Clean up code

E3SM-Project · May 23, 2024 · 10451af · 10451af
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Showing 9 changed files with 76 additions and 113 deletions.
diff --git a/tests/integration/generated/test_bundles_chrysalis.cfg b/tests/integration/generated/test_bundles_chrysalis.cfg
@@ -7,11 +7,11 @@ input = "/lcrc/group/e3sm/ac.forsyth2/E3SMv2/v2.LR.historical_0201"
 input_subdir = archive/atm/hist
 mapping_file = "map_ne30pg2_to_cmip6_180x360_aave.20200201.nc"
 # To run this test, edit `output` and `www` in this file, along with `actual_images_dir` in test_bundles.py
-output = "/lcrc/group/e3sm/ac.forsyth2/zppy_test_bundles_output/test-346/v2.LR.historical_0201"
+output = "/lcrc/group/e3sm/ac.forsyth2/zppy_test_bundles_output/unique_id/v2.LR.historical_0201"
 partition = "compute"
 qos = "regular"
 walltime = "07:00:00"
-www = "/lcrc/group/e3sm/public_html/diagnostic_output/ac.forsyth2/zppy_test_bundles_www/test-346"
+www = "/lcrc/group/e3sm/public_html/diagnostic_output/ac.forsyth2/zppy_test_bundles_www/unique_id"
 
 [bundle]
 

diff --git a/tests/integration/generated/test_complete_run_chrysalis.cfg b/tests/integration/generated/test_complete_run_chrysalis.cfg
@@ -7,10 +7,10 @@ input = "/lcrc/group/e3sm/ac.forsyth2//E3SMv2/v2.LR.historical_0201"
 input_subdir = archive/atm/hist
 mapping_file = "map_ne30pg2_to_cmip6_180x360_aave.20200201.nc"
 # To run this test, edit `output` and `www` in this file, along with `actual_images_dir` in test_complete_run.py
-output = "/lcrc/group/e3sm/ac.forsyth2/zppy_test_complete_run_output/test-346/v2.LR.historical_0201"
+output = "/lcrc/group/e3sm/ac.forsyth2/zppy_test_complete_run_output/unique_id/v2.LR.historical_0201"
 partition = "debug"
 qos = "regular"
-www = "/lcrc/group/e3sm/public_html/diagnostic_output/ac.forsyth2/zppy_test_complete_run_www/test-346"
+www = "/lcrc/group/e3sm/public_html/diagnostic_output/ac.forsyth2/zppy_test_complete_run_www/unique_id"
 
 [climo]
 active = True
@@ -134,7 +134,7 @@ years = "1850:1854:2", "1850:1854:4",
   ref_name = "v2.LR.historical_0201"
   ref_start_yr = 1850
   ref_years = "1850-1851",
-  reference_data_path = "/lcrc/group/e3sm/ac.forsyth2/zppy_test_complete_run_output/test-346/v2.LR.historical_0201/post/atm/180x360_aave/clim"
+  reference_data_path = "/lcrc/group/e3sm/ac.forsyth2/zppy_test_complete_run_output/unique_id/v2.LR.historical_0201/post/atm/180x360_aave/clim"
   run_type = "model_vs_model"
   short_ref_name = "v2.LR.historical_0201"
   swap_test_ref = False
@@ -155,7 +155,7 @@ years = "1850:1854:2", "1850:1854:4",
   ref_name = "v2.LR.historical_0201"
   ref_start_yr = 1850
   ref_years = "1850-1851",
-  reference_data_path = "/lcrc/group/e3sm/ac.forsyth2/zppy_test_complete_run_output/test-346/v2.LR.historical_0201/post/lnd/180x360_aave/clim"
+  reference_data_path = "/lcrc/group/e3sm/ac.forsyth2/zppy_test_complete_run_output/unique_id/v2.LR.historical_0201/post/lnd/180x360_aave/clim"
   run_type = "model_vs_model"
   sets = "lat_lon_land",
   short_ref_name = "same simulation"

diff --git a/tests/integration/generated/test_debug_chrysalis.cfg b/tests/integration/generated/test_debug_chrysalis.cfg
@@ -12,53 +12,46 @@ environment_commands = ""
 input = "/lcrc/group/e3sm/ac.forsyth2//E3SMv2/v2.LR.historical_0201"
 input_subdir = archive/atm/hist
 mapping_file = "map_ne30pg2_to_cmip6_180x360_aave.20200201.nc"
-output = "/lcrc/group/e3sm/ac.forsyth2/zppy_test_debug_output/test-346/v2.LR.historical_0201"
+# To run this test, edit `output` and `www` in this file, along with `actual_images_dir` in test_complete_run.py
+output = "/lcrc/group/e3sm/ac.forsyth2/zppy_test_debug_output/unique_id/v2.LR.historical_0201"
 partition = "debug"
 qos = "regular"
-www = "/lcrc/group/e3sm/public_html/diagnostic_output/ac.forsyth2/zppy_test_debug_www/test-346"
+www = "/lcrc/group/e3sm/public_html/diagnostic_output/ac.forsyth2/zppy_debug_www/unique_id"
 
