Merge remote-tracking branch 'origin/develop' into feature/ss_180

* origin/develop:
  Move to contrib spack-stack on Jet (NOAA-EMC#787)
  a quick workaround for increasing the mpi task numbers on orion for ctest :: rrfs_3denvar_rdasens  (NOAA-EMC#788)
  Recover the capability of handling model fields from operation gfs.v16.3 (NOAA-EMC#785)
  fix a bug in deter_sfc_gmi (NOAA-EMC#781)
  add safeguard to thompson_reff (NOAA-EMC#779)
  Fix incorrect usage of real(i_kind) in mg_input.f90  (NOAA-EMC#760)
  Transition to Thompson Microphysics for Microwave All-sky Assimilation (NOAA-EMC#743)
  Format changes for EUMETSAT metop-sg and CADS debug fix (NOAA-EMC#773)
  Update global_4denvar and global_enkf ctests to reflect GFS v17 (NOAA-EMC#774)
  fix for cris-fsr memory corruption (NOAA-EMC#767)
  Gnssrwnd1.0 (NOAA-EMC#747)

modulefiles/gsi_jet.intel.lua

@@ -1,7 +1,7 @@
 help([[
 ]])
 
-prepend_path("MODULEPATH", "/mnt/lfs4/HFIP/hfv3gfs/role.epic/spack-stack/spack-stack-1.6.0/envs/gsi-addon-dev-rocky8/install/modulefiles/Core")
+prepend_path("MODULEPATH", "/contrib/spack-stack/spack-stack-1.6.0/envs/gsi-addon-intel/install/modulefiles/Core")
 
 local python_ver=os.getenv("python_ver") or "3.11.6"
 local stack_intel_ver=os.getenv("stack_intel_ver") or "2021.5.0"
@@ -20,6 +20,6 @@ load(pathJoin("prod_util", prod_util_ver))
 pushenv("CFLAGS", "-axSSE4.2,AVX,CORE-AVX2")
 pushenv("FFLAGS", "-axSSE4.2,AVX,CORE-AVX2")
 
-pushenv("GSI_BINARY_SOURCE_DIR", "/mnt/lfs4/HFIP/hfv3gfs/glopara/git/fv3gfs/fix/gsi/20240208")
+pushenv("GSI_BINARY_SOURCE_DIR", "/lfs5/HFIP/hfv3gfs/glopara/FIX/fix/gsi/20240208")
 
 whatis("Description: GSI environment on Jet with Intel Compilers")

regression/global_enkf.sh

@@ -76,14 +76,11 @@ export use_correlated_oberrs=${use_correlated_oberrs:-".false."}
 if [ $USE_CORRELATED_OBERRS == "YES" ]; then
  export use_correlated_oberrs=".true."
 fi
-export imp_physics=${imp_physics:-"11"}
 export lupp=${lupp:-".true."}
 export corrlength=${corrlength:-1250}
 export lnsigcutoff=${lnsigcutoff:-2.75}
 export analpertwt=${analpertwt:-0.85}
 export readin_localization_enkf=".false."
-export readin_localization_enkf=${readin_localization_enkf:-".true."}
-export reducedgrid=${reducedgrid:-".true."}
 export letkf_flag=${letkf_flag:-".true."}
 export getkf=${getkf:-".true."}
 export denkf=${denkf:-".true."}

