Feature/gfsv16b (#11)

* First draft to add chgresfcst to rocoto workflow

* Issue #1:  update parm/config/config.base.emc.dyn to be consistent with GFS v16 real-time parallel config.base

* Commit changes from debugging addition of chgresfcst on hera

* add checkout.sh to test on Dell

* Adapting wavepostsbs for running on Hera

* Issue #1 - Hotfix to update anaconda module contrib path on Hera

* modified:   checkout.sh to check out upp_gfsv16_relaese.v1.0.9

output cloud ceiling height and instant total cloud fraction.
output instant cloud fraction at low/mid/high cloud layer.
correct grib2 names of time averaged cloud fraction fraction at low/mid/high cloud layer from "TCDC" into "LCDC, MCDC, HCDC".
output radar reflectivity at 1/4 km above ground and model layer 1/2.
output mixed layer CAPE/CIN.
Remove simulated GOES-12 brightness temperature from gfs product.
Add the bug fix of initializing DBZI from Ruiyu.

* Update exwave_post_sbs.sh

Removing obsolete nm variable entries

* Issue #1 - update Externals.cfg to match updates to checkout.sh

* Issue NOAA-EMC#85:  add cfp option to chgresfcst; enable threads with chgresfcst

* modified:   scripts/run_gfsmos_master.sh.dell to set default verification type o short.
modified:   sorc/checkout.sh  updated to model tag GFS.v16.0.6 to fix contrib issue on HERA

* Issue #1 - sync Externals.cfg with checkout.sh update for FV3 GFSv16.0.6 tag

* update  checkout.sh to switch back to post version upp_gfsv16_release.v1.0.8.   1.0.9 still has issues.

* modified:   run_gfsmos_master.sh.dell to still set range=both as the default for running the real-time parallel

* Issue NOAA-EMC#85:  (1) rename "chgresfcst" as "echgres", (2) add chgres variables to env

* Issue NOAA-EMC#85:  update DA checkout to point at release/gfsda.v16.0.0

* Update config.resources

Generalize setting of echgres threads to be maximum permitted on given platform instead of explicitly setting echgres threads on every platform.

* Update version of upp in Externals.cfg to be consistent with sorc/checkout.sh

* modified:   Externals.cfg and  sorc/checkout.sh to check out model tag GFS.v16.0.7
   and UPP tag upp_gfsv16_release.v1.0.9.  Changes include:

1) Inline POST Issues NOAA-EMC#136 and $142
   * Update ceiling height calculation for global FV3.
   * add low,middle,high instantaneous cloud fraction
   * add radar reflectivity at model layers 1 and 2 , and radar reflectivities at 1 and 4-km height.
   * fix a bug in initializing DBZI
   * output mixed layer CAPE/CIN
   * remove simulated GOES-12 brightness temperature.
   * change the names of time averaged low/mid/high cloud fractions in grib2 files
     from "TCDC" to "LCDC/MCDC/HCDC", respectively.

2) Model Issue NOAA-EMC#152
   * update in-line post control files
   * upgrade post library to 8.0.9 for hera and wcoss_dell_p3

* Update README.md

Remove use/mention of manage_externals until checkout.sh is retired.

* fix for exiting properly with error for wave prep/init scripts

* Issue #1:  HPSS archive and MOS script changes

 * replace enkf member atmi*nc with ratmi*nc in HPSS enkf tarballs

 * add ensemble resolution analysis to HPSS gdas tarball

 * allow variable range to be externally set in run_gfsmos_master scripts

* modified:   config.vrfy to point a different syndat directory on Hera
       export COMROOTp1="/scratch1/NCEPDEV/global/glopara/com"
       export COMINsyn=${COMINsyn:-${COMROOTp1}/gfs/prod/syndat}

* corrected a typo in  hpssarch_gen.sh
-     echo  "${dirname}${head}atma000.ensres${SUFFIX}  " >>gdas.txt
+     echo  "${dirname}${head}atma009.ensres${SUFFIX}  " >>gdas.txt

* modified:   config.vrfy to add
    elif [ $machine = "HERA" ] ; then
        export RUNGFSMOSSH="$HOMEgfs/scripts/run_gfsmos_master.sh.hera"

* Issue NOAA-EMC#94 - generalization updates to link script

- change 'nco' mode to 'prod' mode
- change 'emc' mode to 'dev' mode
- update machine values to match target names

* Issue NOAA-EMC#94 - commit initial version of new installation script

* modified:   jobs/JGLOBAL_FORECAST   parm/config/config.wave   scripts/exglobal_fcst_nemsfv3gfs.sh
    add WW3 break-point restart capability and clean up forecast script.

