Release for HR4 prototypes

What's Changed

• Update to spack-stack 1.6.0 by @DavidHuber-NOAA in #2239
• Removes jlogfile and postmsg instances from workflow by @HenryRWinterbottom in #2312
• Jenkins updates by @TerrenceMcGuinness-NOAA in #2334
• Remove FIX* variables for fix subfolders by @KateFriedman-NOAA in #2337
• Update JEDI ATM to use .nc for obs and generalize x,y layout by @RussTreadon-NOAA in #2336
• Update ufs-waether-model hash by @JessicaMeixner-NOAA in #2338
• Rename the land DA jobs to snow DA to better reflect what they are doing by @CoryMartin-NOAA in #2330
• Fix rocoto forecast hour determination for GEFS by @WalterKolczynski-NOAA in #2351
• Move Jenkinsfile into ci subdirectory by @TerrenceMcGuinness-NOAA in #2355
• Turn on C48mx500_3DVarAOWCDA test on hera by @JessicaMeixner-NOAA in #2363
• Update stage IC to handle ocean perturbations by @NeilBarton-NOAA in #2364
• Sort list of coupler restart files for restart time determination by @DWesl in #2360
• Adding debug option for all build scripts by @HenryRWinterbottom in #2326
• Reduce Jenkins messaging to GitHub by @TerrenceMcGuinness-NOAA in #2370
• Reformat snowDA templates to jinja2 by @aerorahul in #2371
• Add Hercules support for the GSI monitor by @DavidHuber-NOAA in #2373
• Forgotten templated DO_VRFY_OCEANDA by @guillaumevernieres in #2379
• Clean out non-gfs top level variables by @KateFriedman-NOAA in #2366
• Add global-workflow infrastructure for ocean analysis recentering task by @AndrewEichmann-NOAA in #2299
• Add new BUFR table file parm/product/bufr_ij9km.txt for GFSv17 C1152 by @BoCui-NOAA in #2383
• Return ocnanalrun npes resource setting back to previous value by @AndrewEichmann-NOAA in #2386
• Rewrote pr_list_database.py to use wxflow's SQLiteDB Class by @TerrenceMcGuinness-NOAA in #2376
• Add switch to control debug=true on WCOSS2 for development testing by @KateFriedman-NOAA in #2388
• Add JEDI atmosphere only CI by @RussTreadon-NOAA in #2357
• Changed config.atmanl to allow non-hybrid background error yamls by @DavidNew-NOAA in #2394
• remove documentation about generating ICs using global-workflow by @aerorahul in #2397
• Fix KeyError issue in ocean/ice postprocessing job. by @aerorahul in #2398
• Missed a comma from the hotfix this AM by @aerorahul in #2399
• GitHub message error paths by @TerrenceMcGuinness-NOAA in #2401
• Fix ensemble archive groups to include all members by @CatherineThomas-NOAA in #2402
• Parse jediyaml only once by @aerorahul in #2387
• re-enable ci/cases/pr/C48mx500_3DVarAOWCDA.yaml by @JessicaMeixner-NOAA in #2405
• Add initial GSI-based soil analysis capability by @ClaraDraper-NOAA in #2263
• Add GEFS Ocean Perturbation Options by @NeilBarton-NOAA in #2385
• Updates to RTD documentation by @KateFriedman-NOAA in #2418
• Hotfix: send the correct number of build jobs for the UFS by @DavidHuber-NOAA in #2423
• Add WAFS jobs, scripts and ush to GFS v17 workflow repository by @YaliMao-NOAA in #2412
• hotfix to update full path to error logs on CI case fail by @TerrenceMcGuinness-NOAA in #2425
• Fix *earc jobs where the number of members isn't a multiple of 10 by @DavidHuber-NOAA in #2424
• Correct GDASApp paths by @RussTreadon-NOAA in #2435
• Add option to use traditional threading in the UFS by @aerorahul in #2384
• Uploading error logs to GitHub from Jenkins CI Runs by @TerrenceMcGuinness-NOAA in #2429
• Add a rotating subset of members for early-cycle enkf by @TravisElless-NOAA in #2427
• Update global-workflow and subcomponents to Hera/Rocky 8 partition by @HenryRWinterbottom in #2421
• Fix post log arg check and don't create build semaphore by @TerrenceMcGuinness-NOAA in #2440
• Modify APP based on RUN by @WalterKolczynski-NOAA in #2413
