Reorg of where soca is staged/run (#210)

* reorg of where stuff is staged

* Trigger CI

Co-authored-by: Cory Martin <cory.r.martin@noaa.gov>

parm/templates/stage.yaml

@@ -4,6 +4,7 @@ observers: $<< ${OBS_YAML}
 background_dir: '{{background_dir}}'
 staticb_dir: '{{staticb_dir}}'
 COMOUT: '{{COMOUT}}'
+DATA: ${DATA}
 background_time: '{{background_time}}'
 dump: ${CDUMP}
 r2d2_obs_db: ${R2D2_OBS_DB}
@@ -15,5 +16,5 @@ r2d2 window length: ${R2D2_OBS_WINDOW}
 r2d2 window begin: '{{r2d2_window_begin}}'
 fv3jedi_stage_files: $<< $(fv3jedi_stage)
 fv3jedi_stage: ${FV3JEDI_STAGE_YAML}
-stage_dir: $(COMOUT)/analysis
+stage_dir: $(DATA)
 soca_input_fix_dir: '{{soca_input_fix_dir}}'

scripts/exgdas_global_marine_analysis_prep.py

@@ -90,18 +90,20 @@ def gen_bkg_list(window_begin=' ', bkg_path='.', file_type='gdas.t*.ocnf00[3-9]'
 
 comout = os.getenv('COMOUT')
 comin_obs = os.getenv('COMIN_OBS')
+anl_dir = os.getenv('DATA')
 staticsoca_dir = os.getenv('SOCA_INPUT_FIX_DIR')
 
 # create analysis directory for files
-anl_dir = os.path.join(comout, 'analysis')
 ufsda.mkdir(anl_dir)
 
 # create output directory for obs
-diags = os.path.join(comout, 'analysis', 'diags')
+diags = os.path.join(anl_dir, 'diags')
 ufsda.mkdir(diags)
 
 # create output directory for soca DA
-ufsda.mkdir(os.path.join(comout, 'analysis', 'Data'))
+anl_out = os.path.join(comout, 'ocnanal_'+os.getenv('CDATE'), 'Data')
+ufsda.mkdir(anl_out)
+ufsda.symlink(os.path.join(anl_dir, 'Data'), anl_out, remove=False)
 
 
 ################################################################################
@@ -221,7 +223,7 @@ def gen_bkg_list(window_begin=' ', bkg_path='.', file_type='gdas.t*.ocnf00[3-9]'
 
 # link of convenience
 diag_ic = glob.glob(os.path.join(os.getenv('COMIN_GES'), 'gdas.*.ocnf003.nc'))[0]
-ufsda.disk_utils.symlink(diag_ic, os.path.join(comout, 'analysis', 'INPUT', 'MOM.res.nc'))
+ufsda.disk_utils.symlink(diag_ic, os.path.join(anl_dir, 'INPUT', 'MOM.res.nc'))
 
 # prepare input.nml
 mom_input_nml_src = os.path.join(gdas_home, 'parm', 'soca', 'fms', 'input.nml')

test/soca/CMakeLists.txt

@@ -91,7 +91,7 @@ add_test(NAME test_gdasapp_soca_ana_prep
 # -----------------------------------------
 add_test(NAME test_gdasapp_soca_ana_run
          COMMAND ${PROJECT_SOURCE_DIR}/test/soca/test_run.sh ${PROJECT_BINARY_DIR} ${PROJECT_SOURCE_DIR}
-         WORKING_DIRECTORY ${PROJECT_BINARY_DIR}/test/soca/3dvar/analysis)
+         WORKING_DIRECTORY ${PROJECT_BINARY_DIR}/test/soca/3dvar/ocnanal_2018041512)
 set_tests_properties(test_gdasapp_soca_ana_run
       PROPERTIES
           DEPENDS "test_gdasapp_soca_ana_prep"

test/soca/runtime_vars.sh

@@ -14,7 +14,7 @@ export PDY=20180415
 export cyc=12
 export assim_freq=6            # DA window
 export COMOUT=${project_binary_dir}/test/soca/3dvar
-export DATA=${COMOUT}/analysis
+export DATA=${project_binary_dir}/test/soca/3dvar/ocnanal_${CDATE}
 export COMIN_OBS=${project_binary_dir}/test/soca/obs/r2d2-shared
 export COMIN_GES=${project_binary_dir}/test/soca/bkg  # Backgrounds from previous forecast
 export CASE_ANL="C48"           # TODO: Replace with or add OCNRES

test/soca/test_prep.sh

@@ -7,8 +7,7 @@ project_source_dir=$2
 source ${project_source_dir}/test/soca/test_utils.sh
 
