$Header$ -*-text-*-

The netCDF Operators NCO version 4.7.0 are released. 

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

What's new?
Version 4.7.0 adds spit and polish through the toolkit.
Nothing major stands out, except perhaps for easy access
to compression algorithms in ncclimo and ncremap.

Work on NCO 4.7.1 has commenced. Planned changes include
better diagnosis and workarounds for the netCDF CDF5 bug,
and parallel weight generation by ncremap.

Enjoy,
Charlie

NEW FEATURES (full details always in ChangeLog):

A. ncclimo and ncremap accept fl_fmt options for output file format.  
   The option behaves the same as it does for other operators:
   ncclimo [-3 -4 -5 -6 -7] ...
   ncremap [-3 -4 -5 -6 -7] ...
   ncclimo --fl_fmt=netcdf4 ...
   ncremap --fl_fmt=cdf5 ...
   http://nco.sf.net/nco.html#fl_fmt
   http://nco.sf.net/nco.html#autoconversion

B. ncclimo and ncremap accept the dfl_lvl option for compression.
   The value of dfl_lvl is an integer fro 0..9 that specifies the
   DEFLATE (= Lempel-Ziv + Huffman) compression level for netCDF4.
   The option behaves the same as it does for other operators:
   ncclimo --dfl_lvl=3 ...
   ncremap --dfl_lvl=3 ...
   ncclimo -L 3 ...
   ncremap -L 3 ...
   http://nco.sf.net/nco.html#deflate

C. ncclimo accepts the ppc option for Precision-Preserving Compression. 
   Other operators allow multiple, per-variable PPC specification.
   ncclimo allows only one PPC option, equivalent to specifying
   --ppc default=<val> with the compiled operators.  
   NB: regridding does not yet accept PPC.
   ncclimo --ppc=3 ...
   http://nco.sf.net/nco.html#ppc
   http://nco.sf.net/nco.html#bitgrooming

D. ncrename is now quiet by default, like all other operators.
   The old summary line that tallied the numbers of things renamed
   can still be seen by invoking ncrename with -D 1.
   http://nco.sf.net#ncrename

E. CMake: Pedro Vicente contributed a CMake build-engine in 4.6.9. 
   The CMake engine now correctly links ncap2 to intrinsic math
   functions like erf(), gamma(), ... 
   Please give us feedback on any wrinkles in the CMake build. 
   To build with CMake and install in /usr/local: 
   cd nco/cmake
   cmake .. -DCMAKE_INSTALL_PREFIX=/usr/local
   make
   sudo make install
   Additional examples in cmake/build.bat
   http://nco.sf.net#bld

F. The automatic CDF5 bug checker in 4.6.9 has been turned-off.
   It produced too much distracting output in workflows affected
   by the CDF5 bug. To activate this check, build NCO with, e.g.,
   CPPFLAGS='-DNCO_CDF5_BUG_CHK' ./configure ...
   The checker itself has been improved so that, when turned on,
   operators are now quiet when sniffing CDF5 files for corruption,
   until they detect a "large" (> 4 GB) variable.
   In 4.6.9 the sniffing algorithm was noisier, and printed an INFO
   upon closing any CDF5 file.
   http://nco.sf.net#bug_cdf5

BUG FIXES:

A. Fix bug where ncra and ncrcat treated negative record hyperslab
   indices with old (pre-2014) convention, and were off-by-one
   relative to the 2014+ Python-based convention. Previously
   "ncrcat -d time,-1" extracted the penultimate record, now it
   extracts the last. This bug only affected the record dimension
   of the multi-file operators ncra and ncrcat.

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 4.7.0 built/tested under
   MacOS 10.12.6 with netCDF 4.4.1.1 on HDF5 1.10.1 and with
   Linux with netCDF 4.5.1-development (201701101) 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

   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

   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

