Adding WRF baselibs rocky linux

.github/workflows/dockerhub.yml

@@ -38,6 +38,6 @@ jobs:
         uses: docker/build-push-action@v4
         with:
           context: .
-          file: ./requirements/Dockerfile.baselibs
+          file: ./requirements/Dockerfile.Baselibs
           push: true
           tags: nasanccs/wrf-baselibs:latest

requirements/{Dockerfile.baselibs → Dockerfile.Baselibs}

@@ -15,11 +15,12 @@ RUN dnf -y update && dnf -y install epel-release \
         openssh-clients openssh-server net-tools fontconfig libgfortran \
         libXext libXrender ImageMagick ImageMagick-devel git flex \
         flex-devel byacc bzip2-devel gzip libcurl-devel zlib-devel \
-        php-devel php-pear \
+        php-devel php-pear openssl-devel bzip2-devel libffi-devel xz-devel \
+    && dnf -y groupinstall "Development Tools" \
     && dnf -y clean all --enablerepo='*' \
     && rm -rf /var/cache/dnf
 
-# Setting system
+# Set up base systems
 RUN groupadd wrf -g 9999
 RUN useradd -u 9999 -g wrf -G wheel -M -d /wrf wrfuser
 RUN mkdir /wrf \
@@ -27,8 +28,8 @@ RUN mkdir /wrf \
  &&  chmod 6755 /wrf
 
 # Build OpenMPI
-RUN mkdir -p /wrf/libs/openmpi/BUILD_DIR \
- && cd /wrf/libs/openmpi/BUILD_DIR \
+RUN mkdir -p /wrf/libs/openmpi/BUILD_DIR
+RUN 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 \
@@ -42,8 +43,8 @@ RUN mkdir -p /wrf/libs/openmpi/BUILD_DIR \
  && rm -rf /wrf/libs/openmpi/BUILD_DIR
 
 # Build HDF5 libraries
-RUN mkdir -p /wrf/libs/hdf5/BUILD_DIR \
- && cd /wrf/libs/hdf5/BUILD_DIR \
+RUN mkdir -p /wrf/libs/hdf5/BUILD_DIR
+RUN cd /wrf/libs/hdf5/BUILD_DIR \
  && wget https://www2.mmm.ucar.edu/people/duda/files/mpas/sources/hdf5-1.10.5.tar.bz2 \
  && tar -xf hdf5-1.10.5.tar.bz2 \
  && cd hdf5-1.10.5 \
@@ -57,8 +58,8 @@ ENV LD_LIBRARY_PATH /usr/local/lib
 
 # Build netCDF C libraries
 ENV NETCDF /wrf/libs/netcdf
-RUN mkdir -p ${NETCDF}/BUILD_DIR \
- && cd ${NETCDF}/BUILD_DIR \
+RUN mkdir -p ${NETCDF}/BUILD_DIR
+RUN cd ${NETCDF}/BUILD_DIR \
  && curl -L -O https://github.com/Unidata/netcdf-c/archive/refs/tags/v4.7.4.tar.gz \
  && curl -L -O https://github.com/Unidata/netcdf-fortran/archive/refs/tags/v4.6.0.tar.gz \
  && curl -L -O https://github.com/Unidata/netcdf4-python/archive/v1.5.3rel.tar.gz \
@@ -81,131 +82,29 @@ RUN cd ${NETCDF}/BUILD_DIR \
  && echo dummy printout to keep travis happy ncf make \
  && cd /
 
