdf5-1_10_4 \
&& ./configure --enable-fortran --enable-cxx --enable-shared --prefix=/usr/local/ &> /wrf/libs/build_log_hdf5_config \
&& echo dummy printout to keep travis happy hdf5 config \
&& make install &> /wrf/libs/build_log_hdf5_make \
&& echo dummy printout to keep travis happy hdf5 make \
&& rm -rf /wrf/libs/hdf5/BUILD_DIR
ENV LD_LIBRARY_PATH /usr/local/lib
# Build netCDF C libraries
RUN yum -y install libcurl-devel zlib-devel
ENV NETCDF /wrf/libs/netcdf
RUN mkdir -p ${NETCDF}/BUILD_DIR
RUN source /opt/rh/devtoolset-9/enable \
&& cd ${NETCDF}/BUILD_DIR \
&& curl -L -O https://github.com/Unidata/netcdf-c/archive/v4.6.2.tar.gz \
&& curl -L -O https://github.com/Unidata/netcdf-fortran/archive/v4.4.5.tar.gz \
&& curl -L -O https://github.com/Unidata/netcdf4-python/archive/v1.5.3rel.tar.gz \
&& tar -xf v4.6.2.tar.gz \
&& cd netcdf-c-4.6.2 \
&& ./configure --enable-shared --prefix=${NETCDF} &> /wrf/libs/build_log_ncc_config \
&& echo dummy printout to keep travis happy ncc config \
&& make install &> /wrf/libs/build_log_ncc_make \
&& echo dummy printout to keep travis happy ncc make
# Build netCDF Fortran libraries
RUN source /opt/rh/devtoolset-9/enable \
&& env \
&& cd ${NETCDF}/BUILD_DIR \
&& tar -xf v4.4.5.tar.gz \
&& cd netcdf-fortran-4.4.5/ \
&& export LD_LIBRARY_PATH=${NETCDF}/lib:${LD_LIBRARY_PATH} \
&& CPPFLAGS=-I${NETCDF}/include LDFLAGS=-L${NETCDF}/lib ./configure --enable-shared --prefix=${NETCDF} &> /wrf/libs/build_log_ncf_config \
&& echo dummy printout to keep travis happy ncf config \
&& make install &> /wrf/libs/build_log_ncf_make \
&& echo dummy printout to keep travis happy ncf make
# Setup up python3.6
RUN yum -y install python36 \
&& yum -y install python36-devel \
&& yum -y install python36-pip \
&& yum -y install python36-setuptools \
&& easy_install-3.6 pip \
&& python3.6 -m pip install numpy \
&& python3.6 -m pip install --upgrade pip \
&& python3.6 -m pip install --upgrade setuptools
RUN ldconfig -v
# Build netCDF4-python libraries
RUN source /opt/rh/devtoolset-9/enable \
&& cd ${NETCDF}/BUILD_DIR \
&& tar -xf v1.5.3rel.tar.gz \
&& cd netcdf4-python-1.5.3rel/ \
&& export LD_LIBRARY_PATH=${NETCDF}/lib:${LD_LIBRARY_PATH} \
&& export NETCDF4_DIR=${NETCDF} \
&& export HDF5_DIR=/usr/local \
&& python3.6 -m pip install wheel \
&& python3.6 setup.py build \
&& CPPFLAGS="-I${NETCDF}/include -I/usr/local/include" LDFLAGS="-L${NETCDF}/lib -L/usr/local/lib" python3.6 setup.py install \
&& echo dummy printout to keep travis happy ncf4-python install
RUN mkdir -p /var/run/sshd \
&& ssh-keygen -A \
&& sed -i 's/#PermitRootLogin yes/PermitRootLogin yes/g' /etc/ssh/sshd_config \
&& sed -i 's/#RSAAuthentication yes/RSAAuthentication yes/g' /etc/ssh/sshd_config \
&& sed -i 's/#PubkeyAuthentication yes/PubkeyAuthentication yes/g' /etc/ssh/sshd_config
RUN mkdir -p /wrf/WPS_GEOG /wrf/wrfinput /wrf/wrfoutput \
&& chown -R wrfuser:wrf /wrf /wrf/WPS_GEOG /wrf/wrfinput /wrf/wrfoutput /usr/local \
