From 23e6bfff859c7fdc119a2e6d0b7884b2635897fe Mon Sep 17 00:00:00 2001
From: RussTreadon-NOAA <26926959+RussTreadon-NOAA@users.noreply.github.com>
Date: Mon, 26 Feb 2024 09:22:26 -0500
Subject: [PATCH] Update nc suffix and bufr file path for atmospheric
 observation yamls and bufr2ioda converters (#933)

---
 parm/atm/obs/config/aircraft.yaml                    |  4 ++--
 parm/atm/obs/config/amsua_n19.yaml                   | 12 ++++++------
 parm/atm/obs/config/atms_n20.yaml                    |  8 ++++----
 parm/atm/obs/config/atms_npp.yaml                    |  8 ++++----
 parm/atm/obs/config/cris-fsr_n20.yaml                | 12 ++++++------
 parm/atm/obs/config/cris-fsr_npp.yaml                | 12 ++++++------
 parm/atm/obs/config/gnssro.yaml                      |  2 +-
 parm/atm/obs/config/iasi_metop-a.yaml                |  8 ++++----
 parm/atm/obs/config/iasi_metop-b.yaml                |  8 ++++----
 parm/atm/obs/config/lgetkf_amsua_n19.yaml            | 12 ++++++------
 parm/atm/obs/config/lgetkf_sondes.yaml               |  4 ++--
 parm/atm/obs/config/omi_aura.yaml                    |  4 ++--
 parm/atm/obs/config/ompsnp_npp.yaml                  |  4 ++--
 parm/atm/obs/config/ompstc8_npp.yaml                 |  4 ++--
 parm/atm/obs/config/satwind.yaml                     |  4 ++--
 parm/atm/obs/config/satwind_ahi_h8.yaml              |  2 +-
 parm/atm/obs/config/sfc.yaml                         |  4 ++--
 parm/atm/obs/config/sfcship.yaml                     |  4 ++--
 parm/atm/obs/config/sondes.yaml                      |  4 ++--
 parm/atm/obs/config/ssmis_f17.yaml                   |  8 ++++----
 parm/atm/obs/config/ssmis_f18.yaml                   |  8 ++++----
 test/atm/global-workflow/config.atmanl               |  8 ++++----
 test/atm/global-workflow/config.yaml                 | 10 ++++++++++
 test/atm/global-workflow/jjob_ens_init.sh            | 10 +++++++---
 test/atm/global-workflow/jjob_var_init.sh            | 12 ++++++++----
 .../bufr2ioda/bufr2ioda_acft_profiles_prepbufr.py    |  2 +-
 ush/ioda/bufr2ioda/bufr2ioda_adpsfc_prepbufr.py      |  2 +-
 .../bufr2ioda/bufr2ioda_conventional_prepbufr_ps.py  |  2 +-
 ush/ioda/bufr2ioda/bufr2ioda_sfcshp_prepbufr.py      |  2 +-
 29 files changed, 101 insertions(+), 83 deletions(-)

diff --git a/parm/atm/obs/config/aircraft.yaml b/parm/atm/obs/config/aircraft.yaml
index 4920a90db..e0d292e26 100644
--- a/parm/atm/obs/config/aircraft.yaml
+++ b/parm/atm/obs/config/aircraft.yaml
@@ -3,7 +3,7 @@ obs space:
   obsdatain:
     engine:
       type: H5File
-      obsfile: $(DATA)/obs/$(OPREFIX)aircraft.${{ current_cycle | to_YMDH }}.nc4
+      obsfile: $(DATA)/obs/$(OPREFIX)aircraft.${{ current_cycle | to_YMDH }}.nc
     obsgrouping:
       group variables: ["stationIdentification"]
       sort variable: "pressure"
@@ -11,7 +11,7 @@ obs space:
   obsdataout:
     engine:
       type: H5File
-      obsfile: $(DATA)/diags/diag_aircraft_${{ current_cycle | to_YMDH }}.nc4
+      obsfile: $(DATA)/diags/diag_aircraft_${{ current_cycle | to_YMDH }}.nc
   io pool:
     max pool size: 1
   simulated variables: [windEastward, windNorthward, airTemperature, specificHumidity]
diff --git a/parm/atm/obs/config/amsua_n19.yaml b/parm/atm/obs/config/amsua_n19.yaml
index be40d9650..d866569b6 100644
--- a/parm/atm/obs/config/amsua_n19.yaml
+++ b/parm/atm/obs/config/amsua_n19.yaml
@@ -3,11 +3,11 @@ obs space:
   obsdatain:
     engine:
       type: H5File
-      obsfile: $(DATA)/obs/$(OPREFIX)amsua_n19.{{ current_cycle | to_YMDH }}.nc4
+      obsfile: $(DATA)/obs/$(OPREFIX)amsua_n19.{{ current_cycle | to_YMDH }}.nc
   obsdataout:
     engine:
       type: H5File
-      obsfile: $(DATA)/diags/diag_amsua_n19_{{ current_cycle | to_YMDH }}.nc4
+      obsfile: $(DATA)/diags/diag_amsua_n19_{{ current_cycle | to_YMDH }}.nc
   io pool:
     max pool size: 1
   simulated variables: [brightnessTemperature]
@@ -22,8 +22,8 @@ obs operator:
     EndianType: little_endian
     CoefficientPath: $(DATA)/crtm/
 obs bias:
-  input file: $(DATA)/obs/$(GPREFIX)amsua_n19.satbias.nc4
-  output file: $(DATA)/bc/$(APREFIX)amsua_n19.satbias.nc4
+  input file: $(DATA)/obs/$(GPREFIX)amsua_n19.satbias.nc
+  output file: $(DATA)/bc/$(APREFIX)amsua_n19.satbias.nc
   variational bc:
     predictors:
     - name: constant
@@ -46,11 +46,11 @@ obs bias:
     step size: 1.0e-4
     largest analysis variance: 10000.0
     prior:
-      input file: $(DATA)/obs/$(GPREFIX)amsua_n19.satbias_cov.nc4
+      input file: $(DATA)/obs/$(GPREFIX)amsua_n19.satbias_cov.nc
       inflation:
         ratio: 1.1
         ratio for small dataset: 2.0
-    output file: $(DATA)/bc/$(APREFIX)amsua_n19.satbias_cov.nc4
+    output file: $(DATA)/bc/$(APREFIX)amsua_n19.satbias_cov.nc
 obs filters:
 - filter: BlackList
   filter variables:
diff --git a/parm/atm/obs/config/atms_n20.yaml b/parm/atm/obs/config/atms_n20.yaml
index 5cb9c27f3..d32ce2489 100644
--- a/parm/atm/obs/config/atms_n20.yaml
+++ b/parm/atm/obs/config/atms_n20.yaml
@@ -27,8 +27,8 @@ obs operator:
     Absorbers: [H2O, O3]
 
