Merge branch 'develop' into feature/ygyu/NPW_1_file

CHANGELOG.md

@@ -9,12 +9,15 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Added
 
+- Added optional start_date and start_time to control the output window for each History collection. No output will be written before then. If not specified, these default to the beginning of the experiment.
+- Added utility to prepare inputs for ExtDatDriver.x so that ExtData can simulate a real GEOS run
 - Added loggers when writing or reading weight files
 - Added new option to AGCM.rc `overwrite_checkpoint` to allow checkpoint files to be overwritten. By default still will not overwrite checkpoints
 - Added use_NWP_1_file=1 option in Trajectory sampler (HISTORY.rc) to generate the correct location_index_ioda array, mapping back to location points in the single IODA observation input file
 
 ### Changed
 
+- Changed MAPL_ESMFRegridder to require the dstMaskValues to be added as grid attribute to use fixed masking, fixes UFS issue
 - Increased formatting width of time index in ExtData2G diagnostic print
 
 ### Fixed

Tests/generate_extdatadriver_input.md

@@ -0,0 +1,58 @@
+# Introduction
+This is a simple utility to generate inputs for ExtDataDriver.x so that ExtData can simulate a real GEOS run. It requires 3 things that are passed in
+- A list of items ExtData needs to fill. This can be found by looking at the GEOS log
+- The import spec of the GCM component from using the printspec option to GEOS
+- all the needed yaml files in a directory, name of directory is passed
+
+This will generate the import and optionally the export (as well as History) defition for ExtDataDriver.x to spare the human the tedious work.
+
+# Example Inputs
+To get the list of ExtDate items, just grab all the lines that look like this to a file:
+```
+        EXTDATA: INFO: ---- 00001: BC_AIRCRAFT
+        EXTDATA: INFO: ---- 00002: BC_ANTEBC1
+        EXTDATA: INFO: ---- 00003: BC_ANTEBC2
+        EXTDATA: INFO: ---- 00004: BC_AVIATION_CDS
+        EXTDATA: INFO: ---- 00005: BC_AVIATION_CRS
+        EXTDATA: INFO: ---- 00006: BC_AVIATION_LTO
+        EXTDATA: INFO: ---- 00007: BC_BIOFUEL
+        EXTDATA: INFO: ---- 00008: BC_BIOMASS
+        EXTDATA: INFO: ---- 00009: BC_SHIP
+        EXTDATA: INFO: ---- 00010: BRC_AIRCRAFT
+        EXTDATA: INFO: ---- 00011: BRC_ANTEBRC1
+        EXTDATA: INFO: ---- 00012: BRC_ANTEBRC2
+        EXTDATA: INFO: ---- 00013: BRC_AVIATION_CDS
