Merge branch 'NOAA-EMC:develop' into gaea_build

NOAA-EMC · May 1, 2024 · 8168053 · 8168053
2 parents 011c1fc + 13d5b6d
commit 8168053
Show file tree

Hide file tree

Showing 21 changed files with 375 additions and 714 deletions.
diff --git a/.github/workflows/gcc.yml b/.github/workflows/gcc.yml
@@ -9,7 +9,7 @@ defaults:
     shell: bash -leo pipefail {0}
 
 env:
-  cache_key: gcc2  # The number (#) following the cache_key "gcc" is to flush Action cache.
+  cache_key: gcc3  # The number (#) following the cache_key "gcc" is to flush Action cache.
   CC: gcc-10
   FC: gfortran-10
   CXX: g++-10
@@ -60,6 +60,7 @@ jobs:
           sudo apt install cmake
           spack external find
           spack add [email protected]
+          spack add doxygen
           spack concretize
           spack install -v --fail-fast --dirty
           spack clean --all
@@ -91,6 +92,6 @@ jobs:
           export FC=mpif90
           cd UPP
           mkdir -p build && cd build
-          cmake -DCMAKE_INSTALL_PREFIX=../install ..
+          cmake -DENABLE_DOCS=ON -DCMAKE_INSTALL_PREFIX=../install ..
           make -j2 VERBOSE=1
           make install
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -87,9 +87,8 @@ endif()
 if(BUILD_POSTEXEC)
   if(BUILD_WITH_NEMSIO)
     find_package(nemsio REQUIRED)
+    find_package(sigio REQUIRED)
   endif()
-  find_package(sfcio REQUIRED)
-  find_package(sigio REQUIRED)
   find_package(sp REQUIRED)
   find_package(w3emc REQUIRED)
   if(BUILD_WITH_WRFIO)
@@ -119,7 +118,7 @@ add_subdirectory(parm)
 # If desired, build the doxygen docs.
 if(ENABLE_DOCS)
   find_package(Doxygen REQUIRED)
-  add_subdirectory(docs)
+  add_subdirectory(doc)
 endif()
 
 ### Package config

diff --git a/doc/Doxyfile.in b/doc/Doxyfile.in
@@ -846,8 +846,8 @@ WARN_LOGFILE           =
 # spaces. See also FILE_PATTERNS and EXTENSION_MAPPING
 # Note: If this tag is empty the current directory is searched.
 
-INPUT                  = @abs_top_srcdir@/docs/user_guide.md \
-                       = @abs_top_srcdir@/docs/2D-decomp.md \
+INPUT                  = @abs_top_srcdir@/doc/user_guide.md \
+                       = @abs_top_srcdir@/doc/2D-decomp.md \
                          @abs_top_srcdir@/sorc/ncep_post.fd \
                          @config_srcdir@
 
@@ -1007,7 +1007,7 @@ FILTER_SOURCE_PATTERNS =
 # (index.html). This can be useful if you have a project on for instance GitHub
 # and want to reuse the introduction page also for the doxygen output.
 
-USE_MDFILE_AS_MAINPAGE = @abs_top_srcdir@/docs/sp_user_guide.md
+USE_MDFILE_AS_MAINPAGE = @abs_top_srcdir@/doc/user_guide.md
 
 # By default, all characters from position 72 are to be considered as comment.
 # This prevents Doxygen from recognizing certain variables as undocumented

diff --git a/modulefiles/noaacloud.lua b/modulefiles/noaacloud.lua
@@ -0,0 +1,23 @@
+help([[
+Load environment to build UPP on NOAA Cloud
+]])
+
+
+prepend_path("MODULEPATH", "/contrib/spack-stack/spack-stack-1.6.0/envs/unified-env/install/modulefiles/Core")
+
+stack_intel_ver=os.getenv("stack_intel_ver") or "2021.3.0"
+load(pathJoin("stack-intel", stack_intel_ver))
+
+stack_impi_ver=os.getenv("stack_impi_ver") or "2021.3.0"
+load(pathJoin("stack-intel-oneapi-mpi", stack_impi_ver))
+
+cmake_ver=os.getenv("cmake_ver") or "3.23.1"
+load(pathJoin("cmake", cmake_ver))
+
+load("upp_common")
+
+setenv("CC","mpiicc")
+setenv("CXX","mpiicpc")
+setenv("FC","mpiifort")
+
+whatis("Description: UPP build environment")
diff --git a/modulefiles/upp_common.lua b/modulefiles/upp_common.lua
@@ -19,7 +19,6 @@ local ufs_modules = {
   {["w3emc"]           = "2.10.0"},
   {["nemsio"]          = "2.5.4"},
   {["sigio"]           = "2.3.2"},
-  {["sfcio"]           = "1.4.1"},
   {["wrf-io"]          = "1.2.0"},
 }
 

