From c87f5ae0795a739f128845ab8fcb35b27000cc41 Mon Sep 17 00:00:00 2001 From: chan-hoo Date: Sat, 5 Mar 2022 21:55:16 +0000 Subject: [PATCH 1/3] clean up wcoss_cray and unnecessary modules on wcoss --- docs/UsersGuide/source/Chapter2.rst | 5 ++--- .../tasks/wcoss_cray/get_extrn_ics.local | 11 ----------- .../tasks/wcoss_cray/get_extrn_lbcs.local | 11 ----------- modulefiles/tasks/wcoss_cray/get_obs.local | 9 --------- modulefiles/tasks/wcoss_cray/make_grid.local | 15 --------------- modulefiles/tasks/wcoss_cray/make_ics.local | 17 ----------------- modulefiles/tasks/wcoss_cray/make_lbcs.local | 17 ----------------- modulefiles/tasks/wcoss_cray/make_orog.local | 12 ------------ .../tasks/wcoss_cray/make_sfc_climo.local | 12 ------------ modulefiles/tasks/wcoss_cray/run_fcst.local | 15 --------------- modulefiles/tasks/wcoss_cray/run_post.local | 18 ------------------ modulefiles/tasks/wcoss_cray/run_vx.local | 13 ------------- .../tasks/wcoss_dell_p3/get_extrn_ics.local | 3 --- .../tasks/wcoss_dell_p3/get_extrn_lbcs.local | 3 --- modulefiles/tasks/wcoss_dell_p3/run_post.local | 7 ------- 15 files changed, 2 insertions(+), 166 deletions(-) delete mode 100644 modulefiles/tasks/wcoss_cray/get_extrn_ics.local delete mode 100644 modulefiles/tasks/wcoss_cray/get_extrn_lbcs.local delete mode 100644 modulefiles/tasks/wcoss_cray/get_obs.local delete mode 100644 modulefiles/tasks/wcoss_cray/make_grid.local delete mode 100644 modulefiles/tasks/wcoss_cray/make_ics.local delete mode 100644 modulefiles/tasks/wcoss_cray/make_lbcs.local delete mode 100644 modulefiles/tasks/wcoss_cray/make_orog.local delete mode 100644 modulefiles/tasks/wcoss_cray/make_sfc_climo.local delete mode 100644 modulefiles/tasks/wcoss_cray/run_fcst.local delete mode 100644 modulefiles/tasks/wcoss_cray/run_post.local delete mode 100644 modulefiles/tasks/wcoss_cray/run_vx.local delete mode 100644 modulefiles/tasks/wcoss_dell_p3/run_post.local diff --git a/docs/UsersGuide/source/Chapter2.rst b/docs/UsersGuide/source/Chapter2.rst index cbcd116d4..37e84442d 100644 --- a/docs/UsersGuide/source/Chapter2.rst +++ b/docs/UsersGuide/source/Chapter2.rst @@ -193,7 +193,7 @@ To build the FV3SAR pre-processing utilities on theia: % cd ${BASEDIR}/regional_workflow/regional % ./build_regional theia >& out.build_regional -Other supported build platforms are ``"cheyenne``, ``wcoss_cray``, or ``odin``. +Other supported build platforms are ``"cheyenne``, or ``odin``. When the build completes, there should be 9 executables under ``${BASEDIR}/regional_workflow/exec``: .. code-block:: console @@ -214,7 +214,7 @@ Note the following: * The second argument to the ``compile.sh`` script is ``theia.intel``, not just ``theia``. Other build targets are: - ``cheyenne.gnu, cheyenne.intel, cheyenne.pgi, odin, theia.gnu, theia.intel, theia.pgi`` or ``wcoss_cray``. + ``cheyenne.gnu, cheyenne.intel, cheyenne.pgi, odin, theia.gnu, theia.intel`` or ``theia.pgi``. * This is a production build, not a debug build. We don't do the debug build because it is very slow to run, and you'll time out in the queue. @@ -258,7 +258,6 @@ cleaning step, which will speed up repeating compilation, which is useful for de Currently all the fixed fields necessary to run a uniform global case without a nest are in subdirectories on each supported machine: -* ``/gpfs/hps3/emc/global/noscrub/emc.glopara/git/fv3gfs/fix/fix_fv3`` on the cray * ``/scratch4/NCEPDEV/global/save/glopara/git/fv3gfs/fix/fix_fv3`` on theia * ``/glade/p/ral/jntp/GMTB/FV3GFS_V1_RELEASE/fix/fix_am/`` on Cheyenne diff --git a/modulefiles/tasks/wcoss_cray/get_extrn_ics.local b/modulefiles/tasks/wcoss_cray/get_extrn_ics.local deleted file mode 100644 index d540aea2c..000000000 --- a/modulefiles/tasks/wcoss_cray/get_extrn_ics.local +++ /dev/null @@ -1,11 +0,0 @@ -#%Module##################################################### -## Module file for get_extrn_ics task. -############################################################# - -module purge - -module use /usrx/local/prod/modulefiles -module load hpss/4.1.0.3 - -module use /usrx/local/nceplibs/modulefiles -module load srw-app-python/1.0.0 diff --git a/modulefiles/tasks/wcoss_cray/get_extrn_lbcs.local b/modulefiles/tasks/wcoss_cray/get_extrn_lbcs.local deleted file mode 100644 index d7ec3794e..000000000 --- a/modulefiles/tasks/wcoss_cray/get_extrn_lbcs.local +++ /dev/null @@ -1,11 +0,0 @@ -#%Module##################################################### -## Module file for get_extrn_lbcs task. -############################################################# - -module purge - -module use /usrx/local/prod/modulefiles -module load hpss/4.1.0.3 - -module use /usrx/local/nceplibs/modulefiles -module load srw-app-python/1.0.0 diff --git a/modulefiles/tasks/wcoss_cray/get_obs.local b/modulefiles/tasks/wcoss_cray/get_obs.local deleted file mode 100644 index 43ce12ebb..000000000 --- a/modulefiles/tasks/wcoss_cray/get_obs.local +++ /dev/null @@ -1,9 +0,0 @@ -#%Module##################################################### -## Module file for get_obs_ccpa, get_obs_mrms, get_obs_ndas -############################################################# - -module purge - -module use /usrx/local/prod/modulefiles -module load hpss/4.1.0.3 - diff --git a/modulefiles/tasks/wcoss_cray/make_grid.local b/modulefiles/tasks/wcoss_cray/make_grid.local deleted file mode 100644 index edee5d724..000000000 --- a/modulefiles/tasks/wcoss_cray/make_grid.local +++ /dev/null @@ -1,15 +0,0 @@ -#%Module - -module use /opt/cray/ari/modulefiles -module load alps -module load gni-headers -module load pmi/5.0.11 -module load rca -module load udreg -module load ugni -module load xpmem - -module use /usrx/local/nceplibs/modulefiles -module load srw-app-python/1.0.0 - -module list diff --git a/modulefiles/tasks/wcoss_cray/make_ics.local b/modulefiles/tasks/wcoss_cray/make_ics.local deleted file mode 100644 index 04eb686e1..000000000 --- a/modulefiles/tasks/wcoss_cray/make_ics.local +++ /dev/null @@ -1,17 +0,0 @@ -#%Module - -module use /opt/cray/ari/modulefiles -module load alps -module load gni-headers -module load pmi/5.0.11 -module load rca -module load udreg -module load ugni -module load xpmem - -module use /usrx/local/prod/modulefiles -module load hpss/4.1.0.3 - -module use /usrx/local/nceplibs/modulefiles -module load srw-app-python/1.0.0 - diff --git a/modulefiles/tasks/wcoss_cray/make_lbcs.local b/modulefiles/tasks/wcoss_cray/make_lbcs.local deleted file mode 100644 index 04eb686e1..000000000 --- a/modulefiles/tasks/wcoss_cray/make_lbcs.local +++ /dev/null @@ -1,17 +0,0 @@ -#%Module - -module use /opt/cray/ari/modulefiles -module load alps -module load gni-headers -module load pmi/5.0.11 -module load rca -module load udreg -module load ugni -module load xpmem - -module use /usrx/local/prod/modulefiles -module load hpss/4.1.0.3 - -module use /usrx/local/nceplibs/modulefiles -module load srw-app-python/1.0.0 - diff --git a/modulefiles/tasks/wcoss_cray/make_orog.local b/modulefiles/tasks/wcoss_cray/make_orog.local deleted file mode 100644 index c43175532..000000000 --- a/modulefiles/tasks/wcoss_cray/make_orog.local +++ /dev/null @@ -1,12 +0,0 @@ -#%Module - -module use /opt/cray/ari/modulefiles -module load alps -module load gni-headers -module load pmi/5.0.11 -module load rca -module load udreg -module load ugni -module load xpmem - -module list diff --git a/modulefiles/tasks/wcoss_cray/make_sfc_climo.local b/modulefiles/tasks/wcoss_cray/make_sfc_climo.local deleted file mode 100644 index c43175532..000000000 --- a/modulefiles/tasks/wcoss_cray/make_sfc_climo.local +++ /dev/null @@ -1,12 +0,0 @@ -#%Module - -module use /opt/cray/ari/modulefiles -module load alps -module load