Sync bridge branch back into develop

Externals.cfg

@@ -2,7 +2,7 @@
 required = True
 repo_url = git@github.com:GEOS-ESM/ESMA_env.git
 local_path = ./@env
-tag = v2.1.1 
+tag = v2.1.3+intel19.1.0
 protocol = git
 
 [ESMA_cmake]
@@ -25,15 +25,14 @@ sparse = ../../../config/GMAO_Shared.sparse
 required = True
 repo_url = git@github.com:GEOS-ESM/MAPL.git
 local_path = ./src/Shared/@MAPL
-tag = v2.1.1
+tag = v2.1.3
 protocol = git
 
 [GEOSgcm_GridComp]
 required = True
 repo_url = git@github.com:GEOS-ESM/GEOSgcm_GridComp.git
 local_path = ./src/Components/GEOSldas_GridComp/@GEOSgcm_GridComp
 branch = develop
-#tag = v1.6.0
 protocol = git
 sparse = ../../../../config/GEOSgcm_GridComp_ldas.sparse
 

doc/CHANGELOG.md

@@ -30,17 +30,69 @@ In 2019, GEOS LDAS version control transferred from CVS to Git.
 This README file contains the history of stable GEOSldas versions ("tags") in Git, followed by older, CVS LDASsa and GEOSldas versions and change logs.
 
 
-[Unreleased] Features:
---------------------
-_These are additions put in development, that will be in the next stable tag_
+Overview of Git Releases:
+============================
 
+[v17.9.0-beta.5](https://github.com/GEOS-ESM/GEOSldas/releases/tag/v17.9.0-beta.5) - 2020-05-11
+------------------------------
+- Pre-release meant for use under SLES12 at NCCS.  Still works for SLES11.
 
+- New/Updated Science Functionality:
 
+  - Forecast error covariance inflation with scalar (globally constant) factor.
 
+- New/Updated Infrastructure:
 
-Overview of Git tags:
-============================
+  - Support for GEOS FP forcing with generic ("seamless") file names.
+  - Resource parameter changes:
+    - Renamed NUM_ENSEMBLE to NUM_LDAS_ENSEMBLE in "exeinp" file to be consistent with LDAS.rc.
+    - Renamed MONTHLY_OUTPUT to POSTPROC_HIST.
+  - Updated utilities to MAPL v2.1.3, ESMA_env v2.1.3+intel19.1.0.
+
+- Bug Fixes and Other Minor Changes:
+
+  - Added basic protections for concatenation of sub-daily into daily nc4 files and for generation of monthly-mean nc4 files.
+  - Write ObsFcstAna and smapL4SMaup files into ./scratch, then move to ana/ens_avg/year/month dir in postprocessing.
+  - Some cleanup of obsolete LDASsa code.
+
+------------------------------
+[v17.9.0-beta.4-SLES12](https://github.com/GEOS-ESM/GEOSldas/releases/tag/v17.9.0-beta.4-SLES12) - 2020-04-24
+------------------------------
+- Pre-release meant for use under SLES12 at NCCS, otherwise identical to v17.9.0-beta.4-SLES11.
+- Works under SLES12 using the Intel-19 compiler.
+- Also works under SLES11 using the Intel-18 compiler but is not zero-diff across compilers/operating systems.
+
+------------------------------
+[v17.9.0-beta.4-SLES11](https://github.com/GEOS-ESM/GEOSldas/releases/tag/v17.9.0-beta.4-SLES11) - 2020-04-23
+------------------------------
+- Pre-release meant for use under SLES11 at NCCS. Under SLES12, use v17.9.0-beta.4-SLES12 (or newer).
+- Uses the Intel-18 compiler and also appears to work under SLES12. However, LDASsa with Intel-18 under SLES12 was found to create bad Fortran sequential binary files out of a subroutine that is very similar in LDASsa and GEOSldas.
+- Zero-diff vs. v17.9.0-beta.3 for Catchment only (except SMAP L1C Tb fore-minus-aft check).
+- Not zero-diff for CatchCN (via v1.8.3 of GEOS_GCMGridComp).
+
+- New/Updated Science Functionality:
+
+  - Resurrected SMAP L1C Tb fore-minus-aft check.
+
+- New/Updated Infrastructure:
+
+  - Updated utilities to MAPL v2.1.1, ESMA_env v2.1.1., ESMA_cmake v3.0.1.
+  - New GEOS_SurfaceGridComp.rc file (via v1.8.3 of GEOS_GCMGridComp).
+  - Parallel post-processing.
+  - Cross-stream support for FP f525_p5 forcing.
+  - ~sbatch~ submission for pre-processing of restarts to comply with SLES12 requirements.
+  - Subdaily-to-daily concatenation processes before month is complete.
+  - Temporary solution to create directories for ObsFcstAna files to enable extending an existing GEOSldas run without going through setup.
+
+- Bug Fixes and Other Minor Changes:
+
+  - Updated README.md.
+  - ~obspertrseed~ restart file name when restarting from existing run.
+  - Subdaily-to-daily nc4 concatenation (indent error).
+  - Fixes for GNU compiler in debug mode.
+  - Fixed ~landpert~ checkpoint output when on cube-sphere tiles.
 