• Turn GEFS CI test on for Hera by @TerrenceMcGuinness-NOAA in #2442
• Refactor gempak jobs for new COM and style by @WalterKolczynski-NOAA in #2374
• Add GEFS ENS Atmos options by @NeilBarton-NOAA in #2392
• Archive the snow DA analysis into HPSS by @jiaruidong2017 in #2414
• Remove the reset of upper layer humidity by @CatherineThomas-NOAA in #2449
• Fix rotating member bugs by @TravisElless-NOAA in #2443
• Reenable the minimization monitor on Hera by @DavidHuber-NOAA in #2446
• Move bash utility functions out of preamble by @WalterKolczynski-NOAA in #2447
• Rename generate_com to declare_from_tmpl by @WalterKolczynski-NOAA in #2453
• Turn off reducedgrid in the EnKF by @CatherineThomas-NOAA in #2456
• The soca fix path is needed in config.prepoceanobs by @guillaumevernieres in #2460
• Add new data sources used in GFS v16.3.12 by @ADCollard in #2283
• Flip the build for GFS and GEFS with waves by @aerorahul in #2462
• Check the DO_JEDISNOWDA condition before adding snow DA analysis to the list by @jiaruidong2017 in #2471
• Improve error messaging to resolve bugzilla by @KateFriedman-NOAA in #2468
• Add support for CADS IR cloud detection scheme in the GSI by @wx20jjung in #2478
• Add oceanalecn to workflow generator by @AndrewEichmann-NOAA in #2409
• Fix paths in prepocnobs task by @AndrewEichmann-NOAA in #2459
• Update parm files for atm product by @WenMeng-NOAA in #2486
• Update fbwind for COM refactor by @WalterKolczynski-NOAA in #2479
• Upadte and tested CI Bash for WCOSS2 by @TerrenceMcGuinness-NOAA in #2481
• Add mean/spread for atmos grib2 by @WalterKolczynski-NOAA in #2482
• Revert file name changes in off-line post by @WenMeng-NOAA in #2499
• Add rocoto sh tag, script to check netcdf file and apply this to check ocean output by @aerorahul in #2484
• Fix paths for refactored prepocnobs task by @AndrewEichmann-NOAA in #2504
• Add C768 and C1152 S2SW test cases by @JessicaMeixner-NOAA in #2509
• CI Refactoring and STALLED case detection by @TerrenceMcGuinness-NOAA in #2488
• Enable using the FV3_global_nest_v1 CCPP suite by @guoqing-noaa in #2512
• Update gsi_enkf.sh hash to 457510c by @RussTreadon-NOAA in #2514
• Adding more cycles to gempak script gfs_meta_sa2.sh by @GwenChen-NOAA in #2518
• Update gdas_gsibec_ver to 20240416 by @RussTreadon-NOAA in #2497
• Update parm/transfer list files to match vetted GFSv16 set by @KateFriedman-NOAA in #2517
• Add restart on failure capability for the forecast executable by @aerorahul in #2510
• Hotfix to disable STALLED in CI as an error by @TerrenceMcGuinness-NOAA in #2523
• New "atmanlfv3inc" Rocoto job by @DavidNew-NOAA in #2420
• Add CCPP suite and FASTER option to UFS build by @guoqing-noaa in #2521
• Fix comment indentation by @WalterKolczynski-NOAA in #2526
• Hot fix for bash CI on WCOSS2 by @TerrenceMcGuinness-NOAA in #2536
• Add CADS use flexibility by @wx20jjung in #2540
• Retire AWIPS GRIB1 products by @GwenChen-NOAA in #2547
• Add option to link different orog/ugwd fix files for global nest by @guoqing-noaa in #2532
• Turn C48mx500_3DVarAOWCDA back on by @JessicaMeixner-NOAA in #2543
• Launch Multiple Platforms to Jenkins with polling by @TerrenceMcGuinness-NOAA in #2548
• Link ensemble analysis increment files to COMROOT for warm_start by @RussTreadon-NOAA in #2553
• Fixes sea ice archiving by @AndrewEichmann-NOAA in #2541
• Remove implicit symlink names by @WalterKolczynski-NOAA in #2527
• Utilize scale-dependent localization for atmospheric analysis by @TravisElless-NOAA in #2542
• Updated GEMPAK version and APRUN launcher. by @HenryRWinterbottom in #2555
• Build the gfs_utils submod within the global workflow on Gaea by @DavidBurrows-NCO in #2556
