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NOTICE: This version of the NSF Unidata web site (archive.unidata.ucar.edu) is no longer being updated.
Current content can be found at unidata.ucar.edu.
To learn about what's going on, see About the Archive Site.
The netCDF Operators NCO version 4.3.3 are ready. http://nco.sf.net (Homepage) http://dust.ess.uci.edu/nco (Homepage "mirror") The current release brings full group support to ncwa and ncrename. Now seven operators fully support group hierarchies: ncbo, ncecat, ncflint, ncks, ncpdq, ncrename, and ncwa. ncks has a new, highly-configurable printing mode which displays data from files with groups with friendlier indentation and annotation, including in CDL and XML modes. The new formats involve many choices for indentation and spacing. We would be happy to learn what format changes would make analyzing your data easier. The old "traditional" ncks printing format remains the default, though this may change in the future. Please let us know if you find any substantive (non-whitespace) differences outputting CDL from ncdump and ncks. Work on NCO 4.3.4 is underway and includes improved netCDF4 support for more NCO operators (ncatted, ncra, ncea, ncrcat) and improved support for HDF4 files. Enjoy, Charlie "New stuff" in 4.3.3 summary (full details always in ChangeLog): NEW FEATURES: A. ncwa now supports groups, Group Path Editing (GPE) and list unions, the same options supported by ncbo, ncecat, ncflint, ncks, and ncpdq. Features are controlled by -g, -G and --union, respectively. ncwa -a lon -g g1 -v v1 -G dude -O -p ~/nco/data in_grp.nc ~/foo.nc http://nco.sf.net/nco.html#ncwa http://nco.sf.net/nco.html#gpe http://nco.sf.net/nco.html#union B. ncrename will rename groups when compiled (with -DNC_HAVE_RENAME_GRP) against the latest version (~20130720) of libnetcdf.a (which will eventually be released as version 4.3.1). This is much faster than using GPE and ncks to rename groups. Note that the location of the new group is the same as the old. To move groups around, one still needs to use GPE. ncrename -g g1,obama in_grp.nc out.nc http://nco.sf.net/nco.html#ncrename http://nco.sf.net/nco.html#gpe C. ncks will write the MD5 digest of each variable as an NC_CHAR attribute named MD5. Activate this with the --md5_wrt or --md5_write_attribute long options. ncks -O -C --md5_wrt -v md5_.? ~/nco/data/in.nc ~/out.nc http://nco.sf.net/nco.html#md5 D. ncks -5 supports a new, group-friendly printing format. This format uses indentation to indicate group level. Groups are arranged alphabetically, and variable metadata and data are printed alphabetically within each group. Otherwise the information printed is in "traditional" ncks format (but see --cdl switch below for another possibility). Feedback welcome! ncks -5 ~/nco/data/in_grp.nc http://nco.sf.net/nco.html#ncks E. ncks --cdl prints results in CDL format. CDL is the human-readable lingua franca of netCDF imported by ncgen and exported by ncdump. "Traditional" ncks printing was designed for flat netCDF3 files, and for examining hyperslabs of data values. CDL printing is friendlier for examining group hierarchies, and the CDL output is directly usable by ncgen. Moreover, ncks outputs the minimal CDL that matches the user's request, and CDL mode plays well with other ncks options like hyperslabs: ncks --cdl ~/nco/data/in_grp.nc ncks --cdl ~/nco/data/in.nc ncks --cdl -v v1 ~/nco/data/in_grp.nc ncks --cdl -v three_dmn_rec_var -d lon,2 ~/nco/data/in_grp.nc http://nco.sf.net/nco.html#cdl F. ncks --xml prints metadata in NcML XML format. NcML is also exported by ncdump -x. ncks outputs the minimal NcML that matches the user's request. ncks --xml ~/nco/data/in_grp.nc ncks --xml ~/nco/data/in.nc ncks --xml -v