 obs bias:
-  input file: $(DATA)/obs/$(GPREFIX)atms_n20.satbias.nc4
-  output file: $(DATA)/bc/$(APREFIX)atms_n20.satbias.nc4
+  input file: $(DATA)/obs/$(GPREFIX)atms_n20.satbias.nc
+  output file: $(DATA)/bc/$(APREFIX)atms_n20.satbias.nc
   variational bc:
     predictors:
     - name: constant
@@ -51,11 +51,11 @@ obs bias:
     step size: 1.0e-4
     largest analysis variance: 10000.0
     prior:
-      input file: $(DATA)/obs/$(GPREFIX)atms_n20.satbias_cov.nc4
+      input file: $(DATA)/obs/$(GPREFIX)atms_n20.satbias_cov.nc
       inflation:
         ratio: 1.1
         ratio for small dataset: 2.0
-    output file: $(DATA)/bc/$(APREFIX)atms_n20.satbias_cov.nc4
+    output file: $(DATA)/bc/$(APREFIX)atms_n20.satbias_cov.nc
 
 obs pre filters:
 # Step 0-A: Create Diagnostic Flags
diff --git a/parm/atm/obs/config/atms_npp.yaml b/parm/atm/obs/config/atms_npp.yaml
index 0a9b633b6..30926fc20 100644
--- a/parm/atm/obs/config/atms_npp.yaml
+++ b/parm/atm/obs/config/atms_npp.yaml
@@ -27,8 +27,8 @@ obs operator:
     Absorbers: [H2O, O3]
 
 obs bias:
-  input file: $(DATA)/obs/$(GPREFIX)atms_npp.satbias.nc4
-  output file: $(DATA)/bc/$(APREFIX)atms_npp.satbias.nc4
+  input file: $(DATA)/obs/$(GPREFIX)atms_npp.satbias.nc
+  output file: $(DATA)/bc/$(APREFIX)atms_npp.satbias.nc
   variational bc:
     predictors:
     - name: constant
@@ -51,11 +51,11 @@ obs bias:
     step size: 1.0e-4
     largest analysis variance: 10000.0
     prior:
-      input file: $(DATA)/obs/$(GPREFIX)atms_npp.satbias_cov.nc4
+      input file: $(DATA)/obs/$(GPREFIX)atms_npp.satbias_cov.nc
       inflation:
         ratio: 1.1
         ratio for small dataset: 2.0
-    output file: $(DATA)/bc/$(APREFIX)atms_npp.satbias_cov.nc4
+    output file: $(DATA)/bc/$(APREFIX)atms_npp.satbias_cov.nc
 
