Bienvenue sur le netCDF Operator (NCO) site
Current stable NCO version is 4.6.3 released [an error occurred while processing this directive]
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The NCO toolkit manipulates and analyzes data stored in
netCDF-accessible
formats, including
DAP,
HDF4, and
HDF5.
It exploits the geophysical expressivity of many
CF
(Climate & Forecast) metadata conventions,
the flexible description of physical dimensions translated by
UDUnits,
the network transparency of
OPeNDAP,
the storage features (e.g., compression, chunking, groups) of
HDF (the Hierarchical Data Format),
and many powerful mathematical and statistical algorithms of
GSL (the GNU Scientific Library).
NCO is
fast,
powerful,
and
free.
Recent Releases & Milestones
- 2017 Jan ??: 4.6.4 (In progress)
- 2016 Dec 23: 4.6.3 (Minor features)
- 2016 Nov 16: 4.6.2 (JSON)
- 2016 Sep 19: Geosci. Model Dev. publishes PPC paper
- 2016 Aug 06: 4.6.1 (Stability)
- 2016 Jul 06: Submitted Layer-packing manuscript to Geosci. Model Dev.
- 2016 May 12: 4.6.0 (ncclimo)
- 2016 Apr 06: Poster at NASA ESDSWG, Greenbelt
- 2016 Apr 05: Talk at NASA GES DISC, Greenbelt
- 2016 Mar 22: Submitted PPC manuscript to Geosci. Model Dev.
- 2016 Feb 17: 4.5.5 (Stability)
- 2016 Jan 07: 4.5.4 (ncremap)
- 2015 Dec 16: Poster at Fall AGU, San Francisco
- 2015 Nov 04: Talk at DOE ACME, Albuquerque
- 2015 Oct 20: 4.5.3 (Curvilinear)
- 2015 Sep 06: 4.5.2 (Generate SCRIP)
- 2015 Sep 01: NSF EarthCube project commences
- 2015 Jul 10: 4.5.1 (Stability)
- 2015 Jun 11: 4.5.0 (Regridding)
- 2015 May 21: 4.4.9 (ncra weights)
- 2015 Feb 16: 4.4.8 (Precision-Preserving Compression)
- 2014 Dec 15: DOE ACME project commences
- 2014 Nov 26: 4.4.7 (Chunking features)
- 2014 Oct 01: 4.4.6 (ncra, ncwa packing bugfixes, stride optimization)
- 2014 Aug 26: 4.4.5 (Stability)
- 2014 Jul 01: NASA ACCESS 2013 project commences
- Milestones from 200301–201406 (versions 2.8.4–4.4.4)
- News and Announcements from 199801–200212 (version 1.1.0–2.8.3) and earlier
What is NCO?
The netCDF Operators (NCO) comprise about a dozen standalone,
command-line programs that take
netCDF,
HDF, and/or
DAP
files as input, then operate (e.g., derive new data, compute
statistics, print, hyperslab, manipulate metadata) and output the
results to screen or files in text, binary, or netCDF formats.
NCO aids analysis of gridded scientific data.
The shell-command style of NCO allows users to manipulate and analyze
files interactively, or with expressive scripts that avoid some
overhead of higher-level programming environments.
Traditional geoscience data analysis requires users to work with
numerous flat (data in one level or namespace) files.
In that paradigm instruments or models produce, and then repositories
archive and distribute, and then researchers request and analyze,
collections of flat files.
NCO works well with that paradigm, yet it also embodies the necessary
algorithms to transition geoscience data analysis from relying solely
on traditional (or “flat”) datasets to allowing newer
hierarchical (or “nested”) datasets.
The next logical step is to support and enable combining all
datastreams that meet user-specified criteria into a
single or small number of files that hold all the
science-relevant data organized in hierarchical structures.
NCO (and no other software to our knowledge) can do this now.
We call the resulting data storage, distribution, and analysis
paradigm Group-Oriented Data Analysis and Distribution
(GODAD).
GODAD lets the scientific question organize the data, not the
ad hoc granularity of all relevant datasets.