+------------------------------
 [v17.9.0-beta.3](https://github.com/GEOS-ESM/GEOSldas/releases/tag/v17.9.0-beta.3) - 2020-03-18
 ------------------------------
 - Additional RESTART options, incl. from re-tiling MERRA-2, FP, or other restarts on different tile space or with different boundary conditions
@@ -240,6 +292,15 @@ reichle-LDASsa_m3-16_6_p1                9 Jul 2018  Added GEOS-5.21 FP function
 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
 reichle-LDASsa_m3-16_6_p2                7 Mar 2019  Added GEOS-5.22 FP functionality
                                                      (patch targeted for NRv7.2 and SMAP L4_SM ops)
+- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
+reichle-LDASsa_m3-16_6_p3               30 Jan 2020  Added GEOS-5.25 FP functionality
+                                                     (patch targeted for NRv7.2 and SMAP L4_SM ops)
+- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
+reichle-LDASsa_m3-16_6_p4                3 Apr 2020  Added GEOS-5.25_p5 FP functionality
+                                                     (patch targeted for NRv7.2 and SMAP L4_SM ops)
+- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
+reichle-LDASsa_m3-16_6_p4_SLES12        14 Apr 2020  SLES12 version of *_p4 tag -- NOT zero-diff!!
+                                                     (patch targeted for NRv7.2 and SMAP L4_SM ops)
 
 -------------------------------------------------------------------------------------
 -------------------------------------------------------------------------------------

doc/README.metforcing_and_bcs.md

@@ -72,7 +72,7 @@ SMAP_Nature_v04, SMAP_Nature_v04.1
   MET_PATH : /discover/nobackup/projects/gmao/merra/iau/merra_land/GEOS5_land_forcing/
 ```
 
-SMAP_Nature_v05
+SMAP_Nature_v05, v7.2, v8.1;  SMAP L4_SM Version 4, Version 5
 ```
   MET_PATH : /discover/nobackup/projects/gmao/merra/iau/merra_land/MERRA2_land_forcing/  ! before 1/1/2015
   MET_PATH : /discover/nobackup/projects/gmao/merra/iau/merra_land/GEOS5_land_forcing/   ! after  1/1/2015
@@ -168,12 +168,21 @@ COMMONLY USED values for `MET_TAG`:
   MET_TAG  : cross_d5124_RPFPIT               ! uses "late-look" through present
 ```
 
-#### FP
+#### GEOS FP
 ```
-  MET_TAG  : e5110_fp
-  MET_TAG  : e5130_fp
-  MET_TAG  : e5131_fp
-  MET_TAG  : cross_FP
+  MET_TAG  : e5110_fp      ! starting 11 Jun 2013
+  MET_TAG  : e5130_fp      ! starting 20 Aug 2014
+  MET_TAG  : e5131_fp      ! starting  1 May 2015
+  MET_TAG  : f516_fp       ! starting 24 Jan 2017
+  MET_TAG  : f517_fp       ! starting  1 Nov 2017
+  MET_TAG  : f521_fp       ! starting 11 Jul 2018
+  MET_TAG  : f522_fp       ! starting 13 Mar 2019
+  MET_TAG  : f525_fp       ! starting 30 Jan 2020
+  MET_TAG  : f525_p5_fp    ! starting  7 Apr 2020
+
+  MET_TAG  : cross_FP      ! stitch FP experiment names across years 
+
+  MET_TAG  : GEOS.fp.asm   ! "seamless" FP files (published/generic file names, ~same result as cross_FP)
 ```
 
 #### FP with precip corrections as in pre-beta SMAP L4_SM products
@@ -184,7 +193,7 @@ COMMONLY USED values for `MET_TAG`:
 #### SMAP_Nature_v03
 ```
   MET_TAG  : cross_RPFPIT__precCPCUG5RPFPITv1                ! before 1/1/2014
-  MET_TAG  : cross_FP__precCPCUG5FPv1		            ! after  1/1/2014
+  MET_TAG  : cross_FP__precCPCUG5FPv1		             ! after  1/1/2014
 ```
 
 #### SMAP_Nature_v04      
@@ -199,7 +208,7 @@ COMMONLY USED values for `MET_TAG`:
   MET_TAG  : cross_FP__precCPCUG5FPv2                        ! after  1/1/2015
 ```
 
