… checking (NOAA-EMC#532)

…s multiscale EnVar and parallel ensemble IO for EnVar for FV3-LAM (NOAA-EMC#504)

The following capabilities developed by OU MAP lab are included

(1) Further development for simultaneous multiscale EnVar for both
global and regional DA
(1a) spatial scale-dependent localization (SDL; contributed by Ting Lei
and Daryl Kleist/EMC) is implemented in EnVar as described in Huang et
al 2021, MWR for the global NWP application.
(1b) variable-dependent localization (VDL) method by Wang and Wang 2022,
JAMES is implemented in EnVar.

(2)Development of parallel ensemble IO for EnVar for FV3-LAM 
Implement an approach to simultaneously read in all ensemble members for
EnVar. Specifically, parallel ensemble IO for both conventional and
radar EnVar for FV3-LAM is implemented by reading in all ensemble
members simultaneously.

(3) Direct assimilation of radar reflectivity for EnVar for RRFS
The direct radar reflectivity assimilation approach by Wang and Wang
2017, MWR is implemented and tested for FV3-LAM.

Fixes NOAA-EMC#468

**Description**

Added code to divide hx_modens by qsat, for consistency with treatment
of q as q/qsat.

Fixes issue NOAA-EMC#544

merge changes made in recent GFS v16.3.x implementations into develop

…le for FV3-LAM EnVar (NOAA-EMC#541)

This PR adds options (weight_ens_gfs and weight_ens_fv3sar) to tune
weights of mixed ensemble for FV3-LAM EnVar
(NOAA-EMC#538). Regression tests for
global 3dvar/4denvar/4dvar are not completed yet, but for other tests,
issues are not found except for "failed the scalability test" and
"exceeded maximum allowable hardware memory limit" on Orion.

Fixes NOAA-EMC#538

Co-authored-by: Sho Yokota <[email protected]>

**Description**

This update includes several functions added for dBZ analysis in EnKF:
1, Add dBZ ncdiag output for EnKF analysis
2, Enhanced binary dBZ diag output for EnKF analysis
3, Fix spurious analysis increments when assimilating reflectivity (from
OU MAP)
4, Added EnKF interface for read in dBZ from FV3LAM ensemble forecast
(from OU MAP)

Fixed a bug for read in subdomain surface restart files

Fixes NOAA-EMC#534

**Description**
The ncio and ncdiag modules have been promoted from para to prod on
WCOSS2.  This PR replaces the para load of these modules with prod on
WCOSS2.

Fixes NOAA-EMC#554

…me covariances in EnVar (NOAA-EMC#542)

This PR modifies options (i_ensloccov4{scl,var,tim} ->
r_ensloccov4{scl,var,tim}) to tune cross-scale/variable/time covariances
in EnVar (NOAA-EMC#539). Regression tests
for global 3dvar/4denvar/4dvar are not completed yet, but for other
tests, issues are not found except for "failed the scalability test" and
"exceeded maximum allowable hardware memory limit" on Orion.

Fixes NOAA-EMC#539

Co-authored-by: Sho Yokota <[email protected]>

…C#499)

The enhancements made to the EnKF IO interface are the following:
(1) For enkf I/O: add the handling of precipitation hydrometeors to
parallel netcdf I.O --- preparation of next implementation

… plus changes to make code work for multiscale (bugs introduced in develop). (NOAA-EMC#570)

… conventional data simultaneously without side effects in EnVar (NOAA-EMC#543)

This PR removes forcing pure EnVar and adding an option (if_use_w_vr) to
assimilate radar reflectivity and conventional data simultaneously
without side effects in EnVar
(NOAA-EMC#540). Regression tests for
global 3dvar/4denvar/4dvar are not completed yet, but for other tests,
issues are not found except for "failed the scalability test" and
"exceeded maximum allowable hardware memory limit" on Orion.

Fixes NOAA-EMC#540

Co-authored-by: Sho Yokota <[email protected]>

…OAA-EMC#557)

Resubmit PR for cleaning the unneeded item in the previous PR 
In correspondence to the EMC GSI Issue#566, this PR contains a quick
adding of the clipping of negative values of sphum (q) in the analysis
of FV3-LAM EnKF.
This part of codes are not tested in the current GSI regression tests,
which, hence, are not run.
The current codes are verified using local FV3-LAM case. It is found the
differences from this changes exist for sphum ( maximum values about
0.003 (units) and 0.3 K for T (sensible T). The latter is because the
sphum would be used when the analysis TV is converted to T. All
differences are on spontaneous points and values are reasonable as
expected.
Hence, the code is regarded as verified.

Fixes NOAA-EMC#566

**DUE DATE for this PR is 6/15/2023.** If this PR is not merged into
`develop` by this date, the PR will be closed and returned to the
developer.

… values instead of zeros (NOAA-EMC#578)

<!-- PLEASE READ -->
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- Each PR should only address ONE topic and have an associated issue
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**Description**

Initialization of the operational RRFSv1 will include assimilation of
flash-extent density (FED) observations from the GOES Geostationary
Lightning Mapper (GLM). The current PR is the first of at least 3 that
will be needed to introduce the capability of FED assimilation into the
code and regional workflow. The new capabilities that are added to GSI
are:

* reading NetCDF FED observations
* applying an observation operator that maps the model state to FED.

Much of the code was originally developed by Rong Kong at OU-CAPS (Kong
et al. 2020, Wang et al. 2021, Kong et al. 2022;
https://doi.org/10.1175/MWR-D-19-0192.1,
https://doi.org/10.1175/MWR-D-20-0406.1,
https://doi.org/10.1175/MWR-D-21-0326.1). Recently, the observation
operator has been modified by Amanda Back and Ashley Sebok based on
tests with regional, convection-allowing FV3 forecasts. The new
observation operator includes a cap of 8 flashes / minute for both the
observed and simulated FED.

The observation operator is specific to the 3-km regional FV3
application in RRFS. Development of a more general observation operator
is left to future work.

Fixes NOAA-EMC#588 

<!-- Please include relevant motivation and context. -->
<!-- Please include a summary of the change and which issue is fixed.
-->
<!-- List any dependencies that are required for this change. -->

<!-- Please provide reference to the issue this pull request is
addressing. -->
<!-- For e.g. Fixes #IssueNumber -->

**Type of change**

Please delete options that are not relevant.

- [ ] Bug fix (non-breaking change which fixes an issue)
- [X] New feature (non-breaking change which adds functionality)
- [ ] Breaking change (fix or feature that would cause existing
functionality to not work as expected)
- [ ] This change requires a documentation update

**How Has This Been Tested?**

Initial tests were with NOAA-EMC GSI-EnKF code obtained in April 2023
and modified to include the assimilation of FED observations. A
prototype of RRFSv1 was cycled hourly for 2.5 days, and the EnKF
assimilation included FED data assimilation.

For the current PR, only the GSI observer with FED (and radar
reflectivity) observations was tested. It produces identical results to
those obtained in April 2023.

<!-- Please describe the tests that you ran to verify your changes and
on the platforms these tests were conducted. -->
<!-- Provide instructions so we can reproduce. -->
<!-- Please also list any relevant details for your test configuration
-->
  
**Checklist**

- [ ] My code follows the style guidelines of this project
- [X] I have performed a self-review of my own code
- [ ] I have commented my code, particularly in hard-to-understand areas
- [ ] New and existing tests pass with my changes
- [ ] Any dependent changes have been merged and published

**DUE DATE for this PR is 8/24/2023.** If this PR is not merged into
`develop` by this date, the PR will be closed and returned to the
developer.

---------

Co-authored-by: Ming Hu <[email protected]>

…#618) (NOAA-EMC#619)

**Description**
PR NOAA-EMC#591 removed jacobian information from the netcdf ozone diagnostic
file. This caused `enkf.x` to crash. This PR adds the removed ozone
jacobian arrays back to the netcdf ozone diagnostic file.

Fixes NOAA-EMC#618

**Type of change**
- [x] Bug fix (non-breaking change which fixes an issue)


**How Has This Been Tested?**
The revised code was tested in the 20210814 18 gdas cycle of a C192L127
enkf parallel. The updated `gsi.x` created an oznstat file which was
successfully processed by `enkf.x`.
  
**Checklist**
- [x] My code follows the style guidelines of this project
- [x] I have performed a self-review of my own code
- [x] New and existing tests pass with my changes

 * caveat - the wcoss2 build remains at intel/19

---------

Co-authored-by: David Huber <[email protected]>
Co-authored-by: Natalie Perlin <[email protected]>
Co-authored-by: RussTreadon-NOAA <[email protected]>

**Description**
This PR updates the `fix` submodule to bring in GFS v16.3.9 updates to
`global_convinfo.txt` and `global_ozinfo.txt`. Issue NOAA-EMC#620 provides
additional information on the GFS v16.3.9 updates.