The User Guide illustrates
GODAD
techniques for climate data analysis:
Note that the “averagers”
(ncra and ncwa) are misnamed because they perform
many non-linear statistics as well, e.g., total, minimum, RMS.
Moreover, ncap2 implements a powerful domain language which
handles arbitrarily complex algebra, calculus, and statistics (using GSL).
The operators are as general as
netCDF
itself: there are no restrictions on the contents of input file(s).
NCO's internal routines are completely dynamic and impose no limit on
the number or sizes of dimensions, variables, and files.
NCO is designed to be used both interactively and with large batch jobs.
The default operator behavior is often sufficient for everyday needs,
and there are numerous command line (i.e., run-time) options, for
special cases.
How to Contribute: Volunteer, Endorse, or Donate
NCO has always (since 1995) been GPL'd Open Source.
SourceForge.net started hosting NCO
in March, 2000.
This facilitated collaboration, code contributions, and support.
In March, 2015, NCO development moved to GitHub.com.
We continue to use the SourceForge discussion fora for historical
continuity (seventeen years of searchable Q&A).
No matter what your programming background there is a task you can help with.
From re-organizing the TODO list itself, to improving this cheesy
webpage, to documentation, to designing and implementing new features
and interfaces, we need your help!
The project homepage
contains mailing lists, discussion forums, and instructions to make
contributing to NCO easy.
Many users feel unable to volunteer their time.
An equally effective contribution in the long-run would be your
endorsement, which may make the difference
between a declined and an accepted proposal.
An endorsement can be a few sentences that describes how NCO benefits your work or research.
E-mail your endorsement to
Charlie “my surname is zender” Zender
with Subject: “NCO Proposal Endorsement”.
This information is useful advocating for more NCO support.
“What future proposals?” you ask, “Aren't you already funded?”
Yes, in 2012 NASA funded us to implement netCDF4 groups and HDF support,
and in 2014 NASA funded us to improve SLD handling.
These funds are/were primarily for development and maintainance of
specific features.
To realize our grander ambition, i.e., to shift geoscience data
analysis from a flat- to a hierarchical-paradigm
(GODAD),
will require a sustained effort and software ecosystem that
understands and implement hierarchical dataset concepts.
And it's hard to sell a federal agency on the wisdom of investing in a paradigm shift!
Other more prosaic tasks that need work are, for example,
I/O parallelization (!!!), user-defined and non-atomic types, more CF conventions,
cloud-services, JSON back-end, and user-defined ncap2 functions.
If you send an endorsement, please include (at least) your Name, Title, and Institutional affiliation.
Lastly, as of June, 2003, if you're more strapped for time than money
and want to contribute something back, consider a monetary donation.
This may incentivize us to tackle your favorite TODO items.
Inspired by President Obama's plan to bring more transparency to
government investment, these homepage donation counters track the
influence of your monetary donations on NCO development:
Donations received between 20030624 and 20141126: US$144.55. Thank you, donors!
NCO features “incentivized” by these donations: More emoticons in the documentation :)
NSF EarthCube Project
The National Science Foundation Grant
NSF ICER-1541031
funded the Unidata-led
EarthCube Project,
“EarthCube IA: Collaborative Proposal: Advancing netCDF-CF for the Geoscience Community”
from 20150901–20170831 as part of the
Integrative and Collaborative Education and Research
(ICER)
program.
This URL,
http://nco.sf.net#prp_e3,
points to the most up-to-date information on the EarthCube proposal.
UCI's primary role is to help extend CF to cover hierarchical data structures, aka groups.
Groups are the Group-Oriented Data Analysis and Distribution
(GODAD) paradigm we
are developing for geoscience data analysis.
We will convene workshops for interested stakeholders in 2016 and 2017.
Be on the lookout for announcements!
DOE ACME Project
“Lightweight Climate Analysis Tools for ACME”
is a US Department of Energy Cooperative Agreement (CA)
DE-SC0012998
from 20141215–20171214 that funds our
contribution
to the Accelerated Climate Modeling for Energy (ACME)
project,
a part of DOE's Earth System Modeling (ESM)
program.
