Merge pull request #222 from ESCOMP/docker

Add a dockerfile to build CAM-SIMA

.dockerignore

@@ -0,0 +1,11 @@
+# ignore all
+*
+
+# include things to copy
+!Externals*
+!src/
+!cime_config/
+!manage_externals/
+!test/
+!.config_files.xml
+!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

README.md

@@ -21,3 +21,40 @@ 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/).
+
+#### 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`
+```
+cd docker
+docker build -f Dockerfile.esmf -t esmf .
+```
+2. Build the CAM-SIMA image
+```
+cd ../
+docker build -t cam-sima .
+```
+3. Run the image
+```
+docker run --rm -it cam-sima
+```
+4. Submit the case
+```
+./case.submit
+```

docker/Dockerfile.esmf

@@ -0,0 +1,54 @@
+# parts of CAM require x86 architecture (gptl, which relies on the rdtsc x86 assembly instruction)
+FROM --platform=linux/amd64 fedora:latest
+
+###################################################
+## Install necessary packages
+###################################################
+RUN dnf -y update \
+    && dnf -y install \
+      blas-devel \
+      cmake \
+      gcc-c++ \
+      gcc-gfortran \
+      lapack-devel \ 
+      netcdf-devel \
+      netcdf-fortran-devel \
+      make \
+      mpich \
+      mpich-devel \
+      wget \
+    && dnf clean all
+
+###################################################
+## Make sure the mpi compilers can be found
+###################################################
+ENV PATH="${PATH}:/usr/lib64/mpich/bin/"
+ENV OMP_NUM_THREADS=5
+
+###################################################
+## Build and install ESMF
+###################################################
+
+ENV ESMF_TAG="8.4.2"
+
+# set necessary environment variables
+ENV ESMF_DIR=/esmf-${ESMF_TAG}
+ENV ESMF_COMM=mpich3
+ENV ESMF_BOPT="g"
+ENV ESMF_NETCDF="nc-config"
+ENV ESMF_NETCDFF_INCLUDE=/usr/lib64/gfortran/modules
+ENV ESMF_INSTALL_PREFIX=/usr/local
+ENV ESMF_INSTALL_BINDIR=${ESMF_INSTALL_PREFIX}/bin
+ENV ESMF_INSTALL_DOCDIR=${ESMF_INSTALL_PREFIX}/doc
+ENV ESMF_INSTALL_HEADERDIR=${ESMF_INSTALL_PREFIX}/include
+ENV ESMF_INSTALL_LIBDIR=${ESMF_INSTALL_PREFIX}/lib
+ENV ESMF_INSTALL_MODDIR=${ESMF_INSTALL_PREFIX}/mod
+ENV ESMF_TESTEXHAUSTIVE="OFF"
+
+RUN wget -q https://github.com/esmf-org/esmf/archive/refs/tags/v${ESMF_TAG}.tar.gz && \
+    tar zxf v${ESMF_TAG}.tar.gz && \
+    cd esmf-${ESMF_TAG} && \
+    # This command lets you see what esmf thinks its build options are but may not necessary to build, not sure
+    make info && \
+    make -j 8 && \
+    make install