Please **note** the following
- The change to `global_ozinfo.txt` alters analysis results if ompsnp
observation from NOAA-20, NOAA-21, or NPP are processed by gsi.x or
`enkf.x`.
- The change to `global_convinfo.txt` alters analysis results if
PlanetIQ GPSRO (type 267) is processed by `gsi.x` or `enkf.x`.

Fixes NOAA-EMC#620 

**Type of change**
- [x] Breaking change (fix or feature that would cause existing
functionality to not work as expected)

See the **Note** above for potential impact on analysis results.

**How Has This Been Tested?**
ctests have been run on Hera, Orion, and WCOSS2 (Cactus) with results
posted in issue NOAA-EMC#620.
  
**Checklist**
- [x] My code follows the style guidelines of this project
- [x] I have performed a self-review of my own code

**Description**
Bring in HAFSv1 related maxobs changes and the capability of
assimilating GOES-R high-resolution AMVs.
Resolved NOAA-EMC#599 

**Type of change**
Use "maxobs" as a condition to check whether the number of observations
exceeds the limit, to avoid the out of bound/dimension issue in
read_anowbufr.f90 read_dbz_nc.f90 read_gmi.f90 read_goesglm.f90
read_radar.f90 read_radar_wind_ascii.f90
This update also added the capability of assimilating the CIMSS enhanced
GOES-R AMVs in a new "satwhr" bufr file.
Please delete options that are not relevant.

- [x] Bug fix (non-breaking change which fixes an issue)
- [x] New feature (non-breaking change which adds functionality)

**How Has This Been Tested?**
This updates passed the HAFS related regression tests. All tests are
performed on Orion.
  
**Checklist**

- [x] My code follows the style guidelines of this project
- [x] I have performed a self-review of my own code
- [x] I have commented my code, particularly in hard-to-understand areas
- [x] New and existing tests pass with my changes
- [x] Any dependent changes have been merged and published

**DUE DATE for this PR is 9/21/2023.** If this PR is not merged into
develop by this date, the PR will be closed and returned to the
developer.

---------

Co-authored-by: jswhit <[email protected]>
Co-authored-by: [email protected] <[email protected]>
Co-authored-by: Jili Dong <[email protected]>
Co-authored-by: Bin Liu <[email protected]>
Co-authored-by: daprediction <[email protected]>
Co-authored-by: TingLei-NOAA <[email protected]>
Co-authored-by: TingLei-NOAA <[email protected]>
Co-authored-by: xulu <[email protected]>
Co-authored-by: Li Bi <[email protected]>
Co-authored-by: edward.safford <[email protected]>
Co-authored-by: MichaelLueken-NOAA <[email protected]>
Co-authored-by: RussTreadon-NOAA <[email protected]>
Co-authored-by: Michael Lueken <[email protected]>
Co-authored-by: AndrewEichmann-NOAA <[email protected]>
Co-authored-by: Rahul Mahajan <[email protected]>
Co-authored-by: Emily Liu <[email protected]>
Co-authored-by: emilyhcliu <[email protected]>
Co-authored-by: Andrew Collard <[email protected]>
Co-authored-by: RussTreadon-NOAA <[email protected]>

…EMC#626)

The fix involves setting the pressure to 0.001Pa for ozone obs that have
zero pressure (to avoid Inf when log(p) calculated), and turning off
ob-space vertical localization. Has no effect on current operational
setup which uses model-space vertical localization (modelspace_vloc=T).

---------

Co-authored-by: jswhit2 <[email protected]>

NOAA-EMC#594)

This update improves the efficiency of the GSI, especially for
multiscale runs. Details can be found in issue NOAA-EMC#585

**Description**
This PR fixes two types of bugs discovered when cycling `gsi.x` and
`enkf.x` with intel/2022 in the global workflow
1. modify variables written to netcdf diagnostic files by `gsi.x` to be
consistent with codes which read netcdf diagnostic files
2. modify `lrun_subdirs=.true.` option of `gsi.x` to properly handle the
case in which sub-directories already exist in the run directory

Fixes NOAA-EMC#623

**Type of change**
- [x] Bug fix (non-breaking change which fixes an issue)

**How Has This Been Tested?**
Ctests have been on Hera, Orion, and WCOSS2 (Cactus) with acceptable
behavior. A global parallel covering the period 2021073106 through
2021080118 has been run on Hera, Orion, and WCOSS2 (Cactus). All global
workflow jobs ran as expected.
  
**Checklist**
- [x] My code follows the style guidelines of this project
- [x] I have performed a self-review of my own code
- [x] New and existing tests pass with my changes

… (see issue NOAA-EMC#601) (NOAA-EMC#614)

Adding code to analyze the siginificant wave heigh in GSI 3D Analysis,
esp. for FV3-LAM model based DA, eg. RRFS-DA, RRFS-3DRTMA. (Also see the
issue in EMC GSI github repository: NOAA-EMC#601
 Adding I/O for Analysis of Significant Wave Height for 3DRTMA)

<!-- PLEASE READ -->
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- Each PR should only address ONE topic and have an associated issue
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**Description**

<!-- Please include relevant motivation and context. -->
Significant Wave Height (hereafter as SWH) is one of the standard
products provided by the operational (2D)RTMA. To continuously provide
the same products in 3DRTMA, the next-generation RTMA, some efforts in
GSI code need to be made in order to analyze the SWH in 3D analysis of
GSI.
<!-- Please include a summary of the change and which issue is fixed.
-->
The kernel subroutines to assimilate SWH in GSI (such as stphowv.f90,
setuphowv.f90, inthowv.f90, gsi_howvOper.f90 and m_howvNode.f90) already
had been added for (2D)RTMA years ago by Manuel Pondeca, so for this
issue, the code work mainly focus on adding the I/O of SWH in background
and analysis fields for 3DRTMA (esp. RRFS-based 3DRTMA), and some
necessary modifications in background error, options, variables related
to analysis of SWH, etc.
Modified code in GSI:
1. rapidrefresh_cldsurf_mod.f90: adding a few variables related to the
analysis of howv in 3D analysis
2. gsimod.F90: adding namelist options used for analysis of howv in 3D
analysis
3. m_berror_stats_reg.f90: added some code for the special treatment to
the static background error (BE) of howv
4. read_prepbufr.f90: adding code to decode the observation of howv in
prepbufr file when howv is available in firstguess
5. setuphowv.f90: adding code to use obs of howv when howv is available
in firstguess
6. gsi_rfv3io_mod.f90: adding I/O code to read in howv from firstguess
and write out howv into analysis.


<!-- List any dependencies that are required for this change. -->
No dependencies are required for this change.
<!-- Please provide reference to the issue this pull request is
addressing. -->
This PR is addressing the issue
[NOAA-EMC#601](NOAA-EMC#601): Adding code to
analyze the siginificant wave heigh in GSI 3D Analysis".
<!-- For e.g. Fixes #IssueNumber -->
Fixes NOAA-EMC#601

**Type of change**

Please delete options that are not relevant.


- [*] New feature (non-breaking change which adds functionality)



**How Has This Been Tested?**

<!-- Please describe the tests that you ran to verify your changes and
on the platforms these tests were conducted. -->
- Brief results from ctest (regression test) with the modified code (on
WCOSS2 - Cactus):

 [gang.zhao@clogin07:build] (feature/3drtma_howv)$ ctest -N
Test project /lfs/h2/emc/da/save/gang.zhao/WorkDir/WaveHgt/develop/build
  Test NOAA-EMC#1: global_3dvar
  Test NOAA-EMC#2: global_4dvar
  Test NOAA-EMC#3: global_4denvar
  Test NOAA-EMC#4: hwrf_nmm_d2
  Test NOAA-EMC#5: hwrf_nmm_d3
  Test NOAA-EMC#6: rtma
  Test NOAA-EMC#7: rrfs_3denvar_glbens
  Test NOAA-EMC#8: netcdf_fv3_regional
  Test NOAA-EMC#9: global_enkf

Total Tests: 9
  Test NOAA-EMC#1: global_3dvar
[gang.zhao@clogin04:build] (feature/3drtma_howv)$ ctest -R global_3dvar
Test project /lfs/h2/emc/da/save/gang.zhao/WorkDir/WaveHgt/develop/build
    Start 1: global_3dvar
1/1 Test NOAA-EMC#1: global_3dvar .....................   Passed  1631.12 sec