regression/regression_namelists.sh

@@ -23,12 +23,12 @@ export gsi_namelist="
  crtm_coeffs_path='./crtm_coeffs/',
  newpc4pred=.true.,adp_anglebc=.true.,angord=4,passive_bc=.true.,use_edges=.false.,
  diag_precon=.true.,step_start=1.e-3,emiss_bc=.true.,thin4d=.true.,cwoption=3,
- verbose=.false.,imp_physics=11,lupp=.true.,
+ verbose=.false.,imp_physics=8,lupp=.true.,
  binary_diag=.false.,netcdf_diag=.true.,
  lobsdiag_forenkf=.false.,
  nhr_anal=3,6,9,nhr_obsbin=1,
  l4densvar=.true.,ens_nstarthr=3,nhr_assimilation=6,lwrite4danl=.true.,
- optconv=0.05,cao_check=.true.,ta2tb=.false.,
+ optconv=0.05,cao_check=.true.,ta2tb=.true.,
  tzr_qc=1,sfcnst_comb=.true.,
  write_fv3_incr=.true.,incvars_to_zero= 'liq_wat_inc','icmr_inc','rwmr_inc','snmr_inc','grle_inc',
  incvars_zero_strat='sphum_inc','liq_wat_inc','icmr_inc','rwmr_inc','snmr_inc','grle_inc',incvars_efold=5, use_gfs_ncio=.true.,
@@ -962,8 +962,8 @@ export gsi_namelist="
  sprd_tol=1.e30,paoverpb_thresh=0.98,
  nlons=$LONA,nlats=$LATA,nlevs=$LEVS,nanals=$NMEM_ENKF,
  deterministic=.true.,sortinc=.true.,lupd_satbiasc=.false.,
- reducedgrid=.true.,readin_localization=.true.,
- use_gfs_nemsio=${use_gfs_nemsio},use_gfs_ncio=${use_gfs_ncio},imp_physics=$imp_physics,lupp=$lupp,
+ reducedgrid=.false.,readin_localization=.false.,
+ use_gfs_nemsio=${use_gfs_nemsio},use_gfs_ncio=${use_gfs_ncio},imp_physics=8,lupp=$lupp,
  univaroz=.false.,adp_anglebc=.true.,angord=4,use_edges=.false.,emiss_bc=.true.,
  letkf_flag=${letkf_flag},nobsl_max=${nobsl_max},denkf=${denkf},getkf=${getkf}.,
  nhr_anal=${IAUFHRS_ENKF},nhr_state=${IAUFHRS_ENKF},

regression/regression_namelists_db.sh

@@ -21,7 +21,7 @@ export gsi_namelist="
  crtm_coeffs_path='./crtm_coeffs/',
  newpc4pred=.true.,adp_anglebc=.true.,angord=4,passive_bc=.true.,use_edges=.false.,
  diag_precon=.true.,step_start=1.e-3,emiss_bc=.true.,thin4d=.true.,cwoption=3,
- verbose=.false.,imp_physics=11,lupp=.true.,binary_diag=.false.,netcdf_diag=.true.,
+ verbose=.false.,imp_physics=8,lupp=.true.,binary_diag=.false.,netcdf_diag=.true.,
  lobsdiag_forenkf=.false.,
  nhr_anal=3,6,9,
  l4densvar=.true.,ens_nstarthr=3,nhr_obsbin=1,nhr_assimilation=6,lwrite4danl=.true., tzr_qc=1,sfcnst_comb=.true.,

regression/regression_param.sh

@@ -90,8 +90,8 @@ case $regtest in
  topts[1]="0:05:00" ; popts[1]="40/3/" ; ropts[1]="/1"
  topts[2]="0:05:00" ; popts[2]="40/5/" ; ropts[2]="/1"
  elif [[ "$machine" = "Orion" ]]; then
- topts[1]="0:15:00" ; popts[1]="5/4/" ; ropts[1]="/1"
- topts[2]="0:15:00" ; popts[2]="10/4/" ; ropts[2]="/2"
+ topts[1]="0:15:00" ; popts[1]="20/6/" ; ropts[1]="/1"
+ topts[2]="0:15:00" ; popts[2]="20/12/" ; ropts[2]="/2"
  elif [[ "$machine" = "Hercules" ]]; then
  topts[1]="0:05:00" ; popts[1]="40/3/" ; ropts[1]="/1"
  topts[2]="0:05:00" ; popts[2]="40/5/" ; ropts[2]="/2"

src/enkf/gridio_gfs.f90

@@ -195,9 +195,6 @@ subroutine readgriddata_pnc(vars3d,vars2d,n3d,n2d,levels,ndim,ntimes, &
  sst_ind = getindex(vars2d, 'sst')
  use_full_hydro = ( ql_ind > 0 .and. qi_ind > 0 .and. &
  qr_ind > 0 .and. qs_ind > 0 .and. qg_ind > 0 )
- ! Currently, we do not let precipiation to affect the enkf analysis 
- ! The following line will be removed after testing
- use_full_hydro = .false.
 
  if (.not. isinitialized) call init_spec_vars(nlons,nlats,ntrunc,4)
 
