Merge pull request NOAA-GFDL#86 from NOAA-GFDL/master

Sync with NOAA-GFDL main branch

.github/workflows/build_ubuntu_gnu.yml

@@ -0,0 +1,32 @@
+name: Build libFMS test
+
+on: [push, pull_request]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        distcheck-conf-flags: [--enable-openmp, --disable-openmp, --enable-mixed-mode, --disable-setting-flags]
+        fcflags: ["-I/usr/include", "-fdefault-real-8 -fdefault-double-8 -fcray-pointer -ffree-line-length-none -I/usr/include"]
+        exclude:
+          - distcheck-conf-flags: --disable-setting-flags
+            fcflags: -I/usr/include
+          - distcheck-conf-flags: --enable-mixed-mode
+            fcflags: "-fdefault-real-8 -fdefault-double-8 -fcray-pointer -ffree-line-length-none -I/usr/include"
+    container:
+      image: underwoo/ubuntu_libfms_gnu
+      env:
+        FCFLAGS: "${{ matrix.fcflags }}"
+
+    steps:
+    - name: Checkout code
+      uses: actions/checkout@v2
+    - name: Prepare GNU autoconf for build
+      run: autoreconf -if
+    - name: Configure the build
+      run: ./configure ${{ matrix.distcheck-conf-flags }}
+      env:
+        DISTCHECK_CONFIGURE_FLAGS: "${{ matrix.distcheck-conf-flags }}"
+    - name: Build the library
+      run: make -j distcheck

.github/workflows/lint_fms.yml

@@ -0,0 +1,12 @@
+name: libFMS lint tests
+
+on: [push, pull_request]
+
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v2
+      - name: Run Lint
+        uses: NOAA-GFDL/simple_lint@v1

CHANGELOG.md

@@ -15,11 +15,11 @@ sequential patch number (starting from `01`).
 - AMIP_INTERP: A namelist flag called `use_mpp_io` if set to .true. will use mpp_io. The default is .false. and will use fms2_io.
 - TOPOGRAPHY: A namelist flag called `use_mpp_io` if set to .true. will use mpp_io. The default is .false. and will use fms2_io.
 - DATA_OVERRIDE: A namelist flag called `use_mpp_bug` if set to .true. will use mpp_io. The default is .false. and will use fms2_io.
-- DATA_OVERRIDE: A namelist flag called `reproduce_null_char_bug_flag` if set to .true. and fms2_io is being used, it will reproduce the mpp_io bug where the axis bounds were calculated instead of read. The default is .false. 
+- DATA_OVERRIDE: A namelist flag called `reproduce_null_char_bug_flag` if set to .true. and fms2_io is being used, it will reproduce the mpp_io bug where the axis bounds were calculated instead of read. The default is .false.
 A unit test was added to test the functionality of `get_grid_version_1`
 - FMS2_IO: A unit test was added to test the functionality of `get_valid` and `is_valid`
 ### Changed
-- The autotools build has been changed to copy each subdirectory module (.mod) files to a common .mod directory located at the top of the source directory.  This change simplifies the include path specifications. 
+- The autotools build has been changed to copy each subdirectory module (.mod) files to a common .mod directory located at the top of the source directory.  This change simplifies the include path specifications.
 - Use F90 module files for external libraries (MPI and NetCDF) for improved interface checking, thereby removing the reliance on library header include files.
 ### Removed
 - LIBFMS: The flag -Duse_mpp_io should not be used and will cause a crash
@@ -38,15 +38,15 @@ The fms2_io unit tests were modified so they can work with the AOCC compiler
 - 2020.04-alpha2 (ad9915d83a2f34610cd748fd85889ba1f0f1fc02)
 - 2020.04-alpha3 (e7e48839ab25cc9405abe5d8418e1b6ee6fb2d69)
 - 2020.04-beta1 (6d3ac620423e7ede412e4bb1b36c338775d95193)
- 
+
 ## [2020.03] - 2020-10-08
 ### Added
 - FMS2_IO: Adds header_buffer_val to the fms2io namelist which sets the netcdf header size in bytes. The default value is 16kb
 - FMS2_IO: Adds netcdf_default_format to the fms2io namelist which allows the user to change the netcdf file type. The default value is 64bit.
 - FMS2_IO: Adds support to read netcdf string global attributes
 - FMS2_IO: Adds an optional argument to open_file, `dont_add_res_to_filename`, which indicates that the filename should not be modified (default adds .res to restart file name)
 - FMS2_IO: Modifies the `register_variable_attribute` and `register_global_attribute` interfaces by adding str_len as an argument. This is a workaround to get fms2io to work with PGI because they don't support class (*) with len=*.
-- FMS2_IO: Adds unit test that tests `write_data` and `read_data` when using a domain with a mask table 
+- FMS2_IO: Adds unit test that tests `write_data` and `read_data` when using a domain with a mask table
 - FMS2_IO: Adds fms2io’s version of get_mosaic_tile_grid
 - MPP_IO: Adds `-Duse_mpp_io` compile option for data_override, interpolator, amip_interp, diag_manager, topography, and xgrid to select using mpp_io instead of fms2_io
 - MPP_INIT: Adds unit tests for routines/functions that are called in mpp_init
@@ -57,9 +57,9 @@ The fms2_io unit tests were modified so they can work with the AOCC compiler
 