diff --git a/modulefiles/wcoss2.lua b/modulefiles/wcoss2.lua
@@ -40,11 +40,9 @@ load(pathJoin("w3emc", w3emc_ver))
 
 nemsio_ver=os.getenv("nemsio_ver") or "2.5.2"
 sigio_ver=os.getenv("sigio_ver") or "2.3.2"
-sfcio_ver=os.getenv("sfcio_ver") or "1.4.1"
 wrf_io_ver=os.getenv("wrf_io_ver") or "1.2.0"
 load(pathJoin("nemsio", nemsio_ver))
 load(pathJoin("sigio", sigio_ver))
-load(pathJoin("sfcio", sfcio_ver))
 load(pathJoin("wrf_io", wrf_io_ver))
 
 setenv("CC","cc")

diff --git a/parm/README.make_flatfile b/parm/README.make_flatfile
@@ -6,14 +6,14 @@ To make a .txt flat file for UPP, follow these steps within the parm/ directory:
 
 2) Select, then validate, the associated "postcntrl" file, e.g.,
 
-      xmllint --noout --schema EMC_POST_CTRL_Schema.xsd fv3lam_rrfs.xml
+      xmllint --noout --schema EMC_POST_CTRL_Schema.xsd rrfs_postcntrl.xml
 
 3) If file validation succeeds in steps (1) and (2), generate the .txt flat file, e.g.,
 
-      perl PostXMLPreprocessor.pl fv3lam_rrfs.xml post_avblflds.xml postxconfig-NT-fv3lam_rrfs.txt
+      perl PostXMLPreprocessor.pl rrfs_postcntrl.xml post_avblflds.xml postxconfig-NT-rrfs.txt
 
-   In this example, "fv3lam_rrfs.xml" and "fv3lam_post_avblflds.xml" are input files, read by the perl 
-   script. The "postxconfig-NT-fv3lam_rrfs.txt" flat file is the output file produced by the script, which 
+   In this example, "rrfs_postcntrl.xml" and "post_avblflds.xml" are input files, read by the perl 
+   script. The "postxconfig-NT-rrfs.txt" flat file is the output file produced by the script, which 
    can have any name.
 
    Note that a log file will be created by this script, in addition to the flat file.

diff --git a/parm/makefile b/parm/makefile
@@ -35,7 +35,7 @@ ALL_TXT= \
   postxconfig-NT-GFS-F00-TWO.txt \
   postxconfig-NT-hrrr.txt \
   postxconfig-NT-rap.txt \
-  postxconfig-NT-fv3lam_rrfs.txt \
+  postxconfig-NT-rrfs.txt \
   postxconfig-NT-UFS-aerosol.txt \
   postxconfig-NT-UFS-aerosol-F00.txt \
   postxconfig-NT-GEFS-aerosol.txt \
@@ -65,7 +65,7 @@ postxconfig-NT-GFS-TWO.txt:          postcntrl_gfs_two.xml          post_avblfld
 postxconfig-NT-GFS-F00-TWO.txt:      postcntrl_gfs_f00_two.xml      post_avblflds.xml
 postxconfig-NT-hrrr.txt:             hrrr_postcntrl.xml             post_avblflds_raphrrr.xml
 postxconfig-NT-rap.txt:              rap_postcntrl.xml              post_avblflds_raphrrr.xml
-postxconfig-NT-fv3lam_rrfs.txt:      fv3lam_rrfs.xml                post_avblflds.xml
+postxconfig-NT-rrfs.txt:             rrfs_postcntrl.xml             post_avblflds.xml
 postxconfig-NT-UFS-aerosol.txt:      postcntrl_ufs_aerosol.xml      post_avblflds.xml
 postxconfig-NT-UFS-aerosol-F00.txt:  postcntrl_ufs_aerosol_f00.xml  post_avblflds.xml
 postxconfig-NT-GEFS-aerosol.txt:     postcntrl_gefs_aerosol.xml     post_avblflds.xml