100% tests passed, 0 tests failed out of 1

Total Test time (real) = 1631.14 sec

  Test NOAA-EMC#2: global_4dvar
[gang.zhao@clogin09:build] (feature/3drtma_howv)$ ctest -R global_4dvar
Test project /lfs/h2/emc/da/save/gang.zhao/WorkDir/WaveHgt/develop/build
    Start 2: global_4dvar
1/1 Test NOAA-EMC#2: global_4dvar .....................   Passed  2462.19 sec

100% tests passed, 0 tests failed out of 1

Total Test time (real) = 2462.23 sec

  Test NOAA-EMC#3: global_4denvar
[gang.zhao@clogin04:build] (feature/3drtma_howv)$ ctest -R
global_4denvar
Test project /lfs/h2/emc/da/save/gang.zhao/WorkDir/WaveHgt/develop/build
    Start 3: global_4denvar
1/1 Test NOAA-EMC#3: global_4denvar ...................   Passed  1922.43 sec

100% tests passed, 0 tests failed out of 1

Total Test time (real) = 1922.46 sec

  Test NOAA-EMC#4: hwrf_nmm_d2
[gang.zhao@clogin09:build] (feature/3drtma_howv)$ ctest -R hwrf_nmm_d2
Test project /lfs/h2/emc/da/save/gang.zhao/WorkDir/WaveHgt/develop/build
    Start 4: hwrf_nmm_d2
1/1 Test NOAA-EMC#4: hwrf_nmm_d2 ......................   Passed  1214.10 sec

100% tests passed, 0 tests failed out of 1

Total Test time (real) = 1214.20 sec

  Test NOAA-EMC#5: hwrf_nmm_d3
[gang.zhao@clogin09:build] (feature/3drtma_howv)$ ctest -R hwrf_nmm_d3
Test project /lfs/h2/emc/da/save/gang.zhao/WorkDir/WaveHgt/develop/build
    Start 5: hwrf_nmm_d3
1/1 Test NOAA-EMC#5: hwrf_nmm_d3 ......................   Passed  736.38 sec

100% tests passed, 0 tests failed out of 1

Total Test time (real) = 736.50 sec

  Test NOAA-EMC#6: rtma
[gang.zhao@clogin05:build] (feature/3drtma_howv)$ ctest -R rtma
Test project /lfs/h2/emc/da/save/gang.zhao/WorkDir/WaveHgt/develop/build
    Start 6: rtma
1/1 Test NOAA-EMC#6: rtma .............................   Passed  1027.01 sec

100% tests passed, 0 tests failed out of 1

Total Test time (real) = 1027.01 sec

  Test NOAA-EMC#7: rrfs_3denvar_glbens
[gang.zhao@clogin06:build] (feature/3drtma_howv)$ ctest -R
rrfs_3denvar_glbens
Test project /lfs/h2/emc/da/save/gang.zhao/WorkDir/WaveHgt/develop/build
    Start 7: rrfs_3denvar_glbens
1/1 Test NOAA-EMC#7: rrfs_3denvar_glbens ..............   Passed  484.69 sec

100% tests passed, 0 tests failed out of 1

Total Test time (real) = 484.70 sec

  Test NOAA-EMC#8: netcdf_fv3_regional
[gang.zhao@clogin03:build] (feature/3drtma_howv)$ ctest -R
netcdf_fv3_regional
Test project /lfs/h2/emc/da/save/gang.zhao/WorkDir/WaveHgt/develop/build
    Start 8: netcdf_fv3_regional
1/1 Test NOAA-EMC#8: netcdf_fv3_regional ..............   Passed  483.08 sec

100% tests passed, 0 tests failed out of 1

Total Test time (real) = 483.11 sec

  Test NOAA-EMC#9: global_enkf
[gang.zhao@clogin03:build] (feature/3drtma_howv)$ ctest -R global_enkf
Test project /lfs/h2/emc/da/save/gang.zhao/WorkDir/WaveHgt/develop/build
    Start 9: global_enkf
1/1 Test NOAA-EMC#9: global_enkf ......................   Passed  488.50 sec

100% tests passed, 0 tests failed out of 1

Total Test time (real) = 488.57 sec

- The modified GSI code passed the regression tests (all 9 tasks) on
Hera and WCOSS2 (Cactus).

- adding the analysis of howv only has very trial influences on the
analyses of other variables. Here is the statistics of the differences
of other variables (u/v/t/ps/q/t2m/q2m) from the runs of GSI without
howv vs. with howv (from a testing case 2023-07-12_14:00:00 UTC in 3km
North-American domain):

comparing two netcdf files:
fcst_fv3lam_hyb_betas/INPUT/fv_core.res.tile1.nc
fcst_fv3lam_nodata_noinfo/INPUT/fv_core.res.tile1.nc ...
Variable Group Count Sum AbsSum Min Max Range Mean StdDev
u / 602135550 3926.84 25760.8 -0.1026 0.485788 0.588388 6.52152e-06
0.00115817
v / 620166777 -4891.34 32582.5 -0.835774 0.268402 1.10418 -7.88714e-06
0.00197793
T / 155987083 178.048 6497.51 -0.0246582 0.0384064 0.0630646 1.14143e-06
0.000218737
delp / 19559676 -281.532 3008.29 -0.00292969 0.00219727 0.00512695
-1.43935e-05 0.000183727

comparing two netcdf files:
fcst_fv3lam_hyb_betas/INPUT/fv_tracer.res.tile1.nc
fcst_fv3lam_nodata_noinfo/INPUT/fv_tracer.res.tile1.nc ...
Variable Group Count Sum AbsSum Min Max Range Mean StdDev
sphum / 430707614 0.594287 2.77816 -2.6139e-05 3.1759e-05 5.7898e-05
1.37979e-09 8.03072e-08

comparing two netcdf files: fcst_fv3lam_hyb_betas/INPUT/sfc_data.nc
fcst_fv3lam_nodata_noinfo/INPUT/sfc_data.nc ...
Variable Group Count Sum AbsSum Min Max Range Mean StdDev
t2m / 10665000 43.3899 135.095 -0.00152825 0.00686629 0.00839454
4.06844e-06 5.02866e-05
q2m / 10665000 0.0192553 0.124707 -3.1476e-06 1.77554e-05 2.0903e-05
1.80547e-09 5.89657e-08

It could be seen that the differences are trivial and ignorable.

<!-- Provide instructions so we can reproduce. -->
The regression tests were done by following the instructions of "[GSI
Ctests (regression
tests)](https://github.com/NOAA-EMC/GSI/wiki/GSI-Ctests-(regression-tests))"
in [GSI Wiki](https://github.com/NOAA-EMC/GSI/wiki)
<!-- Please also list any relevant details for your test configuration
-->
The modified code had also been tested with a testing case
2023-07-12_14:00:00 UTC for 3km North-American domain
Here is a brief summary of the test results:
1. Here is the analysis increment of Significant Wave Height (aka howv
hereafter): pure 3dvar, static background error of howv is 0.42 meters,
and the de-correlation length scale is 170km.

![HOWV_var_inc_maprll_datll_reg_ncf](https://github.com/NOAA-EMC/GSI/assets/53267411/4fdeeb82-7258-4344-be69-cce747474312)
2. The following figure shows the distribution of howv in the analysis
(used obs is in green, rejected in red). Obviously the location of used
obs of howv match the area of non-zero analysis increments of howv.

![var_obs_2023071214_howv_maprll_datll_reg_ncf](https://github.com/NOAA-EMC/GSI/assets/53267411/d4ed6013-cfc8-486e-8f47-db07ec0e4e53)
3. The following figure is the analysis increment of howv with hybrid
envar analysis (using gdas ensemble 80 members and the ensemble weight
is 84%), and the static BE of howv is tuned/inflated. The analysis
increments are very similar to the results from pure 3dvar run (see the
first figure)

![HOWV_hyb_betas016_inc_maprll_datll_reg_ncf](https://github.com/NOAA-EMC/GSI/assets/53267411/e6e696e8-932b-42ab-9001-3472e970b21c)
4. The last figure shows the analysis increments of howv with hybrid
envar analysis (using gdas ensemble 80 members and the ensemble weight
is 84%), but the static BE of howv is NOT tuned. It can be observed that
the analysis increments is less than the results from the hybrid run
with tuning the static BE of howv. That is because the weight of static
BE (16%) reduced the background error of howv (ensemble of howv is not
available yet), so the impact of obs is decreased.

![HOWV_hyb_betas016_noTune_inc_maprll_datll_reg_ncf](https://github.com/NOAA-EMC/GSI/assets/53267411/ca25d068-fc86-4d47-a9d2-46e02ac22dac)

  
**Checklist**

- [*] My code follows the style guidelines of this project
- [*] I have performed a self-review of my own code
- [*] I have commented my code, particularly in hard-to-understand areas
- [*] New and existing tests pass with my changes
- [*] Any dependent changes have been merged and published

**DUE DATE for this PR is 10/5/2023.** If this PR is not merged into
`develop` by this date, the PR will be closed and returned to the
developer.

