$Header$ -*-text-*-

netCDF Operators NCO version 5.0.3 are on tap

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

What's new?
Version 5.0.3 contains significant improvements to the quantization
algorithms and fixes to MOAB/mbtempest regridding. NCO now supports
the Digit Round and Granular BitGroom quantization algorithms. The
failed self-test problems that prevented Conda from building NCO
5.0.2 have been fixed, and a 5.0.3 Conda package will soon be
available.

Work on NCO 5.0.4 has commenced and will improve ncremap support
for MOAB, incorporate new MOAB improvements, and further improve
quantization metadata and algorithms.

Enjoy,
Charlie

NEW FEATURES (full details always in ChangeLog):

A. Lossy quantization algorithms have been refactored. First, the
   attribute name that store the level of quantization are now
   algorithm-specific, e.g.,
   QuantizeBitGroomNumberOfSignificantDigits. Previsously, NCO 
   stored the NSD attribute number_of_significant_digits. However,
   this was deemed too ambiguous, given the increasing number of
   supported quantization methods. The new attribute names better
   disambiguate which algorithm was used to quantize the variable.
   Second, the default algorithm has been changed from BitGroom with
   BitRound masks from R. Kouznetsov (2021), to what we call Granular
   BitGroom (GBG). GBG combines the best features of BitGroom,
   BitRound, and DigitRound by Delaunay et al. (2019). GBG improves
   compression ratios by ~20% relative to BitGroom for NSD=3 on
   our benchmark 1 GB climate model output dataset.
   ncks -7 -L 1         --ppc default=3 in.nc out.nc # GranularBitGroom
   ncks -7 -L 1 --baa=0 --ppc default=3 in.nc out.nc # BitGroom
   ncks -7 -L 1 --baa=1 --ppc default=3 in.nc out.nc # BitShave
   ncks -7 -L 1 --baa=2 --ppc default=3 in.nc out.nc # BitSet
   ncks -7 -L 1 --baa=3 --ppc default=3 in.nc out.nc # DigitRound
   ncks -7 -L 1 --baa=4 --ppc default=3 in.nc out.nc # GranularBitGroom
   ncks -7 -L 1 --baa=5 --ppc default=3 in.nc out.nc # BitRound
   ncks -7 -L 1 --baa=6 --ppc default=3 in.nc out.nc # HalfShave
   ncks -7 -L 1 --baa=7 --ppc default=3 in.nc out.nc # BruteForce
   Documentation on Bit-Adjustment-Algorithms (BAA) 3-7 will be
   improved in the future. Bit-Groom/Shave/Set are described here:
   http://nco.sf.net/nco.html#ppq
   http://nco.sf.net/nco.html#gbg

BUG FIXES:
   
A. ncremap fixes issues that caused a self-test to fail.
   This prevented Conda from building an NCO 5.0.2 package.
   The tested algorithm is now 'fv2fv_flx' not 'tempest'. The
   MPI-enabled E3SM-Unified (SYSTEM) environment no longer changes
   the behavior of ncremap commands. --mpi_nbr now has complete
   control over whether mpirun (or srun) commands are issued.

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 5.0.3 built/tested under
MacOS 11.6 with netCDF 4.8.0 on HDF5 1.12.0 and with
Linux with netCDF 4.8.0 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

