GEOS-ESM · rtodling · Jun 30, 2026 · Jun 11, 2026 · Jun 11, 2026 · Jun 11, 2026
@@ -392,6 +392,7 @@ my ($landbcs);
 my ($coupled, $ores, $mometc);
 my ($o_servers,$bckend_wrts, $xncpus, $ncpus_per_node);
 my ($skipgsi);
+my ($jedi_ensrpy, $jedi_exprpy);
 
 my ($sysfile, $nodeflg);
 my (@rmTilde);
@@ -2526,6 +2527,9 @@ sub ed_aens_das_replay_acq {
   $replay_arcdir = "/discover/nobackup/projects/gmao/advda/rtodling/archive/x0044";
   $replay_arcdir = query("Replay archive directory?", $replay_arcdir);
 
+  $jedi_ensrpy = $replay_arcdir;
+  $jedi_exprpy = $aens_replay_expid;
+
   $acq = "$fvhome/$mydir/atmens_replay.acq";
   open(SCRIPT,">$acq") or die ">>> ERROR <<< cannot write $acq";
   print  SCRIPT <<"EOF";
@@ -3702,20 +3706,31 @@ sub set_geosjedi {
   if ( ! $ENV{GEOSJEDI} ) { return 0 };
 
   $nogsi = " ";
-  if ( $skipgsi ) { $nogsi = "-nogsi" };
-
-  if( $ENV{OFFLINE_IODA_DIR} ) {
-     $iodadir = $ENV{OFFLINE_IODA_DIR};
+  if ( $skipgsi ) { 
+     $nogsi = "-nogsi";
+     if( $ENV{OFFLINE_IODA_DIR} ) {
+        $iodadir = $ENV{OFFLINE_IODA_DIR};
+     } else {
+#       $iodadir = "/discover/nobackup/projects/gmao/dadev/rtodling/archive/541/Milan/x0050/ioda/";
+        $iodadir = "/discover/nobackup/projects/gmao/dadev/rtodling/archive/544/x0054/ioda/";
+     }
   } else {
-     $iodadir = "/discover/nobackup/projects/gmao/dadev/rtodling/archive/541/Milan/x0050/ioda/";
+     $iodadir = "/dev/null"; # this expects ncdiag files to be created by GSI
+                             # so that JEDIana can convert files to IODA on the fly
+  }
+  $xtra4jedi = "";
+  if ( $jedi_ensrpy ) {
+     $xtra4jedi = "-ensrpy $jedi_ensrpy -exprpy $jedi_exprpy";
   }
-  $jediopts = "-fvhome $fvhome -iodadir $iodadir -archive $acqloc -gcmres $agcm_im $nogsi";
+  $jediopts = "-fvhome $fvhome -iodadir $iodadir -archive $acqloc -gcmres $agcm_im $nogsi $xtra4jedi";
 
   if ( $ENV{JEDI_ATMVAR_SCHEME} ) {
       $jedivar = $ENV{JEDI_ATMVAR_SCHEME};
   } else {
     if ( $hyb_ens < 3 ) { 
       $jedivar = "3dfgat";
+    } elsif ( $hyb_ens == 3 ) { 
+      $jedivar = "hyb3denvar";
     } else {
       $jedivar = "hyb4denvar";
     }

@@ -1,9 +1,10 @@
 add_subdirectory(etc)
 
 file(GLOB perlscripts *.pl)
+file(GLOB pythonscripts *.py)
 file(GLOB pmscripts *.pm)
 file(GLOB cshscripts *.csh)
 
 install(
-   PROGRAMS ${perlscripts} ${pmscripts} ${cshscripts}
+   PROGRAMS ${perlscripts} ${pmscripts} ${pythonscripts} ${cshscripts}
    DESTINATION bin)
@@ -0,0 +1,40 @@
+#!/usr/bin/perl
+use strict;
+use warnings;
+use File::Spec;
+
+# Need at least: dir + one file + output
+die "Usage: perl combine.pl <dir> <file1> [file2 ...] <output>\n"
+    unless @ARGV >= 3;
+
+my $dir = shift @ARGV;        # directory
+my $output_file = pop @ARGV;  # last arg = output file
+my @files = @ARGV;            # remaining = input files
+
+open(my $out_fh, ">", $output_file)
+    or die "Cannot open output file '$output_file': $!";
+
+foreach my $file (@files) {
+
+    my $fullpath = File::Spec->catfile($dir, $file);
+
+    unless (-f $fullpath) {
+        warn "Skipping '$fullpath' (not found or not a regular file)\n";
+        next;
+    }
+
+    open(my $in_fh, "<", $fullpath)
+        or die "Cannot open file '$fullpath': $!";
+
+    print $out_fh "#==== $file ====\n";  # optional separator
+
+    while (my $line = <$in_fh>) {
+        print $out_fh $line;
+    }
+
+    close($in_fh);
+}
+
+close($out_fh);
+
+print "Files have been combined into $output_file\n";
@@ -2,12 +2,14 @@ set (ALLETC
    JEDIanaConfig.csh
    SWELLConfig.csh
    diffstates_geos.yaml
+   diag2ioda.yaml
    geos_3dvar.yaml
    geos_3dfgat.yaml
    geos_hyb3dcenvar.yaml
    geos_hyb4dcenvar.yaml
+   geos_hyb4dcenvar_seq.yaml
+   geos_hyb3denvar.yaml
    geos_hyb4denvar.yaml
-   geos_jediobs.yaml
    jedi_acquire_bkg.j
    jedi_acquire_ebkg.j
    jedi_acquire_ioda.j
@@ -24,3 +26,7 @@ install (
    DESTINATION etc/jedi
    )
 