The ACME project provides the resources to implement support for
parallel regridding and workflows in NCO accessible through UV-CDAT.
Spatially intelligent, parallelized analysis tools are a key component
of the Group-Oriented Data Analysis and Distribution
(GODAD) paradigm we
are developing for geoscience data analysis.
NASA ACCESS Project
The National Aeronautics and Space Administration (NASA) Cooperative
Agreement NNX14AH55A
funds our
project,
“Easy Access to and Analysis of NASA and Model Swath-like Data”
from 20140701–20160630 as part of the
Advancing Collaborative Connections for Earth System Science
(ACCESS)
program.
This URL,
http://nco.sf.net#prp_axs,
points to the most up-to-date information on the ACCESS 2013 project.
This ACCESS project provides resources to implement support in NCO
for Swath-like data (SLD), i.e., dataset with non-rectangular and/or
time-varying spatial grids in which one or more coordinates are multi-dimensional.
It is often challenging and time-consuming to work with SLD,
including all NASA Level 2 satellite-retrieved data, non-rectangular
subsets of Level 3 data, and model data (e.g., CMIP5) that are
increasingly stored on non-rectangular grids.
Spatially intelligent software tools is a key component of the
Group-Oriented Data Analysis and Distribution
(GODAD) paradigm we
are developing for geoscience data analysis.
We are currently recruiting a programmer (aka software engineer)
or postdoc based at UCI for at least two years, to accomplish our
ACCESS objectives.
As described in the proposal, this person will be responsible for
incorporating geospatial features and parallelism into NCO.
See the ads for more details.
(PDF,
TXT).
Publications and Presentations
-
Zender, C. S. (2016), Bit Grooming: Statistically accurate precision-preserving quantization with compression, evaluated in the netCDF Operators (NCO, v4.4.8+), Geosci. Model Dev., 9, 3199–3211, doi:10.5194/gmd-9-3199-2016.
PDF
-
Zender, C. S. (2016): Regrid Curvilinear, Rectangular, and Unstructured Data (CRUD) with ncremap, a new netCDF Operator. Presented to the Earth Science Data Systems Working Group (ESDSWG) Meeting, Greenbelt, MD, April 6--8, 2016.
PDF
-
Zender, C. S. (2016): Regridding Swath, Curvilinear, Rectangular, and Unstructured Data (SCRUD). Presented to the NASA Goddard Earth Sciences (GES) Data and Information Services Center (DISC), Goddard Space Flight Center, Greenbelt, MD, April 5, 2016.
PDF
-
Zender, C. S. (2015): Regrid Curvilinear, Rectangular, and Unstructured Data (CRUD) with ncremap, a new netCDF Operator. Presented to the American Geophysical Union Fall Meeting, San Francisco, CA, December 14--18, 2015. Eos Trans. AGU, 95(54), Fall Meet. Suppl., Abstract IN31A-1744.
PDF
-
Zender, C. S. (2015): Optimizing Intrinsic Parallelism to generate climatologies with netCDF Operators (NCO). Presented to the DOE Accelerated Climate Modeling for Energy (ACME) PI Meeting, Albuquerque, NM, November 2--4, 2015.
PDF
-
Zender, C. S., P. Vicente, and W. Wang (2015): Use netCDF Operators (NCO) to Improve Data Interoperability and Usability. Presented to the Earth Science Data Systems Working Group (ESDSWG) Meeting, Greenbelt, MD, March 24--26, 2015.
PDF
-
Zender, C. S., P. Vicente, and W. Wang (2014): Simplifying and accelerating model evaluation by NASA satellite data. Presented to the Earth Science Data Systems Working Group (ESDSWG) Meeting, Greenbelt, MD, March 24--26, 2014.
PDF
-
Zender, C. S. (2014): Use Hierarchical Storage and Analysis to Exploit Intrinsic Parallelism. Presented to the NASA Goddard Earth Sciences (GES) Data and Information Services Center (DISC), Goddard Space Flight Center, Greenbelt, MD, March 27, 2014.
