$Header$ -*-text-*-

netCDF Operators NCO version 5.2.4 tip the spear

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

What's new?
Version 5.2.4 fully implements the CF lossy metadata convention
for three the three NCO internal quantization algorithms that
are also in libnetCDF. It also improves ncclimo diagnostics.
No major new features are implemented.
Skip this release if these changes are not important to you.

Work on NCO 5.2.5 has commenced and will add support for Zarr S3 
stores, and will enhance the vertical regridder.

Enjoy,
Charlie

NEW FEATURES (full details always in ChangeLog):

A. All numeric operators now support --qnt as a synonym for --ppc.
Previous one could only use --quantize as a synonym, and --qnt
just seemed like it needed to be one too. The first three are the same:
ncks --ppc default=3 --ppc prs_sfc=5 in.nc out.nc # Granular Bitround
ncks --qnt default=3 --qnt prs_sfc=5 in.nc out.nc
ncks --quantize default=3 --quantize prs_sfc=5 in.nc out.nc
ncks --baa=8 --ppc default=12 --ppc prs_sfc=15 in.nc out.nc # Bitround
http://nco.sf.net/nco.html#qnt
http://nco.sf.net/nco.html#ppc
http://nco.sf.net/nco.html#quantize

B. All numeric operators now write CF-compliant metadata for quantization
algorithms through the NCO internal algorithms. (Previously NCO wrote CF
metadata only for quanitzation performed by the netCDF library.) 
NCO no longer writes the really long quantization metadata attributes
such as QuantizeBitGroomNumberOfSignificantDigits. Note that libnetcdf
still does write these attributes (prepended by an underscore) when
its quantization functions are invoked.
% ncks -O -7 --baa=8 --qnt prs_sfc=6 --cmp='shf|zst' in.nc out.nc
% ncks -m -v prs_sfc,compression_info out.nc
netcdf foo2 {
  dimensions:
    lat = 2 ;
    lon = 4 ;
    time = UNLIMITED ; // (10 currently)

  variables:
    char compression_info ;
      compression_info:family = "quantize" ;
      compression_info:algorithm = "BitRound" ;
      compression_info:implementation = "NCO version 5.2.4" ;

    float prs_sfc(time,lat,lon) ;
      prs_sfc:long_name = "Surface pressure" ;
      prs_sfc:units = "pascal" ;
      prs_sfc:lossy_compression = "compression_info" ;
      prs_sfc:lossy_compression_nsb = 6 ;
} // group /

BUG FIXES:
   
A. None

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 5.2.0 built/tested under
MacOS 14.4.1 with netCDF 4.9.3-dev on HDF5 1.14.3 and with
Linux FC38 with netCDF 4.9.2 on HDF5 1.14.1.

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

