Merge pull request #1272 from razamora-nasa/fix/s2s_75patch

Fix/s2s 75patch

lis/dataassim/perturb/gmaopert/gmaopert_Mod.F90

@@ -2036,6 +2036,7 @@ subroutine gmaopert_readrestart()
       integer, allocatable      :: pertdata1d_obs_int(:)
       integer, allocatable      :: pertdata1d_patch_int(:)
       real, allocatable         :: dummy_var(:,:,:)
+      logical                   :: file_exists
 
       do n = 1, LIS_rc%nnest
 
@@ -2062,6 +2063,13 @@ subroutine gmaopert_readrestart()
             endif
          endif
 
+         inquire( file=trim(LIS_rc%pertRestartFile(n)), exist=file_exists ) 
+         if(file_exists .neqv. .true.) then
+            write(LIS_logunit,*) '[ERR] Reading perturbations restart file MISSING: ',&
+                  trim(LIS_rc%pertRestartFile(n))
+            call LIS_endrun()
+         endif
+
          open(ftn,file=trim(LIS_rc%pertRestartFile(n)), form='unformatted')
          write(LIS_logunit,*) '[INFO] Reading perturbations restart file ',&
               trim(LIS_rc%pertRestartFile(n))

lis/utils/usaf/s2s/README_GHI-S2S_LIS7.5

@@ -3,7 +3,7 @@
  Subseasonal-to-Seasonal (S2S) End-to-End System (E2ES) Master Doc
 
   NASA/GSFC GHI-S2S Team 
-  Last Modified 30 November 2022
+  Last Modified 01 February 2023
 
 		TABLE OF CONTENTS
 		_________________
@@ -103,12 +103,11 @@ Postprocessing of LIS-based NoahMP4.0.1 and HYMAP2 is supported in terms
   LISFDIR: [DIRECTORY_PATH_OF_YOUR_LISF_TOP-LEVEL-CODE_DIRECTORY]
   E2ESDIR: [YOUR_LOCAL_WORKING-RUN_DIRECTORY_PATH]
   METFORC: [MAIN_USAF_FORCING_AND_SATELLITE_DATA_DIRECTORY_PATH]
-  AF10KM:  [YOUR_GLOBAL_USAF_FORCING_GRIB_INPUT_DIRECTORY_PATH]
   LISFMOD: lisf_7.5_intel_2021.4.0_s2s  [OR LOCAL MACHINE LISF MODULE LIBRARY LIST]
   SPCODE: s1189    [YOUR LOCAL MACHINE GROUPID CODE]
   DATATYPE: forecast  [OPTIONS INCLUDE:  "forecast" or "hindcast"]
   supplementarydir:  [YOUR GHI_S2S/supplementary_files DIRECTORY PATH WITH RUNTIME INPUT FILES]
-  ldtinputfile:  [PATH FOR LDT-GENERATED MODEL INPUT PARAMETER FILE] 
+  ldtinputfile:  [FILENAME FOR THE LDT-GENERATED MODEL INPUT PARAMETER FILE] 
 
   * The "ldtinputfile" file will be provided as part of the E2ES 
     use-case input file package, with the naming convention of:
@@ -325,20 +324,49 @@ Postprocessing of LIS-based NoahMP4.0.1 and HYMAP2 is supported in terms
 
   4.1 DOWNLOADING FORECAST INPUT FORCINGS
 
-    4.1.1 Downloading CFSv2 forcings
+    4.1.1 Downloading CFSv2 forcing files
 
     - To download the CFSv2 forecast files used for the forecast
        E2ES setup, the following script has been provided for reference:
 
        s2s_app/wget_cfsv2_oper_ts_e2es.sh   
+
+    * Note: We have observed on a rare occasion that some CFSv2 files
+        posted by NCEP/NCEI could be corrupted. Currently, the approach
+        we have used is to run the below steps, and if a file may be corrupted,
+        then the download will stop or crash the E2E runtime. 
+        Here is a solution that we have tested for such situations:
+
+       a) Delete the month that just crashed
+
+           s2s_app/s2s_run.sh -y YEAR -m MONTH -c CONFIG_FILE -d Y
+
+       b) Apply criterion to choose an appropriate file to be used for patch,
+         and add a line to:
+
+           supplementary_files/bcsd_fcst/patch_files/patch_files_list.txt
+
+       c) Rerun E2ES.
+
 
-    4.1.2 Downloading NMME precipitation forcings
+    4.1.2 Downloading NMME precipitation forcing files
 