PDF
-
Zender, C. S., P. Vicente and W. Wang (2013): Use Hierarchical Storage and Analysis to Exploit Intrinsic Parallelism. Presented at the Fall Meeting of the American Geophysical Union, San Francisco, CA, December 9–13, 2013. Eos Trans. AGU, 93(53), Fall Meet. Suppl., Abstract IN52A-06.
PDF
-
Zender, C. S., P. Vicente and W. Wang (2013): The Future of Model Evaluation. Presented to the Chapman University Symposium on Big Data and Analytics: 44th Symposium on the Interface of Computing Science and Statistics, Chapman University, Orange, CA, April 4–6, 2013. PDF
-
Zender, C. S., P. Vicente and W. Wang (2012): NCO: Simpler and faster model evaluation by NASA satellite data via unified file-level netCDF and HDF-EOS data post-processing tools.. Presented at the Fall Meeting of the American Geophysical Union, San Francisco, CA, December 3–7, 2012. Eos Trans. AGU, 93(53), Fall Meet. Suppl., Abstract IN34A-07.
PDF
-
Zender, C. S., P. Vicente and W. Wang (2012): Simplifying and accelerating model evaluation by NASA satellite data.. Presented to the Earth Science Data Systems Working Group (ESDSWG) Meeting, Annapolis MD, November 13–15, 2012.
PDF
- Presentation and Publications from 2006–2011
Release Highlights
Stable releases receive unique tags and their tarballs are created and stored
here at GitHub.
Identical copies of those tarballs are also stored
here on SourceForge for historical
continuity.
You may retrieve the source of tagged versions directly with, e.g.,
git clone -b 4.6.3 http://github.com/nco/nco.git nco-4.6.3.
- NCO 4.6.5: (Future)
ncks prints human-legible ISO8601 dates;
Chunking bytes not elements, caching;
extensive hashing?;
netCDF4 compound types?;
Optimize diskless files?;
- NCO 4.6.4: (In Progress, features in-progress or completed include)
ncks --xtn better extensive variable treatment;
- NCO 4.6.3: (Current Stable Release)
CMake build option;
ncap2 udunits() function;
ncclimo supports binary climos, annual mode;
ncclimo, ncremap support long-options;
ncks --cdl attribute types as comments;
ncks --json strided brackets for multi-dimensional arrays;
- NCO 4.6.2: (Current Stable Release)
Improved ncclimo, ncremap behavior in module environments;
ncks --json for JSON output;
Multi-argument support for --gaa, --rgr, --ppc, --trr options;
- NCO 4.6.1:
ncclimo incremental mode;
ncflint -N normalization;
- NCO 4.6.0:
ncap2 LHC metadata propagation;
ncatted nappend mode;
ncclimo debut;
ncks reads ENVI bsq/bip/bil images;
ncks Terraref features;
ncks -A append consistency;
ncpdq fix permutation with multiple groups;
ncra --cb climatology bounds
ncremap uses CF to find coordinates;
ncremap uses $TMPDIR;
- NCO 4.5.5:
All operators support CDF5 format;
ncap2 fix negative dimension indices handling;
ncremap -P airs,hirdls,mls,mpas;
nces/ncra fix -y mebs normalization, add -y tabs;
ncatted/ncrename/ncpdq fix --gaa;
- NCO 4.5.4:
ncap2 syntax simplification/fixes;
ncks -V bugfix;
ncks XML _Unsigned attribute;
ncremap debuts;
ncwa fix whitespace in coordinates attribute;
- NCO 4.5.3:
ncatted fix deletion of all attributes;
ncecat fix gag mode;
ncks infers rectangular and curvilinear grids;
ncks --xtn specifies extensive variables;
ncks regridder fix multi-level field normalization;
- NCO 4.5.2:
All operators support --glb_att_add;
ncks better support for fracarea, mask, and displaced-pole grids;
ncks diagnoses area for bilinear remapping and when area_b equals 0.0;
ncks generates exact Gaussian and equi-angular, rectangular, and regional gridfiles;
ncks regrid with old, new, and regional TempestRemap mapfiles;
ncra -n NINTAP option understands calendar month counting;
ncra -N avoids normalizing by weights;
ncra -w bugfix with missing value normalization;