+install(
+   DIRECTORY obs/
+   DESTINATION etc/jedi/obs
+   )
@@ -0,0 +1,51 @@
+# SLURM specials
+setenv GEOSJEDI_QOS @GEOSJEDI_QOS
+setenv GEOSJEDI_PARTITION  @GEOSJEDI_PARTITION
+
+# 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  @JEDI_IAU_OVERWRITE   # 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 SWELL_INSTALL @SWELL_INSTALL
+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 1              # 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_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_GETINC   @JEDI_RUN_GETINC   # calc cubed inc from diff of cubed ana and bkg
+setenv JEDI_RUN_UPDRST   0   # not desirable
+
+setenv JEDI_DIF_NCPUS    @JEDI_DIF_NCPUS
+setenv JEDI_NCPUS        @JEDI_VAR_NCPUS
+
+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_GETINC_MPIRUN "mpirun -np $JEDI_DIF_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  $FVHOME/fvInput/gsi/etc/JEDI-CRTM-2.4.1j1-GMAO/Little_Endian/
+setenv JEDI_INPUT @JEDI_INPUT
+
+# post
+setenv JEDI_CONCAT_IODA  0
@@ -12,8 +12,10 @@ setenv JEDI_IAU_OVERWRITE  @JEDI_IAU_OVERWRITE   # overwrite GSI-IAU with JEDI-I
 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
+                                                  # caution: not sure aircraft bias cycle properly in JEDI
 
 setenv JEDI_SWELLUSE 0  # bypass use of SWELL for now
+setenv SWELL_INSTALL @SWELL_INSTALL
 setenv OFFLINE_IODA_DIR @OFFLIODADIR # /discover/nobackup/projects/gmao/dadev/rtodling/archive/530/x0049/R2D2DataStore/Local/v2/
 
 # Details ...
@@ -22,9 +24,6 @@ setenv JEDI_OBS_OPT @JEDI_OBS_OPT  # 1= point to xexp-like set (data in tar-ball
                                    # 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
@@ -33,12 +32,14 @@ setenv JEDI_RUN_CNVANA   0   # convert cc ana and/or inc output to ll
 setenv JEDI_RUN_GETINC   @JEDI_RUN_GETINC   # calc cubed inc from diff of cubed ana and bkg
 setenv JEDI_RUN_UPDRST   0   # not desirable
 
+setenv JEDI_DIF_NCPUS    @JEDI_DIF_NCPUS
+setenv JEDI_NCPUS        @JEDI_VAR_NCPUS
+
 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_GETINC_MPIRUN "mpirun -np @JEDI_DIF_NTASKS"
-setenv JEDI_NCPUS @JEDI_VAR_NCPUS
+setenv JEDI_GETINC_MPIRUN "mpirun -np $JEDI_DIF_NCPUS"
 setenv JEDI_FV3VAR_MPIRUN "mpirun -perhost @JEDI_VAR_PERHOST -np $JEDI_NCPUS"
 
 setenv JEDI_MKIAU_MPIRUN "mpirun "

