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Updates to Remaining Chapters (6 & 8-12) of SRW Docs/User's Guide #255

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370bb6c
updated docs
gspetro Feb 11, 2022
a907487
added git submodule
gspetro Feb 11, 2022
b628dd6
fix formatting
gspetro Feb 11, 2022
467071f
added new submodule commits
gspetro Feb 11, 2022
de00e4c
fixed ref links
gspetro Feb 11, 2022
fb34100
finished Intro
gspetro Feb 11, 2022
701f9e9
finish Components & Intro edits
gspetro Feb 14, 2022
cab1c6f
edited Rocoto workflow section of Quickstart
gspetro Feb 14, 2022
290364e
added minor hpc submodule commits
gspetro Feb 15, 2022
80291a1
Updates to Rocoto Workflow in Quick Start
gspetro Feb 16, 2022
ab97b74
add to HPC-stack intro
gspetro Feb 16, 2022
8056200
submodule updates
gspetro Feb 16, 2022
17504fc
added submodule docs edits
gspetro Feb 17, 2022
357e151
hpc-stack updates & formatting fixes
gspetro Feb 17, 2022
acf555b
hpc-stack intro edits
gspetro Feb 17, 2022
36349a6
bibtex attempted fix
gspetro Feb 18, 2022
838271f
add hpc-stack module edits
gspetro Feb 18, 2022
863b7de
update sphinxcontrib version
gspetro Feb 22, 2022
2b100d9
add .readthedocs.yaml file
gspetro Feb 22, 2022
9e58e67
update .readthedocs.yaml file
gspetro Feb 22, 2022
1830b49
update .readthedocs.yaml file
gspetro Feb 22, 2022
54a647e
update conf.py
gspetro Feb 22, 2022
46d381f
updates .readthedocs.yaml with submodules
gspetro Feb 22, 2022
91af03d
updates .readthedocs.yaml with submodules
gspetro Feb 22, 2022
97616fd
submodule updates
gspetro Feb 22, 2022
21d3e27
submodule updates
gspetro Feb 22, 2022
5af69e5
minor Intro edits
gspetro Feb 23, 2022
ee901e6
minor Intro edits
gspetro Feb 23, 2022
f77cba9
minor Intro edits
gspetro Feb 23, 2022
bc0748c
submodule updates
gspetro Feb 23, 2022
fef6d27
fixed typos in QS
gspetro Feb 23, 2022
0d16101
QS updates
gspetro Feb 24, 2022
418a40b
QS updates
gspetro Feb 24, 2022
77d565d
QS updates
gspetro Feb 25, 2022
2e1a03f
updates to InputOutput and QS
gspetro Feb 25, 2022
80519d4
fix I/O doc typos
gspetro Feb 25, 2022
6f11030
pull updates to hpc-stack docs
gspetro Feb 28, 2022
999a417
pull updates to hpc-stack docs
gspetro Mar 1, 2022
f07fe8a
fix table wrapping
gspetro Mar 1, 2022
14db051
Merge branch 'ufs-community:develop' into develop
gspetro-NOAA Mar 3, 2022
b58d661
updates to QS for cloud
gspetro Mar 3, 2022
301ff5f
Merge branch 'develop' of github.com:gspetro-NOAA/ufs-srweather-app i…
gspetro Mar 3, 2022
0b50e04
fix QS export statements
gspetro Mar 3, 2022
8786b32
fix QS export statements
gspetro Mar 3, 2022
3a442d6
QS edits on bind, config
gspetro Mar 3, 2022
0cae160
add bullet points to notes
gspetro Mar 4, 2022
27247a5
running without rocoto
gspetro Mar 4, 2022
805bb81
add HPC-Stack submodule w/docs
gspetro Mar 4, 2022
29cf292
split QS into container/non-container approaches
gspetro Mar 8, 2022
3e30098
added filepath changes for running in container on Orion, et al.