gni-headers -module load pmi/5.0.11 -module load rca -module load udreg -module load ugni -module load xpmem - -module list diff --git a/modulefiles/tasks/wcoss_cray/run_fcst.local b/modulefiles/tasks/wcoss_cray/run_fcst.local deleted file mode 100644 index edee5d724..000000000 --- a/modulefiles/tasks/wcoss_cray/run_fcst.local +++ /dev/null @@ -1,15 +0,0 @@ -#%Module - -module use /opt/cray/ari/modulefiles -module load alps -module load gni-headers -module load pmi/5.0.11 -module load rca -module load udreg -module load ugni -module load xpmem - -module use /usrx/local/nceplibs/modulefiles -module load srw-app-python/1.0.0 - -module list diff --git a/modulefiles/tasks/wcoss_cray/run_post.local b/modulefiles/tasks/wcoss_cray/run_post.local deleted file mode 100644 index 4529dd2f3..000000000 --- a/modulefiles/tasks/wcoss_cray/run_post.local +++ /dev/null @@ -1,18 +0,0 @@ -#%Module - -module use /opt/cray/ari/modulefiles -module load alps -module load gni-headers -module load pmi/5.0.11 -module load rca -module load udreg -module load ugni -module load xpmem - -module use /usrx/local/prod/modulefiles -module load hpss/4.1.0.3 - -module use /usrx/local/nceplibs/modulefiles -module load srw-app-python/1.0.0 - - diff --git a/modulefiles/tasks/wcoss_cray/run_vx.local b/modulefiles/tasks/wcoss_cray/run_vx.local deleted file mode 100644 index 6dbf48c0f..000000000 --- a/modulefiles/tasks/wcoss_cray/run_vx.local +++ /dev/null @@ -1,13 +0,0 @@ -#%Module - -module use /opt/cray/ari/modulefiles -module load alps -module load gni-headers -module load pmi/5.0.11 -module load rca -module load udreg -module load ugni -module load xpmem - -module use /gpfs/hps3/emc/meso/noscrub/emc.metplus/modulefiles -module load met/10.0.0 diff --git a/modulefiles/tasks/wcoss_dell_p3/get_extrn_ics.local b/modulefiles/tasks/wcoss_dell_p3/get_extrn_ics.local index 1502c04d5..9900015d1 100644 --- a/modulefiles/tasks/wcoss_dell_p3/get_extrn_ics.local +++ b/modulefiles/tasks/wcoss_dell_p3/get_extrn_ics.local @@ -4,6 +4,3 @@ module purge module load HPSS/5.0.2.5 - -module use /usrx/local/nceplibs/dev/modulefiles -module load srw-app-python/1.0.0 diff --git a/modulefiles/tasks/wcoss_dell_p3/get_extrn_lbcs.local b/modulefiles/tasks/wcoss_dell_p3/get_extrn_lbcs.local index 74e8f878c..4a8b7431f 100644 --- a/modulefiles/tasks/wcoss_dell_p3/get_extrn_lbcs.local +++ b/modulefiles/tasks/wcoss_dell_p3/get_extrn_lbcs.local @@ -4,6 +4,3 @@ module purge module load HPSS/5.0.2.5 - -module use /usrx/local/nceplibs/dev/modulefiles -module load srw-app-python/1.0.0 diff --git a/modulefiles/tasks/wcoss_dell_p3/run_post.local b/modulefiles/tasks/wcoss_dell_p3/run_post.local deleted file mode 100644 index 9e6f62305..000000000 --- a/modulefiles/tasks/wcoss_dell_p3/run_post.local +++ /dev/null @@ -1,7 +0,0 @@ -#%Module - -module load lsf/10.1 - -module use /usrx/local/nceplibs/dev/modulefiles -module load srw-app-python/1.0.0 - From 91c6a043f1bb1470c250eba94e587238195a62d6 Mon Sep 17 00:00:00 2001 From: chan-hoo Date: Sat, 5 Mar 2022 21:55:57 +0000 Subject: [PATCH 2/3] Fix a new line issue on wcoss_dell_p3 --- ush/generate_FV3LAM_wflow.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/ush/generate_FV3LAM_wflow.sh b/ush/generate_FV3LAM_wflow.sh index 39793b686..1766205bf 100755 --- a/ush/generate_FV3LAM_wflow.sh +++ b/ush/generate_FV3LAM_wflow.sh @@ -558,7 +558,7 @@ resubmit SRW workflow: CRONTAB_LINE = \"${CRONTAB_LINE}\"" if [ "$MACHINE" = "WCOSS_DELL_P3" ]; then - printf "%s" "${CRONTAB_LINE}" >> "/u/$USER/cron/mycrontab" + printf "%s\n" "${CRONTAB_LINE}" >> "/u/$USER/cron/mycrontab" else # Add a newline to the end of crontab_contents only if it is not empty. # This is needed so that when CRONTAB_LINE is printed out, it appears on From 32c95d3177bd842f3287eba356365b032114f785 Mon Sep 17 00:00:00 2001 From: chan-hoo Date: Sun, 6 Mar 2022 00:56:39 +0000 Subject: [PATCH 3/3] Remove docs from regional_workflow --- docs/UsersGuide/Makefile | 19 -- docs/UsersGuide/README | 29 -- docs/UsersGuide/build/.gitignore | 4 - docs/UsersGuide/make.bat | 35 --- docs/UsersGuide/requirements.txt | 1 - docs/UsersGuide/source/Acknowledgement.rst | 20 -- docs/UsersGuide/source/Chapter1.rst | 27 -- docs/UsersGuide/source/Chapter2.rst | 263 ------------------- docs/UsersGuide/source/Chapter3.rst | 170 ------------ docs/UsersGuide/source/Chapter4.rst | 261 ------------------ docs/UsersGuide/source/Introduction.rst | 41 --- docs/UsersGuide/source/_static/custom.css | 6 - docs/UsersGuide/source/_templates/.gitignore | 4 - docs/UsersGuide/source/conf.py | 202 -------------- docs/UsersGuide/source/index.rst | 17 -- docs/UsersGuide/source/prolog.inc | 4 - 16 files changed, 1103 deletions(-) delete mode 100644 docs/UsersGuide/Makefile delete mode 100644 docs/UsersGuide/README delete mode 100644 docs/UsersGuide/build/.gitignore delete mode 100644 docs/UsersGuide/make.bat delete mode 100644 docs/UsersGuide/requirements.txt delete mode 100644 docs/UsersGuide/source/Acknowledgement.rst delete mode 100644 docs/UsersGuide/source/Chapter1.rst delete mode 100644 docs/UsersGuide/source/Chapter2.rst delete mode 100644 docs/UsersGuide/source/Chapter3.rst delete mode 100644 docs/UsersGuide/source/Chapter4.rst delete mode 100644 docs/UsersGuide/source/Introduction.rst delete mode 100644 docs/UsersGuide/source/_static/custom.css delete mode 100644 docs/UsersGuide/source/_templates/.gitignore delete mode 100644 docs/UsersGuide/source/conf.py delete mode 100644 docs/UsersGuide/source/index.rst delete mode 100644 docs/UsersGuide/source/prolog.inc diff --git a/docs/UsersGuide/Makefile b/docs/UsersGuide/Makefile deleted file mode 100644 index 69fe55ecf..000000000 --- a/docs/UsersGuide/Makefile +++ /dev/null @@ -1,19 +0,0 @@ -# Minimal makefile for Sphinx documentation -# - -# You can set these variables from the command line. -SPHINXOPTS = -SPHINXBUILD = sphinx-build -SOURCEDIR = source -BUILDDIR = build - -# Put it first so that "make" without argument is like "make help". -help: - @$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) - -.PHONY: help Makefile - -# Catch-all target: route all unknown targets to Sphinx using the new -# "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS). -%: Makefile - @$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) \ No newline at end of file diff --git a/docs/UsersGuide/README b/docs/UsersGuide/README deleted file mode 100644 index 30617076c..000000000 --- a/docs/UsersGuide/README +++ /dev/null @@ -1,29 +0,0 @@ -Steps to build and use the Sphinx documentation tool: - -1) Get Sphinx and sphinxcontrib-bibtex installed on your desktop from - http://www.sphinx-doc.org/en/master/usage/installation.html - https://sphinxcontrib-bibtex.readthedocs.io/en/latest/quickstart.html#installation - -2) Create a Sphinx documentation root directory: - % mkdir docs - % cd docs - -3) Initialize your Sphinx project (set up an initial directory structure) using - % sphinx-quickstart - - See http://www.sphinx-doc.org/en/master/usage/quickstart.html or - https://sphinx-rtd-tutorial.readthedocs.io/en/latest/sphinx-quickstart.html - - for help. You can answer (ENTER) to most of the questions. - -To build html: - -From the directory above source and build, the sphinx project directory: - -make html - -Sphinx uses Latex to export the documentation as a PDF file. To build pdf: - -make latexpdf - -It will generate a PDF file in ./build/latex/.pdf diff --git a/docs/UsersGuide/build/.gitignore b/docs/UsersGuide/build/.gitignore deleted file mode 100644 index 5e7d2734c..000000000 --- a/docs/UsersGuide/build/.gitignore +++ /dev/null @@ -1,4 +0,0 @@ -# Ignore everything in this directory -* -# Except this file -!.gitignore diff --git a/docs/UsersGuide/make.bat b/docs/UsersGuide/make.bat deleted file mode 100644 index 543c6b13b..000000000 --- a/docs/UsersGuide/make.bat +++ /dev/null @@ -1,35 +0,0 @@ -@ECHO OFF - -pushd %~dp0 - -REM Command file for Sphinx documentation - -if "%SPHINXBUILD%" == "" ( - set SPHINXBUILD=sphinx-build -) -set SOURCEDIR=source -set BUILDDIR=build - -if "%1" == "" goto help - -%SPHINXBUILD% >NUL 2>NUL -if errorlevel 9009 ( - echo. - echo.The 'sphinx-build' command was not found. Make sure you have Sphinx - echo.installed, then set the SPHINXBUILD environment variable to point - echo.to the full path of the 'sphinx-build' executable. Alternatively you - echo.may add the Sphinx directory to PATH. - echo. - echo.If you don't have Sphinx installed, grab it from - echo.http://sphinx-doc.org/ - exit /b 1 -) - -%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% -goto end - -:help -%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% - -:end -popd diff --git a/docs/UsersGuide/requirements.txt b/docs/UsersGuide/requirements.txt deleted file mode 100644 index ef36addc6..000000000 --- a/docs/UsersGuide/requirements.txt +++ /dev/null @@ -1 +0,0 @@ -sphinxcontrib-bibtex diff --git a/docs/UsersGuide/source/Acknowledgement.rst b/docs/UsersGuide/source/Acknowledgement.rst deleted file mode 100644 index f8847c31d..000000000 --- a/docs/UsersGuide/source/Acknowledgement.rst +++ /dev/null @@ -1,20 +0,0 @@ -.. _acknowledgement: -.. include:: prolog.inc - ---------------- -Acknowledgement ---------------- - -This user's guide is constructed with contributions from distributed developers. We give our special acknowledgement to these contributors and reviewers, including, but not limited to: - -National Centers for Environmental Prediction (NCEP) Environmental Modeling Center (EMC): |br| -*Jim Abeles, Eric Aligo, Tom Black, Benjamin Blake, Jacob Carley, Dusan Jovic, Jim Purser, Eric Rogers, Ed Strobach, and Fanglin Yang* - -National Center for Atmospheric Research (NCAR) and Developmental Testbed Center (DTC): |br| -*Laurie Carson, Michael Kavulich, Julie Schramm, Don Stark, and Jamie Wolff* - -National Oceanic and Atmospheric Administration (NOAA) Earth System Research Laboratory (ESRL): |br| -*Jeff Beck, Gerard Ketefian, and Linlin Pan* - -The community support and code management effort is sponsored by NOAA's Office of Oceanic and Atmospheric Research (OAR). This work is also facilitated by NCAR. NCAR is supported by the National Science Foundation (NSF). - diff --git a/docs/UsersGuide/source/Chapter1.rst b/docs/UsersGuide/source/Chapter1.rst deleted file mode 100644 index d416db7f6..000000000 --- a/docs/UsersGuide/source/Chapter1.rst +++ /dev/null @@ -1,27 +0,0 @@ -*************************************** -Summary of the FV3SAR model -*************************************** - -======================== -Basics of the FV3 Solver -======================== - -=========================================== -Handling of Boundary and Initial Conditions -=========================================== - -======================= -The Gnomonic Projection -======================= - ------------------------- -Grid Space Heterogeneity ------------------------- - ------------------------------------------------------------- -Optimization of the Gnomonic Projection for Regional Domains ------------------------------------------------------------- - -================================= -Available Preset Regional Domains -================================= diff --git a/docs/UsersGuide/source/Chapter2.rst b/docs/UsersGuide/source/Chapter2.rst deleted file mode 100644 index 37e84442d..000000000 --- a/docs/UsersGuide/source/Chapter2.rst +++ /dev/null @@ -1,263 +0,0 @@ -*************************************** -Software Installation -*************************************** - -=========================================== -System Requirements -=========================================== -The FV3SAR model is supported on the NOAA HPC Theia and NCAR -Supercomputer Cheyenne. Intel is the only currently supported -compiler for building the pre-processing utilities and the FV3SAR model. - -------------------------------------------- -External Libraries -------------------------------------------- -Several external support libraries are required but not included with -the source code. Most of these libraries are installed as part of the -compiler installation. For FV3SAR, these libraries are: - -* Intel compiler -* impi -* ESMFv7.1.0 -* netCDF -* HDF5 -* pnetCDF - -------------------------------------------- -NCEP Libraries -------------------------------------------- -A number of the NCEP (National Center for Environmental Prediction) production -libraries are necessary for building and running the FV3SAR pre-processing utilities -and model (:numref:`Table %s `). These libraries are not part of the source -code distribution. If they are not already installed on your computer platform, you may -have to download some or all the source code from `NCEP `_ -and build the libraries yourself. Note that these libraries must be built with the same compiler -used to build the pre-processing utilities FV3SAR model. Another option is to clone the `git -repository `_ and follow the build instructions. -This currently includes only the libraries used by the FV3SAR model. - -.. _ncep_libs: - -.. table:: *NCEP libraries necessary to build the FV3SAR pre-processing utilities and the model. - X indicates that the library is required.* - - +------------------------+----------------------+-------------+ - | **NCEP Library** | **Pre-Processing** | **FV3SAR** | - +========================+======================+=============+ - | ``bacio/v2.0.1`` | | X | - +------------------------+----------------------+-------------+ - | ``bacio/v2.0.2`` | X | | - +------------------------+----------------------+-------------+ - | ``gfsio/v1.1.0`` | X | | - +------------------------+----------------------+-------------+ - | ``ip/v2.0.0`` | X | X | - +------------------------+----------------------+-------------+ - | ``ip/v3.0.0`` | X | | - +------------------------+----------------------+-------------+ - | ``landsfcutil/v2.1.0`` | X | | - +------------------------+----------------------+-------------+ - | ``nemsio/v2.2.3`` | X | X | - +------------------------+----------------------+-------------+ - | ``nemsiogfs/v2.0.1`` | X | | - +------------------------+----------------------+-------------+ - | ``sfcio/v1.0.0`` | X | | - +------------------------+----------------------+-------------+ - | ``sigio/v2.0.1`` | X | | - +------------------------+----------------------+-------------+ - | ``sp/v2.0.2`` | X | X | - +------------------------+----------------------+-------------+ - | ``w3emc/v2.0.5`` | X | X | - +------------------------+----------------------+-------------+ - | ``w3emc/v2.2.0`` | X | | - +------------------------+----------------------+-------------+ - | ``w3nco/v2.0.6`` | X | X | - +------------------------+----------------------+-------------+ - -.. _ObtainingCode: - -================================ -Obtaining the FV3SAR Source Code -================================ -In order to run FV3SAR, the user must get the FV3SAR workflow scripts -and the NEMSfv3gfs model source code. These steps assume that the -necessary NCEP libraries are built and available as modules on your machine. - -The source code for the FV3SAR workflow, which includes pre-processing utilities, -and the regional model reside in two separate NOAA VLAB repositories. -You will need a NOAA account to check out the code; the ``${USER}`` -variable used below is your NEMS User ID used to log into VLab, -not to be confused with the NEMS (NOAA Environmental Modeling System) -infrastructure. The pre-processing and workflow utilities are located in the -fv3gfs_workflow repository. To clone this repository, create a -directory called ``${BASEDIR}``, clone the repository and check out the -``community`` branch: - -.. code-block:: console - - % mkdir ${BASEDIR} - % cd ${BASEDIR} - % git clone ssh://${USER}@vlab.ncep.noaa.gov:29418/regional_workflow - % cd regional_workflow - % git checkout community - -The model source code is located in the NEMSfv3gfs repository, which includes -three submodules: FMS, FV3, and NEMS. All four of these repositories are hosted -in VLab. You will need to clone the main repository, -checkout the ``regional_fv3_nemsfv3gfs`` branch, and check out the appropriate -branch for each submodule. - -Normally, the appropriate branches to check out are shown in :numref:`Table %s `: - -.. _repo_branches: - -.. table:: *Branches to check out to obtain NEMSfv3gfs source code and three submodules.