**Description**

Refine the PM2.5 DA for the RRFS_SD model by use of veg_type, which is
used to decide whether the obs is in urban area or not. Different
thresholds for innovations outside/inside urban areas will be used. Add
new namelist parameters, such as threshold for innovations, anowbufr
type
Read in station terrain height, PM10 et al if extended BUFR format for
anow air quality data is used

Fixes NOAA-EMC#606 


**Type of change**

Please delete options that are not relevant.

- [ ] Bug fix (non-breaking change which fixes an issue)
- [X ] New feature (non-breaking change which adds functionality)
- [ ] Breaking change (fix or feature that would cause existing
functionality to not work as expected)
- [ ] This change requires a documentation update

**How Has This Been Tested?**

<!-- This change will only affect PM2.5 DA for RRFS_SD, so it will not
affect any other tests -->

  
**Checklist**

- [X ] My code follows the style guidelines of this project
- [X] I have performed a self-review of my own code
- [X] I have commented my code, particularly in hard-to-understand areas
- [ ] New and existing tests pass with my changes
- [ ] Any dependent changes have been merged and published

**DUE DATE for this PR is 9/22/2023.** If this PR is not merged into
develop by this date, the PR will be closed and returned to the
developer.

…y direct DA (NOAA-EMC#605)

**Description**

To prevent some undefined values found in the radar reflectivity direct
DA (if_model_dbz=T and l_use_dbz_directDA=F), corresponding parts are
fixed. It doesn't change the result except for the case of the execution
with the debug option.

Fixes NOAA-EMC#604

**Type of change**

- [x] Bug fix (non-breaking change which fixes an issue)

**How Has This Been Tested?**

The radar reflectivity DA test with the RRFS setting was done on Orion.
After this modification, EnVar was completed even with the debug option.
This modification didn't change the result in the test without the debug
option.
  
**Checklist**

- [x] My code follows the style guidelines of this project
- [x] I have performed a self-review of my own code
- [x] I have commented my code, particularly in hard-to-understand areas
- [x] New and existing tests pass with my changes
- [x] Any dependent changes have been merged and published

**Due date for this PR is 9/15/2023.** If this PR is not merged into
`develop` by this date, the PR will be closed and returned to the
developer.

Co-authored-by: Sho Yokota <[email protected]>

This PR is to fix a bug in read_obs.F90 missing N21 for EARS and DBnet.

Fixes NOAA-EMC#506

In cplr_get_fv3_regional_ensperts.f90, "write_ens_sprd=.true." is
hard-coded and overwrites the values in namelist.
write_ens_sprd=.true." should be removed.

Fixes NOAA-EMC#634 

**Type of change**

Please delete options that are not relevant.

- [x] Bug fix (non-breaking change which fixes an issue)

A bug is found in setupps and setupspd: un-used observation is also marked as 1 in "Analysis_Usage_Flag".
Remove a print statement in rfv3io to simply stdout.

This is PR fixes NOAA-EMC#637

Add HAFS related regression test into GSI Ctests to solve the issue
NOAA-EMC#600.

Four set of regression tests for the current suite of HAFSv1 GSI:

3DEnvar with GDAS Ensemble plus FGAT capability --
"hafs_3denvar_glbens".
4Denvar with GDAS Ensemble plus FGAT capability --
"hafs_4denvar_glbens".
3Envar with self-cycled HAFS Ensemble -- "hafs_3denvar_hafens".
3Envar with GDAS Ensemble plus self-cycled HAFS Ensemble --
"hafs_3denvar_hybens".

Fixes NOAA-EMC#600 
Partially fixes NOAA-EMC#647 

**Type of change**

- [ ] Bug fix (non-breaking change which fixes an issue)
- [x] New feature (non-breaking change which adds functionality)
- [ ] Breaking change (fix or feature that would cause existing
functionality to not work as expected)
- [ ] This change requires a documentation update

**How Has This Been Tested?**

These changes are tested under Orion through GSI Ctests.
  
**Checklist**

- [x ] My code follows the style guidelines of this project
- [x] I have performed a self-review of my own code
- [x] I have commented my code, particularly in hard-to-understand areas
- [x] New and existing tests pass with my changes
- [x] Any dependent changes have been merged and published

**DUE DATE for this PR is 12/4/2023.** If this PR is not merged into
`develop` by this date, the PR will be closed and returned to the
developer.

- This PR supports RRFS_B GSI FED assimilation. 
- This PR adds a new GSI EnVar FED assimilation capability.

The summary of the changes:
- Read FED background and ensemble from restart phy files
- Add new control/state variable of fed ( in anavinfo, section: metguess, state and control variable)
- Create intfed.f90 and sfpfed.f90 for minimization.
- Other related codes. For example, update hydrometers when either dbz or fed is assimilated, or both are assimilated. Previously the update of hydrometers is done only when dbz is assimilated.

Please see  Fixes NOAA-EMC#622  

This PR was tested with:
- One FED obs DA test
- Real FED DA with pseudo ensemble for code development and debug
- Real FED DA with real  ensemble 
---------
Co-authored-by: David Dowell <[email protected]>

…ecipitation (NOAA-EMC#650)

This PR addresses issue 649: Reflectivity high bias resulting from EnVar
radar-reflectivity data assimilation.

Observation errors for radar-reflectivity observations are changed as
follows:
(1) Increase default observation error standard deviation from 5.0 dBZ
to 10.0 dBZ for reflectivity observations in precipitation (i.e.,
observations >= 5 dBZ). For non-precipitation observations (< 5 dBZ),
keep the existing 5.0 dBZ error standard deviation.
(2) For reflectivity observations in precipitation, further inflate the
error for observations that fail the gross error check by a factor of
1.0-2.0. This change will be combined with a stricter gross error check,
implemented through a separate PR to the regional workflow. Also, the
gross error check won't be applied to non-precipitation reflectivity
observations.
The changes described above were initially discussed by David Dowell,
Jacob Carley, and Sho Yokota in emails on 11 August 2023.

The proposed changes were tested in a prototype CONUS RRFSv1 for a
summer 2022 retrospective period.

…nostic file (NOAA-EMC#656)

…A-EMC#659)

Co-authored-by: Sho Yokota <[email protected]>

…#624)

Co-authored-by: Natalie Perlin <[email protected]>
Co-authored-by: DavidHuber-NOAA <[email protected]>
Co-authored-by: RussTreadon-NOAA <[email protected]>

**Description**
Add Dual-resolution EnVar capability for HAFS ensemble
By Xu Lu and Xuguang Wang from OU. POC: [email protected]
Fixes NOAA-EMC#603

**Type of change**
- [Y] New feature (non-breaking change which adds functionality)

**How Has This Been Tested?**
Did a single observation test to ensure the capability works and the
increments look reasonable compared to the single-resolution increment
on Orion.

**Checklist**
- [Y] My code follows the style guidelines of this project
- [Y] I have performed a self-review of my own code
- [Y] I have commented my code, particularly in hard-to-understand areas
- [Y] Any dependent changes have been merged and published

**DUE DATE for this PR is 12/15/2023**. If this PR is not merged into
`develop` by this date, the PR will be closed and returned to the
developer.

---------

Co-authored-by: Bin.Liu <[email protected]>
Co-authored-by: YongzuoLi-NOAA <[email protected]>

…KF (NOAA-EMC#654)

**Description**

Fixes NOAA-EMC#653

The proposed code changes
(1) add a new "fed" observation type to the EnKF
(2) add localization parameters, with namelist control, for FED
observations
(3) output basic statistics for FED observations.

In the RRFS, the FED observations will be assimilated together with
radar-reflectivity observations. The localization parameters for the
reflectivity observations in RRFS are corrlength=18 and lnsigcutoff=0.5.
However, these tight localization distances don't work well for the
sparse FED observations. Therefore, localization parameters for FED
observations, with namelist control, were added to allow the FED
observations to influence the model state over longer distances. The
default localization parameters for FED observations (corrlength=30 and
lnsigcutoff=2.0) were determined through experimentation with WRF and
FV3 convection-allowing (3-km horizontal grid spacing) ensembles.

**Type of change**

- [X] New feature (non-breaking change which adds functionality)

**How Has This Been Tested?**

Hourly cycling with simultaneous EnKF assimilation of FED and
radar-reflectivity observations has been tested for a CONUS version of
the prototype RRFSv1 for two short (1-2 days) retrospective periods, one
in July 2022 and the other in August 2023. The impacts of the FED
observations on the analyses are greatest over the oceans far from land,
where the radar network does not provide observations.

