$Header$ -*-text-*-

netCDF Operators NCO version 5.1.0 brachiate toward you

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

What's new?
Version 5.1.0 supports the new netCDF 4.9.0 features for filters and
quantization. This is a significant new feature that justifies the
version bump from 5.0.7 to 5.1.0. There is also an ncremap fix for 
sub-sub-gridscale regridding, e.g., landunit-specific regridding.
Users of sub-SGS regridding, and anyone interested is using modern
compression or quantization algorithms such as Bzip2, Zstandard, 
Granular BitGroom, and BitRound.   

Work on NCO 5.1.1 has commenced and will polish support for
quantization/compression algorithms and add support for NCZarr I/O.

Enjoy,
Charlie

NEW FEATURES (full details always in ChangeLog):

A. All numeric NCO operators support new compression features
when linked to a default installation of the latest netCDF, 4.9.0. 
These features and how to access and tune them are extensively
documented in the manual. Suffice it to say that all NCO users
now have transparent access to modern lossless (Bzip2, Zstandard)
and lossy (BitRound, Granular BitRound) compression algorithms.
Codecs from the netCDF C-library, the Community Codec Repository
(CCR), and from user-installed HDF5 filters may all be used.
The commands will look something like this:
ncks --cmp='granularbr,3|shuffle|zstandard,3' ... # Long-names
ncks --cmp='gbr,3|shf|zst,3' ... # Abbreviations and levels
ncks --cmp='gbr|shf|zst' ...     # Default levels
ncks --cmp='f32|gbr|shf|bz2|dfl|zst' ... # Multiple codecs
ncwa --cmp='gbr|shf|zst' ...     # Other operators...
ncbo --cmp='gbr|shf|zst' ...     # All numeric operators, in fact
ncclimo --cmp='btr\|shf\|zstd' ... # Climo generator
ncremap --cmp='btr\|shf\|zstd' ... # Regridder
Full documentation (including figures) is at
http://nco.sf.net/nco.html#compression
Thanks to Ed Hartnett (NOAA) and Dennis Heimbigner (Unidata) for
guiding the addition of these features into the CCR and netCDF.

BUG FIXES:
   
A. NCO 5.0.7 contained a bug in its new feature that allows missing
values in fields with valid SGS area. ncremap < 5.0.7 assumed fields
to be valid wherever sgs_frc > 0.0. This assumption is valid for ~95%
of ELM/CLM fields. However, it low-biased landunit-specific fields
(like TSOI, H2OSOI) in transition areas (e.g., ablation zone) with
valid SGS, and invalid landunit. NCO 5.0.7 mostly fixed that, though
it had a corner-case bug triggered mostly in multi-level fields
(like TLAKE, TSOI). The normalization for multi-level fields is now
correct, thus allowing sub-sub-gridscale regridding to work in all
known cases.
ncremap -P elm --map=map.nc in.nc out.nc
http://nco.sf.net/nco.html#sgs

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 5.1.0 built/tested under
MacOS 12.4 with netCDF 4.9.0 on HDF5 1.12.2 and with
Linux with netCDF 4.9.0 on HDF5 1.8.19.

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

