$Header$ -*-text-*-

The netCDF Operators NCO version 4.9.6 have arrived.

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

What's new?
Version 4.9.6 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 4.9.7 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. ncclimo supports a new option --var_xtr to specify "extra
variables" for the splitter to add to every generated timerseries.
The splitter attempts to keep the generated timeseries as lean as
possible and by default adds only the most useful ancillary variables,  
such as grid coordinates and CF-associated variable, to split
timeseries. Previously, there was no way to add arbitrary variables, 
e.g., the CO2 volume mixing ratio, to a split timeseries. Now users
can specify an arbitrary number of variables to includes in every
split timeseries, e.g.,

ncclimo --var=T,Q --var_xtr=co2vmr,FSDS ...

In this example the splitter produces two output files because there
are two primary variables (T,Q). Each timeseries also contain co2vmr
and FSDS. Inclusion of other variables, e.g., area, depends on context
and on other options
http://nco.sf.net/nco.html#var_xtr

B. This version is forward-compatible with netCDF 4.8.0, which we know 
will contain some backward-incompatibile changes to filter behavior.
Once netCDF 4.8.0 is released, if it becomes the default version of
netCDF on your syste, then you will likely need to upgrade to NCO
4.9.6 as previous versions may be incompatible with netCDF 4.8.0.

C. ncclimo now supports the -P (or --prc_typ) option instead of -m
(or --mdl_nm) to determine the processing type. More importantly,
ncclimo the -P option to ncremap internally, which simplifies some
complex climo/regridding commands. For example, now it is possible to
create regridded climatologies of output that requires sub-gridscale
regridding with a single ncclimo command whereas previouly this
required separate ncclimo and ncremap commands:

ls *elm.h0* | ncclimo -P elm -s 1 -e 500 --map=map.nc 
ls *mpaso* | ncclimo -P mpaso -s 1 -e 500 --map=map.nc 
ls *mpassi* | ncclimo -P mpassi -s 1 -e 500 --map=map.nc 

The ncclimo -m mdl_nm option is still supported, and is required in
some situations, e.g., when the processing type is 'elm' yet the
history filenames use 'clm2' not 'elm'. In such mixed cases both -P
and -m options may be necessary.
http://nco.sf.net/nco.html#ncclimo
http://dust.ess.uci.edu/smn/smn_nco_e3sm_202010.pptx

D. ncclimo and ncremap now support the large memory AMD (cmem) nodes
on Cori when in MPI mode. 


BUG FIXES:

A. ncremap fixes a bug that prevented MPI mode from working on Cori.

B. ncremap always retains (rather than potentially altering) the
input values of masks specified in SCRIP gridfiles when it writes
the output map-file.

C. ncremap correctly infers the final vertices of RLL grids stored
in north-to-south order. Previously, the final vertex could be
misdiagnosed for some counter-clockwise orderings of cells.


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 4.9.6 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