@@ -459,9 +456,6 @@ subroutine readgriddata_pnc(vars3d,vars2d,n3d,n2d,levels,ndim,ntimes, &
  end if
 
  ! cloud derivatives
- ! Currently, we do not let precipiation to affect the enkf analysis 
- ! The following line will be removed after testing
- use_full_hydro = .true.
  if (.not. use_full_hydro .and. iope==0) then
  if (ql_ind > 0 .or. qi_ind > 0) then
  do k=1,nlevs

src/gsi/convinfo.f90

@@ -155,6 +155,8 @@ subroutine convinfo_read
 ! 2009-01-22 todling - protect against non-initialized destroy call
 ! 2010-05-29 todling - interface consistent w/ similar routines
 ! 2014-07-10 carley - add check to bypass blank lines in convinfo file
+! 2023-05-09 s.vetra-carvalho - extended iotype to be 8 characters long to
+! allow for more descriptive observations names
 !
 ! input argument list:
 ! mype - mpi task id
@@ -171,7 +173,7 @@ subroutine convinfo_read
  implicit none
 
  character(len=1)cflg
- character(len=7) iotype
+ character(len=8) iotype
  character(len=140) crecord
  integer(i_kind) lunin,i,nc,ier,istat
  integer(i_kind) nlines
@@ -188,13 +190,13 @@ subroutine convinfo_read
  nlines=0
  read1: do
  cflg=' '
- iotype=' '
+ iotype='  '
  read(lunin,1030,iostat=istat,end=1130)cflg,iotype,crecord
-1030 format(a1,a7,2x,a140)
+1030 format(a1,a8,1x,a140)
  if (istat /= 0) exit
  nlines=nlines+1
  if(cflg == '!')cycle
- if (cflg==' '.and.iotype==' ') then
+ if (cflg==' '.and.iotype=='  ') then
  if(print_verbose)write(6,*) 'Encountered a blank line in convinfo file at line number: ',nlines,' skipping!'
  cycle
  end if
@@ -242,9 +244,9 @@ subroutine convinfo_read
 
  do i=1,nlines
  cflg=' '
- iotype=' '
+ iotype='  '
  read(lunin,1030)cflg,iotype,crecord
- if (cflg==' '.and.iotype==' ') then
+ if (cflg==' '.and.iotype=='  ') then
  if(print_verbose)write(6,*) 'Encountered a blank line in convinfo file at line number: ',i,' skipping!'
  cycle
  end if
@@ -282,7 +284,7 @@ subroutine convinfo_read
  if(print_verbose .and. mype == 0)write(6,1031)ioctype(nc),ictype(nc),icsubtype(nc),icuse(nc),ctwind(nc),ncnumgrp(nc), &
  ncgroup(nc),ncmiter(nc),cgross(nc),cermax(nc),cermin(nc),cvar_b(nc),cvar_pg(nc), &
  ithin_conv(nc),rmesh_conv(nc),pmesh_conv(nc),idum,pmot_conv(nc),ptime_conv(nc),index_sub(nc),ibeta(nc),ikapa(nc)
-1031 format('READ_CONVINFO: ',a7,1x,i3,1x,i4,1x,i2,1x,g13.6,1x,3(I3,1x),5g13.6,i5,2g13.6,i5,2g13.6,3i5)
+1031 format('READ_CONVINFO: ',a8,1x,i3,1x,i4,1x,i2,1x,g13.6,1x,3(I3,1x),5g13.6,i5,2g13.6,i5,2g13.6,3i5)
  enddo
 
  close(lunin)

src/gsi/correlated_obsmod.F90

@@ -422,7 +422,7 @@ subroutine set_(instrument,fname,mask,method,kreq,kmut,ErrorCov)
  ErrorCov%nch_active = coun
  if (.not.GMAO_ObsErrorCov) ErrorCov%nctot = nctot
  call create_(coun,ErrorCov)
- allocate(indxRf(nch_active),indxR(nch_active),Rcov(nctot,nctot))
+ allocate(indxRf(coun),indxR(nch_active),Rcov(nctot,nctot))
 
 ! Read GSI-like channel numbers used in estimating R for this instrument
  read(lu,IOSTAT=ioflag) indxR