 obs pre filters:
 # Step 0-A: Create Diagnostic Flags
diff --git a/parm/atm/obs/config/cris-fsr_n20.yaml b/parm/atm/obs/config/cris-fsr_n20.yaml
index 579439862..3b26fb672 100644
--- a/parm/atm/obs/config/cris-fsr_n20.yaml
+++ b/parm/atm/obs/config/cris-fsr_n20.yaml
@@ -3,11 +3,11 @@ obs space:
   obsdatain:
     engine:
       type: H5File
-      obsfile: $(DATA)/obs/$(OPREFIX)cris-fsr_n20.${{ current_cycle | to_YMDH }}.nc4
+      obsfile: $(DATA)/obs/$(OPREFIX)cris-fsr_n20.${{ current_cycle | to_YMDH }}.nc
   obsdataout:
     engine:
       type: H5File
-      obsfile: $(DATA)/diags/diag_cris-fsr_n20_${{ current_cycle | to_YMDH }}.nc4
+      obsfile: $(DATA)/diags/diag_cris-fsr_n20_${{ current_cycle | to_YMDH }}.nc
   io pool:
     max pool size: 1
   simulated variables: [brightness_temperature]
@@ -53,8 +53,8 @@ obs operator:
     EndianType: little_endian
     CoefficientPath: $(DATA)/crtm/
 obs bias:
-  input file: $(DATA)/obs/$(GPREFIX)cris-fsr_n20.satbias.nc4
-  output file: $(DATA)/bc/$(APREFIX)cris-fsr_n20.satbias.nc4
+  input file: $(DATA)/obs/$(GPREFIX)cris-fsr_n20.satbias.nc
+  output file: $(DATA)/bc/$(APREFIX)cris-fsr_n20.satbias.nc
   variational bc:
     predictors:
     - name: constant
@@ -77,11 +77,11 @@ obs bias:
     step size: 1.0e-4
     largest analysis variance: 10000.0
     prior:
-      input file: $(DATA)/obs/$(GPREFIX)cris-fsr_n20.satbias_cov.nc4
+      input file: $(DATA)/obs/$(GPREFIX)cris-fsr_n20.satbias_cov.nc
       inflation:
         ratio: 1.1
         ratio for small dataset: 2.0
-    output file: $(DATA)/bc/$(APREFIX)cris-fsr_n20.satbias_cov.nc4
+    output file: $(DATA)/bc/$(APREFIX)cris-fsr_n20.satbias_cov.nc
 #
 #obs filters:
 ##  Wavenumber Check
diff --git a/parm/atm/obs/config/cris-fsr_npp.yaml b/parm/atm/obs/config/cris-fsr_npp.yaml
index 55409f454..ff0aabe86 100644
--- a/parm/atm/obs/config/cris-fsr_npp.yaml
+++ b/parm/atm/obs/config/cris-fsr_npp.yaml
@@ -3,11 +3,11 @@ obs space:
   obsdatain:
     engine:
       type: H5File
-      obsfile: $(DATA)/obs/$(OPREFIX)cris-fsr_npp.${{ current_cycle | to_YMDH }}.nc4
+      obsfile: $(DATA)/obs/$(OPREFIX)cris-fsr_npp.${{ current_cycle | to_YMDH }}.nc
   obsdataout:
     engine:
       type: H5File
-      obsfile: $(DATA)/diags/diag_cris-fsr_npp_${{ current_cycle | to_YMDH }}.nc4
+      obsfile: $(DATA)/diags/diag_cris-fsr_npp_${{ current_cycle | to_YMDH }}.nc
   io pool:
     max pool size: 1
   simulated variables: [brightness_temperature]
@@ -53,8 +53,8 @@ obs operator:
     EndianType: little_endian
     CoefficientPath: $(DATA)/crtm/
 obs bias:
-  input file: $(DATA)/obs/$(GPREFIX)cris-fsr_npp.satbias.nc4
-  output file: $(DATA)/bc/$(APREFIX)cris-fsr_npp.satbias.nc4
+  input file: $(DATA)/obs/$(GPREFIX)cris-fsr_npp.satbias.nc
+  output file: $(DATA)/bc/$(APREFIX)cris-fsr_npp.satbias.nc
   variational bc:
     predictors:
     - name: constant
@@ -77,11 +77,11 @@ obs bias:
     step size: 1.0e-4
     largest analysis variance: 10000.0
     prior:
-      input file: $(DATA)/obs/$(GPREFIX)cris-fsr_npp.satbias_cov.nc4
+      input file: $(DATA)/obs/$(GPREFIX)cris-fsr_npp.satbias_cov.nc
       inflation:
         ratio: 1.1
         ratio for small dataset: 2.0
-    output file: $(DATA)/bc/$(APREFIX)cris-fsr_npp.satbias_cov.nc4
+    output file: $(DATA)/bc/$(APREFIX)cris-fsr_npp.satbias_cov.nc
 #obs filters:
 ##  Wavenumber Check
 #- filter: BlackList
diff --git a/parm/atm/obs/config/gnssro.yaml b/parm/atm/obs/config/gnssro.yaml
index 949a4f87b..1b4d1a0dd 100644
--- a/parm/atm/obs/config/gnssro.yaml
+++ b/parm/atm/obs/config/gnssro.yaml
@@ -18,7 +18,7 @@ obs space:
   obsdataout:
     engine:
       type: H5File
-      obsfile: $(DATA)/diags/diag_gnssro_{{ current_cycle | to_YMDH }}.nc4
+      obsfile: $(DATA)/diags/diag_gnssro_{{ current_cycle | to_YMDH }}.nc
   simulated variables: [bendingAngle]
 
 obs filters:
diff --git a/parm/atm/obs/config/iasi_metop-a.yaml b/parm/atm/obs/config/iasi_metop-a.yaml
index f5c7a602a..fdc974d8e 100644
--- a/parm/atm/obs/config/iasi_metop-a.yaml
+++ b/parm/atm/obs/config/iasi_metop-a.yaml
@@ -74,8 +74,8 @@ obs operator:
     Absorbers: [H2O,O3]
 