• Add the global nesting capability by @guoqing-noaa in #2545
• Single Executable for main GDAS JEDI applications by @danholdaway in #2565
• Add task to prepare emissions for GEFS by @aerorahul in #2562
• Add CI test for products by @WalterKolczynski-NOAA in #2567
• Use JCB for assembling JEDI YAML files for atmospheric GDAS by @danholdaway in #2477
• Updates for cold start half cycle, then continuing with IAU for WCDA by @JessicaMeixner-NOAA in #2560
• Migration to Rocky8 spack-stack installations on Jet by @InnocentSouopgui-NOAA in #2458
• Do not use BUILT_semphore to force rebuilds when re-run by @TerrenceMcGuinness-NOAA in #2593
• Update damping and time-step by @yangfanglin in #2575
• Limit gfswavepostpnt to 40 PEs/node by @DavidHuber-NOAA in #2588
• Update CICE and MOM6 fix versions by @KateFriedman-NOAA in #2600
• Update gsi_utils.fd hash by @RussTreadon-NOAA in #2598
• Moving logic for skipping hosts in pr cases by @TerrenceMcGuinness-NOAA in #2573
• Remove existing EXPDIRs and COMROTs when CI is re-run by @TerrenceMcGuinness-NOAA in #2601
• Fix race condition in CI from cross mounted disks between Orion and Hercules by @TerrenceMcGuinness-NOAA in #2604
• Updating CI Machine configs with redundant PTMP by @TerrenceMcGuinness-NOAA in #2605
• Adds jjob and other necessities for marine LETKF task by @AndrewEichmann-NOAA in #2564
• Add remove RUNDIRS step in CI before creating experements by @TerrenceMcGuinness-NOAA in #2607
• Refactored archiving by @DavidHuber-NOAA in #2491
• Sea-ice analysis insertion by @guillaumevernieres in #2584
• Update STMP and PTMP settings in host file for Orion and Hercules by @TerrenceMcGuinness-NOAA in #2614
• Global-workflow (AR) Generic updates for Gaea C5 by @AnilKumar-NOAA in #2515
• Add atmensanlfv3inc job by @DavidNew-NOAA in #2592
• Change GRIB2 parameter names and vertical levels for ocean/ice post by @GwenChen-NOAA in #2611
• Script to keep Jenkins Agent persistent from cron by @TerrenceMcGuinness-NOAA in #2634
• Add C384mx025_3DVarAOWCDA yamls by @JessicaMeixner-NOAA in #2625
• Update to add 1-deg global wave grid by @JessicaMeixner-NOAA in #2619
• Update forecast job to use COMIN/COMOUT by @WalterKolczynski-NOAA in #2622
• Add the capability to use slurm reservation nodes by @guoqing-noaa in #2627
• Switch to Rocky 9 built external packages on Hercules by @WalterKolczynski-NOAA in #2608
• Archiving cleanup by @DavidHuber-NOAA in #2621
• Add IAU to snow DA (and its test) by @CoryMartin-NOAA in #2610
• Update wmo parm files to fix WMO header by @GwenChen-NOAA in #2652
• Update ufs-weather-model by @JessicaMeixner-NOAA in #2646
• Enable wcoss2 ufsda build and module load by @RussTreadon-NOAA in #2620
• Update S4 point of contact in docs by @DavidHuber-NOAA in #2660
• Add links to the ocean insitu obs processing tools by @guillaumevernieres in #2644
• Parameterize some things in config.atmanl and config.atmensanl by @DavidNew-NOAA in #2661
• Update RDHPCS Hera resource for eupd task by @HenryRWinterbottom in #2636
• Add handling to select CRTM cloud optical table based on cloud scheme and update calcanal_gfs.py by @emilyhcliu in #2645
• Add overwrite to creat experiment in BASH CI by @TerrenceMcGuinness-NOAA in #2676
• Update cleanup job to use COMIN/COMOUT by @HenryRWinterbottom in #2649
• Add ability to process ocean/ice products specific to GEFS by @EricSinsky-NOAA in #2561
• Update ufs-weather-model by @JessicaMeixner-NOAA in #2663
• Link both global-nest fix files and non-nest ones at the same time by @guoqing-noaa in #2632
• Add COM template for JEDI obs by @WalterKolczynski-NOAA in #2678
• Replace sleep with wait_for_file by @HenryRWinterbottom in #2586
