Bugfix: fewer obs than mpi processes

src/nemo-feedback/NemoFeedback.h

@@ -63,8 +63,9 @@ class NemoFeedback : public ufo::ObsFilterBase,
   ///        the file during construction of the feedback file. This step should
   ///        ensure that the number of levels and the reference Julian day are
   ///        shared across MPI processes.
-  feedback_io::MetaData setupMetaData(const NemoFeedbackDataCreator& creator)
-    const;
+  feedback_io::MetaData setupMetaData(const NemoFeedbackDataCreator& creator,
+                                      const util::DateTime juldReferenceGlobal,
+                                      const size_t nLevelsGlobal) const;
   /// \brief Setup the NEMO STATION_TYPES and STATION_IDS netCDF variables
   ///        In the case of altimetry data, this requires additional processing
   ///        of the satelliteIdentifier to extract these variables.

src/nemo-feedback/feedback_io/DataIndexer.cc

@@ -29,6 +29,10 @@ DataIndexer::DataIndexer(const size_t nObs, const size_t nLevels,
   nObs_(nObs), nLevels_(nLevels),  sourceDataSize_(sourceDataSize),
   indices_(indices), starts_(starts) {
   counts_.reserve(nObs);
+  if (nObs == 0) {
+    validate();
+    return;
+  }
   for (size_t iProf = 0; iProf < nObs - 1; ++iProf) {
     counts_.push_back(starts[iProf +1] - starts[iProf]);
   }

src/tests/CMakeLists.txt

@@ -55,3 +55,26 @@ ecbuild_add_test( TARGET test_nemo_feedback_hofx_profiles_two_vars_file
                   COMMAND ./mains/compare_nc_cdl.sh
                   TEST_DEPENDS test_nemo_feedback_hofx_profiles_two_vars_writer)
 
+ecbuild_add_test( TARGET test_nemo_feedback_hofx_mpi_2_writer
+                  OMP 1
+                  MPI 2
+                  ARGS testinput/hofx_mpi_2_writer.yaml
+                  COMMAND test_NemoInputsFilters.x )
+
+ecbuild_add_test( TARGET test_nemo_feedback_hofx_mpi_2_file
+                  OMP 1
+                  ARGS testoutput/test_hofx_mpi_2_writer_out_00001.nc testoutput/test_hofx_mpi_2_writer_out_00001_ref.cdl
+                  COMMAND ./mains/compare_nc_cdl.sh
+                  TEST_DEPENDS test_nemo_feedback_hofx_mpi_2_writer)
+
+ecbuild_add_test( TARGET test_nemo_feedback_hofx_mpi_3_writer
+                  OMP 1
+                  MPI 3
+                  ARGS testinput/hofx_mpi_3_writer.yaml
+                  COMMAND test_NemoInputsFilters.x )
+
+ecbuild_add_test( TARGET test_nemo_feedback_hofx_mpi_3_file
+                  OMP 1
+                  ARGS testoutput/test_hofx_mpi_3_writer_out_00001.nc testoutput/test_hofx_mpi_3_writer_out_00001_ref.cdl
+                  COMMAND ./mains/compare_nc_cdl.sh
+                  TEST_DEPENDS test_nemo_feedback_hofx_mpi_3_writer)

src/tests/Data/CMakeLists.txt

@@ -5,10 +5,12 @@ hofx_sic_obs.nc
 hofx_two_vars_obs.nc
 hofx_potm_obs.nc
 hofx_prof_2var_obs.nc
+hofx_mpi_obs.nc
 test_hofx3d_nc_prof_2vars_writer_geovals.nc
 test_hofx_profiles_writer_geovals.nc
 test_hofx_sic_writer_geovals.nc
 test_hofx_two_vars_writer_geovals.nc
+test_hofx_mpi_writer_geovals.nc
 )
 
 foreach(FILENAME ${nemofeedback_test_data})

src/tests/testinput/CMakeLists.txt

@@ -5,6 +5,8 @@ list( APPEND fdbk_writer_test_input
   hofx_two_vars_writer.yaml
   hofx_profiles_writer.yaml
   hofx_profiles_2var_writer.yaml
+  hofx_mpi_2_writer.yaml
+  hofx_mpi_3_writer.yaml
   test_name_map.yaml
 )
 

