Docker Container Improvements

.gitignore

@@ -1,4 +1,4 @@
-build_output.txt
+output_*_build.txt
 *.swp
 *.png
 

Docker/Dockerfile-GNU

@@ -0,0 +1,187 @@
+FROM ubuntu:18.04
+# Ubuntu 18.04 base
+
+MAINTAINER Peter Vaillancourt "[email protected]"
+
+## Use bash for compile
+## This Dockerfile compiles WRF from source during "docker build" step
+SHELL ["/bin/bash","-c"]
+ENV WRF_VERSION=4.2.2
+
+## Ensuring only root user to prepare for singularity conversion
+ARG USER=root
+USER root
+ARG HOME=/root
+
+ARG DEBIAN_FRONTEND=noninteractive
+
+RUN mkdir /opt/wrf
+RUN set -eux
+
+## Stacksize - WRF is greedy
+## See https://forum.mmm.ucar.edu/phpBB3/viewtopic.php?t=133
+## Setting OS stacksize to unlimited, setting OpenMP stacksize to 96GB
+ENV OMP_STACKSIZE=96G
+
+RUN ulimit -s unlimited && \
+    echo ulimit -s unlimited >> /etc/bashrc && \
+    echo export OMP_STACKSIZE=96G >> /etc/bashrc
+
+## Set up some useful environment variables
+ENV MAIN_DIR=/opt/wrf
+ENV WRF_SRC_ROOT_DIR=${MAIN_DIR}/WRF
+ENV DIR=${MAIN_DIR}/LIBRARIES
+ENV CC=gcc
+ENV FC=gfortran
+ENV FCFLAGS=-m64
+ENV F77=mpif90
+ENV FFLAGS=-m64
+ENV JASPERLIB=$DIR/grib2/lib
+ENV JASPERINC=$DIR/grib2/include
+ENV NETCDF=$DIR/NETCDF
+ENV PNETCDF=$DIR/PNETCDF
+ENV PHDF5=$DIR/PHDF5
+ENV LDFLAGS=-L$DIR/grib2/lib
+ENV CPPFLAGS="-I${PHDF5}/include -I${PNETCDF}/include -I${NETCDF}/include -I$DIR/grib2/include"
+ENV PATH=${NETCDF}/bin:${PNETCDF}/bin:$PATH:$DIR/grib2
+ENV LD_LIBRARY_PATH=$PHDF5/lib:$PNETCDF/lib:$NETCDF/lib:$LD_LIBRARY_PATH:$DIR/grib2/lib
+ENV WRFIO_NCD_LARGE_FILE_SUPPORT=1
+ENV WRF_EM_CORE=1
+
+## Set environment for interactive container shells
+RUN echo export MAIN_DIR=/opt/wrf >> /etc/bashrc && \
+    echo export WRF_SRC_ROOT_DIR=${DIR}/WRF >> /etc/bashrc && \
+    echo export DIR=${MAIN_DIR}/LIBRARIES >> /etc/bashrc && \
+    echo export CC=mpicc >> /etc/bashrc && \
+    echo export FC=mpif90 >> /etc/bashrc && \
+    echo export F77=mpif90 >> /etc/bashrc && \
+    echo export FFLAGS=-m64 >> /etc/bashrc && \
+    echo export JASPERINC=$DIR/grib2/include >> /etc/bashrc && \
+    echo export JASPERLIB=$DIR/grib2/lib >> /etc/bashrc && \
+    echo export NETCDF=$DIR/NETCDF >> /etc/bashrc && \
+    echo export PNETCDF=$DIR/PNETCDF >> /etc/bashrc && \
+    echo export PHDF5=$DIR/PHDF5 >> /etc/bashrc && \
+    echo export LDFLAGS=-L$DIR/grib2/lib >> /etc/bashrc && \
+    echo export CPPFLAGS="-I${PHDF5}/include -I${PNETCDF}/include -I${NETCDF}/include -I$DIR/grib2/include" >> /etc/bashrc && \
+    echo export PATH=$PATH:$DIR/grib2 >> /etc/bashrc && \
+    echo export LD_LIBRARY_PATH=$PHDF5/lib:$PNETCDF/lib:$NETCDF/lib:$LD_LIBRARY_PATH:$DIR/grib2/lib >> /etc/bashrc && \
+    echo export WRFIO_NCD_LARGE_FILE_SUPPORT=1 >> /etc/bashrc && \
+    echo export WRF_EM_CORE=1 >> /etc/bashrc
+
+## Install tools, libraries, and dependencies
+WORKDIR $DIR
+
+### Tools
+RUN apt-get update -y && apt-get install -y \
+    cmake \
+    tcsh \
+    wget \
+    unzip \
+    gawk \
+    time \
+    m4 \
+    rsync \
+    curl \
+    file \
+    gcc \
+    gfortran \
+    g++ \
+    gcc-multilib \
+    g++-multilib \
+    hostname \
+    make \
+    ncl-ncarg \
+    perl \
+    tar
+
+### Libraries
+#### zlib 1.2.7
+RUN wget https://zlib.net/fossils/zlib-1.2.7.tar.gz && \
+    tar -xzf zlib-1.2.7.tar.gz && \
+    cd zlib-1.2.7 && \
+    ./configure --prefix=$DIR/grib2 && \
+    make && make install 
+
+#### libpng 1.2.50
+RUN wget https://sourceforge.net/projects/libpng/files/libpng12/older-releases/1.2.50/libpng-1.2.50.tar.gz && \
+    tar -xzf libpng-1.2.50.tar.gz && \
+    cd libpng-1.2.50 && \
+    ./configure --prefix=$DIR/grib2 && \
+    make && make install
+
+#### Jasper 1.900.1
+RUN wget https://www.ece.uvic.ca/~frodo/jasper/software/jasper-1.900.1.zip && \
+    unzip jasper-1.900.1.zip && \
+    cd jasper-1.900.1 && \
+    ./configure --prefix=$DIR/grib2 && \
+    make && make install
+
+### Install Dependencies
+#### Third-party EPEL builds of NetCDF and OpenMPI
+RUN add-apt-repository "deb http://us.archive.ubuntu.com/ubuntu xenial universe"
+RUN apt-get install -y \
+    libnetcdf-dev \
+    libnetcdf11 \
+    libnetcdff-dev \
+    netcdf-bin \
+    libpnetcdf-dev \
+    libpnetcdf0d \
+    pnetcdf-bin \
+    libhdf5-openmpi-dev \
+    openmpi-bin \
+    libopenmpi-dev \
+    mpi-default-bin \
+    mpi-default-dev
+
+RUN ln -sf /usr/include/pnetcdf* $PNETCDF/include && \
+    ln -sf /usr/include/netcdf* $NETCDF/include && \
+    ln -sf /usr/include/openmpi/ $NETCDF/include && \
+    ln -sf /usr/lib/openmpi/lib $NETCDF/lib
+
+#TODO: Check versions of above
+## Intel Version list for reference
+### PHDF5 1.10.4
+### PNetCDF 1.11.0
+### NetCDF-C 4.6.2
+### NetCDF-Fortran 4.5.3
+
+ENV NETCDF4=1
+RUN echo export export NETCDF4=1 >> /etc/bashrc
+
+## Install WRF 4.2.2
+WORKDIR $MAIN_DIR
+
+#ENV LDFLAGS="-lm -lnetcdff -lnetcdf -lpnetcdf"
+#RUN echo export LDFLAGS="-lm -lnetcdff -lnetcdf -lpnetcdf" >> /etc/bashrc
+#
+#### Get WRF v4.2.2 tar archive
+#RUN wget https://github.com/wrf-model/WRF/archive/refs/tags/v4.2.2.tar.gz && \
+#    tar -zxf v4.2.2.tar.gz && \
+#    mv WRF-4.2.2/ WRF
+#
+#WORKDIR $WRF_SRC_ROOT_DIR
+#
+#### Configure WRF
+#RUN ./clean -a && \
+#TODO: Check config option... 66 is Intel
+#    echo '66\n1\n' | ./configure && \
+#    awk -v add=" -L${DIR}/zlib-1.2.7" '/^ZLIB/ {$0=$0add} 1' configure.wrf > temp && mv temp configure.wrf
+#
+#### Compile WRF
+#RUN time ./compile em_real 2>&1 | tee compile_em_real.log
+
+
+#TODO: Add a check that WRF installed correctly, error otherwise
+#TODO: Install WPS?
+
+## For development
+#TODO: Comment these out for production
+RUN apt-get install -y \
+    man \
+    bash-completion \
+    vim \ 
+    htop \
+    tmux 
+
+RUN ldconfig
+