 ### Fixed
 - DATA_OVERRIDE[2]: Fixes a crash when doing ongrid data_override calls with a domain with halos
-- DIAG_MANAGER[2]: Fixes an issue where time_bnds were written incorrectly for the last time stamp 
+- DIAG_MANAGER[2]: Fixes an issue where time_bnds were written incorrectly for the last time stamp
 - DIAG_MANAGER: Regional diagnostics with a mask table now work
-- FMS2_IO: Unit test includes fms2io_init call to improve functionality 
+- FMS2_IO: Unit test includes fms2io_init call to improve functionality
 - MPP: BOZ literals that are used in variable declaration are converted to integers using the int() function.
 - MPP_DOMAINS2: Fixed unit test
 - FMS_IO: Changes the logic in get_tile_string to fix bug where tile numbers 9 and 99 produce an inappropriate error
@@ -86,7 +86,7 @@ The fms2_io unit tests were modified so they can work with the AOCC compiler
 
 ### Removed
 - GENERAL:  References to the macro _ALLOCATABLE have been replaced with “allocatable”, _ALLOCATED has been replaced with “allocated”, and _NULL has been removed.  It is now assumed that all compilers support the Fortran 2003 standard.  The macros still exist in fms_platforms.h for compatibility within other components.
-- DIAG_MANAGER:  “fms_platform.h” is no longer included in any of the diag_manager routines.  Instead, fms_platform_mod is now being use-associated where necessary.  This fixes an issue for debuggers not providing correct line numbers. 
+- DIAG_MANAGER:  “fms_platform.h” is no longer included in any of the diag_manager routines.  Instead, fms_platform_mod is now being use-associated where necessary.  This fixes an issue for debuggers not providing correct line numbers.
 
 ### Tag Commit Hashes
 - 2020.02-beta1 (bbc6f8d33cfb75a411bbcd3f8423fa74b8b7cdfd)

axis_utils/axis_utils2.F90

@@ -179,7 +179,7 @@ subroutine axis_edges(fileobj, name, edge_data, reproduce_null_char_bug_flag)
 
   buffer = ""
   if (variable_att_exists(fileobj, name, "edges")) then
-    !! If the reproduce_null_char_bug flag is turned on fms2io will not remove the null character 
+    !! If the reproduce_null_char_bug flag is turned on fms2io will not remove the null character
     call get_variable_attribute(fileobj, name, "edges", buffer, reproduce_null_char_bug_flag=reproduce_null_char_bug)
 