ncwa bugfix when weights were not found;
- NCO 4.5.1:
cell_method improvments;
ncap2 gets mibs()/mabs()/mebs() methods;
ncatted regular expressions in att_nm;
ncks regrid using TempestRemap mapfiles;
ncra weights with --wgt wgt_nm;
- NCO 4.5.0:
Regridding with ncks --map;
date/time_written updates;
history provenance with -A (append-mode);
ncdismember uploads to NERC;
- NCO 4.4.9:
Output chunking map/policy nco/nco = rew/all is default for netCDF3 input;
Turn-off MM3 workaround for MM3->MM4 copying to speed-up compression-induced chunking;
LFP chunking uses “reasonable defaults” when variable smaller than default chunksize;
Shuffle by default when manually deflating;
Support CF climatology attribute;
Output chunking defaults to rew/all on netCDF3 input;
Unchunking plays nicely with shuffle;
ncra weights with --wgt 1,2,3;
ncks suggests -C with -x -v crd;
ncwa modifies coordinates attribute;
- NCO 4.4.8:
Precision-Preserving Compression with --ppc;
Arithmetic operators -y mabs/mebs/mibs
- NCO 4.4.7:
cnk_min minimum chunksize;
Chunking cnk_map=rew;
Smarter chunking defaults;
- NCO 4.4.6:
-0 hyperslabs;
configure DAP correctly;
HDF4 chunking and deflation;
netCDF4 stride (NC4_SRD) bugfix;
ncap2 command line args with scripts;
ncra --dbl averaging packed variables with missing values bugfix;
ncwa --dbl minimization/maximization of packed variables bugfix;
ncks _SOURCE_FORMAT and -V;
ncrename re-write
- NCO 4.4.5:
DAP on HTTPS;
ancillary_variables for CF;
ncks --grp_xtr_var_xcl subsetting
Chunking cnk_plc=r1d;
Default chunking policy/map is xst/xst;
Fix ncpdq dimension-reversal parsing;
Chunking while hyperslabbing bugfix;
Correctly parse MS Windows volume names like C:\foo
- Release Highlights from 200001–201406 (versions 1.1.47–4.4.4)
Pre-built Executables
Pre-built binary executables are available for many platforms.
Our source tarballs are always up-to-date, and work on our
development systems (Fedora, Ubuntu, and Mac OS X).
We also attempt to provide (theoretically) platform-independent sources
in the most common Linux package formats (Debian and RPM).
Below are one-line installation instructions and links to these and to
packages for other platforms created by volunteers.
Anyone willing to perform regular regression testing and porting
of NCO to other platforms is welcome.
Previous versions of these executables are still available by searching
the directory index here.
AIX on IBM mainframes
- nco-4.2.5.aix53.tar.gz (9.5M): Executables AIX 5.3-compatible (last updated Tuesday, 29-Jan-2013 19:02:41 UTC). Maintained by NCO Project.
Newer (beta- or pre-release) packages are sometimes available for AIX users as described here.
Thanks to NSF for supporting AIX machines at NCAR over the years.
Anaconda is a coordinated,
cross-platform Python environment that utilizes the conda package manager.
Up-to-date versions of NCO for Linux and MacOS are maintained at conda-forge.
Install NCO in your Anaconda framework with one command ‘conda install -c conda-forge nco’.
Or, alternatively, permanently add conda-forge (which has numerous
goodies besides NCO) to your automatically-searched channels with
‘conda config --add channels --conda-forge’, then
install NCO with ‘conda install nco’.
The default NCO installed by conda is generally within a month of the latest release.
- nco-4.6.3 Executables Anaconda-compatible. Maintained by Filipe Fernandes.
Thanks to Rich Signell, Filipe Fernandes (and others?) for developing and maintaining the NCO package for conda.
Fedora, RedHat Enterprise Linux (RHEL), and Community ENTerprise Operating System (CentOS) GNU/Linux
- The Fedora NCO RPMs are usually up-to-date so that ‘dnf install nco’ will install a recent version.