v1 ~/nco/data/in_grp.nc http://nco.sf.net/nco.html#xml BUG FIXES: A. Fixed potential ncpdq bug packing variables in subgroups. B. ncatted supports attributes of type NC_STRING. Earlier versions of ncatted fail when handling NC_STRINGs. ncatted -a string_att,att_var,c,sng,"string, cheese" in.nc out.nc http://nco.sf.net/nco.html#ncatted KNOWN BUGS NOT YET FIXED: This section of ANNOUNCE reports and reminds users of the existence and severity of known, not yet fixed, problems. These problems occur with NCO 4.3.3 built/tested with netCDF 4.3.0 on top of HDF5 hdf5-1.8.9 with these methods: cd ~/nco;./configure --enable-netcdf4 # Configure mechanism -or- cd ~/nco/bld;make dir;make all;make ncap2 # Old Makefile mechanism A. NOT YET FIXED Correctly read netCDF4 input over DAP, write netCDF4 output, then read resulting file. Replacing netCDF4 with netCDF3 in either location of preceding sentence leads to success. DAP non-transparency: Works locally, fails through DAP server. Unclear whether resulting file is "legal" because of dimension ID ordering assumptions. Demonstration: ncks -4 -O -v three_dmn_rec_var http://motherlode.ucar.edu:8080/thredds/dodsC/testdods/in_4.nc ~/foo.nc ncks ~/foo.nc # breaks with "NetCDF: Invalid dimension ID or name" 20130724: Unable to verify since in_4.nc no longer accessible on Unidata DAP server Bug report filed: netCDF #QUN-641037: dimension ID ordering assumptions B. NOT YET FIXED netCDF4 library fails when renaming dimension and variable using that dimension, in either order. Works fine with netCDF3. Problem with netCDF4 library implementation. Demonstration: ncks -O -4 -v lat_T42 ~/nco/data/in.nc ~/foo.nc ncrename -O -D 2 -d lat_T42,lat -v lat_T42,lat ~/foo.nc ~/foo2.nc # Breaks with "NetCDF: HDF error" ncks -m ~/foo.nc 20130724: Verified problem still exists Bug report filed: netCDF #YQN-334036: problem renaming dimension and coordinate in netCDF4 file C. NOT YET FIXED (requires change to DAP protocol) 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://motherlode.ucar.edu:8080/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 report filed: https://www.unidata.ucar.edu/jira/browse/NCF-47 D. NOT YET FIXED (requires change to DAP protocol) 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://motherlode.ucar.edu:8080/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 E. NOT YET FIXED (NCO problem) Correctly read arrays of NC_STRING 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 20130724: Verified problem still exists TODO nco1102 Cause: NCO parsing of ncatted arguments is not yet sophisticated enough to handle arrays of NC_STRINGS with embedded delimiters. "Sticky" reminders: A. Pre-built, up-to-date Debian Sid & Ubuntu packages: http://nco.sf.net#debian B. Pre-built Fedora and CentOS RPMs: http://nco.sf.net#rpm C. Pre-built Windows (native) and Cygwin binaries: http://nco.sf.net#windows D. Pre-built AIX binaries: http://nco.sf.net#aix E. Did you try SWAMP (Script Workflow Analysis for MultiProcessing)? SWAMP efficiently schedules/executes NCO scripts on remote servers: http://swamp.googlecode.com SWAMP can work command-line operator analysis scripts besides NCO. If you must transfer lots of data from a server to your client before you analyze it, then SWAMP will likely speed things up. F. NCO support for netCDF4 features is tracked at http://nco.sf.net/nco.html#nco4 NCO supports netCDF4 atomic data types, compression, chunking, and groups. G. Reminder that ncks, ncecat, ncbo, ncflint, and ncpdq work on many common HDF5 datasets, e.g., NASA AURA HIRDLS HDF-EOS5 NASA ICESat GLAS HDF5 NASA SBUV HDF5... -- Charlie Zender, Earth System Sci. & Computer Sci. University of California, Irvine 949-891-2429 )'(
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