$Header$ -*-text-*-

netCDF Operators NCO version 5.1.8 make the scene

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

What's new?
Version 5.1.8 recognizes NC_STRING as valid alternatives to NC_CHAR
attributes (consistent with CF Conventions), infers MPAS grids stored
in radians when units attributes are not present, and support checks
for adherence to NASA DIWG (and CF) recommendations for valid
identiers, and for the missing_value attribute. It also recognizes
Skip this release if these issues are of no import to you.

Work on NCO 5.1.9 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. NCO operators are now much better, though not perfect,
at recognizing NC_STRING attributes as equivalent and interchangeable
with NC_CHAR attributes, as permitted by CF Conventions since ~2020.
In particular, this prevents annoying WARNINGs when CF attributes
like "bounds" are stored as NC_STRING. Thanks to Abel Aoun for
reporting/suggesting this.

B. ncremap can now infer SCRIP grid-files from MPAS datasets
when the coordinates are in radians yet not marked as such in
the units attribute. The algorithm simply assumes that if the
bounding latitudes and longitudes are within +/-2*pi then the
units are radians. Imperfect, yet unlikely to fail in most
MPAS meshes.
ncremap --dst_fl=AIS_4to20km.nc --grd_dst=ais4to20km_ismip6.nc

C. ncks supports a new flag, --chk_chr, that prints any identifiers
(dimension,group,variable,attribute names) that do not comply with
the CF Conventions. CF-compliant identifiers must match this
regular expression: [A-Za-z][A-Za-z0-9_]*
This is much more restrictive than the NUG, as it eliminates most
special characters.
$ ncks --chk_chr ~/nco/data/in.nc
...
ncks: WARNING nco_chk_chr() reports variable att_var_spc_chr attribute name "at_in_name@" is not CF-compliant
ncks: WARNING nco_chk_chr() reports variable name "var_nm-dash" is not CF-compliant
ncks: WARNING nco_chk_chr() reports variable var_nm-dash attribute name "att_nm-dash" is not CF-compliant
ncks: INFO nco_chk_chr() reports total number of identifiers with CF non-compliant names is 26
$
http://nco.sf.net/nco.htlm/chk_chr

D. ncks supports a new flag, --chk_mss, that reports which variables
(and groups) contain a missing_value attribute.
NASA's Dataset Interoperability Working Group (DIWG) notes that the
missing_value attribute has been semi-deprecated, and recommends that
it should not be used in new Earth Science data products. 
To check a file for compliance with the DIWG recommendation: 
$ ncks --chk_mss ~/nco/data/in.nc
ncks: WARNING nco_chk_mss() reports variable fll_val_mss_val contains "missing_value" attribute
ncks: WARNING nco_chk_mss() reports variable one_dmn_rec_var_missing_value contains "missing_value" attribute
...
ncks: WARNING nco_chk_mss() reports variable rec_var_int_mss_val_flt contains "missing_value" attribute
ncks: INFO nco_chk_mss() reports total number of variables and/or groups with "missing_value" attribute is 11
$
http://nco.sf.net/nco.htlm/chk_mss

E. ncremap and ncclimo now support paths and nodenames on DOE OLCF's
Frontier supercomputer.

BUG FIXES:
   
A. N/A

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 5.1.8 built/tested under
MacOS 13.5.2 (c) with netCDF 4.9.3-dev on HDF5 1.14.2 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