gspetro Mar 9, 2022
53807fa
edits to overview and container QS
gspetro Mar 10, 2022
93bfe9b
moved CodeReposAndDirs.rst info to the Introduction & deleted file
gspetro Mar 11, 2022
eb00397
continued edits to SRWAppOverview
gspetro Mar 11, 2022
f4d2043
combine overview w/non-container docs
gspetro Mar 15, 2022
d1addf8
finish merging non-container guide & SRWOverview, rename/remove files…
gspetro Mar 16, 2022
fc1a1d4
minor edits for Intro & QS
gspetro Mar 17, 2022
acb77c8
updates to BuildRun doc through 3.8.1
gspetro Mar 17, 2022
70a051b
edits to Build/Run and Components
gspetro Mar 17, 2022
99127e7
remove .gitignore
gspetro Mar 18, 2022
b01268d
fix Ch 3 title, 4 supported platform levels note
gspetro Mar 18, 2022
da35184
fix typos, add term links
gspetro Mar 18, 2022
1302868
other minor fixes/suggestions implemented
gspetro Mar 18, 2022
a704a2f
updated Intro based on feedback; changed SRW to SRW App throughout
gspetro Mar 21, 2022
7fc263d
update comment to Intro citation
gspetro Mar 21, 2022
496fcb3
Merge branch 'develop' into develop
gspetro-NOAA Mar 22, 2022
10de71f
add user-defined vertical levels to future work
gspetro Mar 22, 2022
16b0c1a
Merge branch 'develop' of github.com:gspetro-NOAA/ufs-srweather-app i…
gspetro Mar 22, 2022
e294020
Merge branch 'ufs-community:develop' into develop
gspetro-NOAA Mar 23, 2022
92bddca
Add instructions for srw_common module load
gspetro Mar 23, 2022
698613b
Pull changes from upstream
gspetro Mar 23, 2022
6fa5074
fix typo
gspetro Mar 23, 2022
a5ae76e
update Intro & BuildRunSRW based on Mark's feedback
gspetro Mar 23, 2022
ea17b19
minor intro updates
gspetro Mar 23, 2022
1aa9322
1st round of jwolff's edits
gspetro Mar 25, 2022
3d1cddb
2nd round of jwolff updates
gspetro Mar 28, 2022
173b838
update QS intro
gspetro Mar 29, 2022
09581c8
fix minor physics details
gspetro Mar 29, 2022
a714d43
update citation and physics suite name
gspetro Mar 29, 2022
4757b40
add compute node allocation info to QS
gspetro Mar 29, 2022
2c68823
add authoritative hpc-stack docs to Intro
gspetro Mar 29, 2022
a9702bb
Merge branch 'ufs-community:develop' into develop
gspetro-NOAA Mar 30, 2022
5cb4c2c
edit config intro & platform environment sections
gspetro Mar 30, 2022
96123bb
Merge remote-tracking branch 'origin/develop' into textonly/config
gspetro Mar 30, 2022
0f3598f
edit sections on cron & directory parameters, platform & parameters f…
gspetro Mar 30, 2022
4a53366
edit NCO, file-separator, filename params, add some METplus and model…
gspetro Mar 31, 2022
c425bc5
ConfigWorkflow.rst revisions, added METplus to Components, grid info
gspetro Apr 1, 2022
f596267
add grid config details
gspetro Apr 4, 2022
fb0bc01
changes to readme.md
gspetro Apr 6, 2022
8bb70b1
RTD readme.md edits
gspetro Apr 6, 2022
9d9e079
Merge branch 'ufs-community:develop' into develop
gspetro-NOAA Apr 6, 2022
091574a
create MacOS install/build instructions
gspetro Apr 6, 2022
a5fced9
Merge branch 'develop' of github.com:gspetro-NOAA/ufs-srweather-app i…
gspetro Apr 7, 2022
a73c456
update task run and grid parameters
gspetro Apr 8, 2022
ab13f55
fixed file params & workflow task params
gspetro Apr 8, 2022
1335a4d
1st draft of ConfigParameters.inc
gspetro Apr 12, 2022
19a91cc
Merge branch 'ufs-community:develop' into textonly/config
