Fix container paths

.github/workflows/testing.yml

@@ -213,7 +213,7 @@ jobs:
       - name: Cache inputdata
         uses: actions/cache@v3
         with:
-          path: /home/cime/inputdata
+          path: /root/storage/inputdata
           key: inputdata-2
       - name: Install uv
         uses: astral-sh/setup-uv@v7

doc/requirements.txt

@@ -1,8 +1,8 @@
-sphinx
+sphinx<8.0
 sphinxcontrib-programoutput
 sphinx-rtd-theme
 sphinx-copybutton
 evv4esm
 xmlschema
 sphinx-toolbox
-sphinx-autobuild
+sphinx-autobuild

doc/source/contributing-guide.rst

@@ -161,16 +161,15 @@ following example assumes the model is checked out in ``$SRC_PATH``.
 
 .. code-block:: bash
 
-   docker run -it --rm --hostname docker -e CIME_MODEL=e3sm -v ${SRC_PATH}:/root/model -v ./storage:/root/storage -v ./inputdata:/root/inputdata -w /root/E3SM/cime ghcr.io/esmci/cime:latest bash
+   docker run -it --rm --hostname docker -e CIME_MODEL=e3sm -v ${SRC_PATH}:/root/model -v ./storage:/root/storage -w /root/E3SM/cime ghcr.io/esmci/cime:latest bash
 
 This example will drop into a shell where CIME commands or tests can be run.
 The options are broken down below.
 
 - ``--hostname docker`` is required to tell CIME which machine definition to use.
 - ``-e CIME_MODEL=e3sm`` defines the model.
 - ``-v ${SRC_PATH}:/root/E3SM`` passes through the model source.
-- ``-v ./inputdata:/root/inputdata`` persistent input data.
-- ``-v ./storage:/root/storage`` persistent cases, baselines, timings, etc.
+- ``-v ./storage:/root/storage`` persist all data; cases, baselines, archive, inputdata. the bind mounts can be broken out if you only want to persist certain input/outputs.
 - ``-w /root/E3SM/cime`` set the current working directory to CIME's root.
 - ``ghcr.io/esmci/cime:latest`` container image.
 - ``bash`` the command to run in the container.

docker/.cime/config_machines.v2.xml

@@ -12,8 +12,8 @@
     <SAVE_TIMING_DIR>/root/storage/timings</SAVE_TIMING_DIR>
     <SAVE_TIMING_DIR_PROJECTS>CIME</SAVE_TIMING_DIR_PROJECTS>
     <CIME_OUTPUT_ROOT>/root/storage/cases</CIME_OUTPUT_ROOT>
-    <DIN_LOC_ROOT>/root/inputdata</DIN_LOC_ROOT>
-    <DIN_LOC_ROOT_CLMFORC>/root/inputdata-clmforc</DIN_LOC_ROOT_CLMFORC>
+    <DIN_LOC_ROOT>/root/storage/inputdata</DIN_LOC_ROOT>
+    <DIN_LOC_ROOT_CLMFORC>/root/storage/inputdata-clmforc</DIN_LOC_ROOT_CLMFORC>
     <DOUT_S_ROOT>/root/storage/archive/$CASE</DOUT_S_ROOT>
     <BASELINE_ROOT>/root/storage/baselines/$COMPILER</BASELINE_ROOT>
     <CCSM_CPRNC>/root/storage/tools/cprnc</CCSM_CPRNC>

docker/.cime/docker/config_machines.xml

@@ -11,8 +11,8 @@
     <SAVE_TIMING_DIR>/root/storage/timings</SAVE_TIMING_DIR>
     <SAVE_TIMING_DIR_PROJECTS>CIME</SAVE_TIMING_DIR_PROJECTS>
     <CIME_OUTPUT_ROOT>/root/storage/cases</CIME_OUTPUT_ROOT>
-    <DIN_LOC_ROOT>/root/inputdata</DIN_LOC_ROOT>
-    <DIN_LOC_ROOT_CLMFORC>/root/inputdata-clmforc</DIN_LOC_ROOT_CLMFORC>
+    <DIN_LOC_ROOT>/root/storage/inputdata</DIN_LOC_ROOT>
+    <DIN_LOC_ROOT_CLMFORC>/root/storage/inputdata-clmforc</DIN_LOC_ROOT_CLMFORC>
     <DOUT_S_ROOT>/root/storage/archive/$CASE</DOUT_S_ROOT>
     <BASELINE_ROOT>/root/storage/baselines/$COMPILER</BASELINE_ROOT>
     <CCSM_CPRNC>/root/storage/tools/cprnc</CCSM_CPRNC>