 [ts]
 active = True
-e3sm_to_cmip_environment_commands = ""
 walltime = "00:30:00"
 years = "1850:1854:2",
 
-  [[ atm_monthly_glb ]]
-  # Note global average won't work for 3D variables.
+  [[ atm_monthly_180x360_aave ]]
   frequency = "monthly"
   input_files = "eam.h0"
   input_subdir = "archive/atm/hist"
-  mapping_file = "glb"
-  years = "1850:1860:5",
+  ts_fmt = "cmip"
 
-  [[ lnd_monthly_glb ]]
+  [[ atm_daily_180x360_aave ]]
+  frequency = "daily"
+  input_files = "eam.h1"
+  input_subdir = "archive/atm/hist"
+  vars = "PRECT"
+
+  [[ land_monthly ]]
+  e3sm_to_cmip_environment_commands = ""
+  extra_vars = "landfrac"
   frequency = "monthly"
   input_files = "elm.h0"
   input_subdir = "archive/lnd/hist"
-  mapping_file = "glb"
   vars = "LAISHA,LAISUN"
-  years = "1850:1860:5",
+  #vars = "FSH,RH2M"
+  ts_fmt = "cmip"
 
-[mpas_analysis]
+[ilamb]
 active = True
-anomalyRefYear = 1850
-climo_years ="1850-1854", "1855-1860",
-enso_years = "1850-1854", "1855-1860",
-mesh = "EC30to60E2r2"
-parallelTaskCount = 6
+grid = '180x360_aave'
+nodes = 8
 partition = "compute"
-qos = "regular"
-ts_years = "1850-1854", "1850-1860",
-walltime = "00:30:00"
+short_name = 'v2.LR.historical_0201'
+ts_num_years = 2
+years = "1850:1854:2",
 
-[global_time_series]
-active = True
-climo_years ="1850-1854", "1855-1860",
-experiment_name = "v2.LR.historical_0201"
-figstr = "v2_historical_0201"
-moc_file=mocTimeSeries_1850-1860.nc
-plots_lnd = "LAISHA,LAISUN"
-ts_num_years = 5
-ts_years = "1850-1854", "1850-1860",
-walltime = "00:30:00"
-years = "1850-1860",
+  [[ land_monthly ]]
diff --git a/tests/integration/generated/update_bundles_expected_files_chrysalis.sh b/tests/integration/generated/update_bundles_expected_files_chrysalis.sh
@@ -6,9 +6,9 @@
 rm -rf /lcrc/group/e3sm/public_html/zppy_test_resources/expected_bundles
 # Your output will now become the new expectation.
 # Copy output so you don't have to rerun zppy to generate the output.
-cp -r /lcrc/group/e3sm/public_html/diagnostic_output/ac.forsyth2/zppy_test_bundles_www/test-346/v2.LR.historical_0201 /lcrc/group/e3sm/public_html/zppy_test_resources/expected_bundles
+cp -r /lcrc/group/e3sm/public_html/diagnostic_output/ac.forsyth2/zppy_test_bundles_www/unique_id/v2.LR.historical_0201 /lcrc/group/e3sm/public_html/zppy_test_resources/expected_bundles
 mkdir -p /lcrc/group/e3sm/public_html/zppy_test_resources/expected_bundles/bundle_files
-cp -r /lcrc/group/e3sm/ac.forsyth2/zppy_test_bundles_output/test-346/v2.LR.historical_0201/post/scripts/bundle*.bash /lcrc/group/e3sm/public_html/zppy_test_resources/expected_bundles/bundle_files
+cp -r /lcrc/group/e3sm/ac.forsyth2/zppy_test_bundles_output/unique_id/v2.LR.historical_0201/post/scripts/bundle*.bash /lcrc/group/e3sm/public_html/zppy_test_resources/expected_bundles/bundle_files
 zppy_top_level=$(pwd)
 cd /lcrc/group/e3sm/public_html/zppy_test_resources/expected_bundles
 # Remove the image check failures, so they don't end up in the expected files.

