The netCDF operators NCO version 4.0.2 are ready.
http://nco.sf.net (Homepage)
http://dust.ess.uci.edu/nco (Homepage "mirror")
This version contains many minor fixes and improvements.
Short explanations of these appear below.
A special note for Debian/Ubuntu users who want the latest NCO
features before official releases appears at the bottom.
Work on NCO 4.0.3 is underway. Areas of improvement include
Support for spectral transforms, chunking in all operators,
more chunking rulesets.
"New stuff" in 4.0.2 details:
A. Fix off-by-one error in ncatted appends for type NC_CHAR
Extra NULs are no longer inserted with each append
Thanks to A.T. Wittenburg for this bug report.
B. Warn on deflation (compression) and chunking attempts with netCDF3.
Commands like "ncks -3 -L 9 in.nc out.nc" will still attempt to
complete without deflation, and will warn.
C. Allow deflation and chunking on netCDF4_classic filetypes.
Formerly, this was not uniformly implemented.
Thanks to Romain Ramel for pointing this out.
D. Resolve namespace collision between mvapich2, netCDF4, and NCO when
netCDF
(4.1) is compiled with parallel HDF5 (1.8.4).
Thanks to Denis Nadeau for the patches.
E. Fix ncap2 to correctly cast variables with single dimension of size one.
Formerly, ncap2 would write these as scalars in certain situations.
Thanks to Hugo for pointing this out and to Henry Butowsky for fixing it.
F. Update Cygwin (GNU on Microsoft Windows) executables available on the
homepage
G. Update AIX executables available on the homepage
"Sticky" reminders:
J. ncks and ncecat support netCDF4 chunking options:
These options can improve performance on large datasets.
Large file users: Send us suggestions on useful chunking patterns!
More useful chunking patterns may be implemented in NCO 4.0.2.
ncks -O -4 --cnk_plc=all in.nc out.nc
http://nco.sf.net/nco.html#chunking
K. Pre-built, up-to-date Debian Sid & Ubuntu Karmic packages:
http://nco.sf.net#debian
L. Pre-built Fedora and CentOS RPMs:
http://nco.sf.net#rpm
M. 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.
N. NCO support for netCDF4 features is tracked at
http://nco.sf.net/nco.html#nco4
NCO supports netCDF4 atomic data types, compression, and chunking.
NCO 4.0.2 with was built and tested with HDF5 hdf5-1.8.4 and with
netCDF4 netcdf-4.1-snapshot2009111500.
NCO may not build with earlier, and should build with later, netCDF4
releases.
This is particularly true since NCO 4.0.2 takes advantage of an
internal change to the netCDF nc_def_var_chunking() API in June 2009.
export NETCDF4_ROOT=/usr/local/netcdf4 # Set netCDF4 location
cd ~/nco;./configure --enable-netcdf4 # Configure mechanism -or-
cd ~/nco/bld;./make NETCDF4=Y allinone # Old Makefile mechanism
O. Have you seen the NCO logo candidates by Tony Freeman, Rich
Signell, Rob Hetland, and Andrea Cimatoribus?
http://nco.sf.net
Tell us what you think...
Enjoy,
Charlie
GSL functions added to ncap2 in 4.0.2:
none!
(Most desired GSL functions have been merged)
Debian/Ubuntu users who want the latest NCO features before official
releases take heed: The bleeding-edge NCO features are available in
Debian package format long before official releases. New features are
built into pre-release .deb packages as the features are introduced.
Once an (arbritrary) number of new features seems stable, we simply
announce that the current pre-release code is the official (stable)
release code. For example, .deb packages with the 4.0.2 release name
have been at the expected location
http://nco.sourceforge.net/src/nco_4.0.2-1_amd64.deb
for many months, but the NCO homepage for binary package download
only points to this location once the release is official. Until then,
they are rebuilt and replaced as each new feature is added. When the
release is official, the package is frozen and a package with the next
version number
http://nco.sourceforge.net/src/nco_4.0.3-1_amd64.deb
is created. The is not announced until it stabilizes a few months
later. So, with judicious use of dpkg, Debian/Ubuntu users can easily
track NCO feature development more closely than official releases.
Just remove your existing NCO package and replace it with the latest
(unannounced) package that has the feature you want with, e.g.,
wget http://nco.sourceforge.net/src/nco_4.0.3-1_amd64.deb .
sudo dpkg --remove nco
sudo dpkg --install nco_4.0.3-1_*.deb
Caveats:
1. Only amd64 .debs are available early (because that is my
development machine). Knowledgeable users will be able to build the
binary .deb for any architecture using the other files (.changes,
.diff.gz, .dsc, and .tar.gz) found at the same location.
2. Pre-release packages are not for the meek, but getting feedback
on features from those who most need the features is immensely
valuable to stabilizing the code for the final release. So we
encourage users to try these packages. The worst that could happen is
that a pre-release NCO may crush you puppy or eat your cat.
3. These .debs do not yet support netCDF4 (because Debian has been
late in making netCDF4 library .debs available). For netCDF4 support,
you still need to build NCO from source. Or you can use NCO RPMs
(e.g., from Fedora) but those are built until after official NCO
releases so you can't preview features with pre-built RPMs.
--
Charlie Zender, Department of Earth System Science
University of California, Irvine (949) 891-2429 :)
