Update to use the JEDI Skylab v4 (#28)

* update pathsn for EPICHOME and JEDI_INSTALL * update JEDI EXEC * replace srun with mpiexec * correct the TEST_BASEDIR path and clean up * update s3 bucket location * disable git action * Rename auto_doc._yml to auto_doc.yml
ufs-community · Sep 1, 2023 · 8c0f8de · 8c0f8de
1 parent 34e0f54
commit 8c0f8de
Show file tree

Hide file tree

Showing 14 changed files with 31 additions and 38 deletions.
diff --git a/.github/workflows/auto_doc.yml b/.github/workflows/auto_doc.yml
@@ -2,9 +2,9 @@ name: Land DA automatic documentation build
 
 on:
   push:
-    branches: [ "release/public-v1.0.0" ]
+    branches: [ "develop" ]
   pull_request:
-    branches: [ "release/public-v1.0.0" ]
+    branches: [ "develop" ]
 
 jobs:
   build:
@@ -24,7 +24,7 @@ jobs:
 
     - name: Deploy
       uses: peaceiris/actions-gh-pages@v3
-      if: github.ref == 'refs/heads/release/public-v1.0.0'
+      if: github.ref == 'refs/heads/develop'
       with:
         github_token: ${{ secrets.GITHUB_TOKEN }}
         publish_dir: docs/build/html/
diff --git a/DA_update b/DA_update
diff --git a/do_submit_cycle.sh b/do_submit_cycle.sh
@@ -95,9 +95,8 @@ export analdate=${CYCLEDIR}/analdates.sh
 export incdate=${CYCLEDIR}/incdate.sh
 
 export BUILDDIR=${CYCLEDIR}/build
-export JEDI_EXECDIR='/scratch2/NCEPDEV/land/data/jedi/fv3-bundle/build/bin'
-export JEDI_STATICDIR=${DADIR}/jedi/fv3-jedi/Data/
 export INCR_EXECDIR=${DADIR}/add_jedi_incr/exec/
+
 ############################
 # read in dates  
 

diff --git a/docs/requirements.txt b/docs/requirements.txt
@@ -1,4 +1,4 @@
 sphinxcontrib-bibtex
 sphinx_rtd_theme
-docutils==0.16
-urllib3==1.26.15
+docutils>=0.18.1
+urllib3==1.26.15
diff --git a/modulefiles/landda_hera.intel.lua b/modulefiles/landda_hera.intel.lua
@@ -82,7 +82,7 @@ setenv("CXX", "mpiicpc")
 setenv("FC", "mpiifort")
 setenv("CMAKE_Platform", "hera.intel")
 
-setenv("EPICHOME", "/scratch1/NCEPDEV/nems/role.epic")
-setenv("JEDI_INSTALL", pathJoin(os.getenv("EPICHOME"),"contrib/v1.1"))
+setenv("EPICHOME", "/scratch2/NAGAPE/epic/UFS_Land-DA")
+setenv("JEDI_INSTALL", pathJoin(os.getenv("EPICHOME"),"jedi"))
 
 whatis("Description: UFS build environment")
diff --git a/modulefiles/landda_orion.intel.lua b/modulefiles/landda_orion.intel.lua
@@ -81,8 +81,8 @@ setenv("CXX", "mpiicpc")
 setenv("FC", "mpiifort")
 setenv("CMAKE_Platform", "orion.intel")
 
-setenv("EPICHOME", "/work/noaa/epic/role-epic")
-setenv("JEDI_INSTALL", pathJoin(os.getenv("EPICHOME"),"contrib/orion/v1.1"))
+setenv("EPICHOME", "/work/noaa/epic/UFS_Land-DA")
+setenv("JEDI_INSTALL", pathJoin(os.getenv("EPICHOME"),"jedi"))
 
 whatis("Description: UFS build environment")
 
diff --git a/release.environment b/release.environment
@@ -31,13 +31,13 @@ export OBSDIR=${LANDDA_INPUTS}/DA
 
 # temporary directory where experiment is run from
 export WORKDIR=${WORKDIR:-${LANDDAROOT}/workdir}
+
 # directory where output is saved
 export OUTDIR=${LANDDA_EXPTS}/${exp_name}
 
