Merge branch 'develop' into feature/new_ip

Fixes ufs-community#242

.github/workflows/debug-docs-test_coverage.yml

@@ -102,9 +102,11 @@ jobs:
 
     - name: test
       run: |
-        cd ufs_utils/build/tests/chgres_cube/data
-        wget -i files.txt
-        cd ../../..
+        cd ufs_utils/build/tests
+        wget -i ./chgres_cube/data/files.txt -P ./chgres_cube/data
+        wget -i ./sfc_climo_gen/data/files.txt -P ./sfc_climo_gen/data
+        cd ../
+        export LSAN_OPTIONS=suppressions=LSanSuppress.supp
         ctest --rerun-failed --output-on-failure
         export PATH="/home/runner/.local/bin:$PATH"
         gcovr -r .. --html-details -o test-coverage.html

.github/workflows/intel.yml

@@ -163,9 +163,8 @@ jobs:
     
     - name: test
       run: |
-        cd ufs_utils/build/tests/chgres_cube/data
-        wget -i files.txt
-        cd ../../..
+        cd ufs_utils/build/tests
+        wget -i ./chgres_cube/data/files.txt -P ./chgres_cube/data
+        wget -i ./sfc_climo_gen/data/files.txt -P ./sfc_climo_gen/data
+        cd ../
         ctest --rerun-failed --output-on-failure
-
-

.github/workflows/linux-mac-nceplibs-mpi.yml

@@ -217,9 +217,10 @@ jobs:
 
     - name: test
       run: |
-        cd ufs_utils/build/tests/chgres_cube/data
-        wget -i files.txt
-        cd ../../..
+        cd ufs_utils/build/tests
+        wget -i ./chgres_cube/data/files.txt -P ./chgres_cube/data
+        wget -i ./sfc_climo_gen/data/files.txt -P ./sfc_climo_gen/data
+        cd ../
         # Oversubscribe for OpenMPI to run more processes than CPUs
         export OMPI_MCA_rmaps_base_oversubscribe=1
         ctest --rerun-failed --output-on-failure

.github/workflows/netcdf-versions.yml

@@ -78,7 +78,7 @@ jobs:
         key: esmf-8.0.1-${{ runner.os }}-netcdf-${{ matrix.netcdf_version }}
 
     - name: build-esmf
-      if: steps.cache-esmf.outputs.cache-hit != 'true'
+      #if: steps.cache-esmf.outputs.cache-hit != 'true'
       run: |
         pushd ~
         export ESMF_DIR=~/esmf-ESMF_8_0_1
@@ -151,7 +151,9 @@ jobs:
 
     - name: test
       run: |
-        cd ufs_utils/build/tests/chgres_cube/data
-        wget -i files.txt
-        cd ../../..
+        cd ufs_utils/build/tests
+        wget -i ./chgres_cube/data/files.txt -P ./chgres_cube/data
+        wget -i ./sfc_climo_gen/data/files.txt -P ./sfc_climo_gen/data
+        cd ../
+        export LSAN_OPTIONS=suppressions=LSanSuppress.supp
         ctest --rerun-failed --output-on-failure

.gitignore

@@ -1,6 +1,7 @@
 build/
 install/
 exec/
+lib/
 
 *.[ao]
 *.mod
@@ -10,6 +11,3 @@ exec/
 
 *.swp
 *.o
-emcsfc_ice_blend
-ml01rg2.x
-

CMakeLists.txt

@@ -35,7 +35,7 @@ if(CMAKE_Fortran_COMPILER_ID MATCHES "^(Intel)$")
 elseif(CMAKE_Fortran_COMPILER_ID MATCHES "^(GNU)$")
   set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -g -fbacktrace")
   set(CMAKE_Fortran_FLAGS_RELEASE "-O3")
-  set(CMAKE_Fortran_FLAGS_DEBUG "-O0 -ggdb -fno-unsafe-math-optimizations -frounding-math -fsignaling-nans -ffpe-trap=invalid,zero,overflow -fbounds-check -fsanitize=address -fno-omit-frame-pointer")
+  set(CMAKE_Fortran_FLAGS_DEBUG "-O1 -ggdb -fno-unsafe-math-optimizations -frounding-math -fsignaling-nans -ffpe-trap=invalid,zero,overflow -fbounds-check -fsanitize=address -fno-omit-frame-pointer -fno-optimize-sibling-calls")
 endif()
 
 if(CMAKE_C_COMPILER_ID MATCHES "^(Intel)$")
@@ -62,6 +62,7 @@ find_package(sp 2.3.3 REQUIRED)
 find_package(ip 3.3.3 REQUIRED)
 find_package(g2 3.4.0 REQUIRED)
 find_package(wgrib2 2.0.8 REQUIRED)
+find_package(sigio 2.3.0 REQUIRED)
 
 # EMC requires executables in ./exec
 set(exec_dir bin)

README.md

@@ -4,7 +4,7 @@
 Utilities for the NCEP models. This is part of the
 [NCEPLIBS](https://github.com/NOAA-EMC/NCEPLIBS) project.
 