-#### SMAP_Nature_v05
+#### SMAP_Nature_v05, v7.2, v8.1;  SMAP L4_SM Version 4, Version 5
 ```
   MET_TAG  : M2COR_cross__precCPCUGPCP22clim_MERRA2_BMTXS    ! before 1/1/2015
   MET_TAG  : cross_FP__precCPCUG5FPv3                        ! after  1/1/2015
@@ -259,7 +268,7 @@ COMMONLY USED boundary conditions (bcs):
   BCS_PATH = /discover/nobackup/projects/gmao/ssd/land/l_data/geos5/bcs/CLSM_params/mkCatchParam_SMAP_L4SM_v002/
 ```
 
-#### Icarus-NL ("New Land")
+#### Icarus-NL ("New Land"), SMAP_Nature_v7.2
 ```
   BCS_PATH = /discover/nobackup/ltakacs/bcs/Icarus-NL/
 ```
@@ -269,8 +278,7 @@ Notes:
 - This path remains in place to permit recreating experiments that have used this path.
 - The sub-directory "Icarus-NL_MERRA-2/" contains the "new land" bcs.  The string "MERRA-2" in this sub-directory name refers to ocean bcs that are not relevant for GEOSldas.
 
-
-#### Icarus-NL ("New Land") v2
+#### Icarus-NLv2, SMAP L4_SM Version 4
 ```
   BCS_PATH = /discover/nobackup/ltakacs/bcs/Icarus-NLv2/
 ```
@@ -279,7 +287,7 @@ Notes:
 - Icarus-NLv2 is a update to Icarus-NL bcs. A patch has been applied to files green*.data, nirdf*.dat, and visdf*.dat. 
 - DEFAULT for GEOSldas v17.8.0 
 
-#### Icarus-NL ("New Land") v3
+#### Icarus-NLv3, SMAP_Nature_v8.1, SMAP L4_SM Version 5
 ```
   BCS_PATH = /discover/nobackup/ltakacs/bcs/Icarus-NLv3/
 ```

src/Applications/LDAS_App/GEOSldas_LDAS.rc

@@ -41,39 +41,32 @@ LSM_CHOICE: 1
 #      If only whitelist should be used, specify dummy valuessuch that:
 #         MINLON > MAXLON and MINLAT > MAXLAT.
 #
-# MINLON                       : -180.
-# MAXLON                       :  180.
-# MINLAT                       :  -90.
-# MAXLAT                       :   90.
+# MINLON: -180.
+# MAXLON:  180.
+# MINLAT:  -90.
+# MAXLAT:   90.
 #
 #      Specify path and filenames for blacklist and whitelist files:
 #      (May leave blank.)
 #
-# BLACK_FILE                   : '' 
-# WHITE_FILE                   : '' 
+# BLACK_FILE: '' 
+# WHITE_FILE: '' 
 
 
-# ---- Surface meteorological forcing: Time step
-#
-#        Should be set in the exeinp file where MET_PATH is defined
-#        3600 = default
-#
-# FORCE_DTSTEP                 : 3600
-
 # ---- Surface meteorological forcing: Horizonal interpolation 
 #
 #    1 :  bilinear interpolation (default)
 #    0 :  nearest neighbor
 #
-MET_HINTERP                    : 1
+MET_HINTERP: 1
 
 
 # ---- Specify if running model only or data assimilation
 #
 #  NO  : model only (DEFAULT; with --runmodel option)
 #  YES : assimilation (without --runmodel option)
 #
-LAND_ASSIM                     : NO
+LAND_ASSIM: NO
 
 
 # ---- Perturbations: On/off 
@@ -83,11 +76,11 @@ LAND_ASSIM                     : NO
 #    0 : No perturbactions.
 #    1 : With perturbations.
 #
-PERTURBATIONS                  : 0
+PERTURBATIONS: 0
 
 # ---- Perturbations: ID of first ensemble member
 #
-FIRST_ENS_ID                   : 0
+FIRST_ENS_ID: 0
 
 
 # ---- Path to special namelist input files
@@ -98,15 +91,15 @@ FIRST_ENS_ID                   : 0
 #          LDASsa_SPECIAL_inputs_ensprop.nml 
 #          LDASsa_SPECIAL_inputs_catbias.nml 
 #
-# NML_INPUT_PATH               : ''
+# NML_INPUT_PATH: ''
 
 
 # ---- Microwave Radiative Transfer Model (mwRTM) parameter file name (nc4 format) used for Tb assimilation
 #
 #      This file can be converted from binary with the program mwrtm_bin2nc4.x. 
 #      If empty or commented out, GEOSldas will search the restart directory.
 #
-# MWRTM_FILE                   : ''
+# MWRTM_FILE: ''
 