diff --git a/parm/post_avblflds.xml b/parm/post_avblflds.xml
@@ -6857,7 +6857,10 @@
        <pdstmpl>tmpl4_48</pdstmpl>
        <pname>AEMFLX</pname>
        <aerosol_type>particulate_org_matter_dry</aerosol_type>
-       <fixed_sfc1_type>surface</fixed_sfc1_type>
+       <fixed_sfc1_type>entire_atmos_single_lyr</fixed_sfc1_type>
+       <typ_intvl_size>smaller_than_first_limit</typ_intvl_size>
+       <scale_fact_1st_size>7</scale_fact_1st_size>
+       <scale_val_1st_size>25</scale_val_1st_size>
        <scale>5.0</scale>
     </param>
 
@@ -6945,8 +6948,10 @@
     <param>
        <post_avblfldidx>755</post_avblfldidx>
        <shortname>HWP_ON_SURFACE</shortname>
+       <pdstmpl>tmpl4_8</pdstmpl>
        <longname>Hourly Wildfire Potential on surface</longname>
        <pname>WFIREPOT</pname>
+       <stats_proc>AVE</stats_proc>
        <fixed_sfc1_type>surface</fixed_sfc1_type>
        <scale>5.0</scale>
     </param>
@@ -8335,5 +8340,45 @@
        <scale>6.0</scale>
     </param>
 
+    <param>
+       <post_avblfldidx>1015</post_avblfldidx>
+       <shortname>EBB_ON_HYBRID_LVL</shortname>
+       <pdstmpl>tmpl4_48</pdstmpl>
+       <pname>AEMFLX</pname>
+       <aerosol_type>particulate_org_matter_dry</aerosol_type>
+       <fixed_sfc1_type>hybrid_lvl</fixed_sfc1_type>
+       <typ_intvl_size>smaller_than_first_limit</typ_intvl_size>
+       <scale_fact_1st_size>7</scale_fact_1st_size>
+       <scale_val_1st_size>25</scale_val_1st_size>
+       <scale>6.0</scale>
+    </param>
+
+    <param>
+       <post_avblfldidx>1016</post_avblfldidx>
+       <shortname>EBB_ON_ISOBARIC_SFC</shortname>
+       <pdstmpl>tmpl4_48</pdstmpl>
+       <pname>AEMFLX</pname>
+       <aerosol_type>particulate_org_matter_dry</aerosol_type>
+       <fixed_sfc1_type>isobaric_sfc</fixed_sfc1_type>
+       <typ_intvl_size>smaller_than_first_limit</typ_intvl_size>
+       <scale_fact_1st_size>7</scale_fact_1st_size>
+       <scale_val_1st_size>25</scale_val_1st_size>
+       <scale>6.0</scale>
+    </param>
+
+    <param>
+       <post_avblfldidx>1017</post_avblfldidx>
+       <shortname>EBB_ON_SPEC_HGT_LVL_ABOVE_GRND_8m</shortname>
+       <pdstmpl>tmpl4_48</pdstmpl>
+       <pname>AEMFLX</pname>
+       <aerosol_type>particulate_org_matter_dry</aerosol_type>
+       <fixed_sfc1_type>spec_hgt_lvl_above_grnd</fixed_sfc1_type>
+       <level>8.</level>
+       <typ_intvl_size>smaller_than_first_limit</typ_intvl_size>
+       <scale_fact_1st_size>7</scale_fact_1st_size>
+       <scale_val_1st_size>25</scale_val_1st_size>
+       <scale>6.0</scale>
+    </param>
+
   </post_avblflds>
 </postxml>