* - - +-----------------+-----------------------------+ - | **Repository** | **Branch Name** | - +=================+=============================+ - | ``NEMSfv3gfs`` | ``regional_fv3_nemsfv3gfs`` | - +-----------------+-----------------------------+ - | ``FV3`` | ``regional_fv3`` | - +-----------------+-----------------------------+ - | ``FMS`` | ``GFS-FMS`` | - +-----------------+-----------------------------+ - | ``NEMS`` | ``master`` | - +-----------------+-----------------------------+ - -using the following commands: - -.. code-block:: console - - % cd ${BASEDIR} - % git clone --recursive ssh://${USER}@vlab.ncep.noaa.gov:29418/NEMSfv3gfs - % cd NEMSfv3gfs - % git checkout regional_fv3_nemsfv3gfs - % cd FV3 - % git checkout regional_fv3 - % cd ${BASEDIR}/NEMSfv3gfs - % cd FMS - % git checkout GFS-FMS - % cd ${BASEDIR}/NEMSfv3gfs - % cd NEMS - % git checkout master - -However, it turns out that as of 12/13/2018, the code(s) in the “HEAD”s of one or -more of these branches cause(s) one of the post-processing (UPP) tasks in the workflow -for the test run on the RAP domain to hang/fail (the one for forecast hour 6). Thus, -we will for now check out specific commits in these repos that we know will give a -successful run. The hash numbers of these commits are shown in :numref:`Table %s `: - -.. _commit_hashes: - -.. table:: *Specific commits to checkout to achieve a successful run.* - - +-----------------+------------------+ - | **Repository** | **Commit Hash** | - +=================+==================+ - | ``NEMSfv3gfs`` | ``8c97373`` | - +-----------------+------------------+ - | ``FV3`` | ``3ef9be7`` | - +-----------------+------------------+ - | ``FMS`` | ``d4937c8`` | - +-----------------+------------------+ - | ``NEMS`` | ``10325d4`` | - +-----------------+------------------+ - -For convenience, a script named ``checkout_NEMSfv3gfs.sh`` has been created in -the directory ``$BASEDIR/regional_workflow/ush`` to perform these clone and checkout -steps. This script can check out either the heads of the above branches or the -specific commits listed above (the commit hashes are hard-coded into the script). -To have it check out the commits, call this script as follows: - -.. code-block:: console - - % cd ${BASEDIR}/regional_workflow/ush - % ./checkout_NEMSfv3gfs.sh "hash" - -To have the script check out the branch heads, change the first argument from -``hash`` to ``head``, or simply call the script without an argument. - -=========================================== -Building the FV3SAR Source Code -=========================================== -To run the end-to-end FV3SAR forecasting system, the pre-processing utilities, -the FV3SAR model, and the post-porcessing components must be built. This section -describes the steps for the supported compilers on the available platforms. The -directory ``${BASEDIR}`` is assumed to be where the code has been checked -out as described in Section ObtainingCode_. - -To build the FV3SAR pre-processing utilities on theia: - -.. code-block:: console - - % cd ${BASEDIR}/regional_workflow/regional - % ./build_regional theia >& out.build_regional - -Other supported build platforms are ``"cheyenne``, or ``odin``. -When the build completes, there should be 9 executables under ``${BASEDIR}/regional_workflow/exec``: - -.. code-block:: console - - % ls ${BASEDIR}/regional_workflow/exec - filter_topo global_chgres make_solo_mosaic - fregrid make_hgrid ml01rg2.x - fregrid_parallel make_hgrid_parallel shave.x - -To build the FV3 model executable: - -.. code-block:: console - - % cd ${BASEDIR}/NEMSfv3gfs/tests - % ./compile.sh ${BASEDIR}/NEMSfv3gfs/FV3 theia.intel "32BIT=Y" 32bit YES NO >& make.out.32bit - -Note the following: - -* The second argument to the ``compile.sh`` script is ``theia.intel``, not just ``theia``. - Other build targets are: - ``cheyenne.gnu, cheyenne.intel, cheyenne.pgi, odin, theia.gnu, theia.intel`` or ``theia.pgi``. - -* This is a production build, not a debug build. We don't do the debug build because it is very slow - to run, and you'll time out in the queue. - -* The build takes about 12 minutes to complete. If successful, there should be a file named - ``fv3_32bit.exe`` in the directory ``${BASEDIR}/NEMSfv3gfs/tests``. - -There are other command-line options available when running ``compile.sh`` and are shown in -:numref:`Table %s `. - -.. _build_options: - -.. table:: *Command-line options to build FV3SAR.* - - +---------------------+-----------------------+---------------------------------+--------------+ - | **Argument Number** | **Argument Name** | **Example** | **Optional** | - +=====================+=======================+=================================+==============+ - | 1 | path to FV3 directory | ``${PWD}../FV3`` | No | - +---------------------+-----------------------+---------------------------------+--------------+ - | 2 | ``BUILD_TARGET`` | ``theia.intel, cheyenne.intel`` | No | - +---------------------+-----------------------+---------------------------------+--------------+ - | 3 | ``MAKE_OPT`` | ``DEBUG=Y 32BIT=Y REPRO=N`` | Yes | - +---------------------+-----------------------+---------------------------------+--------------+ - | 4 | ``BUILD_NAME`` | ``32bit`` | Yes | - +---------------------+-----------------------+---------------------------------+--------------+ - | 5 | ``clean_before`` | ``YES`` | Yes | - +---------------------+-----------------------+---------------------------------+--------------+ - | 6 | ``clean_after`` | ``YES`` | Yes | - +---------------------+-----------------------+---------------------------------+--------------+ - -To build with debugging flags, add the following quantities to the ``compile.sh`` command: - -.. code-block:: console - - % ./compile.sh ../FV3 ${BUILD_TARGET} "32BIT=Y DEBUG=Y" 32bit [clean_before] [clean_after] >& make.out.32bit - -The last two optional arguments ``clean_before`` and ``clean_after`` control whether or not to run -make clean to remove temporary files. The default values are ``YES``. Specifying ``NO`` will skip -cleaning step, which will speed up repeating compilation, which is useful for debugging. - -Currently all the fixed fields necessary to run a uniform global case without a nest are in subdirectories -on each supported machine: - -* ``/scratch4/NCEPDEV/global/save/glopara/git/fv3gfs/fix/fix_fv3`` on theia -* ``/glade/p/ral/jntp/GMTB/FV3GFS_V1_RELEASE/fix/fix_am/`` on Cheyenne - diff --git a/docs/UsersGuide/source/Chapter3.rst b/docs/UsersGuide/source/Chapter3.rst deleted file mode 100644 index 46f16c792..000000000 --- a/docs/UsersGuide/source/Chapter3.rst +++ /dev/null @@ -1,170 +0,0 @@ -.. _config_regional_workflow: - -*************************************** -Configuring