$Header$ -*-text-*-

netCDF Operators NCO version 5.3.7 beats the buzzer

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

What's new?
Version 5.3.7 contains significant new features and fixes.
ncremap support for MOAB-TempestRemap (mbtempest) has been refactored
to optimize parallel weight generation and support new algorithms.
ncclimo now supports "flexible-months", so input datsets can begin in
an month, not just January. Additionally, ncclimo understands all
consectutive 2-month pairs and 3-month trios as valid seasons.
Other improvements include support for the l2d packing policy
suggested for CMIP7, and for the NetCDF Expansion Pack v.1.5+ API,
ncks fixes JSON-format output regressions, and ncclimo fixes automatic
name generation fixes two corner case bugs. 

Users should consider upgrading to exploit these new features.

Enjoy,
Charlie

NEW FEATURES (full details always in ChangeLog):

A. ncremap support for mbtempest is better optimized and more fully
parallel. mbconvert runs in parallel for input grids of type True
Exodus and netCDF3, and in serial for types netCDF4 and TR Exodus. 
mbpart now uses --inferred to optimize partitioning of destination
grid. 

ncremap --mpi_nbr=8 -a traave --src_grd=src.g --dst_grd=dst.nc -m map.nc

http://nco.sf.net/nco.html#moab
Thanks to Vijay Mahadevan of ANL for advice on MOAB's workflow.

B. ncremap in vertical interpolation mode for hybrid sigma-pressure
coordinates now searches for the surface pressure in the input
datafile before searching any input vertical grid file. When reading
the hybrid coordinate grid from a separate file, ncremap previously
expected the surface pressure to also be in that file. Now ps can
be with the data itself, apart from the input coordinate grid.

ncremap -P eamxx --vrt_in=vrt_L128.nc --vrt_out=vrt_ncep.nc in.nc out.nc

http://nco.sf.net/nco.html#vrt
Thanks to Jill Zhang of PNNL for reporting this issue.

C. ncclimo now supports climos that begin in any month, not just
January! We call this "flexible month" support. Previously all
climatologies needed to begin with January (or December, with the
--wnt_md=scd option), so no starting month argument was needed.
Now input files can begin in any start month, and the --wnt_md option
is replaced by simply supplying datasets that start with December.
Use the --mth_srt and --mth_end options to specify the starting and
ending months, otherwise January and December will be assumed.
This feature works for High-Frequency-Climos (HFC) as well.
(Note that at least 12 months of data must still be supplied).

ncclimo -c caseid -s 2013 -e 2014 --mth_srt=7 --mth_end=6 -i drc_in -o drc_out

http://nco.sf.net/nco.html#ncclimo
(thanks to Copilot for assisting)

D. ncclimo has all consecutive two-month and three-month seasons
defined internally, so users can select any. Two-month seasons
are, e.g., Jan-Feb, Feb-Mar, ... Dec-Jan. Three-month seasons are,
e.g., Jan-Feb-Mar, Feb-Mar-Apr, ... Dec-Jan-Feb. The seasonal
names are simply the two or three letter conjunctions formed by
the first letters of the constituent months, e.g., jf, amj:

ncclimo ... --csn=jas,ond,jfm,amj,nd,nj -i drc_in -o drc_out

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

E. The l2d chunking policy is available on all operators.
This policy forces all variables with one or two dimensions into a
single chunk. It is inspired by the chunking policy followed by
the cmip7repack tool (https://github.com/NCAS-CMS/cmip7_repack).
It is used like any other packing policy, and has the virtue of
being recommended for CMIP7 datasets. NB: When NCO repacks a
dataset, it automatically consolidates the internal metadata.

ncks --cnk_plc l2d in.nc out.nc

http://nco.sf.net/nco.html#chunking
http://nco.sf.net/nco.html#cnk_l2d
http://nco.sf.net/nco.html#ncpdq
Thanks to Ezequiel Cimadevilla and David Hassell of NCAS for
contributing this.

F. NCO now supports the NetCDF Expansion Pack v.1.5+ API.
Support for the v.1.0 API has been dropped. Original NEP features 
like the LZ4 codec are now supported. Newer NEP features such as
reading GRIB2 and GeoTIFF files should also be supported. 
If the host NEP package is installed correctly for NCO to build
with and link to at runtime, then NCO will be able to read
GeoTIFF and Grib2 and CDF files (depending on NEP configureation).
Our goal is to make this occur automagically via Conda and Spack
packaging. 

ncks --cmp='gbr|shf|lz4' in.nc out.nc # LZ4 compression via NEP

https://github.com/Intelligent-Data-Design-Inc/NEP
Thanks to Ed Hartnett for creating NEP.

G. The ncremap tutorial on the E3SM Confluence page
https://e3sm.atlassian.net/wiki/spaces/DOC/pages/edit-v2/754286611
contains still more documentation on how to exploit the three types
of parallelism (node-, workflow-, and thread-level) supported by
ncremap.

BUG FIXES:
   
A. Conversion of input files to JSON has been subtly broken
for some time, as pointed out by Andrew Barna. Variables
were missing their "type" and "shape" specifiers, and attributes
could not add these not matter what --jsn_fmt option was given.
This has been fixed. The workaround is to use an earlier version
of NCO. The solution is to upgrade.
http://nco.sf.net/nco.html#json
http://nco.sf.net/nco.html#jsn_fmt

B. In all previous versions ncclimo failed to handle
starting and ending years specified as 0, 00, or 000.
Year zero had to be specified as 0000. That is now fixed.
The workaround is to use 0000 for year 0. The solution is
to upgrade.