RHEL NCO RPMs are documented at the Fedora site.
OpenSUSE keeps its NCO RPMs here.
A comprehensive list of pre-built RPMs for many OS's is here.
Volunteers have updated and maintained fairly up-to-date NCO packages in Fedora since it was added by Ed Hill in about 2004.
Thanks to Patrice Dumas, Ed Hill, Orion Poplawski, and Manfred Schwarb for packaging NCO RPMs over the years.
Thanks to Gavin Burris and Kyle Wilcox for documenting build procedures for RHEL and CentOS.
The most up-to-date executables are probably those in the tarball below. Those unfamiliar with installing executables from tarballs may try the (older) DMG files (you may need to add /opt/local/bin to your executable path to access those operators).
- nco-4.6.3.macosx.10.12.tar.gz (4.3M): Executables MacOSX 10.12-compatible (last updated Friday, 23-Dec-2016 20:26:10 UTC).
(NB: These executables require
the MacPorts
dependencies for NCO). Maintained by NCO Project.
- nco-4.0.7_x86_10.6.dmg ( 35M): For Mac OS 10.6 (last updated Wednesday, 02-Mar-2011 20:17:21 UTC). Maintained by Chad Cantwell.
- Fink packages for NCO: Currently NCO 3.9.5. Maintained by Alexander Hansen.
- Homebrew packages for NCO: Currently NCO 4.4.2. Maintained by Ian Lancaster (Alejandro Soto's instructions here).
- MacPorts infrastructure for NCO: Portfile for NCO 4.6.0. Maintained by Takeshi Enomoto.
These native Windows executables should be stand-alone, i.e., not
require users to have any additional software.
This is a new feature as of 20120615, please send us feedback.
To build NCO from source yourself using MSVC or Qt, please see the NCO Qt/MSVC build page.
- nco-4.6.3.windows.mvs.exe ( 24M) : Windows Self-Extracting Installer (last updated Thursday, 29-Dec-2016 03:15:48 UTC). Maintained by Pedro Vicente.
Microsoft Windows (running Cygwin environment, compiled with GNU-toolchain)
Before using, first install curl (in the "Web" category of Cygwin Setup), and set export UDUNITS2_XML_PATH='/usr/local/share/udunits/udunits2.xml' (or wherever udunits2.xml is installed).
Thanks to Mark Hadfield and Pedro Vicente for creating Cygwin tarballs.
Thanks to Cygnus Solutions and RedHat Inc. for developing and supporting Cygwin over the years.
The NCO Users Guide is available for reading in these formats:
- DVI Device Independent (kdvi, xdvi)
- HTML Hypertext (any browser)
- Info GNU Info (M-x Info, emacs)
- PDF Portable Document Format (acroread, evince, kpdf, okular, xpdf)
- Postscript Printing (ghostview, kghostview)
- TeXInfo Documentation Source code (emacs)
- Text Plain text (more)
- XML Extensible Markup Language (firefox)
nco.texi is the most up-to-date.
Files nco.dvi, nco.ps, and nco.pdf
contain all the mathematical formulae (typeset with TeX) missing from
the screen-oriented formats.
The screen-oriented formats—nco.html,
nco.info, nco.txt, and nco.xml—contain
all the documentation except the highly mathematical sections.
Wenshan Wang of UCI contributed a Quick Reference Card
(last updated Tuesday, 17-Jan-2017 16:17:06 UTC) suitable for
printing, framing, and/or carrying on your person at all times.
Other documentation:
- This abbreviation key unlocks the mysteries of the source code abbreviations and acronyms.
FAQ: Frequently Asked Questions
These questions show up almost as frequently as my mother.
But they are more predictable:
- I still have questions, how do I contact the NCO project?
The NCO project has various Q&A and discussion forums described
below.
- Where can I find prebuilt NCO executables?
Pre-built executables of some versions of NCO for the operating
systems described above (Debian-compatible
GNU/Linux, Fedora/RedHat GNU/Linux, Gentoo GNU/Linux, and
Mac OS X).
Otherwise, you may be on your own.
