Auto GitFlow - develop → MAPL-v3 - actual 3dfgat

components.yaml

@@ -86,7 +86,7 @@ FMS:
 GEOSana_GridComp:
   local: ./src/Components/@GEOSana_GridComp
   remote: ../GEOSana_GridComp.git
-  tag: v5.42.3
+  tag: v5.42.4
   develop: develop
 
 mksi:

src/Applications/GEOSdas_App/CMakeLists.txt

@@ -1,4 +1,5 @@
 add_subdirectory(testsuites)
+add_subdirectory(jedi)
 
 set(dasscripts
     FixUnblocked.csh  

src/Applications/GEOSdas_App/GEOSdas.csm

@@ -154,6 +154,7 @@
   if ( !($?RADCOR) )              setenv RADCOR        0
   if ( !($?SHORTFCST) )           setenv SHORTFCST     0
   if ( !($?SKIPANA)  )            setenv SKIPANA       0
+  if ( !($?SKIPGSI)  )            setenv SKIPGSI       0
   if ( !($?SKIP_PSAS)  )          setenv SKIP_PSAS     0
   if ( !($?SPLITEXE) )            setenv SPLITEXE      0
   if ( !($?STRICT) )              setenv STRICT        0
@@ -1610,6 +1611,7 @@ exit 1
   Sub CreateIAUincrement4Fcst_()
 # -------------------------------------
   if ( $?ECHO___ ) set echo
+  if ( $SKIPGSI && ! -e $FVHOME/run/AGCM.BOOTSTRAP.rc.tmpl ) exit 0
 
      if ( ! $DO4DIAU ) then
         if ( -e agcm_import_rst ) exit 0  # no need to regenerate IAU increment if already available
@@ -2526,6 +2528,8 @@ exit 1
   if ( $?ECHO___ ) set echo
   set qsub_acquire = 0
 
+# if ( $SKIPGSI && ! -e $FVHOME/run/AGCM.BOOTSTRAP.rc.tmpl ) exit 0
+
   set ecode = 0
   set acq_status = 0
   set acq_status2 = 0
@@ -2879,6 +2883,8 @@ exit 1
 # -------------------------
   if ( $?ECHO___ ) set echo
 
+  if ( $SKIPGSI && ! -e $FVHOME/run/AGCM.BOOTSTRAP.rc.tmpl ) exit 0
+
 # Get info about pre-qc files to be combined for QC
 # ------------------------------------------------------
 
@@ -2974,6 +2980,7 @@ endif
 
    if ( ! $PREPQC ) exit 0
    if (  $SKIPANA ) exit 0
+   if (  $SKIPGSI && ! -e $FVHOME/run/AGCM.BOOTSTRAP.rc.tmpl ) exit 0
 
 # Combine pre-qc files...
 #  ------------------------
@@ -3139,6 +3146,7 @@ endif
   Sub AnalysisRun_( Viter_, Final_ ) 
 # ----------------------------------
   if ( $?ECHO___ ) set echo
+  if ( $SKIPGSI && ! -e $FVHOME/run/AGCM.BOOTSTRAP.rc.tmpl ) exit 0
 
     if ( $DO4DVAR && $Final_ ) exit 0
 
@@ -3264,15 +3272,18 @@ endif
 #
 
   if ( ! -d $FVHOME/run/jedi )  exit (0)
+  if (   -e $FVHOME/run/AGCM.BOOTSTRAP.rc.tmpl )  exit (0) # only run from second cycle of experiment onwards
 
   @ idummy = $VAROFFSET * 60
   set ana_datetime = ( `tick $gcm_nymd0 $gcm_nhms0 $idummy` )
 
   set this_hh0 = `echo $gcm_nhms0 | cut -c1-2`
   set this_hha = `echo $ana_datetime[2] | cut -c1-2`
 
