[nco-announce] netCDF Operators NCO version 4.6.1 are ready

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

The netCDF Operators NCO version 4.6.1 are ready.

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

What's new?

4.6.1 is mainly a stability release to polish existing features and to
add minor new ones. The main new feature is that ncclimo supports
incremental climatologies. ncatted works much better with special
characters in attribute names, while preserving its ability to handle
regular expressions. ncflint gains a weight-normalization option.

Work on NCO 4.6.2 has commenced and will better support regridding
variables whose horizontal dimensions are not most-rapidly-varying.

Enjoy,
Charlie

NEW FEATURES (full details always in ChangeLog):

A. ncks supports new provenance features released in netCDF-4.4.1.
    These provenance (and other) metadata are revealed by the --hdn (or
    --hidden) switch when dumping global metadata from a netCDF4 file:
    ncks --cdl --hdn -M ~/nco/data/in_grp.nc
    http://nco.sf.net/nco.html#ncflint

B. Wenshan Wang of UCI contributed a Quick Reference Card suitable
    for printing. Thanks, Wenshan!
    http://nco.sf.net/nco_rfr_crd.pdf

C. Add ncflint -N, --nrm, --normalize option so w1:=w1/(w1+w2),
    w2:=w2/(w1+w2)
    http://nco.sf.net/nco.html#ncflint

D. ncap2's array() function can now take a dimension list as the
    third argument, e.g., n2=array(1.0,2.0,/$time,$lat,$lon/)
    http://nco.sf.net/nco.html#ncap2

E. ncclimo will now generate incremental climatologies, e.g., it will
    extend an existing climatology with the new files from a simulation
    to create an extended climatology. Only the new monthly files and
    the existing climatolgoy need be accessible---the old monthly files
    are not used. Invoke ncclimo incremental mode with, e.g.,
    ncclimo -c caseid -s 1982 -e 1983 -i raw -o clm -r map.nc -S 1980
    http://nco.sf.net/nco.html#ncclimo

BUG FIXES:

A. ncatted now allows special characters in attribute and variable
    names. Previously, ncatted interpreted most special characters
    as indicating a regular expression. Now ncatted first tries to
    interpret most special characters as literals, and if that does
    not work, then it interprets them as a regular expression.
    Thanks to emontgomery for reporting the problem.

B. ncap2 fixed handling of implicit array bounds for slabs of form
    var(3:). Previously ncap2 would exit with an error.
    http://nco.sf.net/nco.html#ncap2

C. When inferring grid coordinates from 2D files, ncremap in 4.6.0
    sometimes would confuse dimension names with coordinate names.
    This has been fixed. The workaround is to downgrade to 4.5.6 or
    upgrade to 4.6.1.

D. ncremap now automatically chooses distinct output spatial and
    temporal bounds names when for non-rectangular output datasets.
    Previously ncremap might use, e.g., "nbnd" for both. This could
    fail for curvilinear datasets.

E. Resolve an issue that caused spurious warnings from nco_fl_mv().

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 4.6.1 built/tested under
    MacOS with netCDF 4.3.3.1 on HDF5 1.8.16 and with
    Linux with netCDF 4.4.1-development (20160212) on HDF5 1.8.13.

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

    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

-- 
Charlie Zender, Earth System Sci. & Computer Sci.
University of California, Irvine 949-891-2429 )'(