 # Remove previously fetched obs
-rm -f ${project_binary_dir}/test/soca/3dvar/gdas.t12z.sst*.nc4
-rm -f ${project_binary_dir}/test/soca/3dvar/gdas.t12z.adt*.nc4
+rm -f ${project_binary_dir}/test/soca/3dvar/gdas.t12z.{sst,adt,sss,salt}*.nc4
 
 # Export runtime env. variables
 source ${project_source_dir}/test/soca/runtime_vars.sh $project_binary_dir $project_source_dir
@@ -30,7 +29,7 @@ ${project_source_dir}/scripts/exgdas_global_marine_analysis_prep.py
 
 # Test that the obs path in var.yaml exist
 echo "============================= Testing the existence of obs and bkg in var.vaml"
-obslist=`grep 'gdas.t12z' $COMOUT/analysis/var.yaml`
+obslist=`grep 'gdas.t12z' ${DATA}/var.yaml`
 for o in $obslist; do
     echo "----------------------- "$o
     case $o in
@@ -52,9 +51,9 @@ done
 
 # Test that the static files have been linked properly
 echo "============================= Test that the static files have been linked properly"
-test_file $(readlink ${project_binary_dir}/test/soca/3dvar/analysis/diag_table)
-test_file $(readlink ${project_binary_dir}/test/soca/3dvar/analysis/field_table)
-test_file $(readlink ${project_binary_dir}/test/soca/3dvar/analysis/fields_metadata.yaml)
-test_file $(readlink ${project_binary_dir}/test/soca/3dvar/analysis/godas_sst_bgerr.nc)
-test_file $(readlink ${project_binary_dir}/test/soca/3dvar/analysis/rossrad.dat)
-test_file $(readlink ${project_binary_dir}/test/soca/3dvar/analysis/MOM_input)
+test_file $(readlink ${DATA}/diag_table)
+test_file $(readlink ${DATA}/field_table)
+test_file $(readlink ${DATA}/fields_metadata.yaml)
+test_file $(readlink ${DATA}/godas_sst_bgerr.nc)
+test_file $(readlink ${DATA}/rossrad.dat)
+test_file $(readlink ${DATA}/MOM_input)

test/soca/test_run.sh

@@ -8,14 +8,14 @@ source ${project_source_dir}/test/soca/test_utils.sh
 
 # Clean test files created during a previous test
 echo "============================= Test that the grid has been generated"
-rm -f ${project_binary_dir}/test/soca/3dvar/analysis/soca_gridspec.nc
-rm -f  ${project_binary_dir}/test/soca/3dvar/analysis/ocn.bkgerr_stddev.incr.2018-04-15T09:00:00Z.nc
-rm -f  ${project_binary_dir}/test/soca/3dvar/analysis/Data/ocn.iter1.incr.2018-04-15T09:00:00Z.nc
-rm -f  ${project_binary_dir}/test/soca/3dvar/analysis/Data/ocn.3dvarfgat_pseudo.incr.2018-04-15T09:00:00Z.nc
-rm -f  ${project_binary_dir}/test/soca/3dvar/analysis/Data/ocn.3dvarfgat_pseudo.an.2018-04-15T09:00:00Z.nc
-rm -f  ${project_binary_dir}/test/soca/3dvar/analysis/Data/ocn.3dvarfgat_pseudo.an.2018-04-15T12:00:00Z.nc
-rm -f  ${project_binary_dir}/test/soca/3dvar/analysis/Data/ocn.3dvarfgat_pseudo.an.2018-04-15T15:00:00Z.nc
-rm -f  ${project_binary_dir}/test/soca/3dvar/analysis/Data/inc.nc
+rm -f  ${DATA}/soca_gridspec.nc
+rm -f  ${DATA}/ocn.bkgerr_stddev.incr.2018-04-15T09:00:00Z.nc
+rm -f  ${DATA}/Data/ocn.iter1.incr.2018-04-15T09:00:00Z.nc
+rm -f  ${DATA}/Data/ocn.3dvarfgat_pseudo.incr.2018-04-15T09:00:00Z.nc
+rm -f  ${DATA}/Data/ocn.3dvarfgat_pseudo.an.2018-04-15T09:00:00Z.nc
+rm -f  ${DATA}/Data/ocn.3dvarfgat_pseudo.an.2018-04-15T12:00:00Z.nc
+rm -f  ${DATA}/Data/ocn.3dvarfgat_pseudo.an.2018-04-15T15:00:00Z.nc
+rm -f  ${DATA}/Data/inc.nc
 