diff --git a/tests/integration/generated/update_complete_run_expected_files_chrysalis.sh b/tests/integration/generated/update_complete_run_expected_files_chrysalis.sh
@@ -6,7 +6,7 @@
 rm -rf /lcrc/group/e3sm/public_html/zppy_test_resources/expected_complete_run
 # Your output will now become the new expectation.
 # Copy output so you don't have to rerun zppy to generate the output.
-cp -r /lcrc/group/e3sm/public_html/diagnostic_output/ac.forsyth2/zppy_test_complete_run_www/test-346/v2.LR.historical_0201 /lcrc/group/e3sm/public_html/zppy_test_resources/expected_complete_run
+cp -r /lcrc/group/e3sm/public_html/diagnostic_output/ac.forsyth2/zppy_test_complete_run_www/unique_id/v2.LR.historical_0201 /lcrc/group/e3sm/public_html/zppy_test_resources/expected_complete_run
 zppy_top_level=$(pwd)
 cd /lcrc/group/e3sm/public_html/zppy_test_resources/expected_complete_run
 # Remove the image check failures, so they don't end up in the expected files.

diff --git a/tests/integration/template_debug.cfg b/tests/integration/template_debug.cfg
@@ -12,53 +12,46 @@ environment_commands = "#expand environment_commands#"
 input = "#expand user_input#/E3SMv2/v2.LR.historical_0201"
 input_subdir = archive/atm/hist
 mapping_file = "map_ne30pg2_to_cmip6_180x360_aave.20200201.nc"
+# To run this test, edit `output` and `www` in this file, along with `actual_images_dir` in test_complete_run.py
 output = "#expand user_output#zppy_test_debug_output/#expand unique_id#/v2.LR.historical_0201"
 partition = "#expand partition_short#"
 qos = "#expand qos_short#"
-www = "#expand user_www#zppy_test_debug_www/#expand unique_id#"
+www = "#expand user_www#zppy_debug_www/#expand unique_id#"
 
 [ts]
 active = True
-e3sm_to_cmip_environment_commands = "#expand e3sm_to_cmip_environment_commands#"
 walltime = "00:30:00"
 years = "1850:1854:2",
 
-  [[ atm_monthly_glb ]]
-  # Note global average won't work for 3D variables.
+  [[ atm_monthly_180x360_aave ]]
   frequency = "monthly"
   input_files = "eam.h0"
   input_subdir = "archive/atm/hist"
-  mapping_file = "glb"
-  years = "1850:1860:5",
+  ts_fmt = "cmip"
 
-  [[ lnd_monthly_glb ]]
+  [[ atm_daily_180x360_aave ]]
+  frequency = "daily"
+  input_files = "eam.h1"
+  input_subdir = "archive/atm/hist"
+  vars = "PRECT"
+
+  [[ land_monthly ]]
+  e3sm_to_cmip_environment_commands = "#expand e3sm_to_cmip_environment_commands#"
+  extra_vars = "landfrac"
   frequency = "monthly"
   input_files = "elm.h0"
   input_subdir = "archive/lnd/hist"
-  mapping_file = "glb"
   vars = "LAISHA,LAISUN"
-  years = "1850:1860:5",
+  #vars = "FSH,RH2M"
+  ts_fmt = "cmip"
 
-[mpas_analysis]
+[ilamb]
 active = True
-anomalyRefYear = 1850
-climo_years ="1850-1854", "1855-1860",
-enso_years = "1850-1854", "1855-1860",
-mesh = "EC30to60E2r2"
-parallelTaskCount = 6
+grid = '180x360_aave'
+nodes = 8
 partition = "#expand partition_long#"
-qos = "#expand qos_long#"
-ts_years = "1850-1854", "1850-1860",
-walltime = "#expand mpas_analysis_walltime#"
+short_name = 'v2.LR.historical_0201'
+ts_num_years = 2
+years = "1850:1854:2",
 
-[global_time_series]
-active = True
-climo_years ="1850-1854", "1855-1860",
-experiment_name = "v2.LR.historical_0201"
-figstr = "v2_historical_0201"
-moc_file=mocTimeSeries_1850-1860.nc
-plots_lnd = "LAISHA,LAISUN"
-ts_num_years = 5
-ts_years = "1850-1854", "1850-1860",
-walltime = "00:30:00"
-years = "1850-1860",
+  [[ land_monthly ]]
diff --git a/tests/integration/utils.py b/tests/integration/utils.py
@@ -7,7 +7,7 @@
 from mache import MachineInfo
 from PIL import Image, ImageChops, ImageDraw
 
-UNIQUE_ID = "test-346"
+UNIQUE_ID = "unique_id"
 
 # Image checking ##########################################################
 

diff --git a/zppy/templates/coupled_global.py b/zppy/templates/coupled_global.py
@@ -11,7 +11,6 @@
 import matplotlib.pyplot as plt
 import numpy as np
 import xarray
-import xcdat  # noqa: F401
 from netCDF4 import Dataset
 from readTS import TS
 