the FV3SAR Workflow -*************************************** - -The following steps describe how to create a user-specific configuration -file in order to run your experiment in a given environment. - -1. Create a user-specific configuration file named ``config.sh`` in the subdirectory - ``ush`` under the ``$BASEDIR/regional_workflow`` directory containing appropriate - variable settings for your environment, experiment, etc. - - A configuration file named ``config_defaults.sh`` containing default values already - exists in the ``ush`` subdirectory (this file is part of the ``regional_workflow`` - repository). The setup script (called ``setup.sh`` and located in ``ush``) that - will be called in the workflow generation step below first sources ``config_defaults.sh`` - and then sources ``config.sh`` if the latter exists. Thus, any settings in ``config.sh`` - will overwrite the ones in ``config_defaults.sh``. - - Instead of creating a ``config.sh`` script with custom settings, a user can directly - modify the variable settings in ``config_defaults.sh``. However, we do not recommend - this approach because if this file is then pushed to the remote ``regional_workflow`` - repository, that repository will contain in its copy of ``config_defaults.sh`` variable - settings that are specific to your environment and/or experiment. If others then pull - from this repository, they will inherit these settings, but these settings will likely - not be appropriate for their environment and/or experiment. To avoid this situation, - we’ve designed the setup script to read in the local configuration file ``config.sh`` - that users can (and should) create locally in the ush directory and which should remain - out of the repository. We use ``config_defaults.sh`` to document the variables, setting - them to dummy/placeholder values that will be overwritten by the settings in ``config.sh``. - - For the experiment(s) we will run, we do not need to include in ``config.sh`` all the - variables defined in ``config_defaults.sh``; we only need to include the most relevant - ones (the rest will keep their settings in ``config_default.sh``). Thus, include in your - ``config.sh`` the following variable settings: - -.. code-block:: console - - # - MACHINE="THEIA" - ACCOUNT="gsd-fv3" - QUEUE_DEFAULT="debug" - QUEUE_HPSS="service" - QUEUE_RUN_FV3SAR="batch" - # - BASEDIR="/path/to/directory/of/regional_workflow/and/NEMSfv3gfs/clones" - TMPDIR="/path/to/temporary/work/directories" - UPPDIR="/path/to/UPP/executable/directory" - CCPP="false" - # - CDATE="2018060400" - # - fcst_len_hrs="6" - BC_update_intvl_hrs="6" - # - run_title="my_test" - # - #predef_domain="RAP" - predef_domain="HRRR" - # - if [ "$predef_domain" = "RAP" ]; then - layout_x="14" # One possibility: 14 for RAP, 20 for HRRR. - layout_y="14" # One possibility: 14 for RAP, 20 for HRRR. - write_tasks_per_group="14" # One possibility: 14 for RAP, 20 for HRRR. - elif [ "$predef_domain" = "HRRR" ]; then - layout_x="20" # One possibility: 14 for RAP, 20 for HRRR. - layout_y="20" # One possibility: 14 for RAP, 20 for HRRR. - write_tasks_per_group="20" # One possibility: 14 for RAP, 20 for HRRR. - fi - # - preexisting_dir_method="delete" - #preexisting_dir_method="rename" - #preexisting_dir_method="quit" - -Note that the variable values in this code snippet still need to be customized for -your environment and/or experiment. This customization is described in the next step. - -.. warning:: - The following table and the queue information in Step 2 are specific to the NOAA HPC machine theia. - -.. _tasks_queues: - -.. table:: *Workflow task names and the queue submission.* - - +-------------------------+-----------------------------+ - | **Task Name** | **Queue** | - +=========================+=============================+ - | ``make_grid_orog`` | ``QUEUE_DEFAULT`` | - +-------------------------+-----------------------------+ - | ``get_GFS_files`` | ``QUEUE_HPSS`` | - +-------------------------+-----------------------------+ - | ``make_surf_IC_BC0`` | ``QUEUE_DEFAULT`` | - +-------------------------+-----------------------------+ - | ``make_BC1_to_BCend`` | ``QUEUE_DEFAULT`` | - +-------------------------+-----------------------------+ - | ``stage`` | ``QUEUE_DEFAULT`` | - +-------------------------+-----------------------------+ - | ``run_FV3SAR`` | ``QUEUE_RUN_FV3SAR`` | - +-------------------------+-----------------------------+ - | ``post_00 ... post_NN`` | ``QUEUE_DEFAULT`` | - +-------------------------+-----------------------------+ - - -2. Customize the variables in your ``config.sh`` as follows (note that you can find - documentation on what each of these variables represent in ``config_defaults.sh``): - - * Since we're running on theia, leave ``MACHINE`` set to ``"THEIA"``. - - * If you have access to the ``gsd-fv3`` account, leave ``ACCOUNT`` set to ``"gsd-fv3"``. - Otherwise, set ``ACCOUNT`` to one of the accounts you're a member of. - - * Leave ``QUEUE_HPSS`` and ``QUEUE_RUN_FV3SAR`` unchanged, but you can change - ``QUEUE_DEFAULT`` if you like. The workflow tasks and the queues they will - get submitted to are shown in :numref:`Table %s `. - - From :numref:`Table %s `, we can see that the task that gets the - GFS analysis and forecast files (``get_GFS_files``) is submitted to the queue - defined by ``QUEUE_HPSS``, the forecast task (``run_FV3SAR``) is submitted to - the queue defined by ``QUEUE_RUN_FV3SAR``, and all remaining tasks are submitted - to the queue defined by ``QUEUE_DEFAULT``. The theia admins require that any jobs - that access the HPSS run in the ``"service"`` queue, so you have to leave ``QUEUE_HPSS`` - set to ``"service"``. Also, leave ``QUEUE_RUN_FV3SAR`` set to ``"batch"`` because if - you change it to ``“debug”``, the forecast will not complete within the 30 min maximum - walltime of the ``"debug"`` queue, causing the job to time out. For debugging tests, - set ``QUEUE_DEFAULT`` to ``"debug"`` to get the remaining tasks (i.e. the ones other - than ``get_GFS_file`` and ``run_FV3SAR``) in the queue faster. For production runs, - set it to ``"batch"``. - - * Edit ``BASEDIR`` to be your top-level directory. - - * Edit ``TMPDIR`` to be your work directory, wherever you want that to be. A subdirectory - will be created under this directory for each experiment for which you generate a - workflow (using ``generate_FV3SAR_wflow.sh``; see below). Since the run directory that - the setup script (``setup.sh`` in ``ush``) will create will be in ``$BASEDIR/run_dirs``, - it is convenient to set ``TMPDIR`` to ``$BASEDIR/work_dirs`` so that the work and run - directories will be at the same directory level. This is not necessary, however; you - can use another location for ``TMPDIR`` that is independent of ``BASEDIR``. - - * Leave ``UPPDIR`` unchanged for now. This is set to where Jeff's version of UPP is located. - We need to decide where in the SAR directory structure to put UPP and document how to build - it to work with the FV3SAR. - - * Leave ``CDATE``, ``fcst_len_hrs``, and ``BC_update_intvl_hrs`` unchanged since we know - the workflow should complete with these settings. We can explore other values of these - variables later. - - * Change ``run_title`` to a descriptive string for your run. This will get appended to - the end of the names of your run and work directories. - - * Leave ``predef_domain`` set to ``"HRRR"``. If that works, you can later try the - ``"RAP"`` setting. This variable sets the regional domain to one of these two - predefined domains. It does this by setting the grid parameters (i.e. ``RES``, - ``lon_ctr_T6``, etc defined in ``config_defaults.sh``) to predefined