-# OpenMPI version 4.0.5
-#RUN mkdir -p /var/tmp && \
-#    wget -q -nc --no-check-certificate -P /var/tmp https://www.open-mpi.org/software/ompi/v4.0/downloads/openmpi-4.0.5.tar.bz2 && \
-#    mkdir -p /var/tmp && tar -x -f /var/tmp/openmpi-4.0.5.tar.bz2 -C /var/tmp -j && \
-#    cd /var/tmp/openmpi-4.0.5 &&  \
-#    CC=gcc CXX=g++ F77=gfortran F90=gfortran FC=gfortran ./configure --prefix=/usr/local/openmpi --disable-getpwuid --enable-orterun-prefix-by-default --with-verbs && \
-#    make -j$(nproc) && \
-#    make -j$(nproc) install && \
-#    rm -rf /var/tmp/openmpi-4.0.5 /var/tmp/openmpi-4.0.5.tar.bz2
-#ENV LD_LIBRARY_PATH=/usr/local/openmpi/lib:$LD_LIBRARY_PATH \
-#    PATH=/usr/local/openmpi/bin:$PATH
-
-
-
-# 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-python38
-# Enable rh-python scl binary
-#COPY entrypoint.sh /usr/bin/entrypoint.sh
-#RUN chmod +x /usr/bin/entrypoint.sh
-#ENTRYPOINT [ "/usr/bin/entrypoint.sh" ]
-
-
-
-# Install version 10 of GNU compiler
-
-#RUN yum -y install centos-release-scl \
-# && yum -y install devtoolset-10 \
-# && yum -y install devtoolset-10-gcc devtoolset-10-gcc-gfortran devtoolset-10-gcc-c++ \
-# && scl enable devtoolset-10 bash \
-# && scl enable devtoolset-10 tcsh 
-
-
-# Install and setup Python3.8
-#RUN yum -y groupinstall "Development Tools"
-#RUN yum -y install openssl-devel bzip2-devel libffi-devel xz-devel
-#RUN mkdir -p /wrf/libs/python/BUILD_DIR \
-#  && cd /wrf/libs/python/BUILD_DIR \
-#  && wget https://www.python.org/ftp/python/3.8.12/Python-3.8.12.tgz \
-#  && tar -xf Python-3.8.12.tgz \
-#  && cd Python-3.8.12 \
-#  && ./configure --enable-optimizations --prefix=/usr/local  \
-#  && make altinstall \
-#  && cd / \
-#  && rm -rf /wrf/libs/python/BUILD_DIR
-#RUN python3.8 -m pip install numpy \
-# && python3.8 -m pip install --upgrade pip \
-# && python3.8 -m pip install --upgrade setuptools
-#RUN ldconfig -v
-
-# Build netCDF4-python libraries
-#RUN source /opt/rh/devtoolset-10/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 \
-# && python3.8 -m pip install wheel \
-# && python3.8 setup.py build \
-# && CPPFLAGS="-I${NETCDF}/include -I/usr/local/include" LDFLAGS="-L${NETCDF}/lib -L/usr/local/lib" python3.8 setup.py install \
-# && echo dummy printout to keep travis happy ncf4-python install \
-# && cd / \
-# && rm -rf ${NETCDF}/BUILD_DIR
-
-#RUN mkdir -p /var/run/sshd \
-#    && ssh-keygen -A \
-#    && sed -i 's/#PermitRootLogin yes/PermitRootLogin yes/g' /etc/ssh/sshd_config \
-#    && sed -i 's/#RSAAuthentication yes/RSAAuthentication yes/g' /etc/ssh/sshd_config \
-#    && sed -i 's/#PubkeyAuthentication yes/PubkeyAuthentication yes/g' /etc/ssh/sshd_config
-
-#RUN mkdir -p  /wrf/WPS_GEOG /wrf/wrfinput /wrf/wrfoutput \
-# &&  chown -R wrfuser:wrf /wrf /wrf/WPS_GEOG /wrf/wrfinput /wrf/wrfoutput /usr/local \
-# &&  chmod 6755 /wrf /wrf/WPS_GEOG /wrf/wrfinput /wrf/wrfoutput /usr/local
-
-# Download NCL
-#RUN curl -SL https://www.earthsystemgrid.org/api/v1/dataset/ncl.662.dap/file/ncl_ncarg-6.6.2-CentOS7.6_64bit_gnu485.tar.gz | tar zxC /usr/local 