docker/Dockerfile

@@ -58,10 +58,10 @@ RUN curl -LsSf https://astral.sh/uv/install.sh | sh \
 COPY docker/entrypoint.sh /entrypoint.sh
 
 RUN SKIP_ENTRYPOINT=true source /entrypoint.sh \
-  && mkdir -p /root/{tools,inputdata,cases,timings,archive,baselines} \
+  && mkdir -p /root/storage/{tools,inputdata,cases,timings,archive,baselines} \
   && download_input_data
 
-COPY --from=cprnc /root/tools/cprnc /root/tools/cprnc
+COPY --from=cprnc /root/storage/tools/cprnc /root/storage/tools/cprnc
 COPY docker/.cime /root/.cime
 
 ENTRYPOINT ["/entrypoint.sh"]

docker/entrypoint.sh

@@ -6,10 +6,12 @@ export LOGNAME="${USER}"
 
 # Set static home path where .cime exists and container entrypoint options
 SKIP_ENTRYPOINT="${SKIP_ENTRYPOINT:-false}"
+STORAGE_DIR="${HOME}/storage"
 
 # Build the cprnc tool from CIME sources
 function build_cprnc() {
     cprnc_dir="${CPRNC_DIR:-${PWD}/CIME/non_py/cprnc}"
+    tools_dir="${STORAGE_DIR}/tools"
 
     if [[ ! -e "${cprnc_dir}" ]]; then
         echo "CPRNC path does not exist. Change to CIME's root directory."
@@ -22,10 +24,10 @@ function build_cprnc() {
 
     make
 
-    mkdir "${HOME}/tools"
+    [[ ! -e "${tools_dir}" ]] && mkdir -p "${tools_dir}"
 
     # Needs to be copied into the machines configured tool path
-    cp cprnc "${HOME}/tools/cprnc"
+    cp cprnc "${tools_dir}/cprnc"
 
     popd || exit 1
 }
@@ -34,16 +36,16 @@ function build_cprnc() {
 # Download input data needed for model setup
 # required for grid generation tests
 function download_input_data() {
-    mkdir -p "${HOME}/inputdata/cpl/gridmaps/oQU240"
-    mkdir -p "${HOME}/inputdata/share/domains"
+    mkdir -p "${STORAGE_DIR}/inputdata/cpl/gridmaps/oQU240"
+    mkdir -p "${STORAGE_DIR}/inputdata/share/domains"
 
-    wget -O "${HOME}/inputdata/cpl/gridmaps/oQU240/map_oQU240_to_ne4np4_aave.160614.nc" \
+    wget -O "${STORAGE_DIR}/inputdata/cpl/gridmaps/oQU240/map_oQU240_to_ne4np4_aave.160614.nc" \
         https://portal.nersc.gov/project/e3sm/inputdata/cpl/gridmaps/oQU240/map_oQU240_to_ne4np4_aave.160614.nc
 
-    wget -O "${HOME}/inputdata/share/domains/domain.ocn.ne4np4_oQU240.160614.nc" \
+    wget -O "${STORAGE_DIR}/inputdata/share/domains/domain.ocn.ne4np4_oQU240.160614.nc" \
         https://portal.nersc.gov/project/e3sm/inputdata/share/domains/domain.ocn.ne4np4_oQU240.160614.nc
 
-    wget -O "${HOME}/inputdata/share/domains/domain.lnd.ne4np4_oQU240.160614.nc" \
+    wget -O "${STORAGE_DIR}/inputdata/share/domains/domain.lnd.ne4np4_oQU240.160614.nc" \
         https://portal.nersc.gov/project/e3sm/inputdata/share/domains/domain.lnd.ne4np4_oQU240.160614.nc
 }