 obs bias:
-  input file: $(DATA)/obs/$(GPREFIX)iasi_metop-a.satbias.nc4
-  output file: $(DATA)/bc/$(APREFIX)iasi_metop-a.satbias.nc4
+  input file: $(DATA)/obs/$(GPREFIX)iasi_metop-a.satbias.nc
+  output file: $(DATA)/bc/$(APREFIX)iasi_metop-a.satbias.nc
   variational bc:
     predictors:
     - name: constant
@@ -98,11 +98,11 @@ obs bias:
     step size: 1.0e-4
     largest analysis variance: 10000.0
     prior:
-      input file: $(DATA)/obs/$(GPREFIX)iasi_metop-a.satbias_cov.nc4
+      input file: $(DATA)/obs/$(GPREFIX)iasi_metop-a.satbias_cov.nc
       inflation:
         ratio: 1.1
         ratio for small dataset: 2.0
-    output file: $(DATA)/bc/$(APREFIX)iasi_metop-a.satbias_cov.nc4
+    output file: $(DATA)/bc/$(APREFIX)iasi_metop-a.satbias_cov.nc
 
 obs pre filters:
 # Step 0-A: Create Diagnostic Flags
diff --git a/parm/atm/obs/config/iasi_metop-b.yaml b/parm/atm/obs/config/iasi_metop-b.yaml
index 1a4681dc6..2f8f1424e 100644
--- a/parm/atm/obs/config/iasi_metop-b.yaml
+++ b/parm/atm/obs/config/iasi_metop-b.yaml
@@ -74,8 +74,8 @@ obs operator:
     Absorbers: [H2O,O3]
 
 obs bias:
-  input file: $(DATA)/obs/$(GPREFIX)iasi_metop-b.satbias.nc4
-  output file: $(DATA)/bc/$(APREFIX)iasi_metop-b.satbias.nc4
+  input file: $(DATA)/obs/$(GPREFIX)iasi_metop-b.satbias.nc
+  output file: $(DATA)/bc/$(APREFIX)iasi_metop-b.satbias.nc
   variational bc:
     predictors:
     - name: constant
@@ -98,11 +98,11 @@ obs bias:
     step size: 1.0e-4
     largest analysis variance: 10000.0
     prior:
-      input file: $(DATA)/obs/$(GPREFIX)iasi_metop-b.satbias_cov.nc4
+      input file: $(DATA)/obs/$(GPREFIX)iasi_metop-b.satbias_cov.nc
       inflation:
         ratio: 1.1
         ratio for small dataset: 2.0
-    output file: $(DATA)/bc/$(APREFIX)iasi_metop-b.satbias_cov.nc4
+    output file: $(DATA)/bc/$(APREFIX)iasi_metop-b.satbias_cov.nc
 