     - To download the NMME forecast files used for the forecast
        E2ES setup, the following script has been provided for reference:
 
        s2s_app/download_nmme_precip.sh
 
+    * Note: Based on experience, we have found that IRI/Columbia University
+         can take about 8-10 days to upload all NMME model-based files. When running
+         the above script and if not all precipitation files are available yet,
+         a message will be given be along with the following option, for example:
+
+       Precipitation forecasts are available for only 2 NMME models (GEOS5v2 CCM4). 
+       Do you want to continue (Y/N)?
+
+     We recommend the user to wait until all files are available on the IRI/Columbia
+      University server before trying to complete the remaining E2E steps. 
+
 
   4.2 GLOBAL USAF FORCING (Stand-alone step from E2ES)
     global_usaf_forc:  Generate AGRMET Ops atmospheric forcing for S2S
@@ -548,21 +576,20 @@ THIS COMPLETES ALL STEPS IN THE E2ES SEQUENCE.
  ------------------------------
  ├── bcsd_fcst
  │   ├── bcsd_library
- │   │   ├── BCSD_functionfast.py
- │   │   ├── BCSD_function.py
- │   │   ├── BCSD_stats_functions.py
+ │   │   ├── bcsd_function.py
+ │   │   ├── bcsd_stats_functions.py
  │   │   ├── bias_correction_modulefast.py
  │   │   ├── bias_correction_nmme_modulefast.py
- │   │   ├── Calc_and_Write_forecast_climatology.py
- │   │   ├── Calc_and_Write_NMME_forecast_climatology.py
- │   │   ├── Calc_and_Write_observational_climatology.py
+ │   │   ├── calc_and_write_forecast_climatology.py
+ │   │   ├── calc_and_write_nmme_forecast_climatology.py
+ │   │   ├── calc_and_write_observational_climatology.py
  │   │   ├── combine_sub_daily_downscaled_forcings.py
  │   │   ├── convert_forecast_data_to_netcdf.py
  │   │   ├── NMME_CFSv2reorg_H.py
  │   │   ├── nmme_reorg_f.py
  │   │   ├── nmme_reorg_h.py
  │   │   ├── process_forecast_data.py
- │   │   ├── Shrad_modules.py
+ │   │   ├── shrad_modules.py
  │   │   ├── temporal_disaggregation_6hourly_module.py
  │   │   └── temporal_disaggregation_nmme_6hourly_module.py
  │   ├── check_preprocess_forecast_files.py

lis/utils/usaf/s2s/s2s_app/nctool.py

@@ -8,32 +8,35 @@
        (2) compare 2 netcdf files
            a) check closeness at absolute tolerance of 1.e-3: nctool.py file1 file2
            b) check whether the 2 files are identical: nctool.py file1 file2 zero_diff
-       (3) compare all netcdf files with similar names in two directories (including sub directories)
+       (3) compare all netcdf files with similar names in two directories
+              (including sub directories)
            a) check closeness at absolute tolerance of 1.e-3: nctool.py directory1 directory2
            b) check whether the 2 are identical: nctool.py directory1 directory2 zero_diff
        (4) This is also good to print variable value[s] at a specific location. First ncdump -h
            and get exact names of lat, lon and the variable as in the netCDF header.
            nctool.py lat lon latname longname var_name filename
            for e.g.
-           python nctool.py 39.875 25.875 lat lon Evap_tavg /gpfsm/dnb06/projects/p159/GHI_S2S/AFRICOM/E2ES/NRT/lis_darun/output/SURFACEMODEL/202204/LIS_HIST_202204010000.d01.nc
-           python nctool.py -0.8486657635296301 32.97690772217679 latitude longitude anom /gpfsm/dnb06/projects/p159/GHI_S2S/AFRICOM/E2ES/NRT/s2smetric/output/202203/DYN_ANOM/AFRICOM/NOAHMP/GNEMO5_Surface-SM_ANOM_init_monthly_03_2022.nc
+           python nctool.py 39.875 25.875 lat lon Evap_tavg LIS_HIST_202204010000.d01.nc
+           python nctool.py -0.8486657635296301 32.97690772217679 latitude longitude anom
+                             GNEMO5_Surface-SM_ANOM_init_monthly_03_2022.nc
            when j, i indexes at the location is known
-           python nctool.py j_index i_index lat lon Evap_tavg /gpfsm/dnb06/projects/p159/GHI_S2S/AFRICOM/E2ES/NRT/lis_darun/output/SURFACEMODEL/202204/LIS_HIST_202204010000.d01.nc
+           python nctool.py j_index i_index lat lon Evap_tavg LIS_HIST_202204010000.d01.nc
 '''
 
 import os
 import sys
 import numpy as np
 import xarray as xr
 from numpy import unravel_index
-
+#pylint: disable=too-many-arguments, line-too-long
 ZERO_DIFF = False
 ATOL = 1.e-03
 
 def file_info(infile):
     ''' read file info. '''
     def print_summary (arr):
-        str_out =  'Mean :' + str(np.nanmean(arr)) + ' Max:' + str(np.nanmax(arr)) + str(unravel_index(arr.argmax(), arr.shape)) + \
+        str_out =  'Mean :' + str(np.nanmean(arr)) + ' Max:' + str(np.nanmax(arr)) + \
+            str(unravel_index(arr.argmax(), arr.shape)) + \
             ' Min :' + str(np.nanmin(arr)) + str(unravel_index(arr.argmin(), arr.shape))
         return str_out
 