@@ -1,11 +1,2 @@
-
-#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
-
+module use $SWELL_INSTALL/modulefiles/core
+module load swell/swell
@@ -0,0 +1,134 @@
+# What is the experiment id?
+experiment_id: ${EXPID}-convert_ncdiags
+
+# What is the experiment root (the directory where the experiment will be stored)?
+experiment_root: $JEDIWORK
+
+# What is the time of the first cycle (middle of the window)?
+start_cycle_point: '$JEDI_ISO_DATE_ANA'
+
+# What is the time of the final cycle (middle of the window)?
+final_cycle_point: '$JEDI_ISO_DATE_ANA'
+
+# List of models in this experiment
+model_components:
+- geos_atmosphere
+
+# Set the Cylc runahead limit: the maximum number of cycles that may be active ahead of the current cycle (e.g. P1: up to 1 cycle ahead, P3: up to 3 cycles ahead, default P4).
+runahead_limit: P4
+
+# What experiment_id should r2d2 reference for experiment?
+r2d2_experiment_id: swell-convert_ncdiags
+
+# Skip registering and storing results of this experiment in R2D2?
+skip_r2d2: false
+
+# Do you want to use an existing JEDI build or create a new build?
+jedi_build_method: use_existing
+
+# What is the path to the existing JEDI build directory?
+existing_jedi_build_directory: $JEDI_ROOT
+
+# What is the path to the existing JEDI source code directory?
+existing_jedi_source_directory: $JEDI_ROOT/../
+
+# Configurations for the model components.
+models:
+
+  # Configuration for the geos_atmosphere model component.
+  geos_atmosphere:
+
+    # Enter the cycle times for this model.
+    cycle_times:
+    - T00
+    - T06
+    - T12
+    - T18
+
+    # What is the location where GSI bias correction files can be found?
+    path_to_gsi_bc_coefficients: $JEDIWORK/GSIBIAS/*bias*%Y%m%d_%Hz.txt
+
+    # What is the duration for the data assimilation window?
+    window_length: PT6H
+
+    # What is the path to where the GSI ncdiags are stored?
+    path_to_gsi_nc_diags: $JEDIWORK/GSIDIAGS
+
+    # Which observations do you want to include?
+    observations:
+    - abi_g16
+    - abi_g18
+    - aircraft
+    - airs_aqua
+    - amsr2_gcom-w1
+    - amsua_aqua
+    - amsua_metop-b
+    - amsua_metop-c
+    - amsua_n15
+    - amsua_n18
+    - amsua_n19
+    - atms_n20
+    - atms_n21
+    - atms_npp
+    - avhrr3_metop-b
+    - avhrr3_metop-c
+    - avhrr3_n18
+    - avhrr3_n19
+    - cris-fsr_n20
+    - cris-fsr_n21
+    - cris-fsr_npp
+    - gmi_gpm
+    - gps
+    - iasi_metop-b
+    - iasi_metop-c
+    - mhs_metop-b
+    - mhs_metop-c
+    - mhs_n19
+    - mls55_aura
+    - omi_aura
+    - omieff_aura
+    - ompslpnc_n21
+    - ompslpnc_npp
+    - ompsnm_npp
+    - pibal
+    - satwind
+    - scatwind
+    - sfcship
+    - sfc
+    - sondes
+    - ssmis_f17
+
+    # When running the ncdiag to ioda converted do you want to produce GeoVaLs files?
+    produce_geovals: false
+
+    # Is it a single-observation test?
+    single_observations: false
+
+    # Provide a list of patterns that you wish to remove from the cycle directory.
+    clean_patterns:
+    - gsi_bcs/*.nc4
+    - gsi_bcs/*.txt
+    - gsi_bcs/*.yaml
+    - gsi_bcs
+    - gsi_ncdiags/*.nc4
+    - gsi_ncdiags/aircraft/*.nc4
+    - gsi_ncdiags/aircraft
+    - gsi_ncdiags
+
+    # How long before the middle of the analysis window did the background providing forecast begin?
+    background_time_offset: PT9H
+
+    # What is the path to the CRTM coefficient files?
+    crtm_coeff_dir: $JEDI_CRTM_COEFFS
+
+    # What is the path to the Swell formatted observing system records?
+    observing_system_records_path: None
+
+# Datetime this file was created (auto added)
+datetime_created: 20260331_163310Z
+
+# Computing platform to run the experiment
+platform: nccs_discover_sles15
+
+# Record of the suite being executed
+suite_to_run: convert_ncdiags
@@ -106,13 +106,14 @@ cost function:
 #     mole_fraction_of_carbon_dioxide_in_air: co2
   background error:
     covariance model: SABER
+#   covariance type: gsi static covariance
 #   adjoint test: true
     saber central block:
       saber block name: gsi hybrid covariance
       read:
         gsi akbk: ./fv3-jedi/fv3files/akbk@JEDI_BKG_VRES.nc4
-        gsi error covariance file: ./fv3-jedi/gsibec/gsibec_coefficients_c@JEDI_BKGCOV_RESOL.nc4
-        gsi berror namelist file: ./fv3-jedi/gsibec/cli_gsibec_configuration_c@JEDI_BKGCOV_RESOL.nml
+        gsi error covariance file: ./fv3-jedi/gsibec/gsibec_coefficients_l@JEDI_BKG_VRESx@JEDI_GSIBEC_NLONy@JEDI_GSIBEC_NLAT.nc4
+        gsi berror namelist file: ./fv3-jedi/gsibec/gsibec_configuration_l@JEDI_BKG_VRESx@JEDI_GSIBEC_NLONy@JEDI_GSIBEC_NLAT.nml
         processor layout x direction: @JEDI_VAR_GSIXLAYOUT
         processor layout y direction: @JEDI_VAR_GSIYLAYOUT
         debugging mode: false