gspetro-NOAA Apr 12, 2022
563fd8b
minor edits
gspetro Apr 12, 2022
e77110d
Merge branch 'develop' into textonly/config
gspetro Apr 12, 2022
9518b2f
Merge branch 'textonly/config' of github.com:gspetro-NOAA/ufs-srweath…
gspetro Apr 12, 2022
07f4d6e
add stochastic physics var details
gspetro Apr 12, 2022
3070272
update FVCOM, thread affinity params
gspetro Apr 13, 2022
63d2a86
halo_blend, ens, crtm, custom post, subhourly updates
gspetro Apr 13, 2022
7dcb3e7
update HPC-Stack submodule/docs
gspetro Apr 13, 2022
cf0dab0
Merge branch 'develop' into textonly/config
gspetro Apr 13, 2022
0763542
remove extra macinstall document
gspetro Apr 13, 2022
2b4d74e
Rocoto WF tasks & params
gspetro Apr 13, 2022
ef234d9
workflow tasks/params, debug, verbose, pre-existing dir, predefined grid
gspetro Apr 14, 2022
7de4653
move Stochastic physics to CCP section; write component edits
gspetro Apr 14, 2022
a552b00
comp'l forecast, grid gen, NOMADS, user-staged files
gspetro Apr 14, 2022
d8d217b
METplus, model config & forecast params, separator
gspetro Apr 15, 2022
43ecc81
2nd draft complete
gspetro Apr 15, 2022
a51165f
physics updates
gspetro Apr 15, 2022
928417a
remove MacInstall empty file
gspetro Apr 15, 2022
a1ad723
undo hpc-stack submodule update (save for separate PR)
gspetro Apr 15, 2022
9241039
undo hpc-stack install doc update (save for separate PR)
gspetro Apr 15, 2022
580f641
revert hpc-stack submodule update
gspetro Apr 15, 2022
b9d8087
revisions to SPP & LSM physics
gspetro Apr 19, 2022
987abbd
minor edits
gspetro Apr 19, 2022
aaacfe7
update comments in LAM Grid chapter
gspetro Apr 20, 2022
2956ffc
update LSM_SPP_EACH_STEP
gspetro Apr 20, 2022
4939629
revert LSM_SPP_EACH_STEP to original definition
gspetro Apr 26, 2022
c28b32c
combine config info into one doc instead of two
gspetro Apr 26, 2022
ab2fb78
Merge branch 'ufs-community:develop' into develop
gspetro-NOAA Apr 26, 2022
427afb0
Merge branch 'ufs-community:develop' into textonly/vx
gspetro-NOAA Apr 26, 2022
639443c
remove ConfigParameters.inc (contents now appear in ConfigWorkflow.rst)
gspetro Apr 26, 2022
b83a363
update hpc-stack docs submodule
gspetro Apr 26, 2022
104b834
odds & ends
gspetro Apr 27, 2022
4a86c25
Merge branch 'ufs-community:develop' into develop
gspetro-NOAA Apr 27, 2022
0b4e2da
add VX tables, config info, & Rocoto output tables
gspetro Apr 27, 2022
7ba1352
add module use/load statements, fix typos
gspetro Apr 27, 2022
fa05f2c
Merge branch 'ufs-community:develop' into textonly/vx
gspetro-NOAA Apr 28, 2022
41d2195
varied minor details
gspetro Apr 28, 2022
676a351
add workflow svg diagram
gspetro Apr 28, 2022
f316df2
Merge branch 'ufs-community:develop' into develop
gspetro-NOAA Apr 28, 2022
41527b7
edits to rocoto ch
gspetro Apr 28, 2022
c351daa
Merge branch 'ufs-community:develop' into develop
gspetro-NOAA Apr 29, 2022
0591d60
updates to Rocoto chapter
gspetro Apr 29, 2022
50018dd
fix minor formatting/wording issues
gspetro Apr 29, 2022
60fdef2
Merge branch 'ufs-community:develop' into develop
gspetro-NOAA May 2, 2022
5e28faf
updates to LAMgrid chapter
gspetro May 2, 2022
24b2e69
Merge branch 'ufs-community:develop' into develop
gspetro-NOAA May 2, 2022
eaec3c4
Merge branch 'ufs-community:develop' into textonly/other
