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NOTICE: This version of the NSF Unidata web site (archive.unidata.ucar.edu) is no longer being updated.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 4.3.1 are ready. http://nco.sf.net (Homepage) http://dust.ess.uci.edu/nco (Homepage "mirror") This release solidifies group support in ncbo and makes group-related features consistent across ncbo, ncecat, and ncks. These three operators fully support group hierarchies. Work on NCO 4.3.2 is underway and includes improved netCDF4 support for more NCO operators, and better support for Windows builds (enabling DAP and UDUnits by default). Enjoy, Charlie "New stuff" in 4.3.1 summary (full details always in ChangeLog): NEW FEATURES: A. ncbo now supports Group Path Editing (GPE) and list unions. These are the same options already supported by ncks and ncecat. They are invoked with -G and with --union, respectively. ncbo -g g1 -v v1 --union -G dude -O -p ~/nco/data in_grp.nc in_grp.nc ~/foo.nc http://nco.sf.net/nco.html#gpe http://nco.sf.net/nco.html#union B. ncbo now always works when input files are interchanged, i.e., (ncbo fl_1.nc fl_2.nc) = -(ncbo fl_2.nc fl_1.nc). Formerly, ncbo broadcast variables in fl_2 to match the rank of variables in fl_1 when necessary, but would fail rather than broadcast in the opposite direction. Hence one could subtract zonal averages, e.g., from full fields but not the reverse. Now ncbo broadcasts variables both ways. If v1 is larger rank in fl_1 than in fl_2 then both these work: ncbo -v v1 fl_1.nc fl_2.nc out.nc # Now works too! ncbo -v v1 fl_2.nc fl_1.nc out.nc # Always worked C. ncecat now supports Record AGgregation (RAG) mode for netCDF4. Most people have always used RAG mode, the default for ncecat. RAG mode glues files together with a new record dimension. Group AGgregation (GAG) mode, by contrast, is specified with --gag, andwas introduced in NCO 4.2.2 to glue files together by placing them in distinct groups in a netCDF4 output file. GAG mode always worked for both netCDF3 and netCDF4 input files, but RAG mode only worked for netCDF3/classic input files. Now RAG mode works for netCDF4 files too. And it is the default. Existing record dimensions in input netCDF4 files are preserved, and a single glue record dimension is placed in the root group. ncecat -O in_grp.nc in_grp.nc foo.nc http://nco.sf.net/nco.html#ncecat http://nco.sf.net/nco.html#rag http://nco.sf.net/nco.html#gag BUG FIXES: A. Fixed ncbo bug introduced in version 4.3.0 where some special exceptions (a subset of http://nco.sf.net/nco.html#prc_xcp) to variable list processing were inadvertently always turned off. This may cause some grid-related variables (e.g., ntrm and nbdate) and some non-grid variables (e.g., ORO and gw) to be subtracted even when that makes no physical sense in the CF context. http://nco.sf.net#bug_ncbo_ccm_ccsm_cf B. Fixed ncatted bug where leaving the attribute field blank in attribute edit mode structures could trigger a segfault on netCDF4 files. Bug identified and fix provided by Etienne Tourigny. http://nco.sf.net#bug_ncatted_strcmp C. Fixed ncrcat bug that falsely warned of non-monotonicity in input files with multiple variables treated as record coordinates. D. Fixed ncbo bug where history attribute was not appended. 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 4.3.1 built/tested with netCDF 4.3.0-rc4 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 is returned successfully, data is 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 E. NOT YET FIXED netCDF4 library can create dimensions with duplicate IDs if dimension with same name defined in a group and its ancestor group. Problem with HDF5 or with netCDF4 library implementation? Demonstration: ncks -O -v two_dmn_rec_var ~/nco/data/in_grp.nc ~/foo.nc ncks -m ~/foo.nc 20130328: Verified problem still exists (This may be fixed in the netCDF 4.3.0 release...will check again then) Bug report filed 20120312: netCDF #SHH-257980: Re: [netcdfgroup] Dimensions IDs F. NOT YET FIXED ncdump is unable to dump the NCO test file in_grp.nc This is not an NCO problem per se, but may indicate a deeper netCDF bug that affects NCO. Unclear whether problem with ncdump, HDF5, or with netCDF4 library implementation. Demonstration: ncdump ~/nco/data/in_grp.nc # breaks with "NetCDF: Invalid argument Location: file dumplib.c; line 970" 20130319: Verified Bug report not yet filed G. NOT YET FIXED Auxiliary coordinates do not work in ncks versions 4.2.0-4.3.1. This is an NCO problem discovered just before release. Demonstration: ncks -O -X 0.,180.,-30.,30. -v gds_3dvar ~/nco/data/in.nc ~/foo.nc 20130428: Verified This is our top priority to fix in version 4.3.2. The workaround is to use NCO 4.1.9 or earlier. "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 and ncecat 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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