$Header$ -*-text-*-

The netCDF Operators NCO version 4.7.2 have slithered out.

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

What's new?
Version 4.7.2 contains one new cool feature for ncremap, one important
bugfix for the splitter, and assorted minor improvements and fixes.
ncremap now implements E3SM-recommended Tempest remapping algorithms
for all combinations of FV<->SE remapping for flux and state variables. 
The ncclimo splitter functionality has an important bugfix for cases
when the total number requested time-periods (usually years) of
averaging is not evenly divisible by the maximum number of
time-periods per output-file.

Work on NCO 4.7.3 has commenced. Planned changes include
better diagnosis and workarounds for the netCDF CDF5 bug,
parallel weight generation by ncremap, and possibly workarounds for 
using quotation marks with ncap2 in Windows.

Enjoy,
Charlie

NEW FEATURES (full details always in ChangeLog):

A. ncremap implements E3SM-recommended Tempest remapping algorithms. 
   ncremap can now easily generate and use the each of the six
   E3SM-recommended mappings between FV<->SE flux & state variables.
   ncremap automatically employs the "boutique" TempestRemap options 
   so long as Tempest2 is installed.
   ncremap -a se2fv_flx --src_grd=ne30.g --dst_grd=fv.nc -m map.nc
   ncremap -m map.nc in.nc out.nc
   Canonical algorithm names are se2fv_flx, se2fv_stt, se2fv_alt,
   fv2se_flx, fv2se_stt, fv2se_alt.
   http://nco.sf.net/nco.html#ncremap
   
B. ncremap supports "canonical" NCO argument ordering.
   Canonical ordering is: command [options] [input] [output].
   Previously ncremap required the use of options (like -i
   and -o) or pipes to supply filenames:
   ncremap -m map.nc -i in.nc -o out.nc
   ncremap -m map.nc -o out.nc in.nc
   ncremap -m map.nc -O out_dir in1.nc in2.nc
   ls in.nc | ncremap -m map.nc -o out.nc
   ncremap -m map.nc -o out.nc < in.nc
   Now ncremap finally supports the canonical ordering of command line
   arguments most frequently desired for one-off regridding, where a
   single input and output filename are supplied as command-line
   positional arguments without switches, pipes, or redirection:
   ncremap -m map.nc in.nc out.nc
   http://nco.sf.net/nco.html#ncremap
   http://nco.sf.net/nco.html#alg_typ

C. ncremap support a --mss_val=val option for MPAS data.
   ncremap pre-processes MPAS datasets (indicated with -P mpas) and
   annotates their floating point variables with the _FillValue
   attribute. By default it sets _FillValue to the correct value
   for MPAS ocean and sea-ice models. However, the MPAS land-ice model
   uses a different missing value. Hence this option is usually
   invoked as --mss_val=-1.0e36 to facilitate processing of
   MPAS land-ice datasets. 
   ncremap -P mpas --mss_val=-1.0e36 -s ais.nc -i data.nc -g fv.nc -o out.nc
   http://nco.sf.net/nco.html#ncremap
   http://nco.sf.net/nco.html#mss_val_ncremap

D. ncclimo has improved support for NCAR cheyenne batch queues
   Previously ncclimo -p mpi failed on Cheyenne due to differences
   between SGI MPT mpirun and "normal" mpirun syntax.
   Now ncclimo uses mpirun syntax expected by SGI MPT on cheyenne.
   qsub -A SCSG0002 -l select=12:ncpus=36:mpiprocs=1 -l \
   walltime=00:30:00 -q regular -N ncclimo -j oe -m e -o ~/ncclimo.out 
   http://nco.sf.net/nco.html#ncclimo

BUG FIXES:

A. Fix ncclimo splitter bug when the total number requested
   time-periods (usually years) of averaging is not evenly divisible
   by the maximum number of time-periods per output-file.
   Previously the splitter would omit time-series segments.
   The workaround for NCO < 4.7.2 is to specify a maximum number
   of years-per-file that evenly divides the total number of years.
   For example, split a 75 year climatology by setting --ypf
   to 1, 3, 5, 15, 25, or 75 or greater.
   The solution is to upgrade to 4.7.2.
   Then you can use the default (ypf=50) or any other value.

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 4.7.2 built/tested under
   MacOS 10.13.2 with netCDF 4.4.1.1 on HDF5 1.10.1 and with
   Linux with netCDF 4.5.1-development (20180110) 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
   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

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 file is unreadable
   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
   Bug tracking: https://www.unidata.ucar.edu/jira/browse/fxm
   More details: http://nco.sf.net/nco.html#ncrename_crd

C. NOT YET FIXED (netCDF4 library bug)
   Renaming a non-coordinate variable to a coordinate variable fails in netCDF4

   Demonstration:
   ncrename -O -v non_coord,coord ~/nco/data/in_grp.nc ~/foo.nc # Fails (HDF error)

   20170323: Confirmed problem reported by Paolo Oliveri, reported to Unidata
   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

   Bug tracking: https://www.unidata.ucar.edu/jira/browse/fxm
   More details: http://nco.sf.net/nco.html#ncrename_crd

D. FIXED in netCDF Development branch as of 20161116 and in maintenance release 4.4.1.1
   nc-config/nf-config produce erroneous switches that cause NCO builds to fail
   This problem affects netCDF 4.4.1 on all operating systems.
   Some pre-compiled netCDF packages may have patched the problem.
   Hence it does not affect my MacPorts install of netCDF 4.4.1.

   Demonstration:
   % nc-config --cflags # Produces extraneous text that confuses make
   Using nf-config: /usr/local/bin/nf-config
   -I/usr/local/include -I/usr/local/include -I/usr/include/hdf

   If your nc-config output contains the "Using ..." line, you are
   affected by this issue. 

   20161029: Reported problem to Unidata
   20161101: Unidata confirmed reproducibility, attributed to netCDF 4.4.1 changes
   20161116: Unidata patch is in tree for netCDF 4.4.2 release
   20161123: Fixed in maintenance release netCDF 4.4.1.1

E. 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

F. 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