     !! Check for a null character here, if it exists *_bnds will be calculated instead of read in
@@ -189,13 +189,13 @@ subroutine axis_edges(fileobj, name, edge_data, reproduce_null_char_bug_flag)
         if (i > 0) buffer = ""
     endif
   elseif (variable_att_exists(fileobj, name, "bounds")) then
-    !! If the reproduce_null_char_bug flag is turned on fms2io will not remove the null character 
+    !! If the reproduce_null_char_bug flag is turned on fms2io will not remove the null character
     call get_variable_attribute(fileobj, name, "bounds", buffer, reproduce_null_char_bug_flag=reproduce_null_char_bug)
 
     !! Check for a null character here, if it exists *_bnds will be calculated instead of read in
     if (reproduce_null_char_bug) then
         i = 0
-        i = index(buffer, char(0)) 
+        i = index(buffer, char(0))
         if (i > 0) buffer = ""
     endif
   endif

block_control/block_control.F90

@@ -47,7 +47,7 @@ module block_control_mod
   integer, dimension(:),        allocatable :: ibs  , &  !< block extents for mpp-style
                                                ibe  , &  !! decompositions
                                                jbs  , &
-                                               jbe  
+                                               jbe
   type(ix_type), dimension(:),  allocatable :: ix    !< dereference packed index from global index
   !--- packed blocking fields
   integer, dimension(:),        allocatable :: blksz !< number of points in each individual block

configure.ac

@@ -266,7 +266,7 @@ fi
 AC_MSG_CHECKING([if netCDF 4.7.4 is loaded])
 if [ test "`nc-config --version`" == "netCDF 4.7.4" ]; then
   AM_CONDITIONAL([SKIP_FMS2_IO_TESTS], true )
-  AC_MSG_RESULT([yes]) 
+  AC_MSG_RESULT([yes])
 else
   AM_CONDITIONAL([SKIP_FMS2_IO_TESTS], false )
   AC_MSG_RESULT([no])

diag_manager/diag_manager.F90

@@ -618,7 +618,7 @@ INTEGER FUNCTION register_diag_field_array(module_name, field_name, axes, init_t
                   & Contact the developers.'
                 register_diag_field_array = -1
                 RETURN
-             ELSE 
+             ELSE
                 CALL error_mesg ('diag_manager_mod::register_diag_field', 'module/output_field '&
                   &//TRIM(module_name)//'/'// TRIM(field_name)//' AREA and VOLUME CANNOT be the same variable.&
                   & Contact the developers.',&
@@ -636,7 +636,7 @@ INTEGER FUNCTION register_diag_field_array(module_name, field_name, axes, init_t
                   & Contact the model liaison.'
                 register_diag_field_array = -1
                 RETURN
-             ELSE 
+             ELSE
                 CALL error_mesg ('diag_manager_mod::register_diag_field', 'module/output_field '&
                   &//TRIM(module_name)//'/'// TRIM(field_name)//' AREA measures field NOT found in diag_table.&
                   & Contact the model liaison.',&
@@ -652,7 +652,7 @@ INTEGER FUNCTION register_diag_field_array(module_name, field_name, axes, init_t
                   & Contact the model liaison.'
                 register_diag_field_array = -1
                 RETURN
-             ELSE 
+             ELSE
                 CALL error_mesg ('diag_manager_mod::register_diag_field', 'module/output_field '&
                   &//TRIM(module_name)//'/'// TRIM(field_name)//' VOLUME measures field NOT found in diag_table.&
                   & Contact the model liaison.',&

diag_manager/diag_output.F90

@@ -417,7 +417,7 @@ SUBROUTINE write_axis_meta_data_fms2_io(file_unit, axes, fileob, time_ops, time_
                          call mpp_get_global_domain(domain, begin=gstart, end=gend)  !< Get the global indicies
                          call mpp_get_compute_domain(domain, begin=cstart, end=cend, size=clength) !< Get the compute indicies
                          iend =  cend - gstart + 1     !< Get the array indicies for the axis data
-                         istart = cstart - gstart + 1 
+                         istart = cstart - gstart + 1
                          call register_axis(fptr, axis_name, dimension_length=clength)
                          call register_field(fptr, axis_name, "double", (/axis_name/) )
                          call register_variable_attribute(fptr, axis_name, "long_name", trim(axis_long_name), str_len=len_trim(axis_long_name))
@@ -579,9 +579,9 @@ SUBROUTINE write_axis_meta_data_fms2_io(file_unit, axes, fileob, time_ops, time_
              endif
 
