[netcdfgroup] netCDF Operators NCO version 4.5.4 are ready

• To: NCO Announce Mail List <nco-announce@xxxxxxxxxxxxxxxxxxxxx>, netCDF Mail List <netcdfgroup@xxxxxxxxxxxxxxxx>
• Subject: [netcdfgroup] netCDF Operators NCO version 4.5.4 are ready
• From: Charlie Zender <zender@xxxxxxx>
• Date: Thu, 7 Jan 2016 13:27:03 -0800

The netCDF Operators NCO version 4.5.4 are ready.

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

We are pleased to introduce ncremap, a new operator for regridding.
ncremap is a shell script that wraps ncks to produce a friendly
interface to regridding features. Without any external dependencies,
ncremap applies weights from a pre-exisiting mapfile to a source
data file to produce a regridded dataset. Source and destination
datasets may be on any Curvilinear, Rectangular, or Unstructured
Data (CRUD) grid. When necessary ncremap calls ESMF_RegridWeightGen
or TempestRemap to generate weights and uses those to regrid. ncremap
hides the complexity of regridding from the user, who can know
next-to-nothing about regridding.

Work on NCO 4.5.5 has commenced and will better support eliciting
latitude/longitude coordinates using the CF "coordinates" convention
and regridding variables whose horizontal dimensions are not the
most-rapidly-varying, and ncremap support for calling TempestRemap.

Enjoy,
Charlie

NEW FEATURES (full details always in ChangeLog):

A. ncremap: A new netCDF operator for regridding.
   ncremap is a shell script that wraps ncks to produce a friendly
   interface to regridding features. Without any external dependencies,
   ncremap applies weights from a pre-exisiting mapfile to input data
   file(s) to produce a regrided dataset(s). Source and destination
   datasets may be on any Curvilinear, Rectangular, or Unstructured
   Data (CRUD) grid. ncremap will also, when necessary, use external
   programs (ESMF's ESMF_RegridWeightGen (ERWG), or TempestRemap's
   GenerateOverlapMesh/GenerateOfflineMap) to generate weights and
   mapfiles and use those to regrid. ERWG is distributed in binary
   format with NCL, which many (most?) users already have on their
   system. Or ERWG and TempestRemap may be installed from source.
   Please try ncremap and send us your feedback and suggestions.
   Examples:
   ncremap -i src.nc -d dst.nc -o out.nc
   ls gcm14*cam*0007*.nc | ncremap -a conserve -M -d dst_1x1.nc -O ~/rgr
   http://dust.ess.uci.edu/smn/pst_nco_agu_201512.pdf # AGU Poster
   http://nco.sf.net/nco.html#ncremap

B. ncks prints XML "_Unsigned" attribute for unsigned attribute types.
   Formerly, ncks did not preserve the signedness of attributes.
   Thanks to Aleksandar Jelenak and Ed Armstrong for this suggestion.
   % ncks -v att_var --xml ~/nco/data/in_4.nc | grep Unsigned

    <attribute name="uint64_att" type="long" isUnsigned="true" value="0" />
   http://nco.sf.net/nco.html#xml

C. ncap2 now accepts [] and () syntax interchangeably.
   Expressions which formerly had to use one or the other can now
   use either. Brought to you by Henry.

D. ncap2 now conforms arrays by hyperslabbed dimension size rather
   than by dimension name. This mean, e.g., that hyperslabs from
   one dimension can be used to fill-in other dimensions.
   A prototypical example is determining pressure thickness of layers
   as the difference between interface pressure levels.
   For hybrid coordinate system models like CAM, this is now a
   (relatively) simple two-step command with a mixture of different
   dimensions on the LHS and RHS:
   prs_ntf[time,lat,lon,ilev]=P0*hyai+PS*hybi; // Interface pressures

prs_dlt[time,lat,lon,lev]=prs_ntf(:,:,:,1:$ilev.size-1)-prs_ntf(:,:,:,0:$ilev.size-2);
   http://nco.sf.net/nco.html#pdel
   Thanks to Philip Cameron-Smith for suggesting and to Henry Butowsky
   for implementing this new feature.

E. NCO now treats variables named wgt_* as weights and avoids
   performing math on them when possible. E.g., ncbo will preserve
   (and not difference) the variable wgt_1. This is the same behavior
   that NCO uses for coordinates, "gw", and masks (named with msk_*.)
   The idea is that weights are a property of the grid and should not
   be differenced, averaged, etc., unless necesssary.
   http://nco.sf.net/nco.html#prc_xcp

F. ncap2 now accepts "sum" as a synonym for "total" in its methods.
   Additionally, ncap2 has a new function,
   ncap_stats_wvariance(var,wgt) to computed weighted standard
   deviations where missing values may be present.
   Additionally, ncap2 now builds with GSL 2.x. All thanks to Henry.
   http://nco.sf.net/nco.html#ncap2

BUG FIXES:

A. ncks -V in (at least) versions 4.5.1--4.5.3 could segfault.
   NB: This is the "-V" (uppercase) not "-v" (lowercase) option.
   The workaround is not to use -V, solution is to upgrade to 4.5.4.
   Thanks to Patrick Nichols for reporting the problem.

B. After dimension reduction operations, ncra and ncwa excise the
   reduced dimensions from the CF "coordinates" attribute, if any.
   Versions 4.4.9--4.5.3 could, under certain circumstances involving
   multiple dimensions, retain extra whitespace in "coordinates".
   A workaround is to dump (ncks --cdl in.nc > out.cdl) then
   regenerate (ncgen -b out.nc out.cdl) the file.
   The solution is to upgrade to 4.5.4.
   Thanks to Richard Strub for reporting the 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 (20160101) 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)

   Demonstration:

   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?)

   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)

   Demonstration:

   ncks -v one ~/foo.nc

   20150924: Unidata confirmed problem
   20151221: Verified problem still exists in netCDF library

   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:

   20130724: Verified problem still exists.
   Stopped testing because inclusion of var_nm.dot broke all test scripts.

   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:

   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 )'(