- Does NCAR support NCO?
The NCAR CISL Consulting Service Group (CSG) supports NCO like other
software packages.
The NCAR CISL-suported executables are made available through
“modules” so try module load nco.
If you notice problems with the NCO installation on CISL machines, or
if you would benefit from a more recent release or patch, then ask
cislhelp.
If you have a comment, suggestion, or bug report, then contact the
developers as described below.
- Is there an easy way to keep up with new NCO releases?
Subscribe to the
nco-announce
mailing list.
This list is for NCO-related announcements, not for questions.
nco-announce is very low volume—one message every few months.
Help/Support/Contacts:
If you have support questions or comments please contact us via the
Project Forums (rather than personal e-mail) so other users can
benefit from and contribute to our exchange.
Let us know how NCO is working for you—we'd like to hear.
Have you read the documentation and browsed the
forums to see if your question/comment has been reported before?
Please read the Guide's suggestions for productive
Help Requests and Bug Reports.
- Where should I ask my questions on how to use NCO?
On the Help site.
- Where should I post suggestions/comments on NCO features and usage?
On the Discussion site.
- Where are NCO development and bug-squashing discussed?
At the Developer
site.
ANNOUNCE/ChangeLog/README/TODO
Files containing useful information about the current distribution:
- ANNOUNCE Notes on current release
- ChangeLog Change History since 1997 (version 0.9)
- README Platforms and software required
- TODO An unordered list of features and fixes we plan
Source Code
The simplest way to acquire the source is to download the compressed tarball:
-
nco-4.6.3.tar.gz
([an error occurred while processing this directive] compressed tar-file)
The best way to acquire the source and occasionally update to the
latest features is with Git.
The browsable Repository
contains up-to-the-minute sources and is the easiest way to stay
synchronized with NCO features.
Updating NCO source requires some familiarity with development tools,
especially Git and
Make.
You may retrieve any NCO distribution you wish from
GitHub.
Usually you wish to retrieve a recent tagged (i.e., released) version.
This command retrieves the entire NCO repository (< 20 MB) and
then checks out NCO version 4.6.3:
git clone https://github.com/nco/nco.git;cd nco;git checkout 4.6.3
These commands retrieve the current (“bleeding edge”)
development version of NCO into a local directory named nco:
git clone https://github.com/nco/nco.git ~/nco
or
git clone git@github.com:/nco/nco.git
,
Track changes to the development version using
cd nco;git pull
One difference between running a "tagged" release
(e.g., 4.6.3) and the development version is that the
tagged release operators will print a valid version number (e.g.,
4.6.3) when asked to do so with the -r flag
(e.g., ncks -r).
The development version simply places today's date in place of the
version.
Once the autotools builds are working more robustly, the confusion
over versions should largely disappear.
Developer NCO Source Documentation
Automated source documentation, created by the
Doxygen tool is available.
Some developers find this documentation helpful, as it can clarify code and data
relationships in the code.
The Doxygen documentation is infrequently (i.e., never since Daniel left) updated.
Compilation Requirements
Best Practices:
- Although building NCO yourself can be easy, sexy, and lucrative,
we recommend that you first try the pre-built executables for your
system, e.g.,
- brew install homebrew/science/nco # Mac (after installing Homebrew)
- conda install -c conda-forge nco # Any Linux or Mac (after installing Anaconda)
- sudo aptitude install nco # Debian-based Linux systems like Debian, Mint, Ubuntu
- sudo dnf-install nco # Newer RPM-based Linux systems like CentOS, Fedora, openSUSE, RHEL
- sudo yum-install nco # Older RPM-based Linux systems like CentOS, Fedora, openSUSE, RHEL
- sudo port install nco # Mac (after installing MacPorts on Mac OS X)
If pre-built executables do not satisfy you (e.g., are out-of-date)
and you want the latest, greatest features, then the first steps to
build (i.e., compile, for the most part) NCO from source code are to
install the pre-requisites:
ANTLR version 2.7.7 (like this one not version 3.x or 4.x!) (required for ncap2),
GSL (desirable for ncap2),
netCDF (absolutely required),
OPeNDAP (enables network transparency), and
UDUnits (allows dimensional unit transformations).
