The netCDF Operators NCO version 4.4.9 are ready.
http://nco.sf.net (Homepage)
http://dust.ess.uci.edu/nco (Homepage "mirror")
This release includes small feature improvements in chunking,
deflation, and attribute handling during dimension reduction.
Also improvements in clarity and consistency of messages.
While chunking is an esoteric feature for many, its importance
is increasing as the move to netCDF4 (classic) continues.
The chunking defaults and flexibility have reached a new level
of robustness in this release.
The main new awesome feature is that ncra understands weights.
Finally. Applying uneven weights to different input files was
too clunky. This release is dedicated to the intrepid souls who
use NCO to generate climatologies that require uneven weights.
This release should make that task much easier.
Work on NCO 4.5.0 has commenced and will support regridding,
additional ncra flexibility with weights, and easier builds on
supercomputer systems that use modules.
Enjoy,
Charlie
NEW FEATURES (full details always in ChangeLog):
A. NCO has improved default performance of deflation and chunking.
Our "best practices" chunking (map/policy=nco) is now default when
manually deflating netCDF3 files into netCDF4 files.
This invokes Rew's balanced chunking for three-dimensional
variables, and LeFter-Product (cnk_map=lfp) chunking for others.
LFP chunking, in turn, implements more reasonable defaults when
the variable size is smaller than a single chunksize.
This reduces excessive chunk sizes for many small variables.
Shuffle is now turned-on by default when manually deflating files.
This restores behavior from the NCO 4.3.x series, and can improve
compression ratios by 10-30% relative to not shuffling.
Copying multi-dimensional record variables from netCDF3 to netCDF4
files no longer invokes the MM3 workaround.
This speeds-up deflation of netCDF3 datasets.
ncks -O -4 -L 1 netCDF3.nc netCDF4.nc
http://nco.sf.net/nco.html#cnk
B. ncwa now eliminates dimensions from the "coordinates" attribute
after collapsing them. This helps ensure that rank-reduced
variables become completely independent from their former
dimensions. The former presence of collapsed dimensions continues
to be indicated by the "cell_methods" attribute.
ncwa -O -a lat in.nc out.nc
http://nco.sf.net/nco.html#coordinates
http://nco.sf.net/nco.html#cell_methods
http://nco.sf.net/nco.html#ncwa
C. NCO now warns users and suggest workarounds in situations when
operators behave correctly, though perhaps not as expected,
including:
1. When coordinate variables intended to be excluded by -x and -C
may nonetheless appear in output file, and suggest workaround
2. When hyperslabs are specified for multi-dimensional
"coordinates"
D. NCO now respects the CF "climatology" attribute: The variable
pointed to by this attribute is treated as a pseudo-coordinate
variable, and is extracted by default with any referring variable.
Climatology variables now obey the same arithmetic rules as
coordinates and are exempted from certain operations.
Their treatment is identical to that of "bounds" variables.
This command now retrieves the named variable, its coordinates (if
any), and any variables named in the "ancillary_variable",
"bounds", "climatology", and "coordinates" attributes:
ncks -v temperature in.nc out.nc
http://nco.sf.net/nco.html#climatology
E. ncra now accepts user-specified weights with the -w switch.
When no weight is specified, ncra continues its old behavior
and weights each record (e.g., time slice) equally.
Weights specified with -w wgt may take one of two forms.
Fist, the wgt argument may be a comma-separated list of values by
which to weight each input file. Or, the wgt argument may be
the name of a weighting variable present in every input file.
The variable may be a scalar or a one-dimensional record variable.
Scalar weights are applied uniformly to the entire file (i.e., a
per-file weight), while one-dimensional weights apply to each
corresponding record (i.e., per-record weights). Two applications
of weights with ncra include easier generation of accurate averages
of seasonal statistics, and of accurate averages of quantities
sampled with a dynamically changing timestep.
ncra -w 31,31,28 dec.nc jan.nc feb.nc out.nc
ncra -w delta_tm in1.nc in2.nc in3.nc out.nc
http://nco.sf.net/nco.html#ncra
BUG FIXES:
A. Fix ncecat in group aggregation mode (i.e., ncecat --gag) so it
can no longer use uninitialized file pointers.
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 4.4.9 built/tested with netCDF
4.3.3-rc3 (20150129) 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 (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
C. 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. Pre-built Debian Sid & Ubuntu packages:
http://nco.sf.net#debian
B. Pre-built Fedora and CentOS RPMs:
http://nco.sf.net#rpm
C. Pre-built Mac binaries:
http://nco.sf.net#mac
D. Pre-built Windows (native) and Cygwin binaries:
http://nco.sf.net#windows
E. 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 ...
--
Charlie Zender, Earth System Sci. & Computer Sci.
University of California, Irvine 949-891-2429 )'(