C. Since about 2024 the ncclimo automatic name generation
feature has prepended "${caseid}." to the MPAS model default
filenames. This inadvertently prepended just a period when
the --caseid option was not specified. This period is an
unwanted character, and broke the automatic feature from
correctly generating MPAS v1 and v2 filenames. This has
been fixed. The workaround is to create symbolic links
that contain the period to the actual v1 and v2 filenames.
The solution is to upgrade. Thanks to Qi Tang for reporting
this issue.

Full release statement at http://nco.sf.net/ANNOUNCE
    
KNOWN PROBLEMS DUE TO NCO:

This section of ANNOUNCE reports and reminds users of the
existence and severity of known, not yet fixed, problems. 
These problems occur with NCO 5.3.7 built/tested under
MacOS 26.3 with netCDF 4.10.1-development on HDF5 2.1.1
and with Linux FC42 with netCDF 4.9.2 on HDF5 1.14.4.

A. NOT YET FIXED (NCO problem)
   Correctly read arrays of NC_STRING with embedded delimiters in ncatted arguments

   Demonstration:
   ncatted -D 5 -O -a new_string_att,att_var,c,sng,"list","of","str,ings" ~/nco/data/in_4.nc ~/foo.nc
   ncks -m -C -v att_var ~/foo.nc

   20130724: Verified problem still exists
   TODO nco1102
   Cause: NCO parsing of ncatted arguments is not sophisticated
   enough to handle arrays of NC_STRINGS with embedded delimiters.

B. NOT YET FIXED (NCO problem?)
   ncra/ncrcat (not ncks) hyperslabbing can fail on variables with multiple record dimensions

   Demonstration:
   ncrcat -O -d time,0 ~/nco/data/mrd.nc ~/foo.nc

   20140826: Verified problem still exists
   20140619: Problem reported by rmla
   Cause: Unsure. Maybe ncra.c loop structure not amenable to MRD?
   Workaround: Convert to fixed dimensions then hyperslab

KNOWN PROBLEMS DUE TO BASE LIBRARIES/PROTOCOLS:

A. NOT YET FIXED (netCDF4 or HDF5 problem?)
   Specifying strided hyperslab on large netCDF4 datasets leads
   to slowdown or failure with recent netCDF versions.

   Demonstration with NCO <= 4.4.5:
   time ncks -O -d time,0,,12 ~/ET_2000-01_2001-12.nc ~/foo.nc
   Demonstration with NCL:
   time ncl < ~/nco/data/ncl.ncl   
   20140718: Problem reported by Parker Norton
   20140826: Verified problem still exists
   20140930: Finish NCO workaround for problem
   20190201: Possibly this problem was fixed in netCDF 4.6.2 by https://github.com/Unidata/netcdf-c/pull/1001
   Cause: Slow algorithm in nc_var_gets()?
   Workaround #1: Use NCO 4.4.6 or later (avoids nc_var_gets())
   Workaround #2: Convert file to netCDF3 first, then use stride
   Workaround #3: Compile NCO with netCDF >= 4.6.2

B. NOT YET FIXED (netCDF4 library bug)
   Simultaneously renaming multiple dimensions in netCDF4 file can corrupt output

   Demonstration:
   ncrename -O -d lev,z -d lat,y -d lon,x ~/nco/data/in_grp.nc ~/foo.nc # Completes but produces unreadable file foo.nc
   ncks -v one ~/foo.nc

   20150922: Confirmed problem reported by Isabelle Dast, reported to Unidata
   20150924: Unidata confirmed problem
   20160212: Verified problem still exists in netCDF library
   20160512: Ditto
   20161028: Verified problem still exists with netCDF 4.4.1
   20170323: Verified problem still exists with netCDF 4.4.2-development
   20170323: https://github.com/Unidata/netcdf-c/issues/381
   20171102: Verified problem still exists with netCDF 4.5.1-development
   20171107: https://github.com/Unidata/netcdf-c/issues/597
   20190202: Progress has recently been made in netCDF 4.6.3-development
   More details: http://nco.sf.net/nco.html#ncrename_crd

C. NOT YET FIXED (would require DAP protocol change?)
   Unable to retrieve contents of variables including period '.' in name
   Periods are legal characters in netCDF variable names.
   Metadata are returned successfully, data are not.
   DAP non-transparency: Works locally, fails through DAP server.

   Demonstration:
   ncks -O -C -D 3 -v var_nm.dot -p http://thredds-test.ucar.edu/thredds/dodsC/testdods in.nc # Fails to find variable

   20130724: Verified problem still exists. 
   Stopped testing because inclusion of var_nm.dot broke all test scripts.
   NB: Hard to fix since DAP interprets '.' as structure delimiter in HTTP query string.

   Bug tracking: https://www.unidata.ucar.edu/jira/browse/NCF-47

D. NOT YET FIXED (would require DAP protocol change)
   Correctly read scalar characters over DAP.
   DAP non-transparency: Works locally, fails through DAP server.
   Problem, IMHO, is with DAP definition/protocol

   Demonstration:
   ncks -O -D 1 -H -C -m --md5_dgs -v md5_a -p http://thredds-test.ucar.edu/thredds/dodsC/testdods in.nc

   20120801: Verified problem still exists
   Bug report not filed
   Cause: DAP translates scalar characters into 64-element (this
   dimension is user-configurable, but still...), NUL-terminated
   strings so MD5 agreement fails 

"Sticky" reminders:

A. Reminder that NCO works on most HDF4 and HDF5 datasets, e.g., 
   HDF4: AMSR MERRA MODIS ...
   HDF5: GLAS ICESat Mabel SBUV ...
   HDF-EOS5: AURA HIRDLS OMI ...

B. Pre-built executables for many OS's at:
   http://nco.sf.net#bnr