@@ -80,7 +83,8 @@ def getclosest_ij(lats,lons,latpt,lonpt):
         # find squared distance of every point on grid
         dist_sq = (lats-latpt)**2 + (lons-lonpt)**2
         minindex_flattened = dist_sq.argmin()
-        return np.unravel_index(minindex_flattened, lats.shape)
+        ret = np.unravel_index(minindex_flattened, lats.shape)
+        return ret[0], ret[1]
 
     _a = xr.open_dataset(filename)
     lats = np.array(_a[latname].values)
@@ -112,35 +116,35 @@ def getclosest_ij(lats,lons,latpt,lonpt):
         if sys.argv[1] == 'help':
             print (' ')
             print ("\x1B[4m" + "\033[1m" + 'A python script to: ')
-            print ('           (i) Print summary of a netCDF file;')
-            print ('           (ii) Compare 2 individual netCDF files;')
-            print ('           (iii) Compare netCDF files in two directories including all subdirectories; and')
-            print ('           (iv) Print variable value[s] at a specific location.' + "\033[0m" + "\x1B[0m")
+            print ('(i) Print summary of a netCDF file;')
+            print ('(ii) Compare 2 individual netCDF files;')
+            print ('(iii) Compare netCDF files in 2 directories and all subdirectories; and')
+            print ('(iv) Print variable value[s] at a specific location.' + "\033[0m" + "\x1B[0m")
             print ( ' ')
-            print ("\033[1m" +    '(1) print Mean, Maximum (Maxloc) and Minimum (Minloc) of each spatial layer separately for each variable:' +  "\033[0m")
+            print ("\033[1m" + '(1) print Mean, Max (Maxloc) and Min (Minloc) of each spatial layer separately for each variable:' +  "\033[0m")
             print ('            nctool.py file_name')
             print (' ')
-            print ("\033[1m" +    '(2) Compare 2 netcdf files:' + "\033[0m")
+            print ("\033[1m" + '(2) Compare 2 netcdf files:' + "\033[0m")
             print ('         a) check closeness at absolute tolerance of 1.e-3:')
             print ('            nctool.py file1 file2')
             print ('         b) check whether the 2 files are identical:')
             print ('            nctool.py file1 file2 zero_diff')
             print (' ')
-            print ("\033[1m" +    '(3) Compare all netcdf files with similar names in two directories (including sub directories):' +  "\033[0m")
+            print ("\033[1m" + '(3) Compare all netcdf files with similar names in two directories (including sub directories):' +  "\033[0m")
             print ('         a) check closeness at absolute tolerance of 1.e-3:')
             print ('            nctool.py directory1 directory2')
             print ('         b) check whether the 2 are identical:')
             print ('            nctool.py directory1 directory2 zero_diff')
             print (' ')
-            print ("\033[1m" +    '(4) This is also good to print variable value[s] at a specific location specified by lat/lon OR J_INDEX [north-south dimension] and I_INDEX [west-east dimension] as in the netCDF file.' +  "\033[0m")
+            print ("\033[1m" + '(4) This is also good to print variable value[s] at a specific location specified by lat/lon OR J_INDEX [north-south dimension] and I_INDEX [west-east dimension] as in the netCDF file.' +  "\033[0m")
             print ('         First ncdump -h and get exact names of lat, lon and the variable from the netCDF header.')
             print ('         nctool.py lat lon latname longname var_name filename')
             print (' ')
             print ('         Example 1 (when lat/lon at the place are known - the script will map the place on the grid space and indentify the grid cell that where the place is located.): ')
-            print ('         nctool.py -0.8486657635296301 32.97690772217679 latitude longitude anom /gpfsm/dnb06/projects/p159/GHI_S2S/AFRICOM/E2ES/NRT/s2smetric/output/202203/DYN_ANOM/AFRICOM/NOAHMP/GNEMO5_Surface-SM_ANOM_init_monthly_03_2022.nc')
+            print ('         nctool.py -0.8486657635296301 32.97690772217679 latitude longitude anom GNEMO5_Surface-SM_ANOM_init_monthly_03_2022.nc')
             print (' ')
             print ('         Example 2 (when J_INDEX and I_INDEX at the location are known):')
-            print ('         nctool.py j_index i_index lat lon Evap_tavg /gpfsm/dnb06/projects/p159/GHI_S2S/AFRICOM/E2ES/NRT/lis_darun/output/SURFACEMODEL/202204/LIS_HIST_202204010000.d01.nc')
+            print ('         nctool.py j_index i_index lat lon Evap_tavg LIS_HIST_202204010000.d01.nc')
         else:
             file_info(str(sys.argv[1]))
 