           ELSE
-!> @note Check if the time variable is registered.  It's possible that is_time_axis_registered is set to true if using 
-!! time-templated files because they aren't closed when done writing.  An alternative to this set up would be to put 
-!! variable_exists into the if statement with an .or. so that it gets registered. 
+!> @note Check if the time variable is registered.  It's possible that is_time_axis_registered is set to true if using
+!! time-templated files because they aren't closed when done writing.  An alternative to this set up would be to put
+!! variable_exists into the if statement with an .or. so that it gets registered.
                 is_time_axis_registered = variable_exists(fptr,trim(axis_name),.true.)
                 if (allocated(fptr%pelist) .and. .not. is_time_axis_registered) then
                  select type (fptr)
@@ -2110,7 +2110,7 @@ SUBROUTINE diag_flush(file_unit)
 
     CALL mpp_flush (file_unit)
   END SUBROUTINE diag_flush
-!> End of use_mpp_io = true routines/functions  
+!> End of use_mpp_io = true routines/functions
 !! everything else is shared by both
   ! </SUBROUTINE>
 

diag_manager/diag_util.F90

@@ -1772,7 +1772,7 @@ SUBROUTINE init_output_field(module_name, field_name, output_name, output_file,&
   END SUBROUTINE init_output_field
   ! </SUBROUTINE>
 
-!> \brief Open file for output.  
+!> \brief Open file for output.
   SUBROUTINE opening_file(file, time, use_mpp_io)
     ! WARNING: Assumes that all data structures are fully initialized
     INTEGER, INTENT(in) :: file !< File ID.
@@ -2840,7 +2840,7 @@ SUBROUTINE write_static(file, use_mpp_io)
       CALL mpp_close(files(file)%file_unit)
       files(file)%file_unit = -1
     END IF
-   endif  !< use_mpp_io     
+   endif  !< use_mpp_io
   END SUBROUTINE write_static
   ! </SUBROUTINE>
 

docs/Doxyfile.in

@@ -291,7 +291,7 @@ OPTIMIZE_OUTPUT_VHDL   = NO
 # Note that for custom extensions you also need to set FILE_PATTERNS otherwise
 # the files are not read by doxygen.
 
-EXTENSION_MAPPING      = f90=Fortran 
+EXTENSION_MAPPING      = f90=Fortran
 
 # If the MARKDOWN_SUPPORT tag is enabled then doxygen pre-processes all comments
 # according to the Markdown format, which allows for more readable
@@ -687,7 +687,7 @@ FILE_VERSION_FILTER    =
 # DoxygenLayout.xml, doxygen will parse it automatically even if the LAYOUT_FILE
 # tag is left empty.
 
-LAYOUT_FILE            = 
+LAYOUT_FILE            =
 
 # The CITE_BIB_FILES tag can be used to specify one or more bib files containing
 # the reference definitions. This must be a list of .bib files. The .bib
@@ -810,7 +810,7 @@ RECURSIVE              = YES
 # Note that relative paths are relative to the directory from which doxygen is
 # run.
 
-EXCLUDE                = 
+EXCLUDE                =
 
 # The EXCLUDE_SYMLINKS tag can be used to select whether or not files or
 # directories that are symbolic links (a Unix file system feature) are excluded
@@ -1103,7 +1103,7 @@ HTML_STYLESHEET        =
 # list). For an example see the documentation.
 # This tag requires that the tag GENERATE_HTML is set to YES.
 
-HTML_EXTRA_STYLESHEET  = 
+HTML_EXTRA_STYLESHEET  =
 
 # The HTML_EXTRA_FILES tag can be used to specify one or more extra images or
 # other source files which should be copied to the HTML output directory. Note