-export TEST_BASEDIR=${TEST_BASEDIR:-"/scratch2/NAGAPE/epic/UFS_Land-DA/test_base/mem000/restarts/vector"}
-# JEDI directories
-export JEDI_EXECDIR=${JEDI_EXECDIR:-"/scratch2/NCEPDEV/land/data/jedi/fv3-bundle/build/bin/"}
-export JEDI_STATICDIR=${LANDDADIR}/jedi/fv3-jedi/Data/
-
-
+# directory where ctest base dataset is located
+export TEST_BASEDIR=${TEST_BASEDIR:-"${EPICHOME}/test_base/mem000/restarts/vector"}
 
+# JEDI directories
+export JEDI_EXECDIR=${JEDI_EXECDIR:-"${JEDI_INSTALL}/build/bin"}
+export JEDI_STATICDIR=${JEDI_INSTALL}/jedi-bundle/fv3-jedi/test/Data
diff --git a/test/apply_jedi_incr.sh b/test/apply_jedi_incr.sh
@@ -46,7 +46,7 @@ done
 
 echo "============================= calling apply snow increment"
 #
-$MPIRUN -n $NPROC ${EXECDIR}/${TEST_EXEC}
+${MPIRUN} -n $NPROC ${EXECDIR}/${TEST_EXEC}
 
 # move ana tile to ./restarts/ana/tile
 mkdir -p ana/restarts/tile

diff --git a/test/ci/Dockerfile b/test/ci/Dockerfile
@@ -10,11 +10,10 @@ RUN rm -rf $HOME/land-offline_workflow
 COPY . $HOME/land-offline_workflow
 
 # set env vars
-ENV LANDDA_INPUTS=$HOME/landda-data/inputs
+ENV LANDDA_INPUTS=$HOME/inputs
 ENV EPICHOME=/opt
-ENV JEDI_INSTALL=${EPICHOME}
-#ENV TEST_BASEDIR=${EPICHOME}/landda-data/cycle_land/DA_GHCN_test/mem000/restarts/vector
-ENV TEST_BASEDIR=${TEST_BASEDIR:-"/scratch2/NAGAPE/epic/UFS_Land-DA/test_base/mem000/restarts/vector"}
+ENV JEDI_INSTALL=${EPICHOME}/jedi
+ENV TEST_BASEDIR=${EPICHOME}/test_base/mem000/restarts/vector"}
 
 #build & unit testing
 WORKDIR $HOME/land-offline_workflow

diff --git a/test/retrieve_data.sh b/test/retrieve_data.sh
@@ -6,8 +6,8 @@ project_source_dir=$1
 
 # first retrieve test data for landda system
 cd ${project_source_dir}/../
-[[ ! -f landda-test-inps.tar.gz ]] &&  wget https://epic-sandbox-srw.s3.amazonaws.com/landda-test-inps.tar.gz
-[[ ! -d inputs ]] && tar xvfz landda-test-inps.tar.gz
+[[ ! -f landda-test-inps.tar.gz ]] && wget https://noaa-ufs-land-da-pds.s3.amazonaws.com/landda_inputs.tar.gz
+[[ ! -d inputs ]] && tar xvfz landda_inputs.tar.gz
 cd ${project_source_dir}
 
 # Then retrieve data for ufs-datm-lnd model test (RT: datm_cdeps_lnd_gswp3)

diff --git a/test/runtime_vars.sh b/test/runtime_vars.sh
@@ -36,14 +36,13 @@ export EXECDIR=${EXECDIR:-$project_binary_dir/bin}
 export LANDDA_INPUTS=${LANDDA_INPUTS:-"`dirname $project_source_dir`/inputs"}
 
 # set IODA path
-export IODA_BUILD_DIR=${IODA_BUILD_DIR:-"${JEDI_INSTALL}/jedi-bundle/build"}
+export IODA_BUILD_DIR=${IODA_BUILD_DIR:-"${JEDI_INSTALL}/build"}
 export PYTHON_VERSION=`python -c 'import sys; version=sys.version_info[:3]; print("{0}.{1}".format(*version))'`
 export PYTHONPATH=$PYTHONPATH:${IODA_BUILD_DIR}/lib/python${PYTHON_VERSION}/pyioda:${IODA_BUILD_DIR}/lib/pyiodaconv
 