…OAA-EMC#682)

**Description**

Clips negative values from fields in the tracer file before writing.
Fixes NOAA-EMC#680.


**Type of change**

- [ ] Bug fix (non-breaking change which fixes an issue)


**How Has This Been Tested?**

Tested on Hera in a RRFS CONUS workflow with both hybrid_radar_ref and
anal_gsi_input tasks.
See run directory at /scratch2/BMC/zrtrr/aback/hydrometeors_test/
For one hour of the control run without this change, and one hour using
the change contained in this PR, the INPUT directory was saved for
reference/rerunning before each of the tasks: anal_gsi_input_spinup,
hybrid_radar_ref_spinup, cldanl_nonvar_spinup, and run_fcst spinup.
Those directories are at, for example
/scratch2/BMC/zrtrr/aback/hydrometeors_test/INPUT_after_anal_gsi_input_spinup_before_hybrid_radar_ref_spinup
("control") and
/scratch2/BMC/zrtrr/aback/hydrometeors_test/clipped_INPUT_after_anal_gsi_input_spinup_before_hybrid_radar_ref_spinup
(using the code in the PR).
Logs are at
/scratch2/BMC/zrtrr/aback/hydrometeors_test/v0.7.9/logs/rrfs.20230610/08/,
including new logs produced between all the above-listed tasks, showing
all the min and max values in fv_tracer.

  
**Checklist**

The code is Ting Lei's. It looks stylish and understandable to me
(Amanda) but maybe Ting should weigh in on this section.
- [ ] My code follows the style guidelines of this project
- [ ] I have performed a self-review of my own code
- [ ] I have commented my code, particularly in hard-to-understand areas
- [ ] New and existing tests pass with my changes
- [ ] Any dependent changes have been merged and published

**DUE DATE for merger of this PR into `develop` is 2/22/2024 (six weeks
after PR creation).**

---------

Co-authored-by: Ting.Lei-NOAA <[email protected]>

NOAA-EMC#670)

Co-authored-by: henrywinterbottom-wxdev <[email protected]>

Co-authored-by: jswhit2 <[email protected]>
Co-authored-by: guoqing.ge <[email protected]>

…bal_4denvar regr… (NOAA-EMC#681)

In response to Issue:" A indexing out of bounds issue shown in the
global_4denvar regression test in setuprad.f90 NOAA-EMC#676"
(NOAA-EMC#676) and following both online
and off-line discussions, it is decided to retain the abi2km part in
setuprad.f90 ( for potential future development/improvement), while a
simple index-related checks are added to prevent the indexing error when
GSI is built with debug mode.
It is important to note that this indexing error does not impact GSI
results (when GSI is built with optimization options) since abi2km is
currently hardwire consfigured to be not used.

Fixes NOAA-EMC#676 

**DUE DATE for merger of this PR into `develop` is 2/22/2024 (six weeks
after PR creation).**

---------

Co-authored-by: Russ-Treadon-NOAA <[email protected]>

)

**DUE DATE for merger of this PR into `develop` is 2/27/2024 (six weeks
after PR creation).**

**Description**

- Undefined soil_temp and soil_moist for regional because they are not
correctly read in from the RRFS' warm-sart restart file as described in
the issue#677.
- Undefined or zero value of soil temp and moist will affect the
calculation of surface emissivity. Surface emissivity is a factor to
calculate the microwave surface channel radiance.

Resolves NOAA-EMC#677

**Fix**
In gsi_rfv3io_mod.f90, replace 'STC' with 'tslb', replace 'SMC' as
'smois

**How has this need tested?**

- This has been tested on Hera. The values of soil_temp and
soil_moisture have been verified are correct now from the RRFS restart
file.

…agnostic file of conventional Q obs (for 3D RTMA run only) (NOAA-EMC#688)

- Motivation:
In the Auto-QC utility of 3D-RTMA, the dry-bulb air temperature (hereafter as T_dry) which is accompanied with moisture observation is required in the procedure of the quality control for conventional moisture observations (Q obs). Since this auto-qc of 3DRTMA retrieves many information from the observation diagnostic files (output of GSI run), it should be convenient for the sake of auto-qc of Q obs, if the required T_dry could be output into the observation diagnostics file of Q obs in the GSI run.

- Modifications to the code:
**_read_prepbufr.f90_**:
for qob and rtma run, add lines to use tpc to identify the sensible temp and virtual temp, and mark with tvflag, then get tdry with the temp obs in different ways w.r.t the associated tvflag;
**_setupq.f90_**:
add line to use l_rtma3d from module rapidrefresh_cldsurf_mod variable nreal (the length of obs diag information record for each obs) needs to be increased by 2 (for tdry and tvflag, when running GSI for 3DRTMA only)
in subroutine contents_binary_diag_, add line to put tdry into the array rdiagbuff (for binary format obsdaig file)
in subroutine contents_netcdf_diag_, add line to put tdry into metadata (for netcdf format obsdiag file)

This PR is to address the issue NOAA-EMC#666 : Adding the (calculated) dry-bulb temperature in the observation diagnostic file for conventional Q obs (only for 3D RTMA)

…-EMC#695)

**DUE DATE for merger of this PR into `develop` is 4/2/2024 (six weeks
after PR creation).**

**Description**

We found three bugs in RRFS test:
1) add "vars2d_landonly" to regional gridinfo files for compiling. 
2) add terrain to "sfc_var_exist" check
3) fix case selection bug for FED GSI DA.

Resolves NOAA-EMC#704 
Resolves NOAA-EMC#702
Resolves NOAA-EMC#703 

**Type of change**
 Bug fix (non-breaking change which fixes an issue)

**How Has This Been Tested?**
Those fixes are tested with full RRFS cases and with several cycles of
RRFS retro.

**Checklist**

- [x ] My code follows the style guidelines of this project
- [x ] I have performed a self-review of my own code
- [x ] I have commented my code, particularly in hard-to-understand
areas
- [ ] New and existing tests pass with my changes
- [ ] Any dependent changes have been merged and published

…#718)

…8Z (NOAA-EMC#721)

NOAA-EMC#709)

…SI failure … (NOAA-EMC#698)

**DUE DATE for merger of this PR into `develop` is 3/27/2024 (six weeks
after PR creation).**

Resolves NOAA-EMC#693 (Thanks to @edwardhartnett 's suggestions)
Resolves # 694 ( this PR is not able to provide a stable solution, more
details would be given on the issue page)
Resolves # 697: With larger requested memory for each mpi task, it still
showed, for some time, the differences in the analysis files between
loproc vs hiproc for the control runs on hercules. whether integrating
this with the refactored IO part would provide a stable solution remains
to be seen.

This PR resolved the newly emerged issue with IO of netcdf files in the
continuous storage, with upgraded FV3REG IO for the cold start options.
(Co author Ming Hu @hu5970 )
This PR is being worked on in collaboration with Pete Johnson through
RDHPCS help desk, @RussTreadon-NOAA @DavidHuber-NOAA and thanks to help
from @ed Raghue Reddy through RDHPCS help desk.

---------

Co-authored-by: Ting Lei <[email protected]>
Co-authored-by: Ting.Lei-NOAA <[email protected]>

Co-authored-by: Tinglei-daprediction <[email protected]>

…EMC#699) (NOAA-EMC#700)

**DUE DATE for merger of this PR into `develop` is 3/29/2024 (six weeks
after PR creation).**

**Description**

Resolves NOAA-EMC#699

This PR is to add the option to apply Multigrid Beta Filter (MGBF;
[Purser et al. 2022](https://doi.org/10.1175/MWR-D-20-0405.1)) for
ensemble localization instead of Recursive Filter (RF). This work
includes to add an initial version of the MGBF as a subdirectory in GSI.

To apply the MGBF, set "l_mgbf_loc=true" in the namelist and
additionally input "mgbf_loc01.nml". (In Scale/Variable-Dependent
Localization, input also "mgbf_locXX.nml" (XX=02,03,...) with the same
number of grid points.)

