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$Header$ -*-text-*-
netCDF Operators NCO version 5.3.6 makes landfall
http://nco.sf.net (Homepage, Mailing lists, Help)
http://github.com/nco/nco (Source Code, Issues, Releases)
What's new?
Version 5.3.6 consists mainly of bugfixes:
There is a regridder fix that prevent it from failing to work
with some regional destination grids (global grids are not affected).
ncclimo fixes an issue computing global timeseries from ELM/CLM data
on unstructured grids, e.g., from "bigrid" ESM simulations.
Smaller fixes abound, including to the map-checker.
Regridder should upgrade. Others may skip this release.
Enjoy,
Charlie
NEW FEATURES (full details always in ChangeLog):
A. The ncremap tutorial on the E3SM Confluence page
https://e3sm.atlassian.net/wiki/spaces/DOC/pages/edit-v2/754286611
contains still more documentation on how to exploit the three types
of parallelism (node-, workflow-, and thread-level) supported by
ncremap.
BUG FIXES:
A. The map checker (ncks --chk_map) and regridder robustness check
implemented in 5.3.5 contained a bug that affected regional
destination grids. The bug could cause these tools to report correct
mapfiles as invalid. This has been fixed. The solution is to upgrade
to 5.3.6 or downgrade to 5.3.4.
B. The regridder now accepts 'nco_idw' and 'ncoidw' as synonyms for
NCO's inverse-distance-weighted algorithm. 'nco_idw' was not
recognized on some earlier versions. Thanks to Zachary Moon for
reporting this.
C. ncclimo's 5.3.5 feature to automatically detect surface fields
did not recognized the 'lndgrid' dimension of ELM and CLM as
indicating a horizontal spatial dimension. This prevented ncclimo
from constructing automated spatial timeseries averages of datasets
on native unstructured grids. That is now fixed. The workaround is
to downgrade to version 5.3.3 and explicitly specify the desired
fields. The solution is to upgrade.
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 5.3.4 built/tested under
MacOS 15.6.1 with netCDF 4.10-development on HDF5 1.14.6
and with Linux FC42 with netCDF 4.9.2 on HDF5 1.14.4.
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
20190201: Possibly this problem was fixed in netCDF 4.6.2 by https://github.com/Unidata/netcdf-c/pull/1001
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
Workaround #3: Compile NCO with netCDF >= 4.6.2
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 produces unreadable file foo.nc
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
20171107: https://github.com/Unidata/netcdf-c/issues/597
20190202: Progress has recently been made in netCDF 4.6.3-development
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
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