[nco-announce] netCDF Operators NCO version 4.5.3 are ready

[Charlie Z. <ze...@uc...>]

The netCDF Operators NCO version 4.5.3 are ready.

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

This release mainly advances features related to regridding.
The primary advance is support for curvilinear regridding.
Latitude and longitude may now be two-dimensional coordinates.
NCO will now rectangular and curvilinear grids from most
(well-behaved) input data files, so regridding swath-like data (SLD)
(e.g., WRF and much NASA L2 data) just became a lot easier.
The ~/nco/data/sld_nco.sh script integrates the most common regridding
tasks into a (hopefully) turnkey solution in time for Thanksgiving.
Feedback welcome!

According to https://www2.cisl.ucar.edu/resources/yellowstone/software
NCAR CISL supports CDO but not NCO on Yellowstone/Geyser/Caldera.
Please contact the CISL Help Desk cis...@uc... if you would like
CISL to support NCO on these platforms. Thank you.

Work on NCO 4.5.4 has commenced and will better support eliciting
latitude/longitude coordinates using the CF "coordinates" convention,
regridding variables whose horizontal dimensions are not the
most-rapidly-varying.

Enjoy,
Charlie

NEW FEATURES (full details always in ChangeLog):

A. NCO's new configure --disable-doc switch allows NCO (but not its
    documentation) to build on vanilla OSX again.  It has long been
    possible to build/install NCO on MacOSX with a common packaging
    system, e.g., MacPorts, Fink, etc.  However, it recently become
    important to build NCO from source on vanilla MacOSX without any
    packaging system. Apple has not updated some GNU tools (like
    Texinfo) for over 10 years, and maintaining backwards compatibility
    of the documentation on vanilla OSX is not feasible. Docs continue
    to build fine with MacPorts, Fink, etc.

B. ncks --rgr nfr reads any/all grid information from input files,
    infers any necessary but missing information (e.g., estimates cell
    interface locations from cell midpoints), and outputs the gridfile
    in SCRIP-format for easy use by offline regridders. The procedure
    works on input files where NCO can identify lat/lon coordinates.
    ncks --rgr nfr --rgr grid=infer.nc in.nc out.nc
    http://nco.sf.net/nco.html#grid

C. ncks --rgr skl='y' creates a "skeleton" version of a data file
    with the specified geometry. This skeleton file contains grid
    center and interfaces locations and gridcell area. These can be
    more easily be assessed, and continental outlines examined, than
    with the corresponding SCRIP file. The skeleton can also be
    manually populated with data rather than relying on a model.
    # Generate T42 Gaussian grid file t42_SCRIP.nc and skeleton file 
t42_skl.nc
    ncks --rgr skl=${DATA}/grids/t42_skl.nc --rgr 
grid=${DATA}/grids/t42_SCRIP.nc \
      --rgr latlon=64,128 --rgr lat_typ=gss --rgr lon_typ=Grn_ctr \
      ~zender/nco/data/in.nc ~/foo.nc
    http://nco.sf.net/nco.html#skl

D. Generate 2-D regional grids in SCRIP format, and, in conjunction
    with a mapfile, regrid to/from regional bounding boxes.
    During grid generation, specify bounding box edges with
    --rgr wesn=lon_wst,lon_est,lat_sth,lat_nrt or
    --rgr snwe=lat_sth,lat_nrt,lon_wst,lon_est
    This feature debuted 4.5.2 but was not announced because it
    was not yet documented.
    # Regrid global file to regional domain
    ncks --map map_global_to_regional_bilin.nc in.nc out.nc
    http://nco.sf.net/nco.html#grid
    http://nco.sf.net/nco.html#regrid

E. Use --xtn_var or --extensive to specify extensive variables.
    Extensive variables are summed not averaged during regridding.
    The support for extensive variables is not yet robust, yet we
    are ready to receive feedback from early adopters.
    ncks --xtn count --map map.nc in.nc out.nc
    http://nco.sf.net/nco.html#regrid

BUG FIXES:

A. ncks fixes two newly uncovered regridder bugs that were exposed by
    multi-level fields that contain missing values and underwent
    non-conservative (e.g., bilinear) regridding. The bugs were in
    threaded code and show up in compiler-specific ways.
    The solution is to upgrade to 4.5.3.
    Thanks to PNNL for first reporting problems.

B. ncap2 now evaluates logical expressions with a method that does
    not convert the type of the arguments to lesser precision.
    This fixes incorrect results that could occur when an argument
    could not be represented by the lesser precision.
    The solution is to upgrade to 4.5.3. Thanks to Maxim Petrenko for
    reporting this problem, and to Henry Butowsky for fixing it.

C. ncecat version 4.4.9 introduced a problem that could cause it
    to fail when using --gag mode on a single file. This problem
    has been fixed. The solution is to upgrade to 4.5.3, or to use
    versions 4.4.8 and prior if you encounter this problem.
    Thanks to Huan Wu for reporting this problem.

D. ncatted version 4.5.1 introduced a bug that dumps core when
    attribute deletion is requested without a specific attribute name,
    i.e., whenever all attributes are to be deleted. The workaround is
    to specify the attribute name(s) to be deleted, to use versions
    4.5.0 and earlier, or to upgrade to 4.5.3. Thanks to Richard Strub
    for reporting this problem.

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 4.5.3 built/tested with netCDF
    4.4.0-development (20150818) on top of HDF5 hdf5-1.8.13 with:

    cd ~/nco;./configure # Configure mechanism -or-
    cd ~/nco/bld;make dir;make allinone # Old Makefile mechanism

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

    Bug tracking: https://www.unidata.ucar.edu/jira/browse/fxm
    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

C. Running jobs at NCAR, NERSC, ANL, ORNL? NCO is in ~zender/[bin,lib]
-- 
Charlie Zender, Earth System Sci. & Computer Sci.
University of California, Irvine 949-891-2429 )'(