[netcdfgroup] netCDF Operators NCO version 5.2.0 puffs its feathers

• To: NCO Announce Mail List <nco-announce@xxxxxxxxxxxxxxxxxxxxx>, netCDF Mail List <netcdfgroup@xxxxxxxxxxxxxxxx>
• Subject: [netcdfgroup] netCDF Operators NCO version 5.2.0 puffs its feathers
• From: Charlie Zender <zender@xxxxxxx>
• Date: Fri, 16 Feb 2024 14:40:53 -0800

netCDF Operators NCO version 5.2.0 puffs its feathers

http://nco.sf.net (Homepage, Mailing lists, Help)
http://github.com/nco/nco (Source Code, Issues, Releases)

What's new?
Version 5.2.0 includes four major new features and various fixes.
The features: 1) All operators append draft CF Convention behavior
for metadata to encode lossy compression. 2) ncclimo timeseries mode
now supports all input methods (including automatic filename
generation) long-supported by climo mode. 3) ncremap Make-Weight-File
(MWF) mode has been revamped and now support specifiable lists of
algorithms. Last but not least, 4) ncks --s1d now converts CLM/ELM
restart files from their native, inscrutable sparse 1-D (S1D) format
to normal-looking gridded files, without loss of information.

Work on NCO 5.2.1 has commenced and aims to add support for Zarr S3
stores, and to polish support for new codecs..

Enjoy,
Charlie

NEW FEATURES (full details always in ChangeLog):

A. ncks can now help analyze initial condition and restart datasets
produced by the E3SM ELM and CESM CLM/CTSM land-surface models.
Whereas gridded history datasets from these ESMs use a standard
gridded data format, these land-surface "restart files" employ a
custom packing format that unwinds multi-dimensional data into
sparse, 1-D (S1D) arrays that are not easily visualized. ncks can
now convert these S1D files into gridded datasets where all dimensions
are explicitly declared (rather than unrolled or "packed").
Invoke this conversion feature with the --s1d option and point
ncks to a file that contains the horizontal coordinates (which
restart files do not explicitly contain) and the restart file.
The output file is the fully gridded input file, with no loss
of information:
ncks --s1d --hrz=elmv3_history.nc elmv3_restart.nc out.nc
The output file contains all input variables placed on a lat-lon or
unstructured grid, with new dimensions for Plant Funtional Type (PFT)
and multiple elevation class (MEC).
http://nco.sf.net/nco.html#s1d

B. ncclimo timeseries mode now supports all input methods (including
automatic filename generation) long-supported by climo mode. Previously
ncclimo (in timeseries mode) had to receive explicit lists of input
files, either from stdin or from the command line. Now ncclimo will
automatically generate the input file list for files that adhere to
common CESM/E3SM naming conventions (usually for monthly average
files). The syntax is identical to that long used in climo mode:
% ncclimo --split -c $caseid -s 2000 -e 2024 -i $drc_in -o $drc_out
http://nco.sf.net/nco.html#ncclimo

C. ncremap supports --alg_lst=alg_lst, a comma-separated list of the
algorithms that MWF-mode uses to create map-files. This option can
be used to shorten or alter the default list, which is
'esmfaave,esmfbilin,ncoaave,ncoidw,traave,trbilin,trfv2,trintbilin'.
Each name in the list should be the primary name of an algorithm,
not a synonym. For example, use 'esmfaave,traave' not
'aave,fv2fv_flx' (the latter are backward-compatible synonyms
for the former). The algorithm list must be consistent with grid-types
supplied: ESMF algorithms work with meshes in ESMF, SCRIP, or UGRID
formats. NCO algorithms only work with meshes in SCRIP format.
TempestRemap algorithms work with meshes in ESMF, Exodus, SCRIP, or
UGRID formats. On output, ncremap inserts each algorithm name into the
output map-file name in this format: map_src_to_dst_alg.date.nc.
For example,
% ncremap -P mwf --alg_lst=esmfnstod,ncoaave,ncoidw,traave,trbilin \
  -s ocean.QU.240km.scrip.181106.nc -g ne11pg2.nc --nm_src=QU240 \
  --nm_dst=ne11pg2 --dt_sng=20240201
...
% ls map*
map_QU240_to_ne11pg2_esmfnstod.20240201.nc
map_QU240_to_ne11pg2_ncoaave.20240201.nc
map_QU240_to_ne11pg2_ncoidw.20240201.nc
map_QU240_to_ne11pg2_traave.20240201.nc
map_QU240_to_ne11pg2_trbilin.20240201.nc
map_ne11pg2_to_QU240_esmfnstod.20240201.nc
map_ne11pg2_to_QU240_ncoaave.20240201.nc
map_ne11pg2_to_QU240_ncoidw.20240201.nc
map_ne11pg2_to_QU240_traave.20240201.nc
map_ne11pg2_to_QU240_trbilin.20240201.nc

http://nco.sf.net/nco.html#alg_lst
http://nco.sf.net/nco.html#ncremap

D. All NCO operators now support the draft CF Convention on encoding
metadata that describes lossy compression applied to the dataset.
See https://github.com/cf-convention/cf-conventions/issues/403.
For example, all variables quantized by NCO now receive attributes
that contain the level of quantization and that point to a
container variable that describes the algorithm:

% ncks -O -7 --cmp='btr|shf|zst' in.nc foo.nc
% ncks -m -v ts foo.nc
 char compression_info ;
   char compression_info ;
   compression_info:family = "quantize" ;
   compression_info:algorithm = "BitRound" ;

 float ts(time,lat,lon) ;
      ts:standard_name = "surface_temperature" ;
      ts:lossy_compression = "compression_info" ;
      ts:lossy_compression_nsb = 9 ;

http://nco.sf.net/nco.html#qnt

E. ncks supports a new flag, --chk_bnd, that reports whether all
coordinate variables in a file contain associated "bounds" variables.
This check complies with CF Conventions and with NASA's Dataset
Interoperability Working Group (DIWG) recommendations:
$ ncks --chk_bnd ~/nco/data/in.nc

http://nco.sf.net/nco.htlm/chk_bnd

F. ncremap supports the TempestRemap trfv2 algorithm, a 2nd order FV
reconstruction, that is cell-integrated on the target grid.
ncremap --alg_typ=trfv2 -s grd_src.nc -g grd_dst.nc --map=map.nc
http://nco.sf.net/nco.htlm/trfv2

BUG FIXES:

A. ncclimo fixes an error in the climatology_bounds variable
output for the climatological December file in DJF-winter mode
climos. JFD-winter mode climos (used by most people) are unaffected.
There is no workaround. The solution is to upgrade.
ncclimo --wnt_md=djf -c $caseid -s 2000 -e 2024 ...

Full release statement at http://nco.sf.net/ANNOUNCE
--
Charlie Zender, Earth System Sci. & Computer Sci.
University of California, Irvine 949-891-2429 )'(