• Add ability to use GEFS replay ICs by @NeilBarton-NOAA in #2559
• Update gdas.cd and gsi_utils hashes by @RussTreadon-NOAA in #2641
• Add Hercules-EMC to the Jenkins configurable parameter list by @TerrenceMcGuinness-NOAA in #2685
• Remove ocean daily files by @JessicaMeixner-NOAA in #2689
• Add observation preparation job for aerosols DA to workflow by @ypwang19 in #2624
• Update GDASapp hash to move JCB into GDASapp by @danholdaway in #2665
• Optimize wavepostpnt by @DavidHuber-NOAA in #2657
• Turn on high-frequency output in extended test by @WalterKolczynski-NOAA in #2679
• Update archive job to use COMIN/COMOUT by @HenryRWinterbottom in #2668
• Hotfix for bug in template names. by @HenryRWinterbottom in #2697
• Removes misleading "No such file or directory" syntax errors from output files by @HenryRWinterbottom in #2688
• Eliminate post groups by @WalterKolczynski-NOAA in #2667
• Fix and simplify online archiving by @DavidHuber-NOAA in #2687
• Add minimum software requirements by @DavidHuber-NOAA in #2712
• Assign machine- and RUN-specific resources by @DavidHuber-NOAA in #2672
• Update wave jobs to use COMIN/COMOUT by @HenryRWinterbottom in #2643
• Update logic for MOM6 number of layers/exception values by @JessicaMeixner-NOAA in #2681
• Cleanup of stale RUNDIRS from an experiment by @aerorahul in #2719
• Activate snow DA test on WCOSS by @WalterKolczynski-NOAA in #2720
• updated Finalize in Jenkinsfile and added try block around scm checkout by @TerrenceMcGuinness-NOAA in #2692
• Revert PR 2681 by @aerorahul in #2739
• Update for JCB policies and stage DA job files with Jinja2-templates by @RussTreadon-NOAA in #2700
• Fix xml file setup and complete C48 ATM and S2SW runs for CI on Gaea by @DavidBurrows-NCO in #2701
• Hotfix for clusters from #2701 by @aerorahul in #2747
• Update gempak job to run one fcst hour per task by @GwenChen-NOAA in #2671
• Hotfix for undefined CLUSTERS by @DavidHuber-NOAA in #2748
• Update ufs model hash to 20240625 by @JessicaMeixner-NOAA in #2729
• Update (partially) global-workflow for orion+rocky9 by @aerorahul in #2741
• Add fcst dependency to ocnanalprep by @AndrewEichmann-NOAA in #2728
• Fix GDAS group B restart archiving by @DavidHuber-NOAA in #2735
• Adds contents of constructor and initialize methods to marine LETKF class by @AndrewEichmann-NOAA in #2635
• CI maintenance updates and adding CI Unit Tests by @TerrenceMcGuinness-NOAA in #2740
• Updated prepobs and fit2obs versions for Orion Rocky9 by @KateFriedman-NOAA in #2758
• Address issues in creating XML for GFS forecast-only with app S2SWA by @aerorahul in #2757
• Hotfix: Update jcb to avoid git-lfs files by @DavidHuber-NOAA in #2782
• Set METplus process count in config.metp; add verif-global support for Rocky 9 by @DavidHuber-NOAA in #2774
• Add task to process reforecast variables to save on WCOSS2 by @EricSinsky-NOAA in #2680
• Use replace_tmpl Jinja filter instead of namespaces in archiving by @DavidHuber-NOAA in #2775
• Refactoring of the marine B-matrix job by @guillaumevernieres in #2749
• Hot fix: Disable METplus jobs temporarily by @DavidHuber-NOAA in #2796
• HR4 GWD update by @JessicaMeixner-NOAA in #2732
• Remove f000 from atmos rocoto tasks for replay cases by @EricSinsky-NOAA in #2778
• Simplify resource-related variables, remove CDUMP where unneeded by @DavidHuber-NOAA in #2727
• Add fix for metplus jobs when gfs_cyc=2 or 4 by @DavidHuber-NOAA in #2791
• Update the gfs_utils repository hash by @GeorgeGayno-NOAA in #2801
• Update ocean post-processing triggers by @aerorahul in #2784
• Fix erroneous cdump addition by @WalterKolczynski-NOAA in #2803
• Update Java Agent launching script for Jenkins connections by @TerrenceMcGuinness-NOAA in #2762