lis/utils/usaf/s2s/s2s_app/s2s_config_africom

@@ -5,14 +5,14 @@
 #######################################################################
 
 SETUP:
-  LISFDIR: /discover/nobackup/projects/usaf_lis/smahanam/LISF-1/
   E2ESDIR: /discover/nobackup/projects/usaf_lis/smahanam/E2ES_AFRICOM/
-  METFORC: /discover/nobackup/projects/usaf_lis/MET_FORCING/
-  AF10KM:  /discover/nobackup/projects/usaf_lis/MET_FORCING/usaf_lis73rc8_10km/
+  METFORC: /discover/nobackup/projects/usaf_lis/GHI_S2S/USAF_FORCING/
+  supplementarydir: /discover/nobackup/projects/usaf_lis/GHI_S2S/supplementary_files/
+  LISFDIR: /discover/nobackup/projects/usaf_lis/smahanam/LISF-1/
   LISFMOD: lisf_7.5_intel_2021.4.0_s2s
   SPCODE:  s1189
+  CONSTRAINT: cssro
   DATATYPE: forecast
-  supplementarydir: /discover/nobackup/projects/usaf_lis/GHI_S2S/supplementary_files/
   ldtinputfile: lis_input.s2s_africom.noahmp401_hymap2.merit.25km.nc
 
 #######################################################################

lis/utils/usaf/s2s/s2s_app/s2s_config_global_fcst

@@ -5,14 +5,14 @@
 #######################################################################
 
 SETUP:
+  E2ESDIR: /discover/nobackup/projects/usaf_lis/smahanam/E2ES_GLOBAL_2/
+  METFORC: /discover/nobackup/projects/usaf_lis/GHI_S2S/USAF_FORCING/
+  supplementarydir: /discover/nobackup/projects/usaf_lis/GHI_S2S/supplementary_files/
   LISFDIR: /discover/nobackup/projects/usaf_lis/smahanam/LISF-1/
-  E2ESDIR: /discover/nobackup/projects/usaf_lis/smahanam/E2ES_GLOBAL/
-  METFORC: /discover/nobackup/projects/usaf_lis/USAF_FORCING/
-  AF10KM:  /discover/nobackup/projects/usaf_lis/USAF_FORCING/usaf_lis75s2s_gfs2galwem/
   LISFMOD: lisf_7.5_intel_2021.4.0_s2s
   SPCODE:  s1189
+  CONSTRAINT: cssro
   DATATYPE: forecast
-  supplementarydir: /discover/nobackup/projects/usaf_lis/GHI_S2S/supplementary_files/
   ldtinputfile: lis_input.s2s_global.noahmp401_hymap2.25km.nc
 
 #######################################################################

lis/utils/usaf/s2s/s2s_app/s2s_config_global_hcast

@@ -5,14 +5,14 @@
 #######################################################################
 
 SETUP:
-  LISFDIR: /discover/nobackup/projects/usaf_lis/smahanam/LISF-1/
   E2ESDIR: /discover/nobackup/projects/usaf_lis/smahanam/E2ES_GLOBAL/
-  METFORC: /discover/nobackup/projects/usaf_lis/USAF_FORCING/
-  AF10KM:  /discover/nobackup/projects/usaf_lis/smahanam/GLOBAL/MERRA2_CHIRPSM2_NAFPAMod_3hr_9yr/ens1/
+  METFORC: /discover/nobackup/projects/usaf_lis/GHI_S2S/USAF_FORCING/
+  supplementarydir: /discover/nobackup/projects/usaf_lis/GHI_S2S/supplementary_files/
+  LISFDIR: /discover/nobackup/projects/usaf_lis/smahanam/LISF-1/
   LISFMOD: lisf_7.5_intel_2021.4.0_s2s
   SPCODE:  s1189
+  CONSTRAINT: cssro
   DATATYPE: hindcast
-  supplementarydir: /discover/nobackup/projects/usaf_lis/GHI_S2S/supplementary_files/
   ldtinputfile: lis_input.s2s_global.noahmp401_hymap2.25km.nc
 
 #######################################################################