@@ -586,7 +585,7 @@ def set_var(
                     n = 2
                 else:
                     raise RuntimeError(f"Invalid rgn={rgn}")
-                v = v.isel(rgn=n)  # Just use nth column
+                v = v.isel(rgn=n)  # Just use nth region
             elif rgn != "glb":
                 # v only has one dimension -- glb.
                 # Therefore it is not possible to get n or s plots.
@@ -749,24 +748,24 @@ def run(parameters, rgn):  # noqa: C901
     use_ocn = plots_ocn or (not atmosphere_only and has_original_ocn_plots)
     exps: List[Dict[str, Any]] = [
         {
-            "atmos": None
-            if not use_atmos
-            else "{}/post/atm/glb/ts/monthly/{}yr/".format(case_dir, ts_num_years),
-            "ice": None
-            if not plots_ice
-            else "{}/post/ice/glb/ts/monthly/{}yr/".format(case_dir, ts_num_years),
-            "land": None
-            if not plots_lnd
-            else "{}/post/lnd/glb/ts/monthly/{}yr/".format(case_dir, ts_num_years),
-            "ocean": None
-            if not use_ocn
-            else "{}/post/ocn/glb/ts/monthly/{}yr/".format(case_dir, ts_num_years),
-            "moc": None
-            if not use_ocn
-            else "{}/post/ocn/glb/ts/monthly/{}yr/".format(case_dir, ts_num_years),
-            "vol": None
-            if not use_ocn
-            else "{}/post/ocn/glb/ts/monthly/{}yr/".format(case_dir, ts_num_years),
+            "atmos": f"{case_dir}/post/atm/glb/ts/monthly/{ts_num_years}yr/"
+            if use_atmos
+            else None,
+            "ice": f"{case_dir}/post/ice/glb/ts/monthly/{ts_num_years}yr/"
+            if plots_ice
+            else None,
+            "land": f"{case_dir}/post/lnd/glb/ts/monthly/{ts_num_years}yr/"
+            if plots_lnd
+            else None,
+            "ocean": f"{case_dir}/post/ocn/glb/ts/monthly/{ts_num_years}yr/"
+            if use_ocn
+            else None,
+            "moc": f"{case_dir}/post/ocn/glb/ts/monthly/{ts_num_years}yr/"
+            if use_ocn
+            else None,
+            "vol": f"{case_dir}/post/ocn/glb/ts/monthly/{ts_num_years}yr/"
+            if use_ocn
+            else None,
             "name": experiment_name,
             "yoffset": 0.0,
             "yr": ([year1, year2],),
@@ -856,27 +855,5 @@ def run_by_region(parameters):
         run(parameters, rgn)
 
 
-def debug():
-    args = [
-        "coupled_global.py",
-        "/lcrc/group/e3sm/ac.forsyth2/zppy_test_debug_output/test-346/v2.LR.historical_0201",
-        "v2.LR.historical_0201",
-        "v2_historical_0201",
-        "1850",
-        "1860",
-        "Blue",
-        "5",
-        "net_toa_flux_restom,global_surface_air_temperature,toa_radiation,net_atm_energy_imbalance,change_ohc,max_moc,change_sea_level,net_atm_water_imbalance",
-        "False",
-        "None",
-        "None",
-        "LAISHA,LAISUN",
-        "None",
-        "glb,n,s",
-    ]
-    run_by_region(args)
-
-
 if __name__ == "__main__":
     run_by_region(sys.argv)
-    # debug()
diff --git a/zppy/templates/e3sm_diags.bash b/zppy/templates/e3sm_diags.bash
@@ -108,7 +108,7 @@ create_links_ts()
     # xml file will cover the whole period from year1 to year2
     xml_name=${v}_${begin_year}01_${end_year}12.xml
     export CDMS_NO_MPI=true
-    cdscan ${xml_name} ${v}_files.txt
+    cdscan -x ${xml_name} -f ${v}_files.txt
     if [ $? != 0 ]; then
       cd {{ scriptDir }}
       echo "ERROR (${error_num})" > {{ prefix }}.status
@@ -129,7 +129,7 @@ create_links_ts_rof()
   cd ${ts_rof_dir_destination}
   v="RIVER_DISCHARGE_OVER_LAND_LIQ"
   xml_name=${v}_${begin_year}01_${end_year}12.xml
-  cdscan ${xml_name} ${ts_rof_dir_source}/${v}_*.nc
+  cdscan -x ${xml_name} ${ts_rof_dir_source}/${v}_*.nc
   if [ $? != 0 ]; then
     cd {{ scriptDir }}
     echo "ERROR (${error_num})" > {{ prefix }}.status