• Run METplus serially and correct the name of prod tasks by @DavidHuber-NOAA in #2804
• land surface upgrades for hr4 by @HelinWei-NOAA in #2787
• Clean-up temporary rundirs - take 2. by @aerorahul in #2753
• Bugfix for updating label states in Jenkins by @TerrenceMcGuinness-NOAA in #2808
• Revert MSU FIX_DIRs back to glopara by @KateFriedman-NOAA in #2811
• Marine DA updates by @guillaumevernieres in #2802
• Feature/get arch adds an empty archive job to GEFS system by @AntonMFernando-NOAA in #2772
• Check that a PR driver is still running before trying to kill it by @DavidHuber-NOAA in #2799
• Stage atmospheric backgrounds and UFS cubed-sphere history files by @DavidNew-NOAA in #2792
• Add capability to run forecast in segments by @WalterKolczynski-NOAA in #2795
• Add fixes to products for when REPLAY IC's are used by @EricSinsky-NOAA in #2755
• Add support for forecast-only runs on AWS by @weihuang-jedi in #2711
• Add Gaea C5 to CI by @AnilKumar-NOAA in #2814
• Jenkins Pipeline Updates by @TerrenceMcGuinness-NOAA in #2815
• Hotfix: Handle UNAVAILABLE rocoto status in Bash CI by @DavidHuber-NOAA in #2820
• Fixed test on UNAVAILBLE in python Rocoto check by @TerrenceMcGuinness-NOAA in #2842
• Convert staging job to python and yaml by @KateFriedman-NOAA in #2651
• support ATM forecast only on Azure by @weihuang-jedi in #2827
• Add snow DA update and recentering for the EnKF forecasts by @CoryMartin-NOAA in #2690
• Update omega calculation by @XiaqiongZhou-NOAA in #2751
• Add GEFS C48 support on AWS by @weihuang-jedi in #2818
• Support ATM forecast only on Google by @weihuang-jedi in #2832
• Fix gdas build on Gaea and add Gaea to available CI list by @AnilKumar-NOAA in #2857
• Add JEDI ATM lgetkf observer and solver jobs by @RussTreadon-NOAA in #2833
• Support coupling on AWS by @weihuang-jedi in #2859
• Correct ocean MOM.res_# stage copy by @KateFriedman-NOAA in #2868
• Add diffusion/diag B for aerosol DA and some other needed changes by @CoryMartin-NOAA in #2738
• Add 3 and 9 hr increment files to IC staging by @AndrewEichmann-NOAA in #2876
• Support global-workflow GEFS C48 on Google Cloud by @weihuang-jedi in #2861
• Add ability to run CI test C96_atm3DVar.yaml to Gaea-C5 by @DavidBurrows-NCO in #2885
• Update aerosol climatology to 2013-2024 mean by @AnningCheng-NOAA in #2888
• Eliminate race conditions and remove DATAROOT last in cleanup by @DavidHuber-NOAA in #2893
• Reenable Orion Cycling Support by @DavidHuber-NOAA in #2877
• Add an archive task to GEFS system to archive files locally by @AntonMFernando-NOAA in #2816
• Restructure the bufr sounding job by @BoCui-NOAA in #2853
• Create JEDI class by @DavidNew-NOAA in #2805
• Add FAQ page and a caution with using reserved variables by @aerorahul in #2898
• Consolidate python configuration dictionaries by @DavidHuber-NOAA in #2839
• Replace APRUN with APRUN_default by @DavidHuber-NOAA in #2871
• Add new UPP links to .gitignore by @DavidHuber-NOAA in #2904
• Updates for HR4 tag by @aerorahul in #2914

New Contributors

• @DavidNew-NOAA made their first contribution in #2394
• @ClaraDraper-NOAA made their first contribution in #2263
• @wx20jjung made their first contribution in #2478
• @GwenChen-NOAA made their first contribution in #2518
• @DavidBurrows-NCO made their first contribution in #2556
• @danholdaway made their first contribution in #2565
• @InnocentSouopgui-NOAA made their first contribution in #2458
• @ypwang19 made their first contribution in #2624
• @AntonMFernando-NOAA made their first contribution in #2772
• @weihuang-jedi made their first contribution in #2711
• @XiaqiongZhou-NOAA made their first contribution in #2751

Full Changelog: prototype/hr3...hr.v4