src/tests/testinput/hofx_mpi_2_writer.yaml

@@ -0,0 +1,38 @@
+time window:
+  begin: 2024-06-28T12:00:00Z
+  end: 2025-07-18T12:00:00Z
+observations:
+  - obs space:
+      name: Sea Surface Height Anomaly MPI 
+      obsdatain:
+        engine:
+          type: H5File
+          obsfile: Data/hofx_mpi_obs.nc
+      obsdataout:
+        engine:
+          type: H5File
+          obsfile: testoutput/test_hofx_mpi_2_jopa_out.nc
+      simulated variables: [seaSurfaceHeightAnomaly]
+    obs filters:
+    - filter: NEMO Feedback Writer
+      reference date: 2021-06-30T12:00:00Z
+      filename: testoutput/test_hofx_mpi_2_writer_out.nc
+      observation alias file: testinput/test_name_map.yaml
+      where:
+      - variable:
+          name: DiagnosticFlags/ObsToWrite/seaSurfaceHeightAnomaly
+        value: is_true
+      variables:
+      - name: seaSurfaceHeightAnomaly
+        nemo name: SLA
+        long name: Sea Surface Height Anomaly
+        units: Fraction
+        additional variables:
+        - name: seaSurfaceHeightAnomaly
+          feedback suffix: Hx
+          ioda group: HofX
+    benchmarkFlag: 1000 # just to keep the ObsFilters test happy
+    flaggedBenchmark: 0
+    HofX: hofx
+    geovals:
+      filename: Data/test_hofx_mpi_writer_geovals.nc

src/tests/testinput/hofx_mpi_3_writer.yaml

@@ -0,0 +1,34 @@
+time window:
+  begin: 2024-06-28T12:00:00Z
+  end: 2025-07-18T12:00:00Z
+observations:
+  - obs space:
+      name: Sea Surface Height Anomaly MPI 
+      obsdatain:
+        engine:
+          type: H5File
+          obsfile: Data/hofx_mpi_obs.nc
+      obsdataout:
+        engine:
+          type: H5File
+          obsfile: testoutput/test_hofx_mpi_3_jopa_out.nc
+      simulated variables: [seaSurfaceHeightAnomaly]
+    obs filters:
+    - filter: NEMO Feedback Writer
+      reference date: 2021-06-30T12:00:00Z
+      filename: testoutput/test_hofx_mpi_3_writer_out.nc
+      observation alias file: testinput/test_name_map.yaml
+      variables:
+      - name: seaSurfaceHeightAnomaly
+        nemo name: SLA
+        long name: Sea Surface Height Anomaly
+        units: Fraction
+        additional variables:
+        - name: seaSurfaceHeightAnomaly
+          feedback suffix: Hx
+          ioda group: HofX
+    benchmarkFlag: 1000 # just to keep the ObsFilters test happy
+    flaggedBenchmark: 0
+    HofX: hofx
+    geovals:
+      filename: Data/test_hofx_mpi_writer_geovals.nc

src/tests/testinput/test_name_map.yaml

@@ -11,4 +11,5 @@ variable maps:
     alias: sea_water_salinity
   - name: depthBelowWaterSurface
     alias: depth
-
+  - name: seaSurfaceHeightAnomaly
+    alias: sea_surface_height_anomaly

src/tests/testoutput/CMakeLists.txt

@@ -5,6 +5,8 @@ list( APPEND fdbk_writer_test_output
   test_hofx_two_vars_writer_out_ref.cdl
   test_hofx_profiles_writer_out_ref.cdl
   test_hofx3d_nc_prof_2vars_writer_out_ref.cdl
+  test_hofx_mpi_2_writer_out_00001_ref.cdl
+  test_hofx_mpi_3_writer_out_00001_ref.cdl
 )
 
 foreach(FILENAME ${fdbk_writer_test_output})