 # JEDI directories
-#export JEDI_EXECDIR=${JEDI_EXECDIR:-"${JEDI_INSTALL}/jedi-bundle/build/bin"}
-export JEDI_EXECDIR=${JEDI_EXECDIR:-"/scratch2/NCEPDEV/land/data/jedi/fv3-bundle/build/bin/"}
-export JEDI_STATICDIR=${JEDI_STATICDIR:-"${JEDI_EXECDIR}/../fv3-jedi/test/Data"}
+export JEDI_EXECDIR=${JEDI_EXECDIR:-"${JEDI_INSTALL}/build/bin"}
+export JEDI_STATICDIR=${JEDI_INSTALL}/jedi-bundle/fv3-jedi/test/Data
 
 # set executables
 export MPIRUN=${MPIRUN:-`which mpiexec`}

diff --git a/test/test_letkfoi_snowda.sh b/test/test_letkfoi_snowda.sh
@@ -10,8 +10,7 @@ source ${project_source_dir}/test/runtime_vars.sh ${project_binary_dir} ${projec
 
 # set extra paths
 OROG_PATH=$TPATH
-#OBSDIR=${LANDDA_INPUTS}/DA/snow_depth
-OBSDIR=${OBSDIR:-"/scratch2/NCEPDEV/land/data/DA/"}
+OBSDIR=${LANDDA_INPUTS}/DA/
 
 # set executables
 JEDI_EXEC=${JEDI_EXEC:-$JEDI_EXECDIR/fv3jedi_letkf.x}
@@ -73,5 +72,4 @@ ln -fs $JEDI_STATICDIR ./
 
 #
 echo "============================= calling ${JEDI_EXEC}"
-srun -n $NPROC ${JEDI_EXEC} letkf_land.yaml
-#${MPIRUN} -n $NPROC ${JEDI_EXEC} letkf_land.yaml
+${MPIRUN} -n $NPROC ${JEDI_EXEC} letkf_land.yaml
diff --git a/test/test_ufs_land_driver.sh b/test/test_ufs_land_driver.sh
@@ -9,8 +9,7 @@ project_source_dir=$2
 source ${project_source_dir}/test/runtime_vars.sh ${project_binary_dir} ${project_source_dir}
 
 # set baseline dir
-#TEST_BASEDIR=${TEST_BASEDIR:-"${EPICHOME}/landda/cycle_land/DA_GHCN_test/mem000/restarts/vector"}
-TEST_BASEDIR=${TEST_BASEDIR:-"/scratch2/NAGAPE/epic/UFS_Land-DA/test_base/mem000/restarts/vector"}
+export TEST_BASEDIR=${TEST_BASEDIR:-"${EPICHOME}/test_base/mem000/restarts/vector"}
 
 # compute the restart frequency, run_days and run_hours
 FREQ=$(( 3600 * $FCSTHR ))
@@ -51,7 +50,7 @@ ln -fs ${WORKDIR}/ana/restarts/vector/ufs_land_restart.${YY}-${MM}-${DD}_${HH}-0
 
 # submit model
 echo "============================= calling model" 
-$MPIRUN -n $NPROC ${EXECDIR}/${TEST_EXEC} 
+${MPIRUN} -n $NPROC ${EXECDIR}/${TEST_EXEC} 
 
 # check if new restart exits
 if [[ -e "./ufs_land_restart.${nYY}-${nMM}-${nDD}_${nHH}-00-00.nc" ]]; then

diff --git a/test/test_vector2tile.sh b/test/test_vector2tile.sh
@@ -11,8 +11,7 @@ prefix=$4 #bkg or ana
 source ${project_source_dir}/test/runtime_vars.sh ${project_binary_dir} ${project_source_dir}
 
 # set baseline dir
-#TEST_BASEDIR=${TEST_BASEDIR:-"${EPICHOME}/landda/cycle_land/DA_GHCN_test/mem000/restarts/vector"}
-TEST_BASEDIR=${TEST_BASEDIR:-"/scratch2/NAGAPE/epic/UFS_Land-DA/test_base/mem000/restarts/vector"}
+export TEST_BASEDIR=${TEST_BASEDIR:-"${EPICHOME}/test_base/mem000/restarts/vector"}
 
 # set executables
 TEST_EXEC="vector2tile_converter.exe"