Documentation of RTOFS Global scripts

Listing of RTOFS global scripts can be found here.

#	Script Name	Purpose	Dependencies / Calls
1	exrtofs_glo_ncoda_qc.sh	Main driver for NCODA Quality Control. Prepares incoming observation directories. Executes parallel QC scripts for various instruments via MPI (cfp). Runs data alarm to verify data volumes. Copies QC data and logs to COM directory.	Executables: rtofs_ncoda_alarm USH Scripts: rtofs_ncoda_prep_ice.sh rtofs_ncoda_ice_qc.sh rtofs_ncoda_prep_sfc_sfcr_prof.sh rtofs_ncoda_profile_qc.sh rtofs_ncoda_sfcobs_qc.sh rtofs_ncoda_sss_qc.sh rtofs_ncoda_vel_qc.sh rtofs_ncoda_ssh_qc.sh rtofs_ncoda_npp_qc.sh rtofs_ncoda_jpss_qc.sh rtofs_ncoda_metop_qc.sh rtofs_ncoda_himawari_qc.sh rtofs_ncoda_goes_qc.sh rtofs_ncoda_amsr_qc.sh rtofs_ncoda_msg_qc.sh rtofs_ncodaqc2com.sh
2	exrtofs_glo_ncoda_glbl_var.sh	Runs global 2DVAR sea ice, SSS, and SST analyses. Grid: Near-global Mercator (12km equator, 8km mid-lat). Sets up namelists and runs NCODA prep/var/post executables. Copies updated variables/logs to COM directory.	Executables: rtofs_ncoda_setup rtofs_ncoda_prep rtofs_ncoda rtofs_ncoda_post rtofs_ncoda_map (Optional) rtofs_dtg
3	exrtofs_glo_ncoda_polar_var.sh	Runs polar 2DVAR sea ice and SST analyses for NHEM and SHEM. Grid: Polar stereographic (9km resolution). Builds polar namelists and executes NCODA steps. Copies results to COM directory.	Executables: rtofs_ncoda_setup rtofs_ncoda_prep rtofs_ncoda rtofs_ncoda_post rtofs_ncoda_map (Optional) rtofs_dtg
4	exrtofs_glo_ncoda_hycom_var.sh	Runs global 3DVAR multivariate analysis. Grid: Global HYCOM tri-polar (8km equator). Checks for MOM restart files. Builds namelists and executes NCODA 3D steps.	Executables: rtofs_ncoda_setup rtofs_ncoda_prep rtofs_ncoda rtofs_ncoda_post rtofs_ncoda_map (Optional) rtofs_dtg USH Scripts: [RUN]_abort.sh
5	exrtofs_glo_analysis.sh	Generates analysis fields for the RTOFS_GLO model. Locates and stages initial conditions (restarts). Executes the RTOFS HYCOM simulation. Copies generated restart/archive files to COM.	USH Scripts: rtofs_date4restart.sh [RUN]_abort.sh [RUN]_runstaging.sh rtofs_date_normal2hycom.sh [RUN]_iceforcing.sh [RUN]_submit.sh [RUN]_tmp2com.sh date2jday.sh (from $UTILROOT)
6	exrtofs_glo_ncoda_inc.sh	Creates ocean and sea ice increment files. Used to modify restarts for UFS integration. Links to NCODA output files and MOM6 template restarts. Executes increment generation binary.	Executables: rtofs_dtg rtofs_ncodaz_inc2mom6nc_glb_lyr.x USH Scripts: rtofs_glo2d_ice.sh
7	exrtofs_glo_incup.sh	Runs a 6-hour HYCOM cycle with incremental updates. Stages forcing, boundary, and ice data. Runs the HYCOM executable (rtofs_hycom). Packages and moves resulting restarts and archives.	Executables: rtofs_dtg rtofs_hycom USH Scripts: date2jday.sh (from $USHutil) rtofs_date_normal2hycom.sh [RUN]_iceforcing.sh rtofs_date4restart.sh [RUN]_abort.sh
8	exrtofs_glo_analysis_pre.sh	Prepares input fields for the model analysis step. Calculates start/end dates based on $fcstdays. Calls prestaging script to set up inputs.	Executables: ndate USH Scripts: rtofs_date_normal2hycom.sh [RUN]_prestaging.sh
9	exrtofs_glo_forecast_pre.sh	Prepares input fields for the model forecast step. Calculates forecast start/end dates. Calls prestaging script to set up inputs.	Executables: ndate USH Scripts: rtofs_date_normal2hycom.sh [RUN]_prestaging.sh
10	exrtofs_glo_forecast.sh	Generates forecast fields for the RTOFS_GLO model. Handles restart files (either from analysis or previous forecast). Executes the RTOFS HYCOM simulation. Copies products to COM directory.	USH Scripts: rtofs_date4restart.sh [RUN]_abort.sh [RUN]_runstaging.sh rtofs_date_normal2hycom.sh [RUN]_iceforcing.sh [RUN]_submit.sh [RUN]_tmp2com.sh date2jday.sh (from $UTILROOT)
11	exrtofs_glo_post.sh	Post-processing script for Volume data. Loops through forecast hours to generate 3D NetCDF files. Produces daily and 6-hourly regional files. Alerts db_net when files are ready.	USH Scripts: [RUN]_glo3z_daily.sh [RUN]_glo3z_6hrly.sh
12	exrtofs_glo_post_2.sh	Post-processing script for extended (hr 144-192) surface data. Generates 3-hourly 2D NetCDF files for surface variables and ice. Alerts db_net upon completion.	USH Scripts: [RUN]_glo2d.sh [RUN]_glo2d_ice.sh
13	exrtofs_glo_grib2_post.sh	Generates hourly surface NetCDF files (nowcast and 1-72hr). Generates 3-hourly surface NetCDF files (72-144hr). Packs NetCDF into GRIB2 format for 11 regions. Produces NetCDF files specifically for OPC.	Executables: tocgrib2 USH Scripts: [RUN]_glo2d.sh [RUN]_glo2d_ice.sh rtofs_surface_hcasts.sh (or day1-3/day4-5 equivalents) [RUN]_create_regions_mpmd_weights.sh
14	exrtofs_glo_gzip.sh	Compresses (gzipping via pigz or tar) large restart and archive files. Uses MPI (cfp) to compress files in parallel. Alerts db_net when tarballs are created and moved to COM.	None (System utils only)
15	exrtofs_glo_gempak.sh	Converts GRIB2 files into GEMPAK format. Generates hourly grids (00 to 72) for specified regions (Alaska, Bering, W. Atlantic). Uses mpiexec to parallelize GEMPAK generation. Generates missing F000 files using wgrib2 and GEMPAK utilities.	Executables: wgrib2 nagrib2 (GEMPAK) gdcfil (GEMPAK) gddiag (GEMPAK) Scripts: gempak.sh (from $GEMPAKrtofs)

Notes:

• $RUN refers to rtofs in the dependencies listed above.
• Sequence of execution is not necessarily in the order of listing of scripts.