The netCDF operators NCO version 4.0.0 are ready.
http://nco.sf.net (Homepage)
http://dust.ess.uci.edu/nco (Homepage "mirror")
This version offers significant new features:
Chunking on all operators, GSL fitting, bilinear interpolation.
Short explanations of these appear below.
Work on NCO 4.0.1 is underway. Areas of improvement include
Support for spectral transforms, more chunking rulesets.
"New stuff" in 4.0.0 details:
A. Support CF "calendar" attribute = no_leap, 360_day, 365_day.
Now time-based hyperslabs understand common model calendars!
This _greatly_ eases analyzing datasets such as the CMIP3/AR4 GCMs
B. NCO recognizes more variables that are coordinate variables
or multi-dimensional coordinate variables and does not attempt
to arithmetically process (e.g., difference) these in most
situations. This allows more convenient manipulation of datasets
with irregular grids, e.g., CLM and NARCCAP output.
C. ncap2 supports the GSL (Chapter 36) least-squares fitting routines, e.g.,
ncap2 -v -O -s
'defdim("dmn",100);sigma[dmn]=1.0;var1=gsl_ran_gaussian(sigma);var2=gsl_stats_skew(var1);print(var2)'
in.nc out.nc
ncap2 functions added since 3.9.9 are listed below
http://nco.sf.net/nco.html#gsl
D. 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 usefule chunking patterns will be implemented in NCO 4.0.1.
ncks -O -4 --cnk_plc=all in.nc out.nc
http://nco.sf.net/nco.html#chunking
E. NCO improves support for the netCDF4 NC_STRING atomic type.
An "s" trailing double quotes specifies NC_STRING (not NC_CHAR):
ncap2 -4 -O -v -s 'name[lat]={"US"s,"Them"s};' in.nc out.nc
Ragged arrays of strings are finally here! Let's use them.
http://nco.sf.net/nco.html#nco4
F. Dimension-reduction to scalars works with irregular hyperslabs.
Commands that now work include
scalar=avg(three_dmn_var_dbl(0:1,:,0:3));
scalar=total(three_dmn_var_dbl(0:1,:,0:3));
Formerly these required multiple steps to ensure that the
intermediate dimension sizes used in the hyperslabs were present
on disk.
G. OpenSuse packages are now available (Filipe Fernandes)
http://download.opensuse.org/repositories/home:/ocefpaf/openSUSE_11.1
"Sticky" reminders:
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 4.0.0 with was built and tested with HDF5 hdf5-1.8.4 and with
netCDF4 netcdf-4.1-snapshot2009111500.
NCO may not build with earlier, but should build with later, netCDF4
releases.
This is particularly true since NCO 4.0.0 takes advantage of
an internal change to the netCDF API in June 2009 for
nc_def_var_chunking().
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 4.0.0:
ncap2 -f | grep gsl_fit
ncap2 -f | grep bilinear
--
Charlie Zender, Department of Earth System Science
University of California, Irvine (949) 891-2429 :)