gspetro-NOAA May 3, 2022
43cd2ea
LAM Grid edits
gspetro May 3, 2022
6b66abb
Merge branch 'textonly/other' of github.com:gspetro-NOAA/ufs-srweathe…
gspetro May 3, 2022
d2ca2b8
LAM ch: user-defined grid section
gspetro May 3, 2022
a707fc1
add UPP Product tables ch 6
gspetro May 3, 2022
b48d495
I/O edits & glossary terms
gspetro May 4, 2022
2477527
I/O Pt2
gspetro May 5, 2022
7ca1e52
I/O changes
gspetro May 5, 2022
5d2922a
Merge branch 'ufs-community:develop' into develop
gspetro-NOAA May 5, 2022
271bb1a
include updated images
gspetro May 6, 2022
bcf8de7
update docs to reflect changes in PR #238
gspetro May 6, 2022
a900874
Graphics Ch-1st pass
gspetro May 9, 2022
a708016
minor updates to Graphics
gspetro May 10, 2022
0f1c223
minor updates to Graphics
gspetro May 10, 2022
975bce9
edit ConfigNewPlatform sections 1-4
gspetro May 10, 2022
3ae46d9
ConfigNewPlatform edits
gspetro May 11, 2022
5833d41
update to match head of develop
gspetro May 11, 2022
563cc68
resolve merge conflicts
gspetro May 11, 2022
e866ccd
I/O ch edits
gspetro May 11, 2022
bc93840
I/O edits
gspetro May 12, 2022
525dcb5
more I/O edits
gspetro May 12, 2022
4a4642d
hpc-stack submodule updates
gspetro May 12, 2022
1871716
add HPC-Stack MacOs info
gspetro May 12, 2022
6a49c8d
WE2E edits & tables
gspetro May 13, 2022
2e178a0
Merge branch 'ufs-community:develop' into textonly/other
gspetro-NOAA May 16, 2022
8570d6a
fix typo
gspetro May 16, 2022
8a9df5e
Merge branch 'textonly/other' of github.com:gspetro-NOAA/ufs-srweathe…
gspetro May 16, 2022
fc1d87c
minor grammar/typos
gspetro May 16, 2022
f143c44
merge conflict resolution
gspetro May 17, 2022
4f939ff
merge conflict resolution
gspetro May 17, 2022
aebc0ea
fix grid name
gspetro May 17, 2022
8377f21
remove resolved comments
gspetro May 17, 2022
39e62e4
add compact grids
gspetro May 18, 2022
c09769d
file path updates & info for HPC-Stack
gspetro May 18, 2022
5364e99
add SRW prereqs to Intro
gspetro May 18, 2022
f51bb57
change ConfigNewPlatform to a non-container quickstart
gspetro May 18, 2022
3df0596
clean up non-container quickstart
gspetro May 18, 2022
7f6e4e8
update build options for non-container QS
gspetro May 19, 2022
25851cb
update file paths & WE2E
gspetro May 19, 2022
e99cc1d
minor fixes
gspetro May 20, 2022
2bbd9b8
update I/O & Gaea file paths
gspetro May 20, 2022
b666899
update error in non-container QS
gspetro May 20, 2022
90e355e
add warning for users w/o Rocoto
gspetro May 20, 2022
5250e86
add UPP Satellite Product instructions
gspetro May 20, 2022
a2cb4b7
Xlink for UPP satellite output info
gspetro May 20, 2022
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223 changes: 128 additions & 95 deletions docs/UsersGuide/source/BuildRunSRW.rst

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28 changes: 28 additions & 0 deletions docs/UsersGuide/source/CompleteTests.csv
Original file line number Diff line number Diff line change
@@ -0,0 +1,28 @@
Grid,ICS,LBCS,Suite,Date,Time (UTC),Script Name,Test Type
RRFS_CONUS_3km,FV3GFS,FV3GFS,GFS_v16,2019-07-01,00,config.grid_RRFS_CONUS_3km_ics_FV3GFS_lbcs_FV3GFS_suite_GFS_v16.sh,Complete
RRFS_CONUS_25km,HRRR,RAP,RRFS_v1beta,2020-08-10,00,config.grid_RRFS_CONUScompact_25km_ics_HRRR_lbcs_RAP_suite_HRRR.sh,Complete
