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

* updated docs

* added git submodule

* fix formatting

* added new submodule commits

* fixed ref links

* finished Intro

* finish Components & Intro edits

* edited Rocoto workflow section of Quickstart

* added minor hpc submodule commits

* Updates to Rocoto Workflow in Quick Start

* add to HPC-stack intro

* submodule updates

* added submodule docs edits

* hpc-stack updates & formatting fixes

* hpc-stack intro edits

* bibtex attempted fix

* add hpc-stack module edits

* update sphinxcontrib version

* add .readthedocs.yaml file

* update .readthedocs.yaml file

* update .readthedocs.yaml file

* update conf.py

* updates .readthedocs.yaml with submodules

* updates .readthedocs.yaml with submodules

* submodule updates

* submodule updates

* minor Intro edits

* minor Intro edits

* minor Intro edits

* submodule updates

* fixed typos in QS

* QS updates

* QS updates

* QS updates

* updates to InputOutput and QS

* fix I/O doc typos

* pull updates to hpc-stack docs

* pull updates to hpc-stack docs

* fix table wrapping

* updates to QS for cloud

* fix QS export statements

* fix QS export statements

* QS edits on bind, config

* add bullet points to notes

* running without rocoto

* add HPC-Stack submodule w/docs

* split QS into container/non-container approaches

* added filepath changes for running in container on Orion, et al.

* edits to overview and container QS

* moved CodeReposAndDirs.rst info to the Introduction & deleted file

* continued edits to SRWAppOverview

* combine overview w/non-container docs

* finish merging non-container guide & SRWOverview, rename/remove files, update FAQ

* minor edits for Intro & QS

* updates to BuildRun doc through 3.8.1

* edits to Build/Run and Components

* remove .gitignore

* fix Ch 3 title, 4 supported platform levels note

* fix typos, add term links

* other minor fixes/suggestions implemented

* updated Intro based on feedback; changed SRW to SRW App throughout

* update comment to Intro citation

* add user-defined vertical levels to future work

* Add instructions for srw_common module load

* fix typo

* update Intro & BuildRunSRW based on Mark's feedback

* minor intro updates

* 1st round of jwolff's edits

* 2nd round of jwolff updates

* update QS intro

* fix minor physics details

* update citation and physics suite name

* add compute node allocation info to QS

* add authoritative hpc-stack docs to Intro

* edit config intro & platform environment sections

* edit sections on cron & directory parameters, platform & parameters for running without a workflow manager

* edit NCO, file-separator, filename params, add some METplus and model config params

* ConfigWorkflow.rst revisions, added METplus to Components, grid info

* add grid config details

* changes to readme.md

* RTD readme.md edits

* create MacOS install/build instructions

* update task run and grid parameters

* fixed file params & workflow task params

* 1st draft of ConfigParameters.inc

* minor edits

* add stochastic physics var details

* update FVCOM, thread affinity params

* halo_blend, ens, crtm, custom post, subhourly updates

* update HPC-Stack submodule/docs

* remove extra macinstall document

* Rocoto WF tasks & params

* workflow tasks/params, debug, verbose, pre-existing dir, predefined grid

* move Stochastic physics to CCP section; write component edits

* comp'l forecast, grid gen, NOMADS, user-staged files

* METplus, model config & forecast params, separator

* 2nd draft complete

* physics updates

* remove MacInstall empty file

* undo hpc-stack submodule update (save for separate PR)

* undo hpc-stack install doc update (save for separate PR)

* revert hpc-stack submodule update

* revisions to SPP & LSM physics

* minor edits

* update comments in LAM Grid chapter

* update LSM_SPP_EACH_STEP

* revert LSM_SPP_EACH_STEP to original definition

* combine config info into one doc instead of two

* remove ConfigParameters.inc (contents now appear in ConfigWorkflow.rst)

* update hpc-stack docs submodule

* odds & ends

* add VX tables, config info, & Rocoto output tables

* add module use/load statements, fix typos

* varied minor details

* add workflow svg diagram

* edits to rocoto ch

* updates to Rocoto chapter

* fix minor formatting/wording issues

* updates to LAMgrid chapter

* LAM Grid edits

* LAM ch: user-defined grid section

* add UPP Product tables ch 6

* I/O edits & glossary terms

* I/O Pt2

* I/O changes

* include updated images

* update docs to reflect changes in PR #238

* Graphics Ch-1st pass

* minor updates to Graphics

* minor updates to Graphics

* edit ConfigNewPlatform sections 1-4

* ConfigNewPlatform edits

* resolve merge conflicts

* I/O ch edits

* I/O edits

* more I/O edits

* hpc-stack submodule updates

* add HPC-Stack MacOs info

* WE2E edits & tables

* fix typo

* minor grammar/typos

* merge conflict resolution

* merge conflict resolution

* fix grid name

* remove resolved comments

* add compact grids

* file path updates & info for HPC-Stack

* add SRW prereqs to Intro

* change ConfigNewPlatform to a non-container quickstart

* clean up non-container quickstart

* update build options for non-container QS

* update file paths & WE2E

* minor fixes

* update I/O & Gaea file paths

* update error in non-container QS

* add warning for users w/o Rocoto

* add UPP Satellite Product instructions

* Xlink for UPP satellite output info

Co-authored-by: gspetro <gillian.s.petro@gmail.com>

docs/UsersGuide/source/CompleteTests.csv

@@ -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

docs/UsersGuide/source/CompleteTests.rst

@@ -0,0 +1,8 @@
+************************************************************
+Complete WE2E Tests
+************************************************************
+
+.. csv-table::
+   :file: CompleteTests.csv
+   :widths: 20,20,20,20,20,20,20,20
+   :header-rows: 1

docs/UsersGuide/source/Components.rst

@@ -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