-  set this_log = $EXPID.ana_jo.log.${ana_datetime[1]}_${this_hha}z.txt
-  obimp_summary.pl -rc $FVROOT/etc/odsstats4jedi.rc -type diag -josummary -o $this_log $ana_datetime[1] $ana_datetime[2]
+  if ( ! $SKIPGSI && ! -e $FVHOME/run/AGCM.BOOTSTRAP.rc.tmpl ) then
+     set this_log = $EXPID.ana_jo.log.${ana_datetime[1]}_${this_hha}z.txt
+     obimp_summary.pl -rc $FVROOT/etc/odsstats4jedi.rc -type diag -josummary -o $this_log $ana_datetime[1] $ana_datetime[2]
+  endif
 
 
   jedi_driver.csh $gcm_nymd0 $gcm_nhms0 $ana_datetime[1] $ana_datetime[2] |& tee -a $FVWORK/$EXPID.jedi_drv.log.${gcm_nymd0}_${this_hh0}z.txt

src/Applications/GEOSdas_App/gen_silo_arc.pl

@@ -655,6 +655,7 @@ sub append_other_info {
 \${PESTOROOT}%s/jedi/obs/Y%y4/M%m2/%s.jedi_osen.%y4%m2%d2_%h2z.tar
 \${PESTOROOT}%s/jedi/obs/Y%y4/M%m2/%s.jedi_ioda.%y4%m2%d2_%h2z.tar
 \${PESTOROOT}%s/jedi/obs/Y%y4/M%m2/%s.jedi_vbc.%y4%m2%d2_%h2z.tar
+\${PESTOROOT}%s/jedi/rs/Y%y4/M%m2/%s.jedi_agcm_import_rst.%y4%m2%d2_%h2%n2z.%c%c%c
 #
 #               -------------------------
 #                    LSM FILES

src/Applications/GEOSdas_App/jedi/CMakeLists.txt

@@ -0,0 +1,9 @@
+add_subdirectory(etc)
+
+file(GLOB perlscripts *.pl)
+file(GLOB pmscripts *.pm)
+file(GLOB cshscripts *.csh)
+
+install(
+   PROGRAMS ${perlscripts} ${pmscripts} ${cshscripts}
+   DESTINATION bin)

src/Applications/GEOSdas_App/jedi/cmd_jediset.test

@@ -0,0 +1,6 @@
+#!/bin/csh
+setenv FVROOT  `pwd`/../../../../install-SLES15
+$FVROOT/bin/setup_aanajedi.pl 3dfgat j3dfgat 180 \
+     -archive      /discover/nobackup/projects/gmao/dadev/rtodling/archive/JEDI/x51 \
+     -fvhome       /discover/nobackup/projects/gmao/dadev/rtodling/JEDI/x51/j3dfgat \
+     -iodadir      /discover/nobackup/projects/gmao/dadev/rtodling/archive/541/Milan/x0050/ioda   

src/Applications/GEOSdas_App/jedi/etc/CMakeLists.txt

@@ -0,0 +1,21 @@
+set (ALLETC
+   JEDIanaConfig.csh
+   SWELLConfig.csh
+   geos_3dvar.yaml
+   geos_3dfgat.yaml
+   geos_hyb4denvar.yaml
+   jedi_acquire_bkg.j
+   jedi_acquire_ebkg.j
+   jedi_acquire_ioda.j
+   jedi_acquire_vbc.j
+   jedi_run_var.j
+   mkiau.rc.tenv
+   obsop_name_map.yaml
+   ut_jedi.j
+   )
+
+install (
+   FILES ${ALLETC}
+   DESTINATION etc/jedi
+   )
+