 
 # ---- Job segments: Length
@@ -115,7 +108,7 @@ FIRST_ENS_ID                   : 0
 #      Default is the entire simulation period (END_DATE minus BEG_DATE).
 #      Format:            yyyymmdd hhmmss
 #
-# JOB_SGMT                     : 00000100 000000
+# JOB_SGMT: 00000100 000000
 
 # ---- Job segments: Number
 #
@@ -124,31 +117,34 @@ FIRST_ENS_ID                   : 0
 #      Low values for NUM_SGMT are recommended for run-time and storage efficiency.
 #      Default is 1.
 #
-# NUM_SGMT                     : 1
+# NUM_SGMT: 1
 
 
 # ---- Output: Write log file (YES/NO)?
 #
-LDAS_logit                     : YES
+LDAS_logit: YES
 
 # ---- Output: HISTORY definition of model diagnostics
 #
 #      User-defined path and filename of output (HISTORY) specification file.
 #      If empty, ldas_setup will generate a default HISTORY.rc file.
 #
-# HISTRC_FILE                  : ''
+# HISTRC_FILE: ''
 
-# ---- Write only monthly output?
+# ---- Concatenate sub-daily nc4 files into daily nc4 files and write monthly-mean output?
 #
-#      Monthly files can be created from daily files. 
-#      Accurate monthly averages require setting "ref_time" in HISTORY.rc to "000000"
+#      Optional post-processing of model diagnostics output into bundled daily files and monthly means.
+#      Reduces the file count and (optionally) the output volume.
 #
-#    0 : Output bundled into daily files per HISTORY specifications (default).
-#    1 : Monthly files will be created. Daily files will *not* be deleted.
-#    2 : Monthly files will be created and daily files will be deleted automatically.
+#      Accurate monthly-means of time-average Collections require setting "ref_time" to "000000" in HISTRC_FILE!
 #
-# MONTHLY_OUTPUT               : 0
-
+#    0 : No post-processing (default).
+#    1 : For complete days, concatenate (bundle) sub-daily nc4 files, if any, into daily nc4 files.  
+#        For complete months, write monthly-mean nc4 files.  
+#    2 : As in 1, but delete daily nc4 files.
+#
+# POSTPROC_HIST: 0
+
 
 # ---- Name of file containing Surface GridComp resource parameters 
 #
@@ -161,12 +157,12 @@ SURFRC: LDAS.rc
 
 # ---- No dycore for offline
 #
-DYCORE                         : none
+DYCORE: none
 
 # ---- Only one surface level
 #
-LM                             : 1
+LM: 1
 
 # ---- For MAPL_RestartOptional
 #
-MAPL_ENABLE_BOOTSTRAP          : YES
+MAPL_ENABLE_BOOTSTRAP: YES

src/Applications/LDAS_App/LDASsa_DEFAULT_inputs_ensupd.nml

@@ -1,9 +1,10 @@
 ! 
 ! namelist of EnKF inputs for land EnKF update
 !
-! reichle, 28 Jan 2005
-! reichle, 13 Jun 2011 - updated for SMOS angles and downscaling ("FOV")
-! reichle,  8 Jun 2017 - added "%flistpath" and "%flistname"; updated comments
+! reichle,      28 Jan 2005
+! reichle,      13 Jun 2011 - updated for SMOS angles and downscaling ("FOV")
+! reichle,       8 Jun 2017 - added "%flistpath" and "%flistname"; updated comments
+! qliu+reichle, 29 Apr 2020 - added forecast error covariance inflation 
 !
 ! --------------------------------------------------------------------
 
@@ -42,17 +43,8 @@ centered_update = .false.
 
 out_obslog      = .true.
 out_ObsFcstAna  = .false.
-!out_incr        = .false.
 out_smapL4SMaup = .false.
 
-! select format of increments output	
-!  0: standard LDASsa 
-!     (output in LDASsa domain and LDASsa tile order)
-!  1: suitable for land incremental analysis update (LIAU) in GEOS-5 GCM
-!     (output on global domain in GEOS-5 global tile order)
-
-!out_incr_format = 0       
-
 ! ---------------------------------------------------------------------
 !
 ! Compact support parameters - for 3d updates
@@ -63,6 +55,17 @@ out_smapL4SMaup = .false.
 xcompact = 0.           ! [deg] longitude
 ycompact = 0.           ! [deg] latitude
 
+! ---------------------------------------------------------------------
+!
+! forecast error covariance inflaction factor 
+!
+! - assigns more weight to observations in analysis by inflating forecast error covariance 
+! - works on std-dev, i.e.,  var_inflated = var * inflation_fac**2   
+! - typical values: 1 <= inflation_fac <= 1.5
+! - to turn off, set to any negative real number 
+
+fcsterr_inflation_fac = -9999.
+
 ! ---------------------------------------------------------------------
 !		
 ! Definition of measurement species and parameters