Docker/Dockerfile → Docker/Dockerfile-Intel

@@ -18,11 +18,14 @@ ARG HOME=/root
 
 #ARG DEBIAN_FRONTEND=noninteractive  # Intel Dockerfile does this
 
+## Install tools
 RUN apt-get update -y && apt-get install -y \
     cmake \
     tcsh \
     wget \
     unzip \
+    tar \
+    curl \
     gawk \
     time \
     m4 \
@@ -31,6 +34,17 @@ RUN apt-get update -y && apt-get install -y \
 RUN mkdir /opt/wrf
 RUN set -eux
 
+## Stacksize - WRF is greedy
+## See https://forum.mmm.ucar.edu/phpBB3/viewtopic.php?t=133
+## Setting OS stacksize to unlimited, setting OpenMP stacksize to 64GB (KMP_STACKSIZE is for Intel)
+ENV OMP_STACKSIZE=96G
+ENV KMP_STACKSIZE=96G
+
+RUN ulimit -s unlimited && \
+    echo ulimit -s unlimited >> /etc/bashrc && \
+    echo export OMP_STACKSIZE=96G >> /etc/bashrc && \
+    echo export KMP_STACKSIZE=96G >> /etc/bashrc
+
 ## Set up some useful environment variables
 ENV MAIN_DIR=/opt/wrf
 ENV WRF_SRC_ROOT_DIR=${MAIN_DIR}/WRF
@@ -56,10 +70,10 @@ ENV PATH=${NETCDF}/bin:${PNETCDF}/bin:$PATH:$DIR/grib2
 ENV LD_LIBRARY_PATH=$PHDF5/lib:$PNETCDF/lib:$NETCDF/lib:$LD_LIBRARY_PATH:$DIR/grib2/lib
 ENV WRFIO_NCD_LARGE_FILE_SUPPORT=1
 ENV WRF_EM_CORE=1
-ENV KMP_STACKSIZE=512m
 