* further updated exglobal_fcst_nemsfv3gfs.sh to use restart_wave directory for gdas cycle  as well

* Issue #1:  update sorc/checkout.sh to checkout verif_global_v1.9.0

* Issue #1:  set g2o1_obtype_conus_sfc in config.metp to "ONLYSF ADPUPA"

* Issue NOAA-EMC#94 - initial add of COMPONENTatmos variable to scripts

* modified:   checkout.sh to checkout model tag GFS.v16.0.9

 1.   WW3 update: write all restart files in a sub-directory restart_wave
 2.   Port production/GFS.v16 to Orion (NOAA-EMC#129)
    * Update FV3 submodule
    * Update NEMS submodule
    * Add 'ulimit -s unlimited' to Orion job card template
    * Update NEMS submodule to point to fix_moduleinit branch in 'junwang-noaa/NEMS'
    * Update modulefiles/orion.intel/fv3
    * Update regression test configuration on Orion (for gfs_v16)
    * Update NEMS submodule (change /apps/lmod/init path after Orion maintenance)
    * Update NEMS submodule (point to NOAA-EMC/NEMS)

* Issue NOAA-EMC#94 - convert  variables into hard-coded values per feedback

* Issue NOAA-EMC#94 - fix dependencies with  in the path

* Issue #1 - add mod_icec.sh to UPP ush script symlinking in link_fv3gfs.sh

* modified:   ../Externals.cfg  and   checkout.sh to check out
            UPP tag tag upp_gfsv16_release.v1.0.10  and model tag GFS.v16.0.10
            Updated the algorithm used to compute CAPE and CIN in UPP.  The computation
            is now bounded from the surface up to 1 hPa instead of the model top to
            avoid producing erroneous large CAPE and CIN values.

* modified:   config.base.emc.dyn to use obsproc_prep.iss70457.netcdfhistory_atmos

* Revert "modified:   config.base.emc.dyn to use obsproc_prep.iss70457.netcdfhistory_atmos"

This reverts commit 4977271.

* GitHub Issue#94 update gempak's ush scripts

* Issue NOAA-EMC#94 - added  and [wave] back in after feedback from Steven Earle, also renamed the wave scripts to match the correct convention

* Issue NOAA-EMC#94 - updates to wave scripts based on NCO feedback

* Issue NOAA-EMC#94 - remove COMPONENTatmos and COMPONENTwave, use COMIN[COMOUT]atmos[wave] instead

* Issue NOAA-EMC#94 - revert RSTDIR_WAVE if-block compression to retain breakpoint restarting

* Issue NOAA-EMC#94 - fix dirpath in ush/hpssarch_gen.sh

* Issue NOAA-EMC#94 - component checkout updates to use forks and new UPP tag

* Issue #1:  add enkf member sfcf006.nc to enkf tarballs

* Issue NOAA-EMC#94 - new GLDAS tag with atmos directory

* Issue #1:  refactor CFP in DA sections of HERA.env and WCOSS_DELL_P3.env

* Reverting link_fv3gfs.sh, will commit in different changeset

* Issue NOAA-EMC#94 - updating GLDAS and EMC_post tags in Externals.cfg

* Issue NOAA-EMC#94 - add  to gempak scripts and cleanup based on PR feedback

* Issue NOAA-EMC#94 - removing new install script, will introduce via another branch, needs more testing

* Issue NOAA-EMC#94 - retire BASE_SVN

* Issue NOAA-EMC#94 - add default to fhmax in vrfy.sh for when prior tasks disabled and set new path to restructured gfsmos

* Issue NOAA-EMC#94 - reverting GSI and EMC_gfs_wafs checkouts back to authoritative repos ahead of their updating for new , will update EMC_gfs_wafs to new tag when available

* Issue NOAA-EMC#94 - move UFS_UTILS link script step from build_ufs_utils.sh to link_fv3gfs.sh based on feedback from GEFS team

* Issue NOAA-EMC#94 - small fix to updated UFS_UTILS part of link_fv3gfs.sh

* Issue NOAA-EMC#94 - adding -o flag to checkout.sh for optional GTG checkout with EMC_post

* Issue NOAA-EMC#94 - updates for FSU tracker

* Issue NOAA-EMC#94 - fix AWIPS file dependency

* Issue NOAA-EMC#94 - update WCOSS-Dell module versions to prod_util and EnvVars

* Issue NOAA-EMC#94 - update CFP module version on WCOSS-Dell

* Issue #1 - update to prod_util version (1.1.3 -> 1.1.4) on WCOSS-Dell for post P1/P2 removal

* Issue NOAA-EMC#94 - pull in two fixes for wave job setup in free-forecast mode

* Issue NOAA-EMC#94 - fix to messed up shebang in setup_expt_fcstonly.py

Co-authored-by: CoryMartin-NOAA <cory.r.martin@noaa.gov>
Co-authored-by: russ.treadon <Russ.Treadon@noaa.gov>
Co-authored-by: henrique.alves <Henrique.Alves@noaa.gov>
Co-authored-by: Kate.Friedman <Kate.Friedman@noaa.gov>
Co-authored-by: fanglin.yang <fanglin.yang@noaa.gov>
Co-authored-by: Jose-Henrique Alves <47567389+ajhenrique@users.noreply.github.com>
Co-authored-by: RussTreadon-NOAA <26926959+RussTreadon-NOAA@users.noreply.github.com>
Co-authored-by: JessicaMeixner-NOAA <Jessica.Meixner@noaa.gov>
Co-authored-by: BoiVuong-NOAA <Boi.Vuong@noaa.gov>