$Header$ -*-text-*-

netCDF Operators NCO version 5.1.4 smite evil

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

What's new?
Version 5.1.4 introduces vertical interpolation for datasets stored
on depth/height grids, such as ocean data. The interpolation works
on all datasets tested with vertical levels that are either
horizontally varying (e.g., MPAS-Ocean, POP, MOM) or uniform (many
observational datasets including ARGO, SOSE, WOA18).
The algorithms play well with horzontally varying bathymetry.
This release also fixes a vexing issue that can occur with certain
compilers on AMD hardware. This release can be skipped if these
regridding features are not useful to you.

Work on NCO 5.1.5 has commenced and aims to add support for Zarr S3 
stores and to polish support for new codecs.

Enjoy,
Charlie

NEW FEATURES (full details always in ChangeLog):

A. ncremap can now vertically interpolate files/fields stored on
depth/height-based vertical grids. The capability is analogous to
the existing ncremap capability of interpolating data on pure-pressure
or hybrid sigma/pressure vertical grids (all four combinations work):
ncremap --vrt_out=vrt_out.nc in.nc out.nc
ncremap --vrt_in=vrt_in.nc --vrt_in=vrt_out.nc in.nc out.nc
ncremap -P mpas --vrt_out=vrt.nc --map=map.nc in.nc out.nc
ncremap --vrt_out=sose.nc mpas.nc out.nc
ncremap --vrt_out=mpas.nc sose.nc out.nc
ncremap --vrt_out=woa18.nc mpas.nc out.nc
ncremap --vrt_out=mpas.nc woa18.nc out.nc
ncremap --vrt_out=argo.nc mpas.nc out.nc
ncremap --vrt_out=mpas.nc argo.nc out.nc
The depth/height grid may be positive upwards or downwards.
http://nco.sf.net/nco.html#ncremap
http://nco.sf.net/nco.html#vrt_out
This is the first release of vertical interpolation for ocean data,
and we expect some rough edges. Please let us know what features
you want added or fixed.

B. Operators now silently avoid attempting to compress variable-length
datatypes, i.e., variables of type NC_STRING or NC_VLEN. This is
because neither netCDF nor HDF allow compression of these types.
Previously, attempting to compress these types would trigger a netCDF
error. Now the request will be silently ignored and program will
proceed as expected in all other ways.

C. The software stack upon which the Anaconda NCO package depends
has been future-proofed. Specifically the feedstocks for the Antlr2
and NCO packages have been updated to enable building conda-based
packages on newer architectures such as linux-ppc64le, osx-arm64,
and linux-aarch64. Thanks especially to Klaus Zimmerman, Xylar
Asay-Davis, and Filipe Fernandes with this effort, and to Phil
Rasch for spurring the effort in the first place.

BUG FIXES:
   
A. ncremap versions 5.0.7--5.1.3 can, with certain compiler settings
on AMD hardware, produce (obvisously) erroneous regridding results
due to the behavior of OpenMP SIMD pragmas/directives. This is only
known to affect Spack-compiled executables running on compute nodes of 
the PNNL Compy cluster. The workaround is to use executables compiled
any other way, or on any other hardware. The fix is to upgrade.
Thanks to Jill Zhang (PNNL) and Xylar Asay-Davis (LANL) for their help
and patience with finding and fixing this bug.

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 5.1.4 built/tested under
MacOS 13.1 with netCDF 4.9.1-RC2 on HDF5 1.12.2 and with
Linux with netCDF 4.8.1 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

