NetCDF operators (NCO) version 4.4.6

Version 4.4.6 of the netCDF Operators (NCO) has been released. NCO is an Open Source package that consists of a dozen standalone, command-line programs that take netCDF files as input, then operate (e.g., derive new data, average, print, hyperslab, manipulate metadata) and output the results to screen or files in text, binary, or netCDF formats.

The NCO project is coordinated by Professor Charlie Zender of the Department of Earth System Science, University of California, Irvine. More information about the project, along with binary and source downloads, are available on the SourceForge project page.

From the release message:

This is a bugfix, stability, and performance release. It fixes an ncra bug that affects packed records with missing values, and it fixes an ncwa bug that affects minimization and maximization operations on packed variables. Affected users would likely have noticed being bit by these bugs since the answers generated were, well, noticeable. For these reasons alone, we recommend that users of packed datasets upgrade to 4.4.6.

We rewrote ncrename to enhance its group-oriented features. We also implemented a performance optimization that dramatically improves access times to strided hyperslabs in netCDF4 datasets. Minor improvements include new ncks printing and hyperslab options, support for HDF4 chunking/compression, and ncap2 argument passing.

New Features

1. ncrename expanded functionality on group-oriented files: ncrename now supports group attributes and variable attributes with the same syntax, provides distinct options to change only global metatdata or metadata in every group, and works with multiple instances of the same object, e.g., multiple instances of the same variable name in different groups. ncrename -a g1@old_att,new_att in.nc # Rename in g1 only
ncrename -a group@old_att,new_att in.nc # Rename in all groups
ncrename -a global@old_att,new_att in.nc # Rename in root only
   https://nco.sf.net/nco.html#ncrename
2. Optimization of strided hyperslab access to netCDF4 data: Multiple users complain that access to strided hyperslabs of netCDF4 datasets is orders of magnitude slower than expected. This occurs with other languages (like NCL) and appears to be caused by lower-level libraries. Until the problem is solved at the root, we have developed and implemented a transparent workaround that fixes the issue for the common case where strides are taken in only one dimension, e.g., -d time,0,,12. Strided hyperslabs like ncks -O -d time,0,,12 ~/in.nc4 ~/foo.nc now complete in nearly the same amount of time as non-strided. This workaround works transparently with any version of netCDF. 
   https://nco.sf.net#bug_nc4_srd
3. ncap2 command-line and script arguments can now both be specified AND executed. Command-line args are executed before script: ncap2 -v -s "lon=${longitude" -S in_4.nc out.nc} This is useful for passing shell variables into NCO scripts. Pass the shell variables with -s and the -S scripts will use them. Thanks to Henry Butowsky for this. 
   https://nco.sf.net/nco.html#ncap2

4. ncks -V = --var_val is new switch to print only variable values. Compare and contrast -Q, -V, and --no_nm_prn:

   % ncks -v three_dmn_rec_var -C -H in.nc  
   time[0]=1 lat[0]=-90 lon[0]=0 three_dmn_rec_var[0]=1  
   % ncks --no_nm_prn -v three_dmn_rec_var -C -H in.nc  
   1 -90 0 1  
   % ncks -Q -v three_dmn_rec_var -C -H in.nc  
   three_dmn_rec_var[0]=1  
   % ncks -Q --no_nm_prn -v three_dmn_rec_var -C -H in.nc  
   1  
   % ncks -V -v three_dmn_rec_var -C -H in.nc  
   1  

   https://nco.sf.net/nco.html#var_val

5. ncks --cdl --hdn now prints extended file format (i.e., the format of the file or server supplying the data)as _SOURCE_FORMAT:

   % ncks --hdn --cdl ~/nco/data/cmip5.nc  
   ...  
     :_Format = "netCDF-4" ;  
     :_SOURCE_FORMAT = "NC_FORMAT_HDF5" ;  
   ...  

   https://nco.sf.net/nco.html#hdn

6. Hyperslabs specifications now accept -0 (negative zero) to indicate the last element of a dimension. This is consistent with existing (Python) syntax where negative integers indicate the number of elements from the last (-1 is penultimate, -0 is ultimate): 
   ncks -d lon,1,-0 in.nc out.nc # Second through last longitude
   https://nco.sf.net/nco.html#hyp
7. NCO now supports chunking and deflation features of HDF4 datasets when compiled with netCDF library 4.3.3-rc1 or later. Earlier versions of netCDF do not support these features for HDF4. Thanks to Unidata for continuing to improve HDF4 interoperability. 
   https://nco.sf.net/nco.html#hdf4

Additional details are available in the ChangeLog.