src/tests/testoutput/test_hofx_mpi_2_writer_out_00001_ref.cdl

@@ -0,0 +1,172 @@
+netcdf test_hofx_mpi_2_writer_out_00001 {
+dimensions:
+	N_QCF = 2 ;
+	STRINGGRID = 1 ;
+	STRINGJULD = 14 ;
+	STRINGNAM = 8 ;
+	STRINGTYP = 4 ;
+	STRINGWMO = 8 ;
+	N_OBS = 1 ;
+	N_LEVELS = 1 ;
+	N_VARS = 1 ;
+	N_ENTRIES = 1 ;
+variables:
+	char JULD_REFERENCE(STRINGJULD) ;
+		JULD_REFERENCE:long_name = "Date of reference for julian days" ;
+		JULD_REFERENCE:Conventions = "YYYYMMDDHHMMSS" ;
+	char VARIABLES(N_VARS, STRINGNAM) ;
+		VARIABLES:long_name = "List of variables in feedback files" ;
+	char ENTRIES(N_ENTRIES, STRINGNAM) ;
+		ENTRIES:long_name = "List of additional entries for each variable in feedback files" ;
+	double LATITUDE(N_OBS) ;
+		LATITUDE:units = "degrees_north" ;
+		LATITUDE:long_name = "latitude" ;
+	double LONGITUDE(N_OBS) ;
+		LONGITUDE:units = "degrees_east" ;
+		LONGITUDE:long_name = "longitude" ;
+	double DEPTH(N_OBS, N_LEVELS) ;
+		DEPTH:_FillValue = 99999. ;
+		DEPTH:units = "metre" ;
+		DEPTH:long_name = "Depth" ;
+	double JULD(N_OBS) ;
+		JULD:units = "days since JULD_REFERENCE" ;
+		JULD:long_name = "Julian day" ;
+	char STATION_IDENTIFIER(N_OBS, STRINGWMO) ;
+		STATION_IDENTIFIER:long_name = "Station identifier" ;
+	char STATION_TYPE(N_OBS, STRINGTYP) ;
+		STATION_TYPE:long_name = "Code instrument type" ;
+	int DEPTH_QC(N_OBS, N_LEVELS) ;
+		DEPTH_QC:long_name = "Quality on depth" ;
+		DEPTH_QC:Conventions = "U.S. Integrated Ocean Observing System, 2017. Manual for the Use of Real-Time Oceanographic Data Quality Control Flags, Version 1.1" ;
+	int DEPTH_QC_FLAGS(N_OBS, N_LEVELS, N_QCF) ;
+		DEPTH_QC_FLAGS:long_name = "Quality on depth" ;
+		DEPTH_QC_FLAGS:Conventions = "JEDI UFO QC flag conventions" ;
+	int OBSERVATION_QC(N_OBS) ;
+		OBSERVATION_QC:long_name = "Quality on observation" ;
+		OBSERVATION_QC:Conventions = "U.S. Integrated Ocean Observing System, 2017. Manual for the Use of Real-Time Oceanographic Data Quality Control Flags, Version 1.1" ;
+	int OBSERVATION_QC_FLAGS(N_OBS, N_QCF) ;
+		OBSERVATION_QC_FLAGS:long_name = "Quality on observation" ;
+		OBSERVATION_QC_FLAGS:Conventions = "JEDI UFO QC flag conventions" ;
+	int POSITION_QC(N_OBS) ;
+		POSITION_QC:long_name = "Quality on position" ;
+		POSITION_QC:Conventions = "U.S. Integrated Ocean Observing System, 2017. Manual for the Use of Real-Time Oceanographic Data Quality Control Flags, Version 1.1" ;
+	int POSITION_QC_FLAGS(N_OBS, N_QCF) ;
+		POSITION_QC_FLAGS:long_name = "Quality on position" ;
+		POSITION_QC_FLAGS:Conventions = "JEDI UFO QC flag conventions" ;
+	int JULD_QC(N_OBS) ;
+		JULD_QC:long_name = "Quality on date and time" ;
+		JULD_QC:Conventions = "U.S. Integrated Ocean Observing System, 2017. Manual for the Use of Real-Time Oceanographic Data Quality Control Flags, Version 1.1" ;
+	int JULD_QC_FLAGS(N_OBS, N_QCF) ;