 obs pre filters:
 # Step 0-A: Create Diagnostic Flags
diff --git a/parm/atm/obs/config/lgetkf_amsua_n19.yaml b/parm/atm/obs/config/lgetkf_amsua_n19.yaml
index d5fe9691a..a29cb8bdf 100644
--- a/parm/atm/obs/config/lgetkf_amsua_n19.yaml
+++ b/parm/atm/obs/config/lgetkf_amsua_n19.yaml
@@ -6,11 +6,11 @@ obs space:
   obsdatain:
     engine:
       type: H5File
-      obsfile: ./obs/$(OPREFIX)amsua_n19.{{ current_cycle | to_YMDH }}.nc4
+      obsfile: ./obs/$(OPREFIX)amsua_n19.{{ current_cycle | to_YMDH }}.nc
   obsdataout:
     engine:
       type: H5File
-      obsfile: ./diags/diag_amsua_n19_{{ current_cycle | to_YMDH }}.nc4
+      obsfile: ./diags/diag_amsua_n19_{{ current_cycle | to_YMDH }}.nc
   io pool:
     max pool size: 1
   simulated variables: [brightnessTemperature]
@@ -27,8 +27,8 @@ obs operator:
 obs error:
   covariance model: diagonal
 obs bias:
-  input file: $(DATA)/obs/$(GPREFIX)amsua_n19.satbias.nc4
-  output file: $(DATA)/bc/$(APREFIX)amsua_n19.satbias.nc4
+  input file: $(DATA)/obs/$(GPREFIX)amsua_n19.satbias.nc
+  output file: $(DATA)/bc/$(APREFIX)amsua_n19.satbias.nc
   variational bc:
     predictors:
     - name: constant
@@ -51,11 +51,11 @@ obs bias:
     step size: 1.0e-4
     largest analysis variance: 10000.0
     prior:
-      input file: $(DATA)/obs/$(GPREFIX)amsua_n19.satbias_cov.nc4
+      input file: $(DATA)/obs/$(GPREFIX)amsua_n19.satbias_cov.nc
       inflation:
         ratio: 1.1
         ratio for small dataset: 2.0
-    output file: $(DATA)/bc/$(APREFIX)amsua_n19.satbias_cov.nc4
+    output file: $(DATA)/bc/$(APREFIX)amsua_n19.satbias_cov.nc
 obs filters:
 - filter: Bounds Check
   filter variables:
diff --git a/parm/atm/obs/config/lgetkf_sondes.yaml b/parm/atm/obs/config/lgetkf_sondes.yaml
index 4f2358097..8515508a6 100644
--- a/parm/atm/obs/config/lgetkf_sondes.yaml
+++ b/parm/atm/obs/config/lgetkf_sondes.yaml
@@ -6,11 +6,11 @@ obs space:
   obsdatain:
     engine:
       type: H5File
-      obsfile: ./obs/$(OPREFIX)sondes.{{ current_cycle | to_YMDH }}.nc4
+      obsfile: ./obs/$(OPREFIX)sondes.{{ current_cycle | to_YMDH }}.nc
   obsdataout:
     engine:
       type: H5File
-      obsfile: ./diags/diag_sondes_lgetkf_{{ current_cycle | to_YMDH }}.nc4
+      obsfile: ./diags/diag_sondes_lgetkf_{{ current_cycle | to_YMDH }}.nc
   io pool:
     max pool size: 1
   simulated variables: [windEastward, windNorthward, airTemperature]
diff --git a/parm/atm/obs/config/omi_aura.yaml b/parm/atm/obs/config/omi_aura.yaml
index 20cabced5..27fa97004 100644
--- a/parm/atm/obs/config/omi_aura.yaml
+++ b/parm/atm/obs/config/omi_aura.yaml
@@ -3,11 +3,11 @@ obs space:
   obsdatain:
     engine:
       type: H5File
-      obsfile: $(DATA)/obs/$(OPREFIX)omi_aura.${{ current_cycle | to_YMDH }}.nc4
+      obsfile: $(DATA)/obs/$(OPREFIX)omi_aura.${{ current_cycle | to_YMDH }}.nc
   obsdataout:
     engine:
       type: H5File
-      obsfile: $(DATA)/diags/diag_omi_aura_${{ current_cycle | to_YMDH }}.nc4
+      obsfile: $(DATA)/diags/diag_omi_aura_${{ current_cycle | to_YMDH }}.nc
   io pool:
     max pool size: 1
   simulated variables: [ozoneTotal]
diff --git a/parm/atm/obs/config/ompsnp_npp.yaml b/parm/atm/obs/config/ompsnp_npp.yaml
index c18b9abed..f543a693d 100644
--- a/parm/atm/obs/config/ompsnp_npp.yaml
+++ b/parm/atm/obs/config/ompsnp_npp.yaml
@@ -3,7 +3,7 @@ obs space:
   obsdatain:
     engine:
       type: H5File
-      obsfile: $(DATA)/obs/$(OPREFIX)ompsnp_npp.${{ current_cycle | to_YMDH }}.nc4
+      obsfile: $(DATA)/obs/$(OPREFIX)ompsnp_npp.${{ current_cycle | to_YMDH }}.nc
     obsgrouping:
       group variables: ["latitude"]
       sort variable: "pressure"
@@ -11,7 +11,7 @@ obs space:
   obsdataout:
     engine:
       type: H5File
-      obsfile: $(DATA)/diags/diag_ompsnp_npp_${{ current_cycle | to_YMDH }}.nc4
+      obsfile: $(DATA)/diags/diag_ompsnp_npp_${{ current_cycle | to_YMDH }}.nc
   io pool:
     max pool size: 1
   simulated variables: [ozoneLayer]
diff --git a/parm/atm/obs/config/ompstc8_npp.yaml b/parm/atm/obs/config/ompstc8_npp.yaml
index 545983d93..1563c4534 100644
--- a/parm/atm/obs/config/ompstc8_npp.yaml
+++ b/parm/atm/obs/config/ompstc8_npp.yaml
@@ -3,11 +3,11 @@ obs space:
   obsdatain:
     engine:
       type: H5File
-      obsfile: $(DATA)/obs/$(OPREFIX)ompstc8_npp.${{ current_cycle | to_YMDH }}.nc4
+      obsfile: $(DATA)/obs/$(OPREFIX)ompstc8_npp.${{ current_cycle | to_YMDH }}.nc
   obsdataout:
     engine:
       type: H5File
-      obsfile: $(DATA)/diags/diag_ompstc8_npp_${{ current_cycle | to_YMDH }}.nc4
+      obsfile: $(DATA)/diags/diag_ompstc8_npp_${{ current_cycle | to_YMDH }}.nc
   io pool:
     max pool size: 1
   simulated variables: [ozoneTotal]
diff --git a/parm/atm/obs/config/satwind.yaml b/parm/atm/obs/config/satwind.yaml
index 853cbce77..80b74e23c 100644
--- a/parm/atm/obs/config/satwind.yaml
+++ b/parm/atm/obs/config/satwind.yaml
@@ -3,11 +3,11 @@ obs space:
   obsdatain:
     engine:
       type: H5File
-      obsfile: $(DATA)/obs/$(OPREFIX)satwind.${{ current_cycle | to_YMDH }}.nc4
+      obsfile: $(DATA)/obs/$(OPREFIX)satwind.${{ current_cycle | to_YMDH }}.nc
   obsdataout:
     engine:
       type: H5File
-      obsfile: $(DATA)/diags/diag_satwind_${{ current_cycle | to_YMDH }}.nc4
+      obsfile: $(DATA)/diags/diag_satwind_${{ current_cycle | to_YMDH }}.nc
   io pool:
     max pool size: 1