src/Applications/GEOSdas_App/jedi/etc/JEDIanaConfig.csh

@@ -0,0 +1,46 @@
+
+# Top options
+setenv JEDI_SET    1           # bring bkg/obs/ens
+setenv JEDI_RUN    1           # run JEDI var executable
+setenv JEDI_HYBRID @JEDI_HYBRID           # control opts for hyb JEDI
+setenv JEDI_MKIAU  1           # calculates IAU output
+setenv JEDI_POST   0           # process results (move files, etc)
+setenv JEDI_IAU_OVERWRITE  0   # overwrite GSI-IAU with JEDI-IAU (when cycling)
+setenv JEDI_RUN_ADANA_TEST 0   # run adjoint JEDI-Var
+setenv JEDI_VAROFFSET 10800    # background time offset
+setenv JEDI_FEEDBACK_VARBC @JEDI_FEEDBACK_VARBC   # controls whether or not to feedback biases
+
+setenv JEDI_SWELLUSE 0  # bypass use of SWELL for now
+setenv OFFLINE_IODA_DIR @OFFLIODADIR # /discover/nobackup/projects/gmao/dadev/rtodling/archive/530/x0049/R2D2DataStore/Local/v2/
+
+# Details ...
+setenv MAPLFIX      0
+setenv JEDI_OBS_OPT @JEDI_OBS_OPT  # 1= point to xexp-like set (data in tar-balls; data from existing exp)
+                                   # 2= point to existing set of ncdiag-ioda-converted set (swell/.../DATE/geos_atmosphere)
+                                   # 3= generate on the fly based on GSI (nc4) diags (TBD)
+
+setenv JEDI_GSI2IODA 0
+setenv JEDI_OBS_DIR $FVWORK/IODA
+
+setenv JEDI_ROOT @JEDI_ROOT
+
+# Specific to run procedure
+setenv JEDI_RUN_ANA      1
+setenv JEDI_RUN_CNVANA   0   # convert cc ana and/or inc output to ll
+setenv JEDI_RUN_UPDRST   0   # not desirable
+
+setenv JEDI_ADDINC_MPIRUN "mpirun -np 12"
+setenv JEDI_CNVANA_MPIRUN "mpirun -np 12"
+setenv JEDI_CNVENS_MPIRUN "mpirun -np 12"
+setenv JEDI_CNVINC_MPIRUN "mpirun -np 12"
+setenv JEDI_NCPUS @JEDI_VAR_NCPUS
+setenv JEDI_FV3VAR_MPIRUN "mpirun -perhost @JEDI_VAR_PERHOST -np $JEDI_NCPUS"
+
+setenv JEDI_MKIAU_MPIRUN "mpirun "
+
+setenv JEDI_STATIC_FILES @JEDI_STATIC_FILES
+setenv JEDI_CRTM_COEFFS  $JEDI_STATIC_FILES/jedi/crtm_coefficients/2.4.1/
+setenv JEDI_INPUT @JEDI_INPUT
+
+# post
+setenv JEDI_CONCAT_IODA  0

src/Applications/GEOSdas_App/jedi/etc/SWELLConfig.csh

@@ -0,0 +1,11 @@
+
+#source /discover/nobackup/projects/gmao/advda/swell/jedi_modules/spackstack_1.9_intel_bundle
+
+module use -a /discover/nobackup/projects/gmao/advda/swell/dev/modulefiles/core
+module load py_lmod_installer
+
+module use /discover/nobackup/projects/gmao/advda/rtodling/JEDI1/SWELL/SPACK19/opt/modulefiles/core
+module load swell/Mar18
+
+#module unload py-pycodestyle/2.8.0
+

src/Applications/GEOSdas_App/jedi/etc/convertinc_geos.yaml

@@ -0,0 +1,46 @@
+input geometry:
+  fms initialization:
+    namelist filename: ./fv3files/input_geos_c90.nml
+    field table filename: ./fv3files/field_table_gmao
+  layout: [2,1]
+  akbk: ./fv3files/akbk72.nc4
+  npx: $JEDI_BKG_RESOL
+  npy: $JEDI_BKG_RESOL
+  npz: 72
+  field metadata override: ./fieldmetadata/geos.yaml
+output geometry:
+  layout: [2,1]
+  akbk: ./fv3files/akbk72.nc4
+  npx: $JEDI_BKG_RESOL
+  npy: $JEDI_BKG_RESOL
+  npz: 72
+  field metadata override: ./fieldmetadata/geos.yaml
+
+linear variable change:
+  variable change name: Model2GeoVaLs
+  input variables: &inputvars [ua,va,t,ps,q,o3ppmv,ts]
+  output variables: [ua,va,t,ps,q,o3ppmv,ts]
+increments:
+- date: "$JEDI_ISO_DATE_ANA"
+  input variables: *inputvars
+  trajectory:
+    datetime: "$JEDI_ISO_DATE_ANA"
+    state variables: *inputvars
+    filetype: cube sphere history
+    provider: geos
+    datapath: ./bkg
+    filename: $EXPID.bkg_clcv_rst.${AYYYYMMDD_HH}00z.nc4
+  input:
+    datetime: "$JEDI_ISO_DATE_ANA"
+    filetype: cube sphere history
+    provider: geos
+    datapath: ./inc
+    filename: $EXPID.jedi_inc-iter1.ceta.${AYYYYMMDD_HH}00z.nc4
+  output:
+   filetype: auxgrid
+   gridtype: latlon
+   filename: ./inc/$EXPID.jedi_inc1.eta.
+
+#test:
+#  reference filename: testoutput/convertincrement_geos_model2geovals.ref
+#  test output filename: testoutput/convertincrement_geos_model2geovals.test.out