RRFS_CONUS_13km,HRRR,RAP,RRFS_v1beta,2020-08-01,00,config.grid_RRFS_CONUScompact_13km_ics_HRRR_lbcs_RAP_suite_RRFS_v1beta.sh,Complete
RRFS_CONUS_3km,HRRR,RAP,RRFS_v1beta,2020-08-01,00,config.grid_RRFS_CONUScompact_3km_ics_HRRR_lbcs_RAP_suite_RRFS_v1beta.sh,Complete
RRFS_CONUS_25km,HRRR,RAP,HRRR,2020-08-10,00,config.grid_RRFS_CONUScompact_25km_ics_HRRR_lbcs_RAP_suite_HRRR.sh,Complete
RRFS_CONUS_13km,HRRR,RAP,HRRR,2020-08-10,00,config.grid_RRFS_CONUScompact_13km_ics_HRRR_lbcs_RAP_suite_HRRR.sh,Complete
RRFS_CONUS_3km,HRRR,RAP,HRRR,2020-08-10,00,config.grid_RRFS_CONUScompact_3km_ics_HRRR_lbcs_RAP_suite_HRRR.sh,Complete
RRFS_CONUS_25km,FV3GFS,FV3GFS,FV3_GFS_2017_gfdlmp,2019-07-01,"00,12",config.community_ensemble_008mems.sh,Complete/wflow
RRFS_CONUS_25km,FV3GFS,FV3GFS,FV3_GFS_2017_gfdlmp,2019-07-01,"00,12",config.community_ensemble_2mems.sh,Complete/wflow
RRFS_CONUS_25km,FV3GFS,FV3GFS,FV3_GFS_2017_gfdlmp,2019-07-02,"00,12",config.community_ensemble_008mems.sh,Complete/wflow
RRFS_CONUS_25km,FV3GFS,FV3GFS,FV3_GFS_2017_gfdlmp,2019-07-02,"00,12",config.community_ensemble_2mems.sh,Complete/wflow
RRFS_CONUS_25km,FV3GFS,FV3GFS,FV3_GFS_v15p2,2019-07-01,00,config.deactivate_tasks.sh,Complete/wflow
RRFS_CONUS_25km,FV3GFS,FV3GFS,FV3_GFS_v15p2,2019-07-01,00,config.inline_post.sh,Complete/wflow
RRFS_CONUS_25km,FV3GFS,FV3GFS,FV3_GFS_v15p2,2019-06-15,00,config.MET_ensemble_verification.sh,Complete/wflow
RRFS_CONUS_25km,FV3GFS,FV3GFS,FV3_GFS_v15p2,2019-06-15,00,config.MET_verification.sh,Complete/wflow
ESGgrid,FV3GFS,FV3GFS,FV3_GFS_2017_gfdlmp_regional,2019-07-01,00,config.new_ESGgrid.sh,Complete/wflow
GFDLgrid,FV3GFS,FV3GFS,FV3_GFS_2017_gfdlmp,2019-07-01,00,config.new_GFDLgrid.sh,Complete/wflow
GFDLgrid,FV3GFS,FV3GFS,FV3_GFS_2017_gfdlmp,2019-07-01,00,config.new_GFDLgrid__GFDLgrid_USE_GFDLgrid_RES_IN_FILENAMES_eq_FALSE.sh,Complete/wflow
GFDLgrid,FV3GFS,FV3GFS,FV3_GFS_2017_gfdlmp,2019-07-01,00,config.new_GFDLgrid__GFDLgrid_USE_GFDLgrid_RES_IN_FILENAMES_eq_TRUE.sh,Complete/wflow
RRFS_CONUS_25km,FV3GFS,FV3GFS,FV3_GFS_v15p2,2019-07-01,00,config.pregen_grid_orog_sfc_climo.sh,Complete/wflow
RRFS_CONUS_25km,GSMGFS,GSMGFS,FV3_GFS_2017_gfdlmp,2019-05-20,00,config.specify_DOT_OR_USCORE.sh,Complete/wflow
RRFS_CONUScompact_25km,HRRR,RAP,FV3_HRRR,2020-08-01,00,config.specify_DT_ATMOS_LAYOUT_XY_BLOCKSIZE.sh,Complete/wflow
RRFS_CONUS_25km,FV3GFS,FV3GFS,FV3_GFS_v15p2,2021-06-03,06,config.specify_EXTRN_MDL_SYSBASEDIR_ICS_LBCS.sh,Complete/wflow
RRFS_CONUS_25km,FV3GFS,FV3GFS,FV3_GFS_v15p2,2019-07-01,00,config.specify_RESTART_INTERVAL.sh,Complete/wflow
RRFS_CONUScompact_25km,HRRR,RAP,FV3_RRFS_v1beta,2020-08-10,00,config.subhourly_post_ensemble_2mems.sh,Complete/wflow
RRFS_CONUScompact_25km,HRRR,RAP,FV3_RRFS_v1beta,2020-08-10,00,config.subhourly_post.sh,Complete/wflow
RRFS_CONUS_25km,FV3GFS,FV3GFS,FV3_GFS_v15p2,2019-07-01,00,config.specify_template_filenames.sh,Complete/wflow
8 changes: 8 additions & 0 deletions docs/UsersGuide/source/CompleteTests.rst
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************************************************************
Complete WE2E Tests
************************************************************

.. csv-table::
:file: CompleteTests.csv
:widths: 20,20,20,20,20,20,20,20
