updating readme, dupcliating dockerfile to have a base build with hel…

…d suarez

README.md

@@ -22,33 +22,34 @@ git checkout development
 Good luck, and have a great day!
 
 ## Docker
-
 If you don't want to worry about installing our dependencies, 
-you can create a build of CAM-SIMA using docker. To do so, you will need to 
-download and install [docker desktop](https://docs.docker.com/desktop/).
+you can create a build of CAM-SIMA using docker.
+
+### Download docker
+Download and install [docker desktop](https://docs.docker.com/desktop/).
 
 #### Windows
 Follow the installation instructions for Windows [here](https://docs.docker.com/desktop/install/windows-install/)
 
-
 #### Linux
 Follow the installation instructions for Linux [here](https://docs.docker.com/desktop/install/linux-install/)
 
 #### MacOS
 Follow the installation instructions for Mac [here](https://docs.docker.com/desktop/install/mac-install/)
 
-### Download docker
 
-### Build the docker file
-1. First, build the esmf docker image. You must tag the build with `esmf`
+### Build the base docker file
+1. First, build the esmf docker image. You must tag the build with `esmf`. This will take quite some time.
 ```
-cd docker
-docker build -f Dockerfile.esmf -t esmf .
+docker build -f docker/Dockerfile.esmf -t esmf .
 ```
-2. Build the CAM-SIMA image
+
+### CAM-SIMA
+
+1. Build the CAM-SIMA image
 ```
 cd ../
-docker build -t cam-sima .
+docker build -f docker/Dockerfile -t cam-sima .
 ```
 3. Run the image
 ```
@@ -57,4 +58,21 @@ docker run --rm -it cam-sima
 4. Submit the case
 ```
 ./case.submit
+```
+
+### MUSICA
+You can include musica chemistry by using the correct docker file
+
+1. Build the MUSICA image
+```
+cd ../
+docker build -f docker/Dockerfile.musica -t musica .
+```
+3. Run the image
+```
+docker run --rm -it musica
+```
+4. Submit the case
+```
+./case.submit
 ```

docker/Dockerfile

@@ -0,0 +1,85 @@
+# parts of CAM require x86 architecture (gptl, which relies on the rdtsc x86 assembly instruction)
+# esmf is am image you are expected to have built. Read the README file for instructions
+FROM esmf:latest
+
+###################################################
+## Install necessary packages
+###################################################
+RUN dnf -y update \
+    && dnf -y install \
+      ftp \
+      git \
+      hostname \
+      m4 \
+      python \
+      sudo \
+      svn \
+      tree \
+      vim \
+    && dnf clean all
+
+###################################################
+## Make sure the mpi compilers can be found
+###################################################
+ENV PATH="${PATH}:/usr/lib64/mpich/bin/"
+ENV OMP_NUM_THREADS=5
+
+###################################################
+## Build and install Parallel-netcdf
+###################################################
+RUN wget -q https://parallel-netcdf.github.io/Release/pnetcdf-1.12.3.tar.gz
+RUN tar zxf pnetcdf-1.12.3.tar.gz
+RUN cd pnetcdf-1.12.3 && \
+     ./configure --prefix=/usr/local && \
+     make -j 8 install && \
+     ldconfig
+
+###################################################
+## Build CAM-SIMA
+###################################################
+
+# create a user to run the case
+RUN adduser cam_sima_user \
+    && echo "cam_sima_user ALL=(root) NOPASSWD:ALL" > /etc/sudoers.d/cam_sima_user \
+    && chmod 0440 /etc/sudoers.d/cam_sima_user
+
+# copy in the CAM-SIMA code and give the proper user permissions
+COPY --chown=cam_sima_user . /home/cam_sima_user/CAM-SIMA
+
+USER cam_sima_user
+WORKDIR /home/cam_sima_user/CAM-SIMA
+
+# pull the dependencies
+RUN ./manage_externals/checkout_externals
+
+# Copy in the machine information for the container
+RUN cp /home/cam_sima_user/CAM-SIMA/docker/config_machines.xml /home/cam_sima_user/CAM-SIMA/ccs_config/machines/
+
+# Set environment variables needed to create and build the case
+ENV USER=$(whoami)
+ENV CASE_NAME=/home/cam_sima_user/case_name
+ENV CESMDATAROOT=/home/cam_sima_user/cesm_data
+ENV CIME_MACHINE=container
+ENV CIME_MODEL=cesm
+ENV ESMFMKFILE=/usr/local/lib/esmf.mk
+
+# Create a case
+RUN ./cime/scripts/create_newcase --case $CASE_NAME  --compset FPHYStest --res ne5_ne5_mg37 --run-unsupported
+
+WORKDIR $CASE_NAME 
+
+RUN ./case.setup
+
+RUN ./xmlchange CAM_CONFIG_OPTS="--dyn none --physics-suites held_suarez_1994"
+RUN ./xmlchange ROF_NCPL=48
+RUN ./xmlchange STOP_OPTION=nsteps
+RUN ./xmlchange STOP_N=5
+
+# Copy in the grid files and a snapshot file
+RUN chmod +x /home/cam_sima_user/CAM-SIMA/docker/ftp_download.sh
+RUN /home/cam_sima_user/CAM-SIMA/docker/ftp_download.sh
+
+# # add the snapshot file
+RUN echo "ncdata='/home/cam_sima_user/run_heldsuarez_cam6_nt2_bigg_try005.cam.h5.0001-01-01-00000.nc'" >> user_nl_cam
+
+RUN ./case.build