$Header$ -*-text-*- netCDF Operators NCO version 5.3.1 howl at the Moon http://nco.sf.net (Homepage, Mailing lists, Help) http://github.com/nco/nco (Source Code, Issues, Releases) What's new? Version 5.3.1 adds features and fixes to ncremap and ncclimo. The new autoconversion feature allows these scripts to automagically convert netCDF4 string variables to netCDF3 character arrays. The improved treatment of fixed time dimensions allows ncclimo to work with raw MERRA2 files. Together these improvements make possible regridding and vertical interpolation of the new formatting of Copernicus Data Store (CDS) files used for, e.g., ERA5. Skip this release if these changes do not interest you. Work on 5.3.3 is underway and includes improved NC_STRING autoconversion support for other NCO operators. Enjoy, Charlie NEW FEATURES (full details always in ChangeLog): A. Autoconversion of NC_STRING variables, i.e., automatic conversion from type NC_STRING to NC_CHAR as dictated by choosing a netCDF3 output from a netCDF4 input file, work for all attributes, but not for all variables. This is because attributes are at most one-dimensional and may be of any size whereas variables require gridded dimensions that usually do not fit the ragged sizes of text strings. Hence scalar NC_STRING attributes are correctly converted to and stored as NC_CHAR attributes in the netCDF3 output file, but not all NC_STRING variables are correctly converted. As of version 5.3.1, NCO has two distinct levels of support for autoconversion of NC_STRING variables. ncremap fully supports autoconversion of scalar NC_STRING variables in both horizontal regridder and vertical interpolation mode. This means that ncremap will produce netCDF3 output files from netCDF4 input files (if requested) and that any NC_STRING variables in the input files will be translated to NC_CHAR arrays in the netCDF3 output files. There is no loss of information since the entire contents of the string is preserved in the character array. Autoconversion stores the character array with a new dimension named sng_lng_X where X is the smallest power of ten between 10 and 10000 that is capable of containing the string contents (including the terminating NUL character). This type of variable autoconversion fails if the input string length exceeds 10000 (this is a safety measure, and could be expanded if people lobby me). All operators besides ncremap currently retain only the first character of the input NC_STRING array. This loses information. We are working to implement the same feature that ncremap enjoys. Both types of autoconversion fail if the input string variable is multidimensional, i.e., an array of type NC_STRING. A feature to solve that case is tractable, though we have not yet received any requests for it. Thanks to Waler Hannah (LLNL) for prompting this feature. http://nco.sf.net/nco.html#autoconversion http://nco.sf.net/nco.html#ncclimo B. ncremap's vertical interpolator now automatically extrapolates variables named "t" (as in ERA5 raw data) as if they were temperature. Futhermore the interpolator now automatically extrapolates variables named "H" (as in MERRA2 raw data) and VerticalLayerMidpoint (SCREAM) as if they were geopotential height. See the documentation for specifics about the temperature and geopotential height extrapolation algorithms. http://nco.sf.net/nco.html#vrt C. For many years, users at select supercomputer centers have been able to access the latest versions of NCO scripts directly from C. Zender's build directories. However, this feature was not documented until now. Zender's build directories usually contain the latest NCO snapshot, and so may be unstable and are not for everyday use. This feature is instead intended to allow users to test and provide feedback on new features before they are distributed in a public release. Invoking ncclimo and ncremap with the --npo (or long-option equivalent --nco_path_override) flag as the first option (i.e., as $1) causes these scripts to utilize the binary NCO executables in Zender's build directories on the following machines at the national supercomputer centers in parentheses: acme1 (LLNL), andes (ORNL), chrysalis (ANL), compy (PNNL), derecho (NCAR), frontier (ORNL), and perlmutter (NERSC). If the latest features that you want are actually implemented in the NCO binaries or library, then it may suffice to invoke your own version of the scripts, as in the first examples below. However, if the latest features that you want are implemented in the scripts themselves, then you can either invoke Zender's scripts directly (as in the second set of examples), or copy those scripts into your own executable path: @verbatim # Access Zender's latest binaries from your default scripts ncremap --npo -m map.nc in.nc out.nc ncclimo --npo -P elm -c ${caseid} ... # Access Zender's latest binaries from Zender's latest scripts ~zender/bin/ncremap --npo -m map.nc in.nc out.nc ~zender/bin/ncclimo --npo -P elm -c ${caseid} ... @end verbatim @end example In both cases, the --npo flag must be the first option invoked. http://nco.sf.net/nco.html#npo http://nco.sf.net/nco.html#nco_path_override BUG FIXES: A. ncremap's vertical interpolator now understands that the time dimension in input surface pressure fields may be "fixed". Previously the interpolator assumed that the temporal dimension, if any, was an unlimited/record dimension. This could cause it to miscalculate the number of horizontal spatial dimensions, and then to fail. Now the interpolator considers any fixed dimension named "time", or most unlimited dimensions (except certain corner cases) to be temporal dimension. This allows it to interpolate raw MERRA2 or ERA5 data. Thanks to Naser Mahfouz (PNNL) for prompting this fix/feature. http://nco.sf.net/nco.html#vrt 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 5.2.7 built/tested under MacOS 15.2 with netCDF 4.9.4-development on HDF5 1.14.3 and with Linux FC40 with netCDF 4.9.2 on HDF5 1.14.3. 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