+        EXTDATA: INFO: ---- 00014: BRC_AVIATION_CRS
+        EXTDATA: INFO: ---- 00015: BRC_AVIATION_LTO
+        EXTDATA: INFO: ---- 00016: BRC_BIOFUEL
+        EXTDATA: INFO: ---- 00017: BRC_BIOMASS
+        EXTDATA: INFO: ---- 00018: BRC_SHIP
+        EXTDATA: INFO: ---- 00019: BRC_TERPENE
+```
+
+To get the GCM component spec, run with `PRINTSPEC: 1` in the `CAP.rc` and copy lines out that look like this:
+```
+ #IMPORT spec for GCM
+ #COMPONENT, SHORT_NAME, LONG_NAME, UNIT, DIMS, CONTAINER_TYPE
+        GENERIC: INFO: GCM, WSUB_CLIM, stdev in vertical velocity, m s-1,   3, esmf_field
+        GENERIC: INFO: GCM, MEGAN_ORVC, MEGAN_ORVC, kgC/m2/s,   2, esmf_field
+        GENERIC: INFO: GCM, CLM4_PFT_CROP, CLM4_PFT_CROP, 1,   2, esmf_field
+        GENERIC: INFO: GCM, CLM4_PFT_C4_GRSS, CLM4_PFT_C4_GRSS, 1,   2, esmf_field
+        GENERIC: INFO: GCM, CLM4_PFT_C3_NARC_GRSS, CLM4_PFT_C3_NARC_GRSS, 1,   2, esmf_field
+        GENERIC: INFO: GCM, CLM4_PFT_C3_ARCT_GRSS, CLM4_PFT_C3_ARCT_GRSS, 1,   2, esmf_field
+        GENERIC: INFO: GCM, CLM4_PFT_BDLF_DECD_BORL_SHRB, CLM4_PFT_BDLF_DECD_BORL_SHRB, 1,   2, esmf_field
+        GENERIC: INFO: GCM, CLM4_PFT_BDLF_DECD_TMPT_SHRB, CLM4_PFT_BDLF_DECD_TMPT_SHRB, 1,   2, esmf_field
+        GENERIC: INFO: GCM, CLM4_PFT_BDLF_EVGN_SHRB, CLM4_PFT_BDLF_EVGN_SHRB, 1,   2, esmf_field
+        GENERIC: INFO: GCM, CLM4_PFT_BDLF_DECD_BORL_TREE, CLM4_PFT_BDLF_DECD_BORL_TREE, 1,   2, esmf_field
+        GENERIC: INFO: GCM, CLM4_PFT_BDLF_DECD_TMPT_TREE, CLM4_PFT_BDLF_DECD_TMPT_TREE, 1,   2, esmf_field
+        GENERIC: INFO: GCM, CLM4_PFT_BDLF_DECD_TROP_TREE, CLM4_PFT_BDLF_DECD_TROP_TREE, 1,   2, esmf_field
+        GENERIC: INFO: GCM, CLM4_PFT_BDLF_EVGN_TMPT_TREE, CLM4_PFT_BDLF_EVGN_TMPT_TREE, 1,   2, esmf_field
+        GENERIC: INFO: GCM, CLM4_PFT_BDLF_EVGN_TROP_TREE, CLM4_PFT_BDLF_EVGN_TROP_TREE, 1,   2, esmf_field
+        GENERIC: INFO: GCM, CLM4_PFT_NDLF_DECD_BORL_TREE, CLM4_PFT_NDLF_DECD_BORL_TREE, 1,   2, esmf_field
+        GENERIC: INFO: GCM, CLM4_PFT_NDLF_EVGN_BORL_TREE, CLM4_PFT_NDLF_EVGN_BORL_TREE, 1,   2, esmf_field
+        GENERIC: INFO: GCM, CLM4_PFT_NDLF_EVGN_TMPT_TREE, CLM4_PFT_NDLF_EVGN_TMPT_TREE, 1,   2, esmf_field
+```
+
+Finally just grab the right yaml files for ExtData.
+
+To run you will of course need to do some further editing of the produced files and link in the acutal data using the same convention `gcm_run.j` does.

