Mvu25s

jupyter-images/mvu25s/.condarc

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+envs_dirs:
+  - /home/jovyan/additional-envs

jupyter-images/mvu25s/Acknowledgements.ipynb

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+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "id": "c86cd54f-b73c-4781-b6eb-89c79d3d3b22",
+   "metadata": {},
+   "source": [
+    "## Acknowledgements\n",
+    "\n",
+    "Launching this JupyterHub server is the result of a collaboration between several research and academic institutions and their staff. For Jetstream2 and JupyterHub expertise, we thank Andrea Zonca (San Diego Supercomputing Center), Jeremy Fischer, Mike Lowe (Indiana University), the NSF Jetstream2 (`doi:10.1145/3437359.3465565`) team.\n",
+    "\n",
+    "This work employs the NSF Jetstream2 Cloud at Indiana University through allocation EES220002 from the Advanced Cyberinfrastructure Coordination Ecosystem: Services & Support (ACCESS) program, which is supported by National Science Foundation grants #2138259, #2138286, #2138307, #2137603, and #2138296.\n",
+    "\n",
+    "Unidata is one of the University Corporation for Atmospheric Research (UCAR)'s Community Programs (UCP), and is funded primarily by the National Science Foundation (AGS-2403649).\n",
+    "\n",
+    "## To Acknowledge This JupyterHub and the Unidata Science Gateway\n",
+    "\n",
+    "If you have benefited from the Unidata Science Gateway, please cite `doi:10.5065/688s-2w73`. Additional citation information can be found in this [Citation File Format file](https://raw.githubusercontent.com/Unidata/science-gateway/master/CITATION.cff).\n"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.10.6"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}