   simulated variables: [windEastward, windNorthward]
diff --git a/parm/atm/obs/config/satwind_ahi_h8.yaml b/parm/atm/obs/config/satwind_ahi_h8.yaml
index c66afaa67..2cfc17e02 100644
--- a/parm/atm/obs/config/satwind_ahi_h8.yaml
+++ b/parm/atm/obs/config/satwind_ahi_h8.yaml
@@ -7,7 +7,7 @@ obs space:
   obsdataout:
     engine:
       type: H5File
-      obsfile: $(DATA)/diags/diag_satwind_ahi_h8_{{ current_cycle | to_YMDH }}.nc4
+      obsfile: $(DATA)/diags/diag_satwind_ahi_h8_{{ current_cycle | to_YMDH }}.nc
   io pool:
     max pool size: 1
   simulated variables: [windEastward, windNorthward]
diff --git a/parm/atm/obs/config/sfc.yaml b/parm/atm/obs/config/sfc.yaml
index 31fd74c0c..b846e98f0 100644
--- a/parm/atm/obs/config/sfc.yaml
+++ b/parm/atm/obs/config/sfc.yaml
@@ -3,11 +3,11 @@ obs space:
   obsdatain:
     engine:
       type: H5File
-      obsfile: $(DATA)/obs/$(OPREFIX)sfc.${{ current_cycle | to_YMDH }}.nc4
+      obsfile: $(DATA)/obs/$(OPREFIX)sfc.${{ current_cycle | to_YMDH }}.nc
   obsdataout:
     engine:
       type: H5File
-      obsfile: $(DATA)/diags/diag_sfc_${{ current_cycle | to_YMDH }}.nc4
+      obsfile: $(DATA)/diags/diag_sfc_${{ current_cycle | to_YMDH }}.nc
   io pool:
     max pool size: 1
   simulated variables: [stationPressure]
diff --git a/parm/atm/obs/config/sfcship.yaml b/parm/atm/obs/config/sfcship.yaml
index c3530f404..b9f548b53 100644
--- a/parm/atm/obs/config/sfcship.yaml
+++ b/parm/atm/obs/config/sfcship.yaml
@@ -3,12 +3,12 @@ obs space:
   obsdatain:
     engine:
       type: H5File
-      obsfile: $(DATA)/obs/$(OPREFIX)sfcship.${{ current_cycle | to_YMDH }}.nc4
+      obsfile: $(DATA)/obs/$(OPREFIX)sfcship.${{ current_cycle | to_YMDH }}.nc
   obsdataout:
     engine:
       type: H5File
       overwrite: true
-      obsfile: $(DATA)/diags/diag_sfcship_${{ current_cycle | to_YMDH }}.nc4
+      obsfile: $(DATA)/diags/diag_sfcship_${{ current_cycle | to_YMDH }}.nc
   io pool:
     max pool size: 1
   simulated variables: [stationPressure, airTemperature, specificHumidity]
diff --git a/parm/atm/obs/config/sondes.yaml b/parm/atm/obs/config/sondes.yaml
index e9331f7bd..5c83686eb 100644
--- a/parm/atm/obs/config/sondes.yaml
+++ b/parm/atm/obs/config/sondes.yaml
@@ -3,7 +3,7 @@ obs space:
   obsdatain:
     engine: 
       type: H5File
-      obsfile: $(DATA)/obs/$(OPREFIX)sondes.{{ current_cycle | to_YMDH }}.nc4
+      obsfile: $(DATA)/obs/$(OPREFIX)sondes.{{ current_cycle | to_YMDH }}.nc
     obsgrouping:
       group variables: ["stationIdentification"]
       sort variable: "pressure"
@@ -11,7 +11,7 @@ obs space:
   obsdataout:
     engine:
       type: H5File
-      obsfile: $(DATA)/diags/diag_sondes_{{ current_cycle | to_YMDH }}.nc4
+      obsfile: $(DATA)/diags/diag_sondes_{{ current_cycle | to_YMDH }}.nc
   io pool:
     max pool size: 1
   simulated variables: [stationPressure, airTemperature, windEastward, windNorthward, specificHumidity]
diff --git a/parm/atm/obs/config/ssmis_f17.yaml b/parm/atm/obs/config/ssmis_f17.yaml
index 5054951ef..dc16f1581 100644
--- a/parm/atm/obs/config/ssmis_f17.yaml
+++ b/parm/atm/obs/config/ssmis_f17.yaml
@@ -10,16 +10,16 @@ obs space:
   obsdatain:
     engine:
       type: H5File
-      obsfile: $(DATA)/obs/$(OPREFIX)ssmis_f17.${{ current_cycle | to_YMDH }}.nc4
+      obsfile: $(DATA)/obs/$(OPREFIX)ssmis_f17.${{ current_cycle | to_YMDH }}.nc
   obsdataout:
     engine:
       type: H5File
-      obsfile: $(DATA)/diags/diag_ssmis_f17_${{ current_cycle | to_YMDH }}.nc4
+      obsfile: $(DATA)/diags/diag_ssmis_f17_${{ current_cycle | to_YMDH }}.nc
   simulated variables: [brightness_temperature]
   channels: 1-24
 obs bias:
-  input file: $(DATA)/obs/$(GPREFIX)ssmis_f17.satbias.nc4
-  output file: $(DATA)/bc/$(APREFIX)ssmis_f17.satbias.nc4
+  input file: $(DATA)/obs/$(GPREFIX)ssmis_f17.satbias.nc
+  output file: $(DATA)/bc/$(APREFIX)ssmis_f17.satbias.nc
   variational bc:
     predictors:
     - name: constant
diff --git a/parm/atm/obs/config/ssmis_f18.yaml b/parm/atm/obs/config/ssmis_f18.yaml
index 2c757268a..c22598815 100644
--- a/parm/atm/obs/config/ssmis_f18.yaml
+++ b/parm/atm/obs/config/ssmis_f18.yaml
@@ -10,16 +10,16 @@ obs space:
   obsdatain:
     engine:
       type: H5File
-      obsfile: $(DATA)/obs/$(OPREFIX)ssmis_f18.${{ current_cycle | to_YMDH }}.nc4
+      obsfile: $(DATA)/obs/$(OPREFIX)ssmis_f18.${{ current_cycle | to_YMDH }}.nc
   obsdataout:
     engine:
       type: H5File
-      obsfile: $(DATA)/diags/diag_ssmis_f18_${{ current_cycle | to_YMDH }}.nc4
+      obsfile: $(DATA)/diags/diag_ssmis_f18_${{ current_cycle | to_YMDH }}.nc
   simulated variables: [brightness_temperature]
   channels: 1-24
 obs bias:
-  input file: $(DATA)/obs/$(GPREFIX)ssmis_f18.satbias.nc4
-  output file: $(DATA)/bc/$(APREFIX)ssmis_f18.satbias.nc4
+  input file: $(DATA)/obs/$(GPREFIX)ssmis_f18.satbias.nc
+  output file: $(DATA)/bc/$(APREFIX)ssmis_f18.satbias.nc
   variational bc:
     predictors:
     - name: constant
diff --git a/test/atm/global-workflow/config.atmanl b/test/atm/global-workflow/config.atmanl
index a2660e055..c8b6d1d80 100755
--- a/test/atm/global-workflow/config.atmanl
+++ b/test/atm/global-workflow/config.atmanl
@@ -13,11 +13,11 @@ export STATICB_TYPE="identity"
 export BERROR_YAML=${HOMEgfs}/sorc/gdas.cd/parm/atm/berror/staticb_${STATICB_TYPE}.yaml
 export INTERP_METHOD='barycentric'
 