+		JULD_QC_FLAGS:long_name = "Quality on date and time" ;
+		JULD_QC_FLAGS:Conventions = "JEDI UFO QC flag conventions" ;
+	int ORIGINAL_FILE_INDEX(N_OBS) ;
+		ORIGINAL_FILE_INDEX:long_name = "Index in original data file" ;
+	double SLA_OBS(N_OBS, N_LEVELS) ;
+		SLA_OBS:long_name = "Sea Surface Height Anomaly" ;
+		SLA_OBS:units = "Fraction" ;
+		SLA_OBS:_FillValue = 99999. ;
+	double SLA_Hx(N_OBS, N_LEVELS) ;
+		SLA_Hx:long_name = "Sea Surface Height Anomaly Hx" ;
+		SLA_Hx:units = "Fraction" ;
+		SLA_Hx:_FillValue = 99999. ;
+	int SLA_QC_FLAGS(N_OBS, N_QCF) ;
+		SLA_QC_FLAGS:_FillValue = 0 ;
+		SLA_QC_FLAGS:long_name = "quality flags on Sea Surface Height Anomaly" ;
+		SLA_QC_FLAGS:Conventions = "JEDI UFO QC flag conventions" ;
+	int SLA_LEVEL_QC_FLAGS(N_OBS, N_LEVELS, N_QCF) ;
+		SLA_LEVEL_QC_FLAGS:_FillValue = 0 ;
+		SLA_LEVEL_QC_FLAGS:long_name = "quality flags for each level on Sea Surface Height Anomaly" ;
+		SLA_LEVEL_QC_FLAGS:Conventions = "JEDI UFO QC flag conventions" ;
+	int SLA_QC(N_OBS) ;
+		SLA_QC:long_name = "quality on Sea Surface Height Anomaly" ;
+		SLA_QC:Conventions = "U.S. Integrated Ocean Observing System, 2017. Manual for the Use of Real-Time Oceanographic Data Quality Control Flags, Version 1.1" ;
+	int SLA_LEVEL_QC(N_OBS, N_LEVELS) ;
+		SLA_LEVEL_QC:_FillValue = 0 ;
+		SLA_LEVEL_QC:long_name = "quality for each level on Sea Surface Height Anomaly" ;
+		SLA_LEVEL_QC:Conventions = "U.S. Integrated Ocean Observing System, 2017. Manual for the Use of Real-Time Oceanographic Data Quality Control Flags, Version 1.1" ;
+	int SLA_IOBSI(N_OBS) ;
+		SLA_IOBSI:long_name = "ORCA grid search I coordinate" ;
+	int SLA_IOBSJ(N_OBS) ;
+		SLA_IOBSJ:long_name = "ORCA grid search J coordinate" ;
+	int SLA_IOBSK(N_OBS, N_LEVELS) ;
+		SLA_IOBSK:long_name = "ORCA grid search K coordinate" ;
+	char SLA_GRID(STRINGGRID) ;
+		SLA_GRID:long_name = "ORCA grid search grid (T,U,V)" ;
+
+// global attributes:
+		:title = "NEMO observation operator output" ;
+		:Convention = "NEMO unified observation operator output" ;
+data:
+
+ JULD_REFERENCE = "20210630120000" ;
+
+ VARIABLES =
+  "SLA     " ;
+
+ ENTRIES =
+  "Hx      " ;
+
+ LATITUDE = 28.26 ;
+
+ LONGITUDE = 33.350002 ;
+
+ DEPTH =
+  0 ;
+
+ JULD = 1461.1639 ;
+
+ STATION_IDENTIFIER =
+  "1005    " ;
+
+ STATION_TYPE =
+  "1005" ;
+
+ DEPTH_QC =
+  _ ;
+
+ DEPTH_QC_FLAGS =
+  _, _ ;
+
+ OBSERVATION_QC = 0 ;
+
+ OBSERVATION_QC_FLAGS =
+  _, _ ;
+
+ POSITION_QC = _ ;
+
+ POSITION_QC_FLAGS =
+  _, _ ;
+
+ JULD_QC = _ ;
+
+ JULD_QC_FLAGS =
+  _, _ ;
+
+ ORIGINAL_FILE_INDEX = _ ;
+
+ SLA_OBS =
+  0.00099999993 ;
+
+ SLA_Hx =
+  -0.072882071 ;
+
+ SLA_QC_FLAGS =
+  _, _ ;
+
+ SLA_LEVEL_QC_FLAGS =
+  _, _ ;
+
+ SLA_QC = _ ;
+
+ SLA_LEVEL_QC =
+  _ ;
+
+ SLA_IOBSI = _ ;
+
+ SLA_IOBSJ = _ ;
+
+ SLA_IOBSK =
+  _ ;
+
+ SLA_GRID = "T" ;
+}