values. - If you want a domain other than one of these two defaults, then you have to first - set predef_domain to an empty string and then copy the grid parameters from - ``config_defaults.sh`` to ``config.sh`` and set them to the values you want. - But don't do that for now. - - * Leave the ``layout_x``, ``layout_y``, and write_tasks_per_group settings - unchanged for now. You will likely have to change these if you decide to use a custom domain. - - * Set ``preexisting_dir_method`` to the method you want to use to handle pre-existing - versions of run and work directories. The workflow generation script (``generate_FV3SAR_wflow.sh``, - discussed below) will create run and work directories for your experiment. If one or both - of those directories already exist, the setting of ``preexisting_dir_method`` determines what - will be done with them. If this variable is set to ``"delete"``, pre-existing directories will - be deleted and replaced with new ones; if it is set to ``"rename"``, they will get renamed - (by appending ``"_old001"``, ``"_old002"``, etc to their names); and if it is set to ``"quit"``, - the workflow generation script will fail if it finds any pre-existing directories. diff --git a/docs/UsersGuide/source/Chapter4.rst b/docs/UsersGuide/source/Chapter4.rst deleted file mode 100644 index d3ce887c5..000000000 --- a/docs/UsersGuide/source/Chapter4.rst +++ /dev/null @@ -1,261 +0,0 @@ -.. _running_regional_workflow: - -**************************** -Running the FV3SAR Workflow -**************************** -The steps described in this section assume the config.sh file -has been created following the steps outlined in -section :ref:`config_regional_workflow`. In this section, the run and -work directories will be created and a script to run the rocoto -workflow will be generated to run the FV3SAR. - -1. Create the run and work directories and a rocoto workflow XML - for your experiment by running ``generate_FV3SAR_wflow.sh`` in - the ``fv3sar_wflow/ush directory``: - -.. code-block:: console - - % cd $BASEDIR/regional_workflow/ush - % generate_FV3SAR_wflow.sh - -This will create a run directory and a work directory, and it will -put the rocoto workflow XML (called ``FV3SAR_wflow.xml``) in the -run directory. Towards the end of the output that ``generate_FV3SAR_wflow.sh`` -generates, you'll find the locations of the run and work directories -(``RUNDIR=...`` and ``WORKDIR=...``). Note that the workflow always -creates the run directory as a subdirectory under ``$BASEDIR/run_dirs``, -and it creates the work directory as a subdirectory under ``$TMPDIR``. - -The output from ``generate_FV3SAR_wflow.sh`` will contain the commands -you can use to launch the workflow and check on its status (also discussed -in the next step below). It will also contain the line you need to add -to your crontab (using the command ``"crontab -e"``) in order to continuously -resubmit the workflow to the queue. - -2. Regardless of whether or not you added an entry to your crontab for automatic - resubmission, you can go to the run directory and launch the rocoto workflow - as follows (assuming you've already loaded rocoto using ``"module load rocoto"``): - -.. code-block:: console - - % cd $RUNDIR - % rocotorun -w FV3SAR_wflow.xml -d FV3SAR_wflow.db -v 10 - -This will launch the first task in the workflow if it's the first time you're -issuing it. If it's not the first time, it will launch the next task if it -has completed the current one, relaunch the current one if it failed (and -if the number of times you’ve tried to launch the task hasn’t yet exceeded -the maxtries value defined for the task in the workflow XML), or do nothing -if the current one is still running. After issuing this command, you can -check on the status of the workflow using: - -.. code-block:: console - - % rocotostat -w FV3SAR_wflow.xml -d FV3SAR_wflow.db -v 10 - -This will generate a table similar to the following: - -.. code-block:: console - - CYCLE TASK JOBID STATE EXIT STATUS TRIES DURATION - ================================================================================================== - 201806040000 make_grid_orog druby://tfe05:33377 SUBMITTING - 0 0.0 - 201806040000 get_GFS_files - - - - - - 201806040000 make_surf_IC_BC0 - - - - - - 201806040000 make_BC1_to_BCend - - - - - - 201806040000 stage - - - - - - 201806040000 run_FV3SAR - - - - - - 201806040000 post_00 - - - - - - 201806040000 post_01 - - - - - - 201806040000 post_02 - - - - - - 201806040000 post_03 - - - - - - 201806040000 post_04 - - - - - - 201806040000 post_05 - - - - - - 201806040000 post_06 - - - - - - -Note that you first have to issue the ``rocotorun`` command above in order to get -updated results from the ``rocotostat`` command. Since it's inconvenient to have -to keep issuing the ``rocotorun`` command to keep the workflow moving along -(i.e. in order to launch the next task if the current one has completed, etc), -you can modify your crontab as described at the end of the output from -``generate_FV3SAR_wflow.sh`` in order to automatically relaunch the workflow with -some specified frequency (e.g. every 3 minutes). - -If all goes well, the workflow should step through all the tasks and finish. The -workflow will have completed when the ``rocotostat`` command generates a table in -which the ``STATE`` for all tasks is ``SUCCEEDED``, something like this: - -.. code-block:: console - - CYCLE TASK JOBID STATE EXIT STATUS TRIES DURATION - =============================================================================================== - 201806040000 make_grid_orog 36437677 SUCCEEDED 0 1 262.0 - 201806040000 get_GFS_files 36437726 SUCCEEDED 0 1 71.0 - 201806040000 make_surf_IC_BC0 36437730 SUCCEEDED 0 1 293.0 - 201806040000 make_BC1_to_BCend 36437731 SUCCEEDED 0 1 242.0 - 201806040000 stage 36437765 SUCCEEDED 0 1 38.0 - 201806040000 run_FV3SAR 36437802 SUCCEEDED 0 1 1653.0 - 201806040000 post_00 36438577 SUCCEEDED 0 1 309.0 - 201806040000 post_01 36438624 SUCCEEDED 0 1 294.0 - 201806040000 post_02 36438696 SUCCEEDED 0 1 319.0 - 201806040000 post_03 36438705 SUCCEEDED 0 1 288.0 - 201806040000 post_04 36438441 SUCCEEDED 0 2 293.0 - 201806040000 post_05 36438808 SUCCEEDED 0 1 313.0 - 201806040000 post_06 36438809 SUCCEEDED 0 1 304.0 - -If a job fails, you can find the log file for the job under the run directory -in ``$RUNDIR/log``. Each job will have its own log. This directory will also -have the overall log file for the workflow called ``FV3_$CDATE.log``, where -``CDATE`` is the starting date of the forecast that you set in ``config.sh``. - -================================ -Comparing run output to baseline -================================ - -.. warning:: - The this section is specific to the NOAA HPC machine theia. - -Baseline runs have been created for both the RAP and HRRR domains. The run -directories for these are at the following locations: - -RAP: -``/scratch3/BMC/fim/Gerard.Ketefian/FV3SAR_baseline_runs/run_dirs/C384_S0p63_RR3_RAP`` - -HRRR: -``/scratch3/BMC/fim/Gerard.Ketefian/FV3SAR_baseline_runs/run_dirs/C384_S1p65_RR5_HRRR`` - -These baselines have been generated using code from the specific commits of the -``NEMSfv3gfs`` repo and its submodules (``FV3``, ``FMS``, and ``NEMS``) mentioned -above (i.e. the ones for which all tasks in the workflows for both the RAP and -HRRR domains complete successfully). Thus, your runs should match these baselines -(assuming you passed the argument ``"hash"`` to the checkout script ``checkout_NEMSfv3gfs.sh`` -described above). As described next, you can use the script ``cmp_rundirs_ncfiles.sh`` -to compare your runs to the baselines. - -The script ``cmp_rundirs_ncfiles.sh`` in