Tests/generate_extdatadriver_input.py

@@ -0,0 +1,167 @@
+#!/usr/bin/env python3
+from yaml import load,dump
+import argparse
+import os
+import yaml
+import glob
+
+dims_dict = {"2":"xy", "3":"xyz"}
+
+def get_dims(component_map, name):
+    for comp in component_map:
+        if name in component_map[comp]:
+             dims = component_map[comp][name]["dims"]
+    return dims
+
+def get_vars_needed(input_file):
+
+    output_list = []
+    f = open(input_file,"r")
+    lines = f.readlines()
+    f.close()
+    for line in lines:
+        temp = line.split() 
+        output_list.append(temp[4])
+
+    return output_list
+
+def get_extdata_map(input_dir):
+
+    input_files = glob.glob(input_dir+"/*.yaml")
+    export_list = {}
+    for input_file in input_files:
+       f = open(input_file,'r')
+       extdata_def = yaml.safe_load(f)
+       f.close()
+       for short_name in extdata_def["Exports"]:
+           export_list.update({short_name:extdata_def["Exports"][short_name]})
+    return export_list    
+
+def get_block(cvs_file):
+
+    temp = cvs_file[0].split(' ')
+    state_type = temp[1][1:].strip()
+    component = temp[4].strip()
+    i=2
+    for line in cvs_file[2:]:
+        if "spec for" in line:
+            break
+        i=i+1
+    return component,state_type,i
+
+
+def get_component_map(cvs_file):
+
+    i_start = 0
+    i_end = 0
+    n_lines = len(cvs_file)
+    components = {}
+    while i_start < n_lines-1:
+
+       comp_name,state_type,i_end = get_block(cvs_file[i_start:])
+       comp_map = {}
+       for i in range(i_end-2):
+           line = cvs_file[i_start+2+i]
+           values = line.split(',')
+           short_name = values[1].strip()
+           long_name = values[2].strip()
+           units = values[3].strip()
+           dims = values[4].strip()
+           item_type = values[5].strip()
+           comp_map.update({short_name:{"long_name":long_name,"units":units,"item_type":item_type,"dims":dims}})
+       components.update({comp_name+"_"+state_type:comp_map})
+       i_start = i_start + i_end
+
+    return components
+
+def parse_args():
+    p = argparse.ArgumentParser(description='Generarte input files for ExtDataDriver to simulate GEOS')
+    p.add_argument('extdata_provided',type=str,help='a list of items ExtData should fill',default=None)
+    p.add_argument('spec_def',type=str,help='the GEOS gcm import state from the printspec',default=None)
+    p.add_argument('extdata_dir',type=str,help='diretory with all the yaml imputs for extdata',default=None)
+    p.add_argument('-e','--export',action='store_true',help='also include exports for corresponding imports')
+
+    return vars(p.parse_args())
+
+if __name__ == '__main__':
+
+   args = parse_args()
+
+   extdata_list = args['extdata_provided']
+   do_exports = args['export']
+   input_file = args['spec_def']
+   f = open(input_file,"r")
+   input_rc = f.readlines()
+   f.close()
+
+   extdata_directory = args['extdata_dir']
+   extdata_def = get_extdata_map(extdata_directory)
+
+   f_agcm = open("AGCM.rc",'w')
+#  component
+   component_map = {}
+   component_map = get_component_map(input_rc)
+
+   vars_needed = get_vars_needed(extdata_list)
+
+   nl = "\n"
+   cm = " , "
+
+#  Import state
+   written = []
+   f_agcm.write("IMPORT_STATE::"+nl)
+
+   for item in vars_needed:
+      if item in extdata_def:
+         long_name = "NA"
+         units = "NA"
+         dims = get_dims(component_map, item) 
+         cdims = dims_dict[dims]
+
+         if item not in written:
+            f_agcm.write(item+cm+long_name+cm+units+cm+cdims+cm+"c"+nl)
+            written.append(item)
+
+   f_agcm.write("::"+nl)
+
+#  Export state
+   if do_exports:
+       written = []
+       f_agcm.write("EXPORT_STATE::"+nl)
+       for item in vars_needed:
+          if item in extdata_def:
+             long_name = "NA"
+             units = "NA"
+             dims = get_dims(component_map, item) 
+             cdims = dims_dict[dims]
+
+             if item not in written:
+                f_agcm.write(item+cm+long_name+cm+units+cm+cdims+cm+"c"+nl)
+                written.append(item)
+
+       f_agcm.write("::"+nl)
+
+       f_hist = open("HISTORY.rc",'w')
+       f_hist.write("GRID_LABELS:"+nl)
+       f_hist.write("::"+nl)
+       f_hist.write("COLLECTIONS: my_collection"+nl)
+       f_hist.write("::"+nl)
+       f_hist.write("my_collection.template: 'nc4'"+nl)
+       f_hist.write("my_collection.format: 'CFIO'"+nl)
+       f_hist.write("my_collection.frequency: '240000'"+nl)
+       first = True
+       written = []
+       for item in vars_needed:
+          if item in extdata_def:
+             if item not in written:
+                 if first:
+                    first = False
+                    f_hist.write("my_collection.fields:'"+item+"' , 'Root',"+"\n")
+                 else:
+                    f_hist.write("'"+item+"' , 'Root',"+"\n")
+                 written.append(item)
+       f_hist.write("::")
+
+   f_hist.close()
+   f_agcm.close()
+

base/MAPL_EsmfRegridder.F90

@@ -1431,13 +1431,13 @@ subroutine create_route_handle(this, kind, rc)
      real(real64), pointer :: src_dummy_r8(:,:), dst_dummy_r8(:,:)
      type (ESMF_Field) :: src_field, dst_field
 