<details>

**<summary>How to set MGBF parameters in mgbf_locXX.nml</summary>**

An example of mgbf_locXX.nml is as follows:

```
&PARAMETERS_MGBETA
  mg_ampl01=1.125,            ! length of vertical beta filter (standard deviation; filter grid unit)
  mg_ampl02=2.4,              ! length of horizontal beta filter (standard deviation; filter grid unit)
  mg_ampl03=0.85,             ! length of 3D beta filter (standard deviation; filter grid unit)
  mg_weig1=0.,                ! weight of generation 1
  mg_weig2=0.,                ! weight of generation 2
  mg_weig3=0.,                ! weight of generation 3
  mg_weig4=1.,                ! weight of generation 4
  hx=5,                       ! number of halo grid points in x-direction
  hy=5,                       ! number of halo grid points in y-direction
  hz=3,                       ! number of halo grid points in z-direction
  p=2,                        ! beta filter exponent
  mgbf_line=.false.,          ! set false except for mgbf_proc=2,4,7
  mgbf_proc=8,                ! 1-2: 3D filter; 3-5: 2D filter for static B; 6-8: 2D filter for localization (1,3,6: radial filter; 2,4,7: line filter; 5,8: isotropic line filter)
  lm_a=65,                    ! number of vertical layers in analysis grid
  lm=33,                      ! number of vertical layers in filter grid
  km2=0,                      ! number of 2D variables (set 0 for localization)
  km3=1,                      ! number of 3D variables (set 1 for localization)
  n_ens=30,                   ! ensemble size
  l_loc=.true.,               ! set true in localization
  l_filt_g1=.false.,          ! set false in skipping generation 1
  l_lin_vertical=.true.,      ! set true in applying linear vertical interpolation for analysis-filter mapping
  l_lin_horizontal=.true.,    ! set true in applying linear horizontal interpolation for analysis-filter mapping
  l_quad_horizontal=.false.,  ! set true in applying quadratic horizontal interpolation for analysis-filter mapping
  l_new_map=.true.,           ! set true in applying efficient vertical interpolation for analysis-filter mapping
  l_vertical_filter=.true.,   ! set true in applying vertical beta filter outside 2D filter
  ldelta=.false.,             ! (not used)
  lquart=.false.,             ! set true in applying quadratic horizontal interpolation for up/down-sending
  lhelm=.false.,              ! set true in applying Helmholtz differential operator for weighting
  nm0=1975,                   ! number of analysis grid points in x-direction
  mm0=1350,                   ! number of analysis grid points in y-direction
  gm_max=4,                   ! highest generation (max: 4)
  nxPE=79,                    ! number of MPI processors in x-direction
  nyPE=54,                    ! number of MPI processors in y-direction
  im_filt=8,                  ! number of filter grid points in each MPI processor in x-direction
  jm_filt=8,                  ! number of filter grid points in each MPI processor in y-direction
 /
```

Here, to make the result of MGBF-based localization similar to RF-based
one, we can set the beta filter length ( mg_ampl0[12] ) from the
recursive filter length in the GSI namelist ( s_ens_[vh] ) as:

- $\text{mg\\_ampl01} = \left[\text{s\\_ens\\_v (grid unit)} *
\frac{1}{\sqrt{2}} * \frac{\text{lm}-1}{\text{lm\\_a}-1} \right]^2$
- $\text{mg\\_ampl02} = \left[\frac{\text{s\\_ens\\_h
(km)}}{\text{analysis grid interval (km)}} * \frac{1}{\sqrt{2}} *
\frac{\text{im\\_filt} * \text{nxPE}}{\text{nm0}} * \frac{1}{2} *
\frac{1}{2} * \frac{1}{2} \right]^2$ (in case mg_weig[1-4]=[0,0,0,1])

Please note there are some limitations for the other MGBF parameters
such as:

- The number of MPI processors input in GSI should be nxPE x nyPE 
- (nm0, mm0, lm_a) should be the same as the GSI analysis grid
- nm0 should be divisible by nxPE
- mm0 should be divisible by nyPE
- nm0 / nxPE = mm0 / nyPE

</details>

<details>

**<summary>How to run RRFS regression tests with MGBF-based
localization</summary>**

Change settings in regression/ as follows, and run Test#3
(rrfs_3denvar_glbens)

```diff
diff --git a/regression/regression_namelists.sh b/regression/regression_namelists.sh
index 7ca183ef3..671d028ff 100755
--- a/regression/regression_namelists.sh
+++ b/regression/regression_namelists.sh
@@ -457,7 +457,7 @@ OBS_INPUT::
    beta_s0=0.15,s_ens_h=110,s_ens_v=3,
    regional_ensemble_option=1,
    pseudo_hybens = .false.,
-   grid_ratio_ens = 3,
+   grid_ratio_ens = 5.1,
    l_ens_in_diff_time=.true.,
    ensemble_path='',
    i_en_perts_io=1,
@@ -465,6 +465,7 @@ OBS_INPUT::
    fv3sar_bg_opt=0,
    readin_localization=.true.,
    ens_fast_read=.false.,
+   l_mgbf_loc=.true.,
  /
  &RAPIDREFRESH_CLDSURF
    dfi_radar_latent_heat_time_period=20.0,
```

```diff
diff --git a/regression/regression_namelists_db.sh b/regression/regression_namelists_db.sh
index e03917e88..36b8b6a22 100755
--- a/regression/regression_namelists_db.sh
+++ b/regression/regression_namelists_db.sh
@@ -438,7 +438,7 @@ OBS_INPUT::
    beta_s0=0.15,s_ens_h=110,s_ens_v=3,
    regional_ensemble_option=1,
    pseudo_hybens = .false.,
-   grid_ratio_ens = 3,
+   grid_ratio_ens = 5.1,
    l_ens_in_diff_time=.true.,
    ensemble_path='',
    i_en_perts_io=1,
@@ -446,6 +446,7 @@ OBS_INPUT::
    fv3sar_bg_opt=0,
    readin_localization=.true.,
    ens_fast_read=.false.,
+   l_mgbf_loc=.true.,
  /
  &RAPIDREFRESH_CLDSURF
    dfi_radar_latent_heat_time_period=20.0,
```

```diff
diff --git a/regression/regression_param.sh b/regression/regression_param.sh
index 2ac615fc4..6186acdbb 100755
--- a/regression/regression_param.sh
+++ b/regression/regression_param.sh
@@ -87,23 +87,23 @@ case $regtest in
     rrfs_3denvar_glbens)

         if [[ "$machine" = "Hera" ]]; then
-           topts[1]="0:15:00" ; popts[1]="20/1/"  ; ropts[1]="/1"
-           topts[2]="0:15:00" ; popts[2]="20/2/"  ; ropts[2]="/1"
+           topts[1]="0:15:00" ; popts[1]="30/2/"  ; ropts[1]="/1"
+           topts[2]="0:15:00" ; popts[2]="15/4/"  ; ropts[2]="/1"
         elif [[ "$machine" = "Orion" ]]; then
-           topts[1]="0:15:00" ; popts[1]="20/1/" ; ropts[1]="/1"
-           topts[2]="0:15:00" ; popts[2]="20/2/" ; ropts[2]="/2"
+           topts[1]="0:15:00" ; popts[1]="30/2/"  ; ropts[1]="/1"
+           topts[2]="0:15:00" ; popts[2]="15/4/"  ; ropts[2]="/2"
         elif [[ "$machine" = "Hercules" ]]; then
-           topts[1]="0:15:00" ; popts[1]="20/1/" ; ropts[1]="/1"
-           topts[2]="0:15:00" ; popts[2]="20/2/" ; ropts[2]="/2"
+           topts[1]="0:15:00" ; popts[1]="30/2/"  ; ropts[1]="/1"
+           topts[2]="0:15:00" ; popts[2]="15/4/"  ; ropts[2]="/2"
         elif [[ "$machine" = "Jet" ]]; then
-           topts[1]="0:15:00" ; popts[1]="20/1/"  ; ropts[1]="/1"
-           topts[2]="0:15:00" ; popts[2]="20/2/"  ; ropts[2]="/1"
+           topts[1]="0:15:00" ; popts[1]="15/4/"  ; ropts[1]="/1"
+           topts[2]="0:15:00" ; popts[2]="10/6/"  ; ropts[2]="/1"
         elif [[ "$machine" = "Gaea" ]]; then
-           topts[1]="0:15:00" ; popts[1]="18/1/"  ; ropts[1]="/1"
-           topts[2]="0:15:00" ; popts[2]="18/2/"  ; ropts[2]="/1"
+           topts[1]="0:15:00" ; popts[1]="15/4/"  ; ropts[1]="/1"
+           topts[2]="0:15:00" ; popts[2]="10/6/"  ; ropts[2]="/1"
         elif [[ "$machine" = "wcoss2" ]]; then
-           topts[1]="0:15:00" ; popts[1]="64/1/" ; ropts[1]="/1"
-           topts[2]="0:15:00" ; popts[2]="128/2/" ; ropts[2]="/1"
+           topts[1]="0:15:00" ; popts[1]="60/1/"  ; ropts[1]="/1"
+           topts[2]="0:15:00" ; popts[2]="30/2/"  ; ropts[2]="/1"
         fi

         if [ "$debug" = ".true." ] ; then
```

```diff
diff --git a/regression/rrfs_3denvar_glbens.sh b/regression/rrfs_3denvar_glbens.sh
index af5da5117..04fd73d57 100755
--- a/regression/rrfs_3denvar_glbens.sh
+++ b/regression/rrfs_3denvar_glbens.sh
@@ -272,6 +272,46 @@ $gsi_namelist

 EOF

+cat << EOF > mgbf_loc01.nml
+&PARAMETERS_MGBETA
+  mg_ampl01=1.125,            ! length of vertical beta filter (standard deviation; filter grid unit)
+  mg_ampl02=1.615,            ! length of horizontal beta filter (standard deviation; filter grid unit)
+  mg_ampl03=0.85,             ! length of 3D beta filter (standard deviation; filter grid unit)
+  mg_weig1=0.,                ! weight of generation 1
+  mg_weig2=1.,                ! weight of generation 2
+  mg_weig3=0.,                ! weight of generation 3
+  mg_weig4=0.,                ! weight of generation 4
+  hx=4,                       ! number of halo grid points in x-direction
+  hy=4,                       ! number of halo grid points in y-direction
+  hz=3,                       ! number of halo grid points in z-direction
+  p=2,                        ! beta filter exponent
+  mgbf_line=.false.,          ! set false except for mgbf_proc=2,4,7
+  mgbf_proc=8,                ! 1-2: 3D filter; 3-5: 2D filter for static B; 6-8: 2D filter for localization (1,3,6: radial filter; 2,4,7: line filter; 5,8: isotropic line filter)
+  lm_a=65,                    ! number of vertical layers in analysis grid
+  lm=33,                      ! number of vertical layers in filter grid
+  km2=0,                      ! number of 2D variables (set 0 for localization)
+  km3=1,                      ! number of 3D variables (set 1 for localization)
+  n_ens=10,                   ! ensemble size
+  l_loc=.true.,               ! set true in localization
+  l_filt_g1=.false.,          ! set false in skipping generation 1
+  l_lin_vertical=.true.,      ! set true in applying linear vertical interpolation for analysis-filter mapping
+  l_lin_horizontal=.true.,    ! set true in applying linear horizontal interpolation for analysis-filter mapping
+  l_quad_horizontal=.false.,  ! set true in applying quadratic horizontal interpolation for analysis-filter mapping
+  l_new_map=.true.,           ! set true in applying efficient vertical interpolation for analysis-filter mapping
+  l_vertical_filter=.true.,   ! set true in applying vertical beta filter outside 2D filter
+  ldelta=.false.,             ! (not used)
+  lquart=.false.,             ! set true in applying quadratic horizontal interpolation for up/down-sending
+  lhelm=.false.,              ! set true in applying Helmholtz differential operator for weighting
+  nm0=40,                     ! number of analysis grid points in x-direction
+  mm0=24,                     ! number of analysis grid points in y-direction
+  gm_max=2,                   ! highest generation (max: 4)
+  nxPE=10,                    ! number of MPI processors in x-direction
+  nyPE=6,                     ! number of MPI processors in y-direction
+  im_filt=4,                  ! number of filter grid points in each MPI processor in x-direction
+  jm_filt=4,                  ! number of filter grid points in each MPI processor in y-direction
+ /
+EOF
+
 # Copy executable and fixed files to $tmpdir
 if [[ $exp == *"updat"* ]]; then
    $ncp $gsiexec_updat  ./gsi.x
```

