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FRE-NCtools patch release 2023.01.02

FRE-NCtools patch release 2023.01.01
* include 4-dimensional (i.e. diurnal) output in default split-ncvars.pl processing

FRE-NCtools release 19.1, or FRE Bronx-19 patch 1 at GFDL sites
1. Added additional and consistent metadata provenance in the form of NetCDF global attributes: git hash of the tools repository, hostname used to compile the tool, tool arguments, creation time, tools site version, and grid version (tool-specific meaning)
2. Updated compilation settings for GFDL-WS and PP/AN sites to not use the optimized Intel math library, which was discovered to cause round-off floating point differences among nodes with different hardware capability (i.e. AVX)
3. Also, added the -xsse2 option for consistency with the gaea compilation settings, which support reproducibility

FRE-NCtools release 19.0, or FRE Bronx-19 at GFDL sites
Tool updates
- make_hgrid was enhanced with the capability to generate multiple nested telescoping grids on the cubed sphere. This new feature is described in the --nest_grids option documentation and in usage example 8 in the usage help (make_hgrid --help). From Bill Ramstrom, Joseph Mouallem, and Kyle Ahern.
NOTE: Global refinement, a method used to create two grids such that the higher-resolution one overlays the course one with identical intersecting points, is unsupported as we revisit its requirements, though the feature still works for now. See the usage help for instructions, and please create a github issue if you use this feature (https://github.com/NOAA-GFDL/FRE-NCtools/issues)
- remap_land was enhanced to support the new fields and dimensions in lm4.1 and lm4.2 (proposed) restart files
- make_coupler_mosaic includes a fix to reuse the atmos grid for land when they are the same (instead of re-calculating, which has unavoidable inaccuracies) when NOT using the great circle algorithm. (The tool already had the correct behavior when using the great circle algorithm).
- make_coupler_mosaic includes a fix for calculating polygon areas correctly when a polygon side crosses a pole. This occurs mostly for stretched, non-great circle algorithm atmos grids; previously the bug caused tiling errors and holes in the Antarctic land mask.
- create_xgrid includes a fix for certain exchange grid errors for grid cells adjacent to ocean tripolar fold in the vicinity of the Poles (often involving a stretched atmos grid and tripolar ocean).
- fregrid was fixed to set the NetCDF file type of the output file to be the same type as the input file when the user does not specify the type in the command argument list and the --weight_file option is used
- combine_restarts was updated to support icebergs
- iceberg_comb.sh was updated to properly check for prerequisite tool “ncdump”
- New tool nc_null_check was added to diagnose a particular problem with mppio related to reading in latitude and longitude bounds when there is a null string in the latitude/longitude “bounds” variable attribute (https://github.com/NOAA-GFDL/FMS/issues/578). This tool will be removed soon as mppio is deprecated within FMS.
- combine_blobs was removed. (Historically used for combining MOM5 Lagrangian Blobs)

Other updates
- Updates to build environment and compiling procedures
  - Automake macros to better detect NetCDF configurations on systems with broken n[cf]-config
  - Updates for GFDL sites, including NCRC Intel compiler flags for greater reproducibility while being able to run on AMD hardware as well, GDFL-WS and PP/AN updates to use CentOS 7 “Spack” modules, and updated NetCDF and mpich libraries.
  - Adds site configuration files for compiling on NESCC systems
- Numerous C language files were updated to be in compliance with the C99 standard.
- Set the executable rpath to included needed NetCDF libraries
- Copyright and licensing headers standardized throughout the repository.
- Added .editorconfig file to standardize code formatting across varying user editors and IDEs. (https://editorconfig.org)

Bronx-18 minor patch: update split_ncvars.pl shebang with relative path perl

Bronx-18 deployed at GFDL WS, PP/AN, and NCRC gaea
*Use Autotools build system (replacing legacy build script): config files for GFDL-ws, GFDL-pan, ncrc
* Use updated Intel compilers; 18 at GFDL (from 15), 18 at gaea (from 16), 19 at orion
* Expanded CI testing, including basic tests for all tools, and Bronx-16 reference tests for the combiners (mppnccombine, combine-ncc, and decompress-ncc)
* Added site config files for MSU orion site
* Bug fix for make_coupler_mosaic segmentation faults (https://github.com/NOAA-GFDL/FRE-NCtools/issues/4)
* Fix for locating ceil() function on some sites (i.e. Hera) (from Marshall Ward)
* Removed compilation warnings (from Tom Robinson)
* New simple hydrography grid generating script make_simple_hydrog.csh (from Krista Dunne)

Bronx-16 FRE-nctools
split_ncvars
*New option -u to split files without .nc extension (i.e. distributed output files)
*Deprecate old cshell and python split_ncvars (will print warning and call split_ncvars.pl)

list_ncvars
*Make the temporary input namelist file more unique, to help when running in parallel

make_hgrid
*support very high-resolution grid (e.g. 43200 x 21600 lat-lon grid)
*New option --do_cube_transform to re-orient tile #6 upwards
*New option --no_length_angle to not output dx, dy, angle_dx, and angle_dy

make_solo_mosaic
*Extend make_solo_mosaic to be able to create fold-north contact for MOM6 horizontal grid

make_remap_file
*New tool to create low-resolution remap file from high-resolution remap file
*Input and output mosaic files can be cubed-sphere or not

mppncscatter
*bug fix when data has record dimension

Bronx-14 fre-nctools
1. Bug fix for fregrid bilinear interpolation when specifying lat/lon bounds
2. Bug fix for combine_restarts to not load fre-nctools

Patch 2018-9-4: Minor CMIP updates and a fregrid update
* New optional fregrid option --format to write to desired output format: either netcdf4, netcdf4_classic, 64bit_offset, classic
* split_ncvars change to recognize edges when in --cmip mode
* split_ncvars change to pass through GEOLAT/GEOLON in split-out files

Bronx-12 patch 3
* Increase hard-wired dimension limit from 10 to 20