-     integer :: srcTermProcessing
+     integer :: srcTermProcessing, num_mask_values
      integer, pointer :: factorIndexList(:,:)
      integer, allocatable :: dstMaskValues(:)
      real(ESMF_KIND_R8), pointer :: factorList(:)
      type(ESMF_RouteHandle) :: dummy_rh
      type(ESMF_UnmappedAction_Flag) :: unmappedaction
-     logical :: global, isPresent, has_mask
+     logical :: global, isPresent, has_mask, has_dstMaskValues
      type(RegridderSpecRouteHandleMap), pointer :: route_handles, transpose_route_handles
      type(ESMF_RouteHandle) :: route_handle, transpose_route_handle
      character(len=ESMF_MAXPATHLEN) :: rh_file,rh_trans_file
@@ -1512,6 +1512,13 @@ subroutine create_route_handle(this, kind, rc)
            end if
            call ESMF_GridGetItem(spec%grid_out,itemflag=ESMF_GRIDITEM_MASK, &
            staggerloc=ESMF_STAGGERLOC_CENTER, isPresent = has_mask, _RC)
+           call ESMF_AttributeGet(spec%grid_out, name=MAPL_DESTINATIONMASK, isPresent=has_dstMaskValues, _RC)
+           if (has_dstMaskValues) then
+              _ASSERT(has_mask, "masking destination values when no masks is present")
+              call ESMF_AttributeGet(spec%grid_out, name=MAPL_DESTINATIONMASK, itemcount=num_mask_values, _RC)
+              allocate(dstMaskValues(num_mask_values), _STAT)
+              call ESMF_AttributeGet(spec%grid_out, name=MAPL_DESTINATIONMASK, valuelist=dstMaskValues, _RC)
+           end if
 
            counter = counter + 1
 
@@ -1521,7 +1528,6 @@ subroutine create_route_handle(this, kind, rc)
               call ESMF_AttributeGet(spec%grid_in, name='Global',value=global,rc=status)
               if (.not.global) unmappedaction=ESMF_UNMAPPEDACTION_IGNORE
            end if
-           if (has_mask) dstMaskValues = [MAPL_MASK_OUT] ! otherwise unallocated
            select case (spec%regrid_method)
            case (REGRID_METHOD_BILINEAR, REGRID_METHOD_BILINEAR_MONOTONIC)
 

base/MAPL_XYGridFactory.F90

@@ -1037,6 +1037,9 @@ subroutine add_mask(this,grid,rc)
       mask = MAPL_MASK_IN
       where(fptr==MAPL_UNDEF) mask = MAPL_MASK_OUT
 
+      call ESMF_AttributeSet(grid, name=MAPL_DESTINATIONMASK, &
+           itemCount=1, valueList=[MAPL_MASK_OUT], _RC)
+
       _RETURN(_SUCCESS)
     end subroutine add_mask
 

gridcomps/History/MAPL_HistoryCollection.F90

@@ -47,12 +47,15 @@ module MAPL_HistoryCollectionMod
      integer                            :: acc_offset
      integer                            :: ref_date
      integer                            :: ref_time
+     integer                            :: start_date
+     integer                            :: start_time
      integer                            :: end_date
      integer                            :: end_time
      integer                            :: duration
      type(ESMF_Alarm)                   :: his_alarm ! when to write file
      type(ESMF_Alarm)                   :: seg_alarm ! segment alarm controls when to write to new file
      type(ESMF_Alarm)                   :: mon_alarm
+     type(ESMF_Alarm)                   :: start_alarm
      type(ESMF_Alarm)                   :: end_alarm
      integer,pointer                    :: expSTATE (:)
      integer                            :: unit
@@ -70,6 +73,7 @@ module MAPL_HistoryCollectionMod
      integer                            :: verbose
      integer                            :: xyoffset
      logical                            :: disabled
+     logical                            :: skipWriting
      logical                            :: subVm
      logical                            :: backwards ! Adds support for clock running in reverse direction
      logical                            :: useNewFormat