jupyter-images/mvu25s/Dockerfile

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+# Multistage Docker build to include the WRF single column model in a
+# JupyterLab environment
+
+FROM ubuntu as build-wrf
+
+####################################################
+# Begin WRF ideal single column model compilation  #
+####################################################
+
+# Mostly following the steps outlined here:
+# https://forum.mmm.ucar.edu/threads/full-wrf-and-wps-installation-example.12385/
+
+# Dependencies missing from base image
+RUN apt-get update && apt-get install --yes --no-install-recommends \
+      gcc cpp gfortran g++ openmpi-bin libopenmpi-dev git csh perl file \
+      make m4 curl vim ca-certificates && \
+    apt-get clean && rm -rf /var/lib/apt/lists/*
+
+# Run tests recommended by MMM to confirm the fortran and c compilers are
+# functioning as expected
+# https://www2.mmm.ucar.edu/wrf/OnLineTutorial/compilation_tutorial.php#STEP1
+RUN set -x && cd / && mkdir TESTS && cd TESTS && \
+    curl https://www2.mmm.ucar.edu/wrf/OnLineTutorial/compile_tutorial/tar_files/Fortran_C_tests.tar -O && \
+    tar -xf Fortran_C_tests.tar && \
+    gfortran TEST_1_fortran_only_fixed.f && ./a.out && \
+    gfortran TEST_2_fortran_only_free.f90 && ./a.out && \
+    gcc TEST_3_c_only.c && ./a.out && \
+    gcc -c -m64 TEST_4_fortran+c_c.c && gfortran -c -m64 TEST_4_fortran+c_f.f90 && \
+        gfortran -m64 TEST_4_fortran+c_f.o TEST_4_fortran+c_c.o && ./a.out && \
+    ./TEST_csh.csh && \
+    ./TEST_perl.pl && \
+    ./TEST_sh.sh && \
+    cd / && rm -rf TESTS
+
+# Test for other utilities
+RUN which ar awk cat cp cut expr file grep gzip \
+    head hostname ln ls make mkdir mv nm printf rm \
+    sed sleep sort tar touch tr uname wc which m4
+
+###########################################################
+# Library and software versions
+###########################################################
+
+ENV NETCDF_VERSION=4.9.0 \
+    NETCDF_F_VERSION=4.5.3 \
+    WRF_VERSION=4.4.2
+
+###########################################################
+# Library and software PATHS
+###########################################################
+
+ENV DIR=/Build_WRF/LIBRARIES
+ENV NETCDF=$DIR/netcdf
+ENV PATH=$NETCDF/bin:$PATH \
+    LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$NETCDF/lib:/$ZLIB_DIR/lib
+
+RUN mkdir -p $DIR
+
+###########################################################
+# Compiler options
+###########################################################
+
+ENV CC=gcc \
+    CXX=g++ \
+    FC=gfortran \
+    FCFLAGS=-m64 \
+    F77=gfortran \
+    FFLAGS=-m64 \
+    LDFLAGS="-L$NETCDF/lib" \
+    CPPFLAGS="-I$NETCDF/include"
+
+###########################################################
+# Build libraries
+###########################################################
+
+# netcdf-c
+# BUILT WITH "--disable-netcdf4" SO WE COMPILE WRF WITH "NETCDF_classic"
+RUN set -x && \
+    cd / && mkdir -p Build_WRF/LIBRARIES && cd Build_WRF/LIBRARIES && \
+    curl https://downloads.unidata.ucar.edu/netcdf-c/$NETCDF_VERSION/netcdf-c-$NETCDF_VERSION.tar.gz -O && \
+    tar xzvf netcdf-c-$NETCDF_VERSION.tar.gz && \
+    cd netcdf-c-$NETCDF_VERSION && \
+    ./configure --enable-shared --disable-netcdf4 --disable-filter-testing --disable-dap --prefix=$DIR/netcdf && \
+    make && make install && \
+    cd .. && rm -rf netcdf-c-$NETCDF_VERSION*
+
+# netcdf-f
+RUN set -x && \
+    export CPPFLAGS="-I$NETCDF/include -L$NETCDF/lib" && \
+    cd /Build_WRF/LIBRARIES && \
+    curl https://downloads.unidata.ucar.edu/netcdf-fortran/$NETCDF_F_VERSION/netcdf-fortran-$NETCDF_F_VERSION.tar.gz -O && \
+    tar xzvf netcdf-fortran-$NETCDF_F_VERSION.tar.gz && \
+    cd netcdf-fortran-$NETCDF_F_VERSION && \
+    ./configure --prefix=$DIR/netcdf --disable-shared && \
+    make && make install && \
+    cd .. && rm -rf netcdf-fortran-$NETCDF_F_VERSION
+
+###########################################################
+# Verify libraries will play nice with the compilers used to build WRF
+###########################################################
+
+# https://www2.mmm.ucar.edu/wrf/OnLineTutorial/compilation_tutorial.php#STEP3
+
+RUN set -x && \
+    cd / && mkdir TESTS && cd TESTS && \
+    curl https://www2.mmm.ucar.edu/wrf/OnLineTutorial/compile_tutorial/tar_files/Fortran_C_NETCDF_MPI_tests.tar -O && \
+    tar -xf Fortran_C_NETCDF_MPI_tests.tar && \
+    cp ${NETCDF}/include/netcdf.inc . && \
+    gfortran -c 01_fortran+c+netcdf_f.f && \
+    gcc -c 01_fortran+c+netcdf_c.c && \
+    gfortran 01_fortran+c+netcdf_f.o 01_fortran+c+netcdf_c.o -L${NETCDF}/lib -lnetcdff -lnetcdf && \
+    ./a.out && \
+    mpif90 -c 02_fortran+c+netcdf+mpi_f.f && \
+    mpicc -c 02_fortran+c+netcdf+mpi_c.c && \
+    mpif90 02_fortran+c+netcdf+mpi_f.o 02_fortran+c+netcdf+mpi_c.o -L${NETCDF}/lib -lnetcdff -lnetcdf && \
+    mpirun --allow-run-as-root ./a.out && \
+    cd / && rm -rf TESTS
+
+###########################################################
+# Actually build WRF
+###########################################################
+
+# At the moment, the configure script on the repo has an open issue regarding
+# string comparison:
+# https://github.com/wrf-model/WRF/issues/1817
+COPY ./configure /tmp/configure
+COPY ./Registry.EM_COMMON_edit /tmp/Registry.EM_COMMON_edit
+
+# ./configure won't run with the options (33 and 0) if this variable is not set
+ENV NETCDF_classic=1
+
+# Piping the output of "echo '33\r0\r'" tells the script to configure WRF to
+# compile for parallel using smpar and the GNU compilers we have been using (33)
+# and to compile for no nesting (0)
+RUN set -x && \
+    cd /Build_WRF && \
+    git clone --recurse-submodule https://github.com/wrf-model/WRF.git && \
+    cd WRF && \
+    git checkout release-v${WRF_VERSION} && \
+    mv /tmp/Registry.EM_COMMON_edit ./Registry/Registry.EM_COMMON && \
+    mv /tmp/configure ./configure && chmod u+x ./configure && \
+    git diff && \
+    echo '33\r0\r' | ./configure && \
+    ./compile em_scm_xy > log.compile 2>&1
+
+###########################################################
+# Begin JupyterLab Stage
+###########################################################
+
+# Heavily borrowed from docker-stacks/minimal-notebook/
+# https://github.com/jupyter/docker-stacks/blob/main/minimal-notebook/Dockerfile
+
+FROM quay.io/jupyter/minimal-notebook
+
+ENV DEFAULT_ENV_NAME=mvu25s EDITOR=nano VISUAL=nano
+
+LABEL maintainer="Unidata <support-gateway@unidata.ucar.edu>"
+
+USER root
+
+RUN apt-get update && \
+    apt-get install -y --no-install-recommends vim nano curl wget zip unzip \
+    gcc cpp gfortran g++ openmpi-bin libopenmpi-dev git csh perl file \
+    make m4 ca-certificates libgl1 && \
+    apt-get clean && \
+    rm -rf /var/lib/apt/lists/*
+
+USER $NB_UID
+
+ADD environment.yml /tmp
+
+RUN mamba install --quiet --yes \
+      'conda-forge::nb_conda_kernels' \
+      'conda-forge::jupyterlab-git' \
+      'conda-forge::ipywidgets' && \
+    mamba env create --name $DEFAULT_ENV_NAME -f /tmp/environment.yml && \
+    pip install --no-cache-dir nbgitpuller && \
+    mamba clean --all -f -y && \
+    jupyter lab clean -y && \
+    #npm cache clean --force && \
+    rm -rf /home/$NB_USER/.cache/yarn && \
+    rm -rf /home/$NB_USER/.node-gyp && \
+    fix-permissions $CONDA_DIR && \
+    fix-permissions /home/$NB_USER
+
+COPY additional_kernels.ipynb update_material.ipynb Acknowledgements.ipynb \
+    default_kernel.py .condarc /
+
+COPY --from=build-wrf /Build_WRF /Build_WRF
+
+USER root
+RUN chown -R ${NB_UID}:${NB_GID} /Build_WRF/WRF && \
+    ldconfig /Build_WRF/LIBRARIES/netcdf/lib
+
+USER $NB_UID