$Header$ -*-text-*-

The netCDF Operators NCO version 4.9.7 have arrived.

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

What's new?
Version 4.9.7 is a minor NCO release that contains a few new features
and fixes. Unless the features/fixes listed below affect you, no need
to upgrade this time.

Work on NCO 4.9.8 has commenced and will improve analysis of land
surface datasets packed into sparse-1D formats.

Enjoy,
Charlie

NEW FEATURES (full details always in ChangeLog):

A. ncremap can now infer SCRIP grids from MPAS restart files.
This is useful when users lack access to the gridfiles their
model used. This can easily happen when running standalone
MPAS simulations that use non-scientifically validated grids.
Previously inferring MPAS grids produce incomplete (no corners)
and erroneous (degrees not radians in metadata) grids.
Now the inferred grids are complete, consistent, and BFB with
the original grids used in the MPAS simulation.

ncremap -d ~/restart.2001-01-01_00.00.00.nc -g QU120_zach.nc

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

B. ncremap and ncclimo have been updated to work in MPI mode
on the new DOE machines Andes (ORNL) and Chrysalis (ANL LCRC).
http://nco.sf.net/nco.html#par_typ

C. NCO can be built to leverage the Communinty Codec Repository.
The CCR is currently supports two lossless compression filters
(BZip2, Zstandard) and one lossy quantization filter (BitGroom).
More importantly, the CCR is extensible and provides the C/Fortran 
API for defining alternative (non-DEFLATE) compression using
a netCDF-like API at file creation time. The NCO ncap2 operator
will now access these filters for rewriting variables in existing
files:

./configure --enable-ccr; make; make install # Build NCO with CCR
ncap2 -O -7 --ccr=Zstd -L 3 -s 'two=one+one' in.nc out.nc
ncap2 -O -7 --ccr=BitGroom -L 3 -s 'two=one+one' in.nc out.nc
ncks -C --hdn -v three_dmn_rec_var out.nc # Examine data

http://github.com/ccr/ccr
CCR capabilities, and NCO support for them, will expand in 2021. 
Thanks to Ed Hartnett of NOAA (and netCDF4/PIO fame) for partnering
on the CCR! See our poster on the CCR 1.1 release at AMS.

BUG FIXES:

A. ncclimo fixes the bug that caused the --glb_avg option to fail
when invoked in a batch-queue submission. Thanks to Chris Golaz
for reporting. The problem was subtle and only exposed itself when
invoked on multiple input variables on nodes with fast response
times (bug appeared only in batch queues not interactive nodes).
The solution is to upgrade.

B. ncclimo fixes a bug introduced in 4.9.6 that caused the
high-frequency climo mode to diagnose the wrong timesteps-per-day
(tpd) in the input file. Thanks to Jill Chang for reporting.
Workaround is to manually specify with --tpd or to upgrade.

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 4.9.7 built/tested under
   MacOS 11.0.1 with netCDF 4.7.4 on HDF5 1.10.7 and with
   Linux with netCDF 4.8.0-development (2020715) 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