 ## Set environment for interactive container shells
-RUN echo export WRF_SRC_ROOT_DIR=${DIR}/WRF >> /etc/bashrc && \
+RUN echo export MAIN_DIR=/opt/wrf >> /etc/bashrc && \
+    echo export WRF_SRC_ROOT_DIR=${DIR}/WRF >> /etc/bashrc && \
     echo export DIR=${MAIN_DIR}/LIBRARIES >> /etc/bashrc && \
     echo export I_MPI_CC=icc >> /etc/bashrc && \
     echo export I_MPI_CXX=icpc >> /etc/bashrc && \
@@ -80,8 +94,7 @@ RUN echo export WRF_SRC_ROOT_DIR=${DIR}/WRF >> /etc/bashrc && \
     echo export PATH=$PATH:$DIR/grib2 >> /etc/bashrc && \
     echo export LD_LIBRARY_PATH=$PHDF5/lib:$PNETCDF/lib:$NETCDF/lib:$LD_LIBRARY_PATH:$DIR/grib2/lib >> /etc/bashrc && \
     echo export WRFIO_NCD_LARGE_FILE_SUPPORT=1 >> /etc/bashrc && \
-    echo export WRF_EM_CORE=1 >> /etc/bashrc && \
-    echo export KMP_STACKSIZE=512m >> /etc/bashrc
+    echo export WRF_EM_CORE=1 >> /etc/bashrc
 
 ## Install Libraries
 WORKDIR $DIR
@@ -159,7 +172,7 @@ RUN echo export export NETCDF4=1 >> /etc/bashrc
 ## Install WRF 4.2.2
 WORKDIR $MAIN_DIR
 
-ENV LDFLAGS="-lm -lnetcdf -lnetcdff -L${PNETCDF}/lib"
+ENV LDFLAGS="-lm -lnetcdff -lnetcdf -L${PNETCDF}/lib"
 RUN echo export LDFLAGS="-lm -lnetcdff -L${PNETCDF}/lib" >> /etc/bashrc
 
 ### Get WRF v4.2.2 tar archive
@@ -184,7 +197,7 @@ RUN time ./compile em_real 2>&1 | tee compile_em_real.log
 
 ## For development
 #TODO: Comment these out for production
-RUN apt install -y \
+RUN apt-get install -y \
     man \
     bash-completion \
     vim \ 

Docker/gnu-build.sh

@@ -0,0 +1,20 @@
+#!/usr/bin/env bash
+# A simple script for building the GNU/OpenMPI version of the container
+
+export BUILD_OUTPUT_FILE=./output_gnu_build.txt
+echo "**WRF GNU Docker** Build started, output in ${BUILD_OUTPUT_FILE}"
+
+# Save build output log instead of printing to the screen
+#docker build --network=host --tag cornellcac/wrf:4.2.2-gnu - < Dockerfile-GNU 2>&1 > $BUILD_OUTPUT_FILE
+
+# Uncomment below to save build output log AND print to screen
+docker build --network=host --tag cornellcac/wrf:4.2.2-gnu - < Dockerfile-GNU 2>&1 | tee $BUILD_OUTPUT_FILE
+
+# Some useful summary output
+echo "-------------------------------------------------------------"
+echo "Build complete.  Check output file for final status.  Possible Errors:"
+cat $BUILD_OUTPUT_FILE | grep ERROR
+cat $BUILD_OUTPUT_FILE | grep Error
+echo "-------------------------------------------------------------"
+echo "Tail of build output file:"
+cat $BUILD_OUTPUT_FILE | tail

Docker/intel-build.sh

@@ -0,0 +1,20 @@
+#!/usr/bin/env bash
+# A simple script for building the Intel (with Intel MPI) container
+
+export BUILD_OUTPUT_FILE=./output_intel_build.txt
+echo "**WRF Intel Docker** Build started, output in ${BUILD_OUTPUT_FILE}"
+
+# Save build output log instead of printing to the screen
+#docker build --network=host --tag cornellcac/wrf:4.2.2-intel-7415915e0b8e - < Dockerfile-Intel 2>&1 > $BUILD_OUTPUT_FILE
+
+# Uncomment below to save build output log AND print to screen
+docker build --network=host --tag cornellcac/wrf:4.2.2-intel-7415915e0b8e - < Dockerfile-Intel 2>&1 | tee $BUILD_OUTPUT_FILE
+
+# Some useful summary output
+echo "-------------------------------------------------------------"
+echo "Build complete.  Check output file for final status.  Possible Errors:"
+cat $BUILD_OUTPUT_FILE | grep ERROR
+cat $BUILD_OUTPUT_FILE | grep Error
+echo "-------------------------------------------------------------"
+echo "Tail of build output file:"
+cat $BUILD_OUTPUT_FILE | tail