-export layout_x=1
-export layout_y=1
+export layout_x_atmanl=@LAYOUT_X_ATMANL@
+export layout_y_atmanl=@LAYOUT_Y_ATMANL@
 
-export io_layout_x=1
-export io_layout_y=1
+export io_layout_x=@IO_LAYOUT_X@
+export io_layout_y=@IO_LAYOUT_Y@
 
 export JEDIEXE=${HOMEgfs}/exec/fv3jedi_var.x
 export crtm_VERSION="2.4.0"
diff --git a/test/atm/global-workflow/config.yaml b/test/atm/global-workflow/config.yaml
index ec37c4f79..43da40fcf 100644
--- a/test/atm/global-workflow/config.yaml
+++ b/test/atm/global-workflow/config.yaml
@@ -9,3 +9,13 @@ base:
 atmanl:
   OBS_LIST: "@srcdir@/test/atm/global-workflow/gdas_prototype.yaml"
   ATMRES_ANL: "C48"
+  LAYOUT_X_ATMANL: 1
+  LAYOUT_Y_ATMANL: 1
+  IO_LAYOUT_X: 1
+  IO_LAYOUT_Y: 1
+
+atmensanl:
+  LAYOUT_X_ATMENSANL: 1
+  LAYOUT_Y_ATMENSANL: 1
+  IO_LAYOUT_X: 1
+  IO_LAYOUT_Y: 1
diff --git a/test/atm/global-workflow/jjob_ens_init.sh b/test/atm/global-workflow/jjob_ens_init.sh
index 2e5cefc66..1b73a6983 100755
--- a/test/atm/global-workflow/jjob_ens_init.sh
+++ b/test/atm/global-workflow/jjob_ens_init.sh
@@ -68,15 +68,19 @@ RUN=${GDUMP} YMD=${gPDY} HH=${gcyc} generate_com -rx \
 # Link observations
 dpath=gdas.$PDY/$cyc/obs
 mkdir -p $COM_OBS
-flist="amsua_n19.$CDATE.nc4 sondes.$CDATE.nc4"
+flist="amsua_n19.$CDATE sondes.$CDATE"
 for file in $flist; do
-   ln -fs $GDASAPP_TESTDATA/lowres/$dpath/${oprefix}.$file $COM_OBS/${oprefix}.$file
+   ln -fs $GDASAPP_TESTDATA/lowres/$dpath/${oprefix}.${file}.nc4 $COM_OBS/${oprefix}.${file}.nc
 done
 
 # Link radiance bias correction files
 dpath=gdas.$gPDY/$gcyc/analysis/atmos
 mkdir -p $COM_ATMOS_ANALYSIS_PREV
-flist="amsua_n19.satbias.nc4 amsua_n19.satbias_cov.nc4 amsua_n19.tlapse.txt"
+flist="amsua_n19.satbias amsua_n19.satbias_cov"
+for file in $flist; do
+   ln -fs $GDASAPP_TESTDATA/lowres/$dpath/$gprefix.${file}.nc4 $COM_ATMOS_ANALYSIS_PREV/$gprefix.${file}.nc
+done
+flist="amsua_n19.tlapse.txt"
 for file in $flist; do
    ln -fs $GDASAPP_TESTDATA/lowres/$dpath/$gprefix.$file $COM_ATMOS_ANALYSIS_PREV/$gprefix.$file
 done
diff --git a/test/atm/global-workflow/jjob_var_init.sh b/test/atm/global-workflow/jjob_var_init.sh
index 32fc19537..49fdf4eb0 100755
--- a/test/atm/global-workflow/jjob_var_init.sh
+++ b/test/atm/global-workflow/jjob_var_init.sh
@@ -70,17 +70,21 @@ RUN=${GDUMP} YMD=${gPDY} HH=${gcyc} generate_com -rx \
 # Link observations
 dpath=gdas.$PDY/$cyc/obs
 mkdir -p $COM_OBS
-flist="amsua_n19.$CDATE.nc4 sondes.$CDATE.nc4"
+flist="amsua_n19.$CDATE sondes.$CDATE"
 for file in $flist; do
-   ln -fs $GDASAPP_TESTDATA/lowres/$dpath/${oprefix}.$file $COM_OBS/${oprefix}.$file
+   ln -fs $GDASAPP_TESTDATA/lowres/$dpath/${oprefix}.${file}.nc4 $COM_OBS/${oprefix}.${file}.nc
 done
 