</details>

**Type of change**

Please delete options that are not relevant.

- [ ] Bug fix (non-breaking change which fixes an issue)
- [x] New feature (non-breaking change which adds functionality)
- [ ] Breaking change (fix or feature that would cause existing
functionality to not work as expected)
- [ ] This change requires a documentation update

**How Has This Been Tested?**

EnVar for NA-domain RRFS was tested with "mgbf_locXX.nml" (XX=01) shown
above on Orion. The resulting analysis increment was similar to the
original and the computation time for localization became short.
  
**Checklist**

- [x] My code follows the style guidelines of this project
- [x] I have performed a self-review of my own code
- [x] I have commented my code, particularly in hard-to-understand areas
- [x] New and existing tests pass with my changes
- [x] Any dependent changes have been merged and published

Co-authored-by: Sho Yokota <[email protected]>

Tiny fix to allow modelling of sub-fov variability for NOAA-21 ATMS.

**DUE DATE for merger of this PR into `develop` is 2/19/2024 (six weeks
after PR creation).**
**DUE DATE for this PR is extended to 3/19/2024 because @XuLu-NOAA is on
leave.**
**Description**

Xu Lu ([email protected]) and Biju Thomas ([email protected]) fixed bugs
regarding HAFS GSI debug build and run issues. This is in corresponding
to issue NOAA-EMC#661

Fixes NOAA-EMC#661

1. In read_radar.f90, uninitialized toff is making all the ground-based
radar observations be placed at -3h instead of 0h, which creates wrong
increments for FGAT and 4DEnVar.
2. In read_radar.f90, uninitialized zsges will crash the debug mode.
3. In read_radar.f90, t4dvo should be used instead of t4dv in the
read_radar_l2rw_novadqc subroutine.
4. In radinfo.90, maxscan should be increased to at least 252 to allow
more scans, or it will crash the debug mode.
5. In read_fl_hdob.f90, dlnpsob is replaced with 1000. since the SFMR
does not sample surface pressure, and the uninitialized dlnpsob creates
issues later in setupspd.f90 in the debug mode.
6. In mod_fv3_lola.f90, (i,j+1) should be used instead of (i+1,j) in
searching for V edges.
7. In stpcalc.f90, when tried to find the best stepsize from outpen
around L838-864, the minimum outstp(i) is stored in stp(ii), but the
istp_use is asigned with i instead of ii. Create inconsistency when
assigning stp(istp_use) to stpinout at L872. Should use istp_use=ii
instead.

**Type of change**
- [Yes] Bug fix (non-breaking change which fixes an issue)

**How Has This Been Tested?**
Regression test on Orion:
```
Test project /work/noaa/hwrf/save/xulu/mergeversions/GSI/build
CMake Warning (dev) at CTestTestfile.cmake:9 (subdirs):  Syntax Warning in cmake code at /work/noaa/hwrf/save/xulu/mergeversions/GSI/build/regression/CTestTestfile.cmake:7:10
1/7 Test NOAA-EMC#4: [=[netcdf_fv3_regional]=] ........   Passed  365.11 sec
2/7 Test NOAA-EMC#7: [=[global_enkf]=] ................   Passed  430.29 sec
3/7 Test NOAA-EMC#3: [=[rrfs_3denvar_glbens]=] ........   Passed  605.35 sec
4/7 Test NOAA-EMC#2: [=[rtma]=] .......................   Passed  969.78 sec
5/7 Test NOAA-EMC#6: [=[hafs_3denvar_hybens]=] ........***Failed  1455.47 sec
6/7 Test NOAA-EMC#1: [=[global_4denvar]=] .............   Passed  1682.40 sec
7/7 Test NOAA-EMC#5: [=[hafs_4denvar_glbens]=] ........***Failed  1758.90 sec
```

The failed hafs_3denvar and 4denvar are within expectation due to the
fix for toff. As demonstrated in the single observation tests in the
following figure, the uninitialized toff can result in increment
degradations due to wrongly assigned observation times:

![image](https://github.com/NOAA-EMC/GSI/assets/26603014/0de870e1-f8c8-4b6d-8039-57f417b76367)

…er AMVs (NOAA-EMC#724)

**Description**
This is an update of the QC process for the enhanced high-resolution
GOES-R mesoscale floater AMVs to resolve the issue NOAA-EMC#713.
As mentioned in the issue, enhanced AMV data are derived from IR band,
which turns out to be not reliable in the mid-layer of atmosphere.
Adding additional QC process to remove data in those layers are
necessary and proved to enhance the Hurricane intensity forecast.

**Type of change**

Please delete options that are not relevant.