the ``ush`` directory compares the NetCDF -files in two specified run directories and their ``INPUT`` subdirectories. Run it as follows: - -.. code-block:: console - - % cd $BASEDIR/regional_workflow/ush - % ./cmp_rundirs_ncfiles.sh "$rundir1" "$rundir2" - -Here, ``rundir1`` and ``rundir2`` are the two run directories you want to compare. -Thus, for example, to compare your RAP run to the baseline, you would use your run -directory for ``rundir1`` and the baseline RAP directory listed above for ``rundir2`` -(or vice versa). - -Below is sample output from running the ``cmp_rundirs_ncfiles.sh`` script to compare -a RAP run to the baseline. You can see that all NetCDF files in the INPUT subdirectory -and the main run directory are identical to their counterparts in the baseline except -for the file ``C384_mosaic.nc``. This is normal because this file contains variables -that contain the full paths to grid files in the run or work directories, and those -full paths will be different because the two run or work directories are different. - -.. code-block:: console - - % ./cmp_rundirs_ncfiles.sh /scratch3/BMC/fim/Gerard.Ketefian/FV3SAR_test_gsk/run_dirs/C384_S0p63_RR3_RAP_my_test /scratch3/BMC/fim/Gerard.Ketefian/FV3SAR_baseline_runs/run_dirs/C384_S0p63_RR3_RAP - - rundir1 = "/scratch3/BMC/fim/Gerard.Ketefian/FV3SAR_test_gsk/run_dirs/C384_S0p63_RR3_RAP_my_test" - rundir2 = "/scratch3/BMC/fim/Gerard.Ketefian/FV3SAR_baseline_runs/run_dirs/C384_S0p63_RR3_RAP" - - Comparing files in subdirectory "INPUT" ... - =========================================== - - Comparing file "C384_grid.tile7.halo3.nc" in subdirectory "INPUT" ... - Files are identical. - - Comparing file "C384_grid.tile7.halo4.nc" in subdirectory "INPUT" ... - Files are identical. - - File "C384_grid.tile7.nc" in "/scratch3/BMC/fim/Gerard.Ketefian/FV3SAR_test_gsk/run_dirs/C384_S0p63_RR3_RAP_my_test/INPUT" is a symbolic link. Skipping. - - Comparing file "C384_mosaic.nc" in subdirectory "INPUT" ... - DIFFER : VARIABLE : gridlocation : POSITION : [34] : VALUES : F <> r - ===>>> FILES ARE DIFFERENT!!! - - Comparing file "C384_oro_data.tile7.halo0.nc" in subdirectory "INPUT" ... - Files are identical. - - Comparing file "C384_oro_data.tile7.halo4.nc" in subdirectory "INPUT" ... - Files are identical. - - Comparing file "gfs_bndy.tile7.000.nc" in subdirectory "INPUT" ... - Files are identical. - - Comparing file "gfs_bndy.tile7.006.nc" in subdirectory "INPUT" ... - Files are identical. - - Comparing file "gfs_ctrl.nc" in subdirectory "INPUT" ... - Files are identical. - - File "gfs_data.nc" in "/scratch3/BMC/fim/Gerard.Ketefian/FV3SAR_test_gsk/run_dirs/C384_S0p63_RR3_RAP_my_test/INPUT" is a symbolic link. Skipping. - - Comparing file "gfs_data.tile7.nc" in subdirectory "INPUT" ... - Files are identical. - - File "grid_spec.nc" in "/scratch3/BMC/fim/Gerard.Ketefian/FV3SAR_test_gsk/run_dirs/C384_S0p63_RR3_RAP_my_test/INPUT" is a symbolic link. Skipping. - - File "grid.tile7.halo4.nc" in "/scratch3/BMC/fim/Gerard.Ketefian/FV3SAR_test_gsk/run_dirs/C384_S0p63_RR3_RAP_my_test/INPUT" is a symbolic link. Skipping. - - File "oro_data.nc" in "/scratch3/BMC/fim/Gerard.Ketefian/FV3SAR_test_gsk/run_dirs/C384_S0p63_RR3_RAP_my_test/INPUT" is a symbolic link. Skipping. - - File "oro_data.tile7.halo4.nc" in "/scratch3/BMC/fim/Gerard.Ketefian/FV3SAR_test_gsk/run_dirs/C384_S0p63_RR3_RAP_my_test/INPUT" is a symbolic link. Skipping. - - File "sfc_data.nc" in "/scratch3/BMC/fim/Gerard.Ketefian/FV3SAR_test_gsk/run_dirs/C384_S0p63_RR3_RAP_my_test/INPUT" is a symbolic link. Skipping. - - - Comparing file "sfc_data.tile7.nc" in subdirectory "INPUT" ... - Files are identical. - - Comparing files in subdirectory "." ... - ======================================= - - Comparing file "atmos_static.nc" in subdirectory "." ... - Files are identical. - - Comparing file "dynf000.nc" in subdirectory "." ... - Files are identical. - - Comparing file "dynf001.nc" in subdirectory "." ... - Files are identical. - - Comparing file "dynf002.nc" in subdirectory "." ... - Files are identical. - - Comparing file "dynf003.nc" in subdirectory "." ... - Files are identical. - - Comparing file "dynf004.nc" in subdirectory "." ... - Files are identical. - - Comparing file "dynf005.nc" in subdirectory "." ... - Files are identical. - - Comparing file "dynf006.nc" in subdirectory "." ... - Files are identical. - - Comparing file "grid_spec.nc" in subdirectory "." ... - Files are identical. - - Comparing file "phyf000.nc" in subdirectory "." ... - Files are identical. - - Comparing file "phyf001.nc" in subdirectory "." ... - Files are identical. - - Comparing file "phyf002.nc" in subdirectory "." ... - Files are identical. - - Comparing file "phyf003.nc" in subdirectory "." ... - Files are identical. - - Comparing file "phyf004.nc" in subdirectory "." ... - Files are identical. - - Comparing file "phyf005.nc" in subdirectory "." ... - Files are identical. - - Comparing file "phyf006.nc" in subdirectory "." ... - Files are identical. - diff --git a/docs/UsersGuide/source/Introduction.rst b/docs/UsersGuide/source/Introduction.rst deleted file mode 100644 index 3b304d9e9..000000000 --- a/docs/UsersGuide/source/Introduction.rst +++ /dev/null @@ -1,41 +0,0 @@ -.. _introduction: -.. include:: prolog.inc - ------------- -Introduction ------------- - -This document contains the Finite-Volume Cubed-Sphere Standalone Regional (FV3SAR) Model User's Guide. It provides an overview of the FV3SAR, the fundamentals of obtaining, building and running the FV3SAR. There is also a description of the FV3SAR community workflow and its components. - -For the latest version of the released code, please visit the `FV3SAR DTC Website `_ - -Please send questions and comments to the help desk: `xxx-help@ucar.edu` - -This document and the annual releases are made available through a community effort jointly led by the Developmental Testbed Center (DTC) and the National Centers for Environmental Prediction (NCEP) Environmental Modeling Center (EMC), in collaboration with other developers. To help sustain this effort, we recommend for those who use the community release, the helpdesk, the User's Guide, and other DTC services, please refer to this community effort in their work and publications. - - -How To Use This Document ------------------------- - -This table describes the type changes and symbols used in this guide. - -+------------------------+------------------------------+---------------------------------------+ -| **Typeface or Symbol** | **Meaning** | **Example** | -+========================+==============================+=======================================+ -| ``AaBbCc123`` | The names of commands, | Edit your ``.bashrc`` |br| | -| | files, and directories; |br| | Use ``ls -a`` to list all files. |br| | -| | on-screen computer output | ``host$ You have mail!