 # Link radiance bias correction files
 dpath=gdas.$gPDY/$gcyc/analysis/atmos
 mkdir -p $COM_ATMOS_ANALYSIS_PREV
-flist="amsua_n19.satbias.nc4 amsua_n19.satbias_cov.nc4 amsua_n19.tlapse.txt"
+flist="amsua_n19.satbias amsua_n19.satbias_cov"
 for file in $flist; do
-   ln -fs $GDASAPP_TESTDATA/lowres/$dpath/$gprefix.$file $COM_ATMOS_ANALYSIS_PREV/$gprefix.$file
+   ln -fs $GDASAPP_TESTDATA/lowres/$dpath/$gprefix.${file}.nc4 $COM_ATMOS_ANALYSIS_PREV/$gprefix.${file}.nc
+done
+flist="amsua_n19.tlapse.txt"
+for file in $flist; do
+   ln -fs $GDASAPP_TESTDATA/lowres/$dpath/$gprefix.${file} $COM_ATMOS_ANALYSIS_PREV/$gprefix.${file}
 done
 
 # Link atmospheric background on gaussian grid
diff --git a/ush/ioda/bufr2ioda/bufr2ioda_acft_profiles_prepbufr.py b/ush/ioda/bufr2ioda/bufr2ioda_acft_profiles_prepbufr.py
index 477ac26ca..2e04e8f38 100755
--- a/ush/ioda/bufr2ioda/bufr2ioda_acft_profiles_prepbufr.py
+++ b/ush/ioda/bufr2ioda/bufr2ioda_acft_profiles_prepbufr.py
@@ -98,7 +98,7 @@ def bufr_to_ioda(config, logger):
 
     bufrfile = f"{cycle_type}.t{hh}z.{data_format}.acft_profiles"
     DATA_PATH = os.path.join(dump_dir, f"{cycle_type}.{yyyymmdd}", str(hh),
-                             bufrfile)
+                             'atmos', bufrfile)
 
     # ============================================
     # Make the QuerySet for all the data we want
diff --git a/ush/ioda/bufr2ioda/bufr2ioda_adpsfc_prepbufr.py b/ush/ioda/bufr2ioda/bufr2ioda_adpsfc_prepbufr.py
index 98509b945..a0086293a 100755
--- a/ush/ioda/bufr2ioda/bufr2ioda_adpsfc_prepbufr.py
+++ b/ush/ioda/bufr2ioda/bufr2ioda_adpsfc_prepbufr.py
@@ -70,7 +70,7 @@ def bufr_to_ioda(config, logger):
 
     bufrfile = f"{cycle_type}.t{hh}z.{data_format}"
     DATA_PATH = os.path.join(dump_dir, f"{cycle_type}.{yyyymmdd}",
-                             str(hh), bufrfile)
+                             str(hh), 'atmos', bufrfile)
 
     logger.debug(f"The DATA_PATH is: {DATA_PATH}")
 
diff --git a/ush/ioda/bufr2ioda/bufr2ioda_conventional_prepbufr_ps.py b/ush/ioda/bufr2ioda/bufr2ioda_conventional_prepbufr_ps.py
index 66fb0b112..8352b9f63 100755
--- a/ush/ioda/bufr2ioda/bufr2ioda_conventional_prepbufr_ps.py
+++ b/ush/ioda/bufr2ioda/bufr2ioda_conventional_prepbufr_ps.py
@@ -101,7 +101,7 @@ def bufr_to_ioda(config, logger):
 
     bufrfile = f"{cycle_type}.t{hh}z.{data_format}"
     DATA_PATH = os.path.join(dump_dir, f"{cycle_type}.{yyyymmdd}",
-                             str(hh), bufrfile)
+                             str(hh), 'atmos', bufrfile)
 
     logger.debug(f"The DATA_PATH is: {DATA_PATH}")
 
diff --git a/ush/ioda/bufr2ioda/bufr2ioda_sfcshp_prepbufr.py b/ush/ioda/bufr2ioda/bufr2ioda_sfcshp_prepbufr.py
index 47207a3e9..84aaa7a22 100755
--- a/ush/ioda/bufr2ioda/bufr2ioda_sfcshp_prepbufr.py
+++ b/ush/ioda/bufr2ioda/bufr2ioda_sfcshp_prepbufr.py
@@ -60,7 +60,7 @@ def bufr_to_ioda(config, logger):
 
     bufrfile = f"{cycle_type}.t{hh}z.{data_format}"
     DATA_PATH = os.path.join(dump_dir, f"{cycle_type}.{yyyymmdd}",
-                             str(hh), bufrfile)
+                             str(hh), 'atmos', bufrfile)
 
     logger.debug(f"The DATA_PATH is: {DATA_PATH}")