&& chmod 6755 /wrf /wrf/WPS_GEOG /wrf/wrfinput /wrf/wrfoutput /usr/local
# Download NCL
RUN curl -SL https://ral.ucar.edu/sites/default/files/public/projects/ncar-docker-wrf/nclncarg-6.3.0.linuxcentos7.0x8664nodapgcc482.tar.gz | tar zxC /usr/local
ENV NCARG_ROOT /usr/local
# Set environment for interactive container shells
RUN echo export LDFLAGS="-lm" >> /etc/bashrc \
&& echo export NETCDF=${NETCDF} >> /etc/bashrc \
&& echo export JASPERINC=/usr/include/jasper/ >> /etc/bashrc \
&& echo export JASPERLIB=/usr/lib64/ >> /etc/bashrc \
&& echo export LD_LIBRARY_PATH="/opt/rh/devtoolset-9/root/usr/lib/gcc/x86_64-redhat-linux/9:/usr/lib64/openmpi/lib:${NETCDF}/lib:${LD_LIBRARY_PATH}" >> /etc/bashrc \
&& echo export PATH=".:/opt/rh/devtoolset-9/root/usr/bin:/usr/lib64/openmpi/bin:${NETCDF}/bin:$PATH" >> /etc/bashrc
RUN echo setenv LDFLAGS "-lm" >> /etc/csh.cshrc \
&& echo setenv NETCDF "${NETCDF}" >> /etc/csh.cshrc \
&& echo setenv JASPERINC "/usr/include/jasper/" >> /etc/csh.cshrc \
&& echo setenv JASPERLIB "/usr/lib64/" >> /etc/csh.cshrc \
&& echo setenv LD_LIBRARY_PATH "/opt/rh/devtoolset-9/root/usr/lib/gcc/x86_64-redhat-linux/9:/usr/lib64/openmpi/lib:${NETCDF}/lib:${LD_LIBRARY_PATH}" >> /etc/csh.cshrc \
&& echo setenv PATH ".:/opt/rh/devtoolset-9/root/usr/bin:/usr/lib64/openmpi/bin:${NETCDF}/bin:$PATH" >> /etc/csh.cshrc
RUN mkdir /wrf/.ssh ; echo "StrictHostKeyChecking no" > /wrf/.ssh/config
COPY default-mca-params.conf /wrf/.openmpi/mca-params.conf
RUN mkdir -p /wrf/.openmpi
RUN chown -R wrfuser:wrf /wrf/
# all root steps completed above, now below as regular userID wrfuser
USER wrfuser
WORKDIR /wrf
# Download data
ARG argname=tutorial
RUN echo DAVE $argname
RUN if [ "$argname" = "tutorial" ] ; then curl -SL https://www2.mmm.ucar.edu/wrf/src/wps_files/geog_low_res_mandatory.tar.gz | tar -xzC /wrf/WPS_GEOG ; fi
RUN if [ "$argname" = "tutorial" ] ; then curl -SL https://www2.mmm.ucar.edu/wrf/TUTORIAL_DATA/colorado_march16.new.tar.gz | tar -xzC /wrf/wrfinput ; fi
RUN if [ "$argname" = "tutorial" ] ; then curl -SL https://www2.mmm.ucar.edu/wrf/src/namelists_v$NML_VERSION.tar.gz | tar -xzC /wrf/wrfinput ; fi
RUN if [ "$argname" = "tutorial" ] ; then curl -SL https://www2.mmm.ucar.edu/wrf/TUTORIAL_DATA/WRF_NCL_scripts.tar.gz | tar -xzC /wrf ; fi
RUN if [ "$argname" = "regtest" ] ; then curl -SL https://www2.mmm.ucar.edu/wrf/dave/data_smaller.tar.gz | tar -xzC /wrf ; fi
ENV JASPERINC /usr/include/jasper
ENV JASPERLIB /usr/lib64
ENV NETCDF_classic 1
ENV LD_LIBRARY_PATH /opt/rh/devtoolset-9/root/usr/lib/gcc/x86_64-redhat-linux/9:/usr/lib64/openmpi/lib:${NETCDF}/lib:${LD_LIBRARY_PATH}
ENV PATH .:/opt/rh/devtoolset-9/root/usr/bin:/usr/lib64/openmpi/bin:${NETCDF}/bin:$PATH
RUN ssh-keygen -f /wrf/.ssh/id_rsa -t rsa -N '' \
&& chmod 600 /wrf/.ssh/config \
&& chmod 700 /wrf/.ssh \
&& cp /wrf/.ssh/id_rsa.pub /wrf/.ssh/authorized_keys
#