-Documentation for the chgres_cube utility can be found at
+Documentation for chgres_cube and other utilities can be found at
 https://noaa-emcufs-utils.readthedocs.io/en/latest/.
 
 Complete documentation can be found at
@@ -17,18 +17,20 @@ Utility | Programmer(s)
 chgres_cube | George Gayno, Jeff Beck, Larissa Reames
 emcsfc_ice_blend | George Gayno
 emcsfc_snow2mdl | George Gayno
+fre-nctools | GFDL progammer
 fvcom_tools | David Wright, University of Michigan, Ming Hu, GSD/AMB
 global_cycle | George Gayno, Shrinivas Moorthi, Mark Iredell, Xu Li, Hang Lei
 grid_tools | R. J. Purser (regional_esg_grid), Tom Black/Ben Blake (shave.fd), Gerard Ketefian (global_equiv_resol), Tsukasa Fujita, JMA (pmat2), GFDL programmer (topo filtering code).
 orog_mask_tools | Ning Wang, Jordan Alpert, Shan Sun and Ning Wang
 sfc_climo_gen | George Gayno
+gblevents | Hang Lei
 vcoord_gen | Fanglin Yang, Mark Iredell
 
-UFS_UTILS Code managers: George Gayno, Kyle Gerheiser
+UFS_UTILS Code managers: George Gayno, Kyle Gerheiser, Jeff Beck, Larissa Reames
 
 ## Prerequisites
 
-This package requires the following NCEPLIBS packages:
+This package uses the [hpc-stack](https://github.com/NOAA-EMC/hpc-stack) for the following NCEPLIBS packages:
  - [NCEPLIBS-sfcio](https://github.com/NOAA-EMC/NCEPLIBS-sfcio)
  - [NCEPLIBS-w3nco](https://github.com/NOAA-EMC/NCEPLIBS-w3nco)
  - [NCEPLIBS-bacio](https://github.com/NOAA-EMC/NCEPLIBS-bacio)
@@ -39,13 +41,15 @@ This package requires the following NCEPLIBS packages:
  - [NCEPLIBS-g2](https://github.com/NOAA-EMC/NCEPLIBS-g2)
  - [NCEPLIBS-wgrib2](https://github.com/NOAA-EMC/NCEPLIBS-wgrib2)
 
-This package also requires:
+And for the following third party libraries:
 
  - [netcdf-c Library](https://github.com/Unidata/netcdf-c)
  - [netcdf-fortran Library](https://github.com/Unidata/netcdf-fortran)
  - [ESMF](https://github.com/esmf-org/esmf)
  - [Jasper](https://github.com/jasper-software/jasper)
-
+ - [Zlib](www.zlib.net)
+ - [HDF5](https://www.hdfgroup.org/solutions/hdf5/)
+ - [PNG](http://www.libpng.org/pub/png/)
 
 ## Installing
 
@@ -101,6 +105,9 @@ documentation build, as well as some markdown files which are part of
 the documentation. It also contains (in the source subdirectory) the
 ReadTheDocs documentation files.
 
+The cmake directory contains CMake package find utilities, and utilities to
+run units tests on some supported HPC platforms.
+
 ## References
 
 Gayno G., Beck J., Carson L., [Pre-Processing:

VERSION

@@ -1 +1 @@
-1.3.0
+1.5.0

build_all.sh

@@ -10,7 +10,6 @@ set -eux
 
 target=${target:-"NULL"}
 compiler=${compiler:-"intel"}
-
 export MOD_PATH
 
 if [[ "$target" == "linux.*" || "$target" == "macosx.*" ]]; then
@@ -28,6 +27,7 @@ else
 fi
 
 CMAKE_FLAGS="-DCMAKE_INSTALL_PREFIX=../ -DEMC_EXEC_DIR=ON"
+#CMAKE_FLAGS="-DCMAKE_INSTALL_PREFIX=../ -DEMC_EXEC_DIR=ON -DENABLE_DOCS=ON"
 
 rm -fr ./build
 mkdir ./build && cd ./build

cmake/gblevents-package-config.cmake

@@ -0,0 +1,16 @@
+@PACKAGE_INIT@
+
+# Include targets file.  This will create IMPORTED target @PROJECT_NAME@
+include("${CMAKE_CURRENT_LIST_DIR}/gblevents-targets.cmake")
+include(CMakeFindDependencyMacro)
+
+find_dependency(nemsio CONFIG)
+find_dependency(sigio CONFIG)
+find_dependency(NetCDF COMPONENTS Fortran)
+
+get_target_property(gblevents_BUILD_TYPES gblevents::gblevents IMPORTED_CONFIGURATIONS)
+
+check_required_components("gblevents")
+
+get_target_property(location gblevents::gblevents LOCATION)
+message(STATUS "Found gblevents: ${location} (found version \"@PROJECT_VERSION@\")")

cmake/mpiexec.hera

@@ -6,7 +6,7 @@
 #   $2+ - Executable and its arguments
 #
 
-ACCOUNT=
+ACCOUNT=gsd-fv3
 QOS=debug
 
 NP=$1