 # Export runtime env. variables
 source ${project_source_dir}/test/soca/runtime_vars.sh $project_binary_dir $project_source_dir
@@ -25,15 +25,15 @@ echo "============================= Testing exgdas_global_marine_analysis_run.sh
 ${project_source_dir}/scripts/exgdas_global_marine_analysis_run.sh > exgdas_global_marine_analysis_run.log
 
 echo "============================= Test that the grid has been generated"
-test_file  ${project_binary_dir}/test/soca/3dvar/analysis/soca_gridspec.nc
+test_file  ${DATA}/soca_gridspec.nc
 
 echo "============================= Test that the parametric diag of B was generated"
-test_file  ${project_binary_dir}/test/soca/3dvar/analysis/ocn.bkgerr_stddev.incr.2018-04-15T09:00:00Z.nc
+test_file  ${DATA}/ocn.bkgerr_stddev.incr.2018-04-15T09:00:00Z.nc
 
 echo "============================= Test that an increment and an analysis were created"
-test_file  ${project_binary_dir}/test/soca/3dvar/analysis/Data/ocn.iter1.incr.2018-04-15T09:00:00Z.nc
-test_file  ${project_binary_dir}/test/soca/3dvar/analysis/Data/ocn.3dvarfgat_pseudo.incr.2018-04-15T09:00:00Z.nc
-test_file  ${project_binary_dir}/test/soca/3dvar/analysis/Data/ocn.3dvarfgat_pseudo.an.2018-04-15T09:00:00Z.nc
-test_file  ${project_binary_dir}/test/soca/3dvar/analysis/Data/ocn.3dvarfgat_pseudo.an.2018-04-15T12:00:00Z.nc
-test_file  ${project_binary_dir}/test/soca/3dvar/analysis/Data/ocn.3dvarfgat_pseudo.an.2018-04-15T15:00:00Z.nc
-test_file  ${project_binary_dir}/test/soca/3dvar/analysis/Data/inc.nc
+test_file  ${DATA}/Data/ocn.iter1.incr.2018-04-15T09:00:00Z.nc
+test_file  ${DATA}/Data/ocn.3dvarfgat_pseudo.incr.2018-04-15T09:00:00Z.nc
+test_file  ${DATA}/Data/ocn.3dvarfgat_pseudo.an.2018-04-15T09:00:00Z.nc
+test_file  ${DATA}/Data/ocn.3dvarfgat_pseudo.an.2018-04-15T12:00:00Z.nc
+test_file  ${DATA}/Data/ocn.3dvarfgat_pseudo.an.2018-04-15T15:00:00Z.nc
+test_file  ${DATA}/Data/inc.nc

ush/ufsda/disk_utils.py

@@ -52,12 +52,15 @@ def copyfile(src, dest):
         logging.info(f"copy of {src} to {dest}")
 
 
-def symlink(src, dest):
+def symlink(src, dest, remove=True):
     try:
         os.symlink(src, dest)
         logging.info(f"Symbolically linked {src} to {dest}")
     except FileExistsError:
-        os.remove(dest)
-        logging.info(f"{dest} exists, removing...")
-        os.symlink(src, dest)
-        logging.info(f"Symbolically linked {src} to {dest}")
+        if remove:
+            os.remove(dest)
+            logging.info(f"{dest} exists, removing...")
+            os.symlink(src, dest)
+            logging.info(f"Symbolically linked {src} to {dest}")
+        else:
+            logging.info(f"{dest} exists, do nothing.")

ush/ufsda/stage.py

@@ -377,8 +377,8 @@ def background(config):
     """
     rst_dir = os.path.join(config['background_dir'], 'RESTART')
     ges_dir = os.path.join(config['background_dir'], 'RESTART_GES')
-    jedi_bkg_dir = os.path.join(config['COMOUT'], 'analysis', 'bkg')
-    jedi_anl_dir = os.path.join(config['COMOUT'], 'analysis', 'anl')
+    jedi_bkg_dir = os.path.join(config['DATA'], 'bkg')
+    jedi_anl_dir = os.path.join(config['DATA'], 'anl')
 
     # copy RESTART to RESTART_GES
     try:
@@ -400,15 +400,11 @@ def obs(config):
     based on input `config` dict
     """
     # create directory
-    obs_dir = os.path.join(config['COMOUT'], 'analysis', 'obs')
+    obs_dir = os.path.join(config['DATA'], 'obs')
     mkdir(obs_dir)
     for ob in config['observers']:
         obname = ob['obs space']['name'].lower()
         outfile = ob['obs space']['obsdatain']['engine']['obsfile']
-        # the above path is what 'FV3-JEDI' expects, need to modify it
-        outpath = outfile.split('/')
-        outpath[0] = 'analysis'
-        outpath = '/'.join(outpath)
         # grab obs using R2D2
         window_begin = config['window begin']
         window_begin = parser.parse(window_begin, fuzzy=True)