docker/config_machines.xml

@@ -0,0 +1,95 @@
+<?xml version="1.0"?>
+
+<!--
+
+===============================================================
+COMPILER and COMPILERS
+===============================================================
+If a machine supports multiple compilers - then
+- the settings for COMPILERS should reflect the supported compilers
+as a comma separated string
+- the setting for COMPILER should be the default compiler
+(which is one of the values in COMPILERS)
+
+===============================================================
+MPILIB and MPILIBS
+===============================================================
+If a machine supports only one MPILIB is supported - then
+the setting for  MPILIB and MPILIBS should be blank ("")
+If a machine supports multiple mpi libraries (e.g. mpich and openmpi)
+- the settings for MPILIBS should reflect the supported mpi libraries
+as a comma separated string
+
+The default settings for COMPILERS and MPILIBS is blank (in config_machines.xml)
+
+Normally variable substitutions are not made until the case scripts are run, however variables
+of the form $ENV{VARIABLE_NAME} are substituted in create_newcase from the environment
+variable of the same name if it exists.
+
+===============================================================
+PROJECT_REQUIRED
+===============================================================
+A machine may need the PROJECT xml variable to be defined either because it is
+used in some paths, or because it is used to give an account number in the job
+submission script. If either of these are the case, then PROJECT_REQUIRED
+should be set to TRUE for the given machine.
+
+
+mpirun: the mpirun command that will be used to actually launch the model.
+The attributes used to choose the mpirun command are:
+
+mpilib: can either be 'default' the name of an mpi library, or a compiler name so one can choose the mpirun
+based on the mpi library in use.
+
+the 'executable' tag must have arguments required for the chosen mpirun, as well as the executable name.
+
+unit_testing: can be 'true' or 'false'.
+This allows using a different mpirun command to launch unit tests
+
+-->
+
+<config_machines version="2.0">
+
+  <machine MACH="container">
+    <DESC>
+      Containerized development environment (Docker/Singularity) for CESM w/ GNU compilers
+    </DESC>
+    <OS>LINUX</OS>
+    <COMPILERS>gnu</COMPILERS>
+    <MPILIBS>mpich</MPILIBS>
+    <CIME_OUTPUT_ROOT>$ENV{HOME}/scratch</CIME_OUTPUT_ROOT>
+    <DIN_LOC_ROOT>$ENV{CESMDATAROOT}/inputdata</DIN_LOC_ROOT>
+    <DIN_LOC_ROOT_CLMFORC>$DIN_LOC_ROOT/atm/datm7</DIN_LOC_ROOT_CLMFORC>
+    <DOUT_S_ROOT>$ENV{HOME}/archive/$CASE</DOUT_S_ROOT>
+    <GMAKE>make</GMAKE>
+    <GMAKE_J>4</GMAKE_J>
+    <BATCH_SYSTEM>none</BATCH_SYSTEM>
+    <SUPPORTED_BY>cgd</SUPPORTED_BY>
+    <MAX_TASKS_PER_NODE>4</MAX_TASKS_PER_NODE>
+    <MAX_MPITASKS_PER_NODE>4</MAX_MPITASKS_PER_NODE>
+    <PROJECT_REQUIRED>FALSE</PROJECT_REQUIRED>
+    <mpirun mpilib="mpich">
+      <executable>mpiexec</executable>
+      <arguments>
+        <arg name="anum_tasks"> -n {{ total_tasks }}</arg>
+      </arguments>
+    </mpirun>
+    <module_system type="none">
+    </module_system>
+    <environment_variables>
+      <env name="NETCDF_PATH">/usr/local</env>
+      <env name="PNETCDF_PATH">/usr/local</env>
+      <env name="FPATH">/usr/lib64</env>
+      <env name="CPATH">/usr/lib64</env>
+    </environment_variables>
+    <resource_limits>
+      <resource name="RLIMIT_STACK">-1</resource>
+    </resource_limits>
+  </machine>
+
+  <default_run_suffix>
+    <default_run_exe>${EXEROOT}/cesm.exe </default_run_exe>
+    <default_run_misc_suffix> >> cesm.log.$LID 2>&amp;1 </default_run_misc_suffix>
+  </default_run_suffix>
+
+</config_machines>

docker/ftp_download.sh

@@ -0,0 +1,19 @@
+#!/bin/sh
+
+FTP_HOST="cesm-inputdata-lowres1.cgd.ucar.edu"
+FTP_USER="anonymous"
+FTP_PASS="[email protected]"
+
+
+FILES_TO_DOWNLOAD=(
+    "/testdata/run_heldsuarez_cam6_nt2_bigg_try005.cam.h5.0001-01-01-00000.nc"
+)
+
+# Download the file using FTP
+ftp -inv $FTP_HOST << EOF
+user $FTP_USER $FTP_PASS
+binary
+cd $(dirname ${FILES_TO_DOWNLOAD[0]})
+get $(basename ${FILES_TO_DOWNLOAD[0]}) /home/cam_sima_user/$(basename ${FILES_TO_DOWNLOAD[0]})
+bye
+EOF