:header-rows: 1
6 changes: 2 additions & 4 deletions docs/UsersGuide/source/Components.rst
Original file line number Diff line number Diff line change
Expand Up @@ -74,14 +74,12 @@ After running ``manage_externals/checkout_externals``, the visualization scripts
Build System and Workflow
=========================

The SRW Application has a portable build system and a user-friendly, modular, and
expandable workflow framework.
The SRW Application has a portable build system and a user-friendly, modular, and expandable workflow framework.

An umbrella CMake-based build system is used for building the components necessary for running the end-to-end SRW Application, including the UFS Weather Model and the pre- and post-processing software. Additional libraries necessary for the application (e.g., :term:`NCEPLIBS-external` and :term:`NCEPLIBS`) are not included in the SRW Application build system but are available pre-built on pre-configured platforms. On other systems, they can be installed via the HPC-Stack (see :numref:`Chapter %s: Installing the HPC-Stack <InstallHPCStack>`). There is a small set of system libraries and utilities that are assumed to be present on the target computer: the CMake build software, a Fortran, C, and C++ compiler, and an :term:`MPI` library.

Once built, the provided experiment generator script can be used to create a Rocoto-based
workflow file that will run each task in the system in the proper sequence (see `Rocoto documentation
<https://github.com/christopherwharrop/rocoto/wiki/Documentation>`_). If Rocoto and/or a batch system is not present on the available platform, the individual components can be run in a stand-alone, command line fashion with provided run scripts. The generated namelist for the atmospheric model can be modified in order to vary settings such as forecast starting and ending dates, forecast length hours, the :term:`CCPP` physics suite, integration time step, history file output frequency, and more. It also allows for configuration of other elements of the workflow; for example, whether to run some or all of the pre-processing, forecast model, and post-processing steps.
workflow file that will run each task in the system in the proper sequence (see :numref:`Chapter %s <RocotoInfo>` or the `Rocoto documentation <https://github.com/christopherwharrop/rocoto/wiki/Documentation>`_) for more information. If Rocoto and/or a batch system is not present on the available platform, the individual components can be run in a stand-alone, command line fashion with provided run scripts. The generated namelist for the atmospheric model can be modified in order to vary settings such as forecast starting and ending dates, forecast length hours, the :term:`CCPP` physics suite, integration time step, history file output frequency, and more. It also allows for configuration of other elements of the workflow; for example, whether to run some or all of the pre-processing, forecast model, and post-processing steps.

This SRW Application release has been tested on a variety of platforms widely used by
researchers, such as the NOAA Research and Development High-Performance Computing Systems
Expand Down
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