- [ ] Bug fix (non-breaking change which fixes an issue)
- [x] New feature (non-breaking change which adds functionality)
- [ ] Breaking change (fix or feature that would cause existing
functionality to not work as expected)
- [ ] This change requires a documentation update

**How Has This Been Tested?**
This change has been tested with GSI regression test on Hera.
  
**Checklist**

- [x] My code follows the style guidelines of this project
- [x] I have performed a self-review of my own code
- [x] I have commented my code, particularly in hard-to-understand areas
- [x] New and existing tests pass with my changes
- [x] Any dependent changes have been merged and published

…ed 3DRTMA (NOAA-EMC#730)

<!-- PLEASE READ -->
<!--
Before opening a PR, please note these guidelines:

- Each PR should only address ONE topic and have an associated issue
- No hardcoded or paths to personal directories should be present
- No temporary or backup files should be committed
- Any code that was disabled by being commented out should be removed
-->

**Description**

<!-- Please include relevant motivation and context. -->
<!-- Please include a summary of the change and which issue is fixed.
-->
<!-- List any dependencies that are required for this change. -->
To improve the analysis of the near-surface wind gust in 3DRTMA, the
observations of near-surface wind gust would be analyzed directly in GSI
(3DVar and Hybrid 3DEnVar), instead of being a derived product from the
near-surface wind analysis.

Since the core subroutines for direct variational assimilation of wind
gust (e.g., setupgust.f90, intgust.f90, stpgust.f90, etc.) had already
been implemented in GSI for 2DRTMA, so in the work the development in
GSI mainly focus on adding I/O of 2-D wind gust firstguess and analysis
fields for RRFS-based 3DRTMA, and some minor modifications in
observation and background error for wind gust, options to control the
analysis of wind gust, etc.
<!-- Please provide reference to the issue this pull request is
addressing. -->
<!-- For e.g. Fixes #IssueNumber -->
This PR is to address the issue NOAA-EMC#726 : Adding I/O for direct analysis of
near-surface wind gust for RRFS-based 3DRTMA
Fixes NOAA-EMC#726
**Type of change**

Please delete options that are not relevant.

- [x] New feature (non-breaking change which adds functionality)

**How Has This Been Tested?**

<!-- Please describe the tests that you ran to verify your changes and
on the platforms these tests were conducted. -->
<!-- Provide instructions so we can reproduce. -->
<!-- Please also list any relevant details for your test configuration
-->
  
**Checklist**

- [x] My code follows the style guidelines of this project
- [x] I have performed a self-review of my own code
- [x] I have commented my code, particularly in hard-to-understand areas
- [x] New and existing tests pass with my changes
      tested with a real case - 2024-02-20_12:00Z, 
1. dry-run (using my updated GSI code with wind gust analysis, but
actually no wind gust obs is analyzed, so-called dryrun) is compared to
control-run (original GSI code running without wind gust obs): the
results are identical. This indicates that if without analyzing
wind-gust obs, then the updated code generates the analysis identical to
the analysis of original/control code. Or say, the added code does not
have influence on the other part of code.
2. real case run with updated GSI code to analyze the obs of wind gust:
The following figure shows the used observations of near-surface wind
gust:

![var_obs_2024022012_gust_used_maprll_datll_reg_ncf](https://github.com/NOAA-EMC/GSI/assets/53267411/ecbe479a-03c6-490f-a179-9e0027291468)
the following figure shows the analysis increments:

![GUST_hyb_hwllp90_corptuned_inc_incrintrp_maprll_datrll_reg_grb2](https://github.com/NOAA-EMC/GSI/assets/53267411/a01fca0d-dc1f-438b-b8eb-e624de35a631)
- [x] Any dependent changes have been merged and published
- [x] Regression tests on WCOSS2 (Cactus) and Hera (Rocky-8) : my
updated GSI commit
[#f91f247d](GangZhao-NOAA@f91f247))
vs control/original GSI code (commit
[#6d9ebbb7](NOAA-EMC@6d9ebbb))
Here is the reports of the regression tests on WCOSS2 (Cactus):
~~~
[gang.zhao@clogin02:build] (feature/windgust_in_3dvar_for_3drtma)$ ctest
-j 7
Test project
/lfs/h2/emc/da/save/gang.zhao/WorkDir/ProdGSI_Dev/gsi_dev/build
    Start 1: global_4denvar
    Start 2: rtma
    Start 3: rrfs_3denvar_glbens
    Start 4: netcdf_fv3_regional
    Start 5: hafs_4denvar_glbens
    Start 6: hafs_3denvar_hybens
    Start 7: global_enkf
1/7 Test NOAA-EMC#4: netcdf_fv3_regional ..............   Passed  483.15 sec
2/7 Test NOAA-EMC#3: rrfs_3denvar_glbens ..............   Passed  486.74 sec
3/7 Test NOAA-EMC#7: global_enkf ......................   Passed  850.98 sec
4/7 Test NOAA-EMC#2: rtma .............................   Passed  970.28 sec
5/7 Test NOAA-EMC#6: hafs_3denvar_hybens ..............   Passed  1152.82 sec
6/7 Test NOAA-EMC#5: hafs_4denvar_glbens ..............   Passed  1213.93 sec
7/7 Test NOAA-EMC#1: global_4denvar ...................   Passed  1683.16 sec

100% tests passed, 0 tests failed out of 7

Total Test time (real) = 1683.19 sec
~~~
Here is the reports of the regression tests on Hera (Rocky8):
~~~
(base) [Gang.Zhao@hfe11:build] (feature/windgust_in_3dvar_for_3drtma)$
ctest -j 7
Test project /scratch1/NCEPDEV/da/Gang.Zhao/ProdGSI_dev/gsi_dev/build
    Start 1: global_4denvar
    Start 2: rtma
    Start 3: rrfs_3denvar_glbens
    Start 4: netcdf_fv3_regional
    Start 5: hafs_4denvar_glbens
    Start 6: hafs_3denvar_hybens
    Start 7: global_enkf
1/7 Test NOAA-EMC#4: netcdf_fv3_regional ..............   Passed  491.53 sec
2/7 Test NOAA-EMC#3: rrfs_3denvar_glbens ..............***Failed  495.27 sec
3/7 Test NOAA-EMC#2: rtma .............................   Passed  982.45 sec
4/7 Test NOAA-EMC#6: hafs_3denvar_hybens ..............   Passed  1168.99 sec
5/7 Test NOAA-EMC#7: global_enkf ......................   Passed  1239.77 sec
6/7 Test NOAA-EMC#5: hafs_4denvar_glbens ..............***Failed  1347.87 sec
7/7 Test NOAA-EMC#1: global_4denvar ...................   Passed  1974.45 sec

71% tests passed, 2 tests failed out of 7

Total Test time (real) = 1974.91 sec

The following tests FAILED:
          3 - rrfs_3denvar_glbens (Failed)
          5 - hafs_4denvar_glbens (Failed)
Errors while running CTest
Output from these tests are in:
/scratch1/NCEPDEV/da/Gang.Zhao/ProdGSI_dev/gsi_dev/build/Testing/Temporary/LastTest.log
Use "--rerun-failed --output-on-failure" to re-run the failed cases
verbosely.
(base) [Gang.Zhao@hfe11:build] (feature/windgust_in_3dvar_for_3drtma)$
ctest -R rrfs_3denvar_glbens
Test project /scratch1/NCEPDEV/da/Gang.Zhao/ProdGSI_dev/gsi_dev/build
    Start 3: rrfs_3denvar_glbens
1/1 Test NOAA-EMC#3: rrfs_3denvar_glbens ..............   Passed  430.52 sec

100% tests passed, 0 tests failed out of 1

Total Test time (real) = 430.55 sec
(base) [Gang.Zhao@hfe11:build] (feature/windgust_in_3dvar_for_3drtma)$
ctest -R hafs_4denvar_glbens
Test project /scratch1/NCEPDEV/da/Gang.Zhao/ProdGSI_dev/gsi_dev/build
    Start 5: hafs_4denvar_glbens
1/1 Test NOAA-EMC#5: hafs_4denvar_glbens ..............   Passed  1225.37 sec

100% tests passed, 0 tests failed out of 1

Total Test time (real) = 1225.39 sec
~~~
**Note**: 
_When I was running the regression tests, GSI code was just updated to
the latest commit
[#b53740a7](GangZhao-NOAA@f91f247).
Considering the frequent update in EMC GSI code recently and saving the
time, after this PR has been reviewed and approved by peer-reviewers, I
will update the code to latest EMC GSI commit, then re-run the
regression tests for final approval.

This PR addresses GSI NOAA-EMC#731. It modifies the satthin.F90 routine to allow
data to be processed unthinned in the GSI without requiring exorbitant
resources and it removes an unnecessary thinning from the read_atms.f90
routine.

The change to satthin reduces the value of `itxmax` from 1.e9 to 1.e7
which should be sufficient for most sensors. But if a larger number is
required for a sensor, this may be passed in via optional argument.

This change will change results for ATMS only as documented in the
issue.

- Update Jet module file to use Rocky8 installation of spack-stack;

…-EMC#740)

In read_radar.f90, the value of nread should be "nsuper2_kept" and
shouldn't be reset to zero after processing TDR data.

- [x] Bug fix (non-breaking change which fixes an issue)