-#ENV NCARG_ROOT /usr/local
-
-# Set environment for interactive container shells
-#RUN echo export LDFLAGS="-lm" >> /etc/bashrc \
-# && echo export NETCDF=${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-10/root/usr/lib/gcc/aarch64-redhat-linux/10:/usr/lib64/openmpi/lib:${NETCDF}/lib:${LD_LIBRARY_PATH}" >> /etc/bashrc  \
-# && echo export PATH=".:/opt/rh/devtoolset-10/root/usr/bin:/usr/lib64/openmpi/bin:${NETCDF}/bin:$PATH" >> /etc/bashrc \
-# && echo export NCARG_ROOT=/usr/local >> /etc/bashrc
-
-#RUN echo setenv LDFLAGS "-lm" >> /etc/csh.cshrc \
-# && echo setenv NETCDF "${NETCDF}" >> /etc/csh.cshrc \
-# && echo setenv JASPERINC "/usr/include/jasper/" >> /etc/csh.cshrc \
-# && echo setenv JASPERLIB "/usr/lib64/" >> /etc/csh.cshrc \
-# && echo setenv LD_LIBRARY_PATH "/opt/rh/devtoolset-10/root/usr/lib/gcc/aarch64-redhat-linux/10:/usr/lib64/openmpi/lib:${NETCDF}/lib:${LD_LIBRARY_PATH}" >> /etc/csh.cshrc \
-# && echo setenv PATH ".:/opt/rh/devtoolset-10/root/usr/bin:/usr/lib64/openmpi/bin:${NETCDF}/bin:$PATH" >> /etc/csh.cshrc \
-# && echo setenv NCARG_ROOT /usr/local >> /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 [ "$argname" = "regtest" ]  ; then curl -SL https://www2.mmm.ucar.edu/wrf/dave/data_smaller.tar.gz | tar -xzC /wrf ; fi
-
-#ENV JASPERINC /usr/include/jasper
-#ENV JASPERLIB /usr/lib64
-#ENV NETCDF_classic 1
-#ENV LD_LIBRARY_PATH /opt/rh/devtoolset-10/root/usr/lib/gcc/aarch64-redhat-linux/10:/usr/lib64/openmpi/lib:${NETCDF}/lib:${LD_LIBRARY_PATH}
-#ENV PATH  .:/opt/rh/devtoolset-10/root/usr/bin:/usr/lib64/openmpi/bin:${NETCDF}/bin:$PATH
-
-#RUN ssh-keygen -f /wrf/.ssh/id_rsa -t rsa -N '' \
-#    && chmod 600 /wrf/.ssh/config \
-#    && chmod 700 /wrf/.ssh \
-#    && cp /wrf/.ssh/id_rsa.pub /wrf/.ssh/authorized_keys
-#
+# Some sshd configurations for mpi
+RUN mkdir -p /var/run/sshd \
+    && ssh-keygen -A \
+    && sed -i 's/#PermitRootLogin yes/PermitRootLogin yes/g' /etc/ssh/sshd_config \
+    && sed -i 's/#RSAAuthentication yes/RSAAuthentication yes/g' /etc/ssh/sshd_config \
+    && sed -i 's/#PubkeyAuthentication yes/PubkeyAuthentication yes/g' /etc/ssh/sshd_config
+
+# Create WRF working directories
+RUN mkdir -p  /wrf/WPS_GEOG /wrf/wrfinput /wrf/wrfoutput \
+ &&  chown -R wrfuser:wrf /wrf /wrf/WPS_GEOG /wrf/wrfinput /wrf/wrfoutput /usr/local \
+ &&  chmod 6755 /wrf /wrf/WPS_GEOG /wrf/wrfinput /wrf/wrfoutput /usr/local
+
+# Some additional configurations
+RUN mkdir /wrf/.ssh ; echo "StrictHostKeyChecking no" > /wrf/.ssh/config
+COPY default-mca-params.conf /wrf/.openmpi/mca-params.conf
+RUN mkdir -p /wrf/.openmpi
+RUN chown -R wrfuser:wrf /wrf/
+
+# Setting up environment variables
+ENV NETCDF "${NETCDF}"
+ENV LDFLAGS="-lm"
+ENV JASPERINC /usr/include/jasper
+ENV JASPERLIB /usr/lib64
+ENV NETCDF_classic 1
+ENV LD_LIBRARY_PATH /usr/local/lib/openmpi:/wrf/libs/netcdf/lib:${LD_LIBRARY_PATH}
+ENV PATH  .:/usr/bin:/usr/local/bin:/wrf/libs/netcdf/bin:$PATH

requirements/default-mca-params.conf

@@ -0,0 +1,4 @@
+btl=tcp,self
+plm_rsh_no_tree_spawn=1
+btl_base_warn_component_unused=0
+pml=ob1