`` | -+------------------------+------------------------------+---------------------------------------+ -| :mod:`AaBbCc123` | What you type contrasted | ``host$`` :mod:`su` | -| | with on-screen computer | | -| | output | | -+------------------------+------------------------------+---------------------------------------+ -| ``%`` | Command-line prompt | ``% cd $TOP_DIR`` | -+------------------------+------------------------------+---------------------------------------+ - -Following these typefaces and conventions, shell commands, code examples, namelist varialbes, etc. -will be presented in this style: - -.. code-block:: console - - % mkdir ${TOP_DIR} diff --git a/docs/UsersGuide/source/_static/custom.css b/docs/UsersGuide/source/_static/custom.css deleted file mode 100644 index 25f207a22..000000000 --- a/docs/UsersGuide/source/_static/custom.css +++ /dev/null @@ -1,6 +0,0 @@ -.red { color: red; } -.bolditalic { - font-family: "Courier New", Courier, monospace; - font-weight: bold; - font-style: italic; -} diff --git a/docs/UsersGuide/source/_templates/.gitignore b/docs/UsersGuide/source/_templates/.gitignore deleted file mode 100644 index 5e7d2734c..000000000 --- a/docs/UsersGuide/source/_templates/.gitignore +++ /dev/null @@ -1,4 +0,0 @@ -# Ignore everything in this directory -* -# Except this file -!.gitignore diff --git a/docs/UsersGuide/source/conf.py b/docs/UsersGuide/source/conf.py deleted file mode 100644 index b95750740..000000000 --- a/docs/UsersGuide/source/conf.py +++ /dev/null @@ -1,202 +0,0 @@ -# -*- coding: utf-8 -*- -# -# Configuration file for the Sphinx documentation builder. -# -# This file does only contain a selection of the most common options. For a -# full list see the documentation: -# http://www.sphinx-doc.org/en/master/config - -# -- Path setup -------------------------------------------------------------- - -# If extensions (or modules to document with autodoc) are in another directory, -# add these directories to sys.path here. If the directory is relative to the -# documentation root, use os.path.abspath to make it absolute, like shown here. -# -import os -import sys -sys.path.insert(0, os.path.abspath('.')) - - -# -- Project information ----------------------------------------------------- - -project = 'FV3SAR' -copyright = '2019, ' -author = ' ' - -# The short X.Y version -version = '' -# The full version, including alpha/beta/rc tags -release = 'v1.0' - -numfig = True - -# -- General configuration --------------------------------------------------- - -# If your documentation needs a minimal Sphinx version, state it here. -# -# needs_sphinx = '1.0' - -# Add any Sphinx extension module names here, as strings. They can be -# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom -# ones. -extensions = [ - 'sphinx.ext.autodoc', - 'sphinx.ext.doctest', - 'sphinx.ext.intersphinx', - 'sphinx.ext.todo', - 'sphinx.ext.coverage', - 'sphinx.ext.mathjax', - 'sphinx.ext.ifconfig', - 'sphinx.ext.viewcode', - 'sphinx.ext.githubpages', - 'sphinx.ext.napoleon', - 'sphinxcontrib.bibtex' -] - -# Add any paths that contain templates here, relative to this directory. -templates_path = ['_templates'] - -# The suffix(es) of source filenames. -# You can specify multiple suffix as a list of string: -# -# source_suffix = ['.rst', '.md'] -source_suffix = '.rst' - -# The master toctree document. -master_doc = 'index' - -# The language for content autogenerated by Sphinx. Refer to documentation -# for a list of supported languages. -# -# This is also used if you do content translation via gettext catalogs. -# Usually you set "language" from the command line for these cases. -language = None - -# List of patterns, relative to source directory, that match files and -# directories to ignore when looking for source files. -# This pattern also affects html_static_path and html_extra_path. -exclude_patterns = [] - -# The name of the Pygments (syntax highlighting) style to use. -pygments_style = None - - -# -- Options for HTML output ------------------------------------------------- - -# The theme to use for HTML and HTML Help pages. See the documentation for -# a list of builtin themes. -# -html_theme = 'classic' - -# Theme options are theme-specific and customize the look and feel of a theme -# further. For a list of options available for each theme, see the -# documentation. -# -# html_theme_options = {} -html_theme_options = {"body_max_width": "none"} - -# Add any paths that contain custom static files (such as style sheets) here, -# relative to this directory. They are copied after the builtin static files, -# so a file named "default.css" will overwrite the builtin "default.css". -html_static_path = ['_static'] - -def setup(app): - app.add_stylesheet('custom.css') # may also be an URL - -# Custom sidebar templates, must be a dictionary that maps document names -# to template names. -# -# The default sidebars (for documents that don't match any pattern) are -# defined by theme itself. Builtin themes are using these templates by -# default: ``['localtoc.html', 'relations.html', 'sourcelink.html', -# 'searchbox.html']``. -# -# html_sidebars = {} - - -# -- Options for HTMLHelp output --------------------------------------------- - -# Output file base name for HTML help builder. -htmlhelp_basename = 'FV3SAR' - - -# -- Options for LaTeX output ------------------------------------------------ - -latex_elements = { - # The paper size ('letterpaper' or 'a4paper'). - 'papersize': 'letterpaper', - - # The font size ('10pt', '11pt' or '12pt'). - 'pointsize': '11pt', - - # Additional stuff for the LaTeX preamble. - 'preamble': r''' - \usepackage{charter} - \usepackage[defaultsans]{lato} - \usepackage{inconsolata} - ''', - # Latex figure (float) alignment - # - # 'figure_align': 'htbp', -} - -# Grouping the document tree into LaTeX files. List of tuples -# (source start file, target name, title, -# author, documentclass [howto, manual, or own class]). -latex_documents = [ - (master_doc, 'FV3SAR.tex', 'FV3SAR Documentation', - ' ', 'manual'), -] - - -# -- Options for manual page output ------------------------------------------ - -# One entry per manual page. List of tuples -# (source start file, name, description, authors, manual section). -man_pages = [ - (master_doc, 'FV3SAR', 'FV3SAR Documentation', - [author], 1) -] - - -# -- Options for Texinfo output ---------------------------------------------- - -# Grouping the document tree into Texinfo files. List of tuples -# (source start file, target name, title, author, -# dir menu entry, description, category) -texinfo_documents = [ - (master_doc, 'FV3SAR', 'FV3SAR Documentation', - author, 'FV3SAR', 'One line description of project.', - 'Miscellaneous'), -] - - -# -- Options for Epub output ------------------------------------------------- - -# Bibliographic Dublin Core info. -epub_title = project - -# The unique identifier of the text. This can be a ISBN number -# or the project homepage. -# -# epub_identifier = '' - -# A unique identification for the text. -# -# epub_uid = '' - -# A list of files that should not be packed into the epub file. -epub_exclude_files = ['search.html'] - - -# -- Extension configuration ------------------------------------------------- - -# -- Options for intersphinx extension --------------------------------------- - -# Example configuration for intersphinx: refer to the Python standard library. -intersphinx_mapping = {'https://docs.python.org/': None} - -# -- Options for todo extension ---------------------------------------------- - -# If true, `todo` and `todoList` produce output, else they produce nothing. -todo_include_todos = True diff --git a/docs/UsersGuide/source/index.rst b/docs/UsersGuide/source/index.rst deleted file mode 100644 index 1a0a50a93..000000000 --- a/docs/UsersGuide/source/index.rst +++ /dev/null @@ -1,17 +0,0 @@ -.. ccpp_docs documentation master file, created by - sphinx-quickstart on Tue Feb 12 08:48:32 2019. - You can adapt this file completely to your liking, but it should at least - contain the root `toctree` directive. - -FV3SAR User's Guide -=================== - -.. toctree:: - :maxdepth: 3 - - Introduction - Chapter1 - Chapter2 - Chapter3 - Chapter4 - Acknowledgement diff --git a/docs/UsersGuide/source/prolog.inc b/docs/UsersGuide/source/prolog.inc deleted file mode 100644 index 516e6eb6a..000000000 --- a/docs/UsersGuide/source/prolog.inc +++ /dev/null @@ -1,4 +0,0 @@ -.. # define a hard line break for HTML -.. |br| raw:: html - -