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NOTICE: This version of the NSF Unidata web site (archive.unidata.ucar.edu) is no longer being updated.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 4.3.2 are ready. http://nco.sf.net (Homepage) http://dust.ess.uci.edu/nco (Homepage "mirror") Did you enjoy the break after a rapid string of NCO releases? Good, because it's over. The current release brings group support to two more operators, ncflint and ncpdq. Now five operators fully support group hierarchies: ncbo, ncecat, ncflint, ncks, and ncpdq. There is also a long-overdue bugfix for support of CF "coordinates" attributes which is how NCO understands Reduced Horizontal Grids and Unstructured Grids. Work on NCO 4.3.2 is underway and includes improved netCDF4 support for more NCO operators (ncwa, ncra, ncea, ncrcat), and better support for Windows builds (enabling DAP and UDUnits by default). Enjoy, Charlie "New stuff" in 4.3.2 summary (full details always in ChangeLog): NEW FEATURES: A. ncflint and ncpdq now supports groups, Group Path Editing (GPE) and list unions, the same options supported by ncbo, ncecat, and ncks. Features are controlled by -g, -G and --union, respectively. ncflint -g g1 -v v1 --union -G dude -w 0.5 -O -p ~/nco/data in_grp.nc in_grp.nc ~/foo.nc ncpdq -g g1 -v v1 -G dude -O -p ~/nco/data in_grp.nc ~/foo.nc http://nco.sf.net/nco.html#ncflint http://nco.sf.net/nco.html#ncpdq http://nco.sf.net/nco.html#gpe http://nco.sf.net/nco.html#union B. NCO takes advantage of improved Windows support in netCDF 4.3.0+. NCO executables built with Visual Studio on Windows now support OPenDAP. Formerly it was much more difficult to obtain OPenDAP support on MS Windows. http://nco.sf.net/nco.html#wnd BUG FIXES: A. Fixed ncks auxiliary coordinate (-X) bug introduced in ~4.2.0. What we call auxiliary coordinates are what CF defines as the variables stored in the "coordinates" attributes of variables. These make possible easy analysis of Reduced/Unstructured Grids. Auxiliary coordinates do not work in ncks versions 4.2.0-4.3.1, though they do work in the other hyperslabbing NCO operators. Auxiliary coordinates now also work in netCDF4 group files. ncks -O -X 0.,180.,-30.,30. -v gds_3dvar ~/nco/data/in.nc ~/foo.nc http://nco.sf.net#bug_ncks_aux B. Global history attribute once again always works in ncecat C. Group Path Editing (GPE) once again always works in ncecat 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 4.3.2 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" 20120731: 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 20130319: 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 20120731: 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 -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, NUL-terminated strings so MD5 agreement fails "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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