If possible, install this software stack from pre-built executables
(commands to do so on Debian, Mac, and RPM systems follow below).
ANTLR executables from major distributions are pre-built with the source
patch necessary to allow NCO to link to ANTLR.
If you must build the source stack yourself (e.g., due to lack of root
access, or systems without packages such as AIX), build all libraries
with the same compiler and switches.
The ANTLR source file CharScanner.hpp must include this line:
#include <cstring> or else ncap2 will not
compile (this
tarball is already patched).
Recent versions of netCDF automatically build OPeNDAP and UDUnits.
NCO is mostly written in C99, and although you may mix and
match compilers, this is often difficult in practice and is not recommended.
The exception is ncap2 which is written in C++.
ANTLR, OPeNDAP, and NCO must be built with the same C++ compiler
to properly resolve the C++ name-mangling.
NCO does not yet support newer ANTLR versions because the
ANTLR 3.x and 4.x C++ interfaces are incomplete.
For the reasons explained above (compiler compatibility) install as
much pre-requisite and optional software as possible from pre-compiled
packages.
This is easy on modern package-oriented OSs.
The NCL/ESMF packages provide ESMF_RegridWeightGen for use
by ncremap, they are not required to build NCO.
Remember, to compile NCO from source, you need not only the library
dependencies the "devel" versions
(which include the header files) of the
For Debian-based systems (like Ubuntu) (aptitude is similar to and interchangeable, I think, with apt-get):
- sudo aptitude install antlr libantlr-dev # ANTLR
- sudo aptitude install libcurl4-gnutls-dev libexpat1-dev libxml2-dev # DAP-prereqs (curl, expat XML parser)
- sudo aptitude install bison flex gcc g++ # GNU toolchain
- sudo aptitude install gsl-bin libgsl0-dev # GSL
- sudo aptitude install libnetcdf11 libnetcdf-dev netcdf-bin # netCDF and DAP
- sudo aptitude install libhdf5-serial-dev # HDF5
- sudo aptitude install ncl-ncarg # ESMF_RegridWeightGen (for ncremap)
- sudo aptitude install udunits-bin libudunits2-0 libudunits2-dev # UDUnits
For RPM-based systems like Fedora and CentOS (substitute yum for dnf on older systems):
- sudo dnf install antlr antlr-C++ -y # ANTLR
- sudo dnf install curl-devel libxml2-devel -y # DAP-prereqs
- sudo dnf install expat expat-devel -y # expat XML parser, a UDUnits-prereq (RHEL only?)
- sudo dnf install libdap libdap-devel -y # DAP
- sudo dnf install bison flex gcc gcc-c++ -y # GNU toolchain
- sudo dnf install ncl # ESMF_RegridWeightGen (for ncremap)
- sudo dnf install gsl gsl-devel -y # GSL
- sudo dnf install netcdf netcdf-devel -y # netCDF
- sudo dnf install librx librx-devel -y # RX
- sudo dnf install udunits2 udunits2-devel -y # UDUnits
For Mac OS X with MacPorts:
- sudo port install antlr # Antlr
- sudo port install esmf # ESMF_RegridWeightGen (for ncremap)
- sudo port install libdap # DAP
- sudo port install gsl # GSL
- sudo port install netcdf # netCDF
- sudo port install udunits2 # UDUnits
Without MacPorts, the system TeXInfo may be too old to build the
documentation.
In this case use configure --disable-doc.
For Windows with Cygwin, select and install the following packages with Cygwin Setup:
- curl # DAP and wget pre-req
- expat # expat XML parser for UDUnits
- gsl # GSL
- hdf5 # HDF
- netcdf # netCDF
- udunits2 # UDUnits
As of 20131101 there is no Cygwin package for Antlr, and the netcdf package does not yet support DAP.
Users should instead first download and install the Antlr found here.
- Once you have installed the pre-requisites as shown above, you may
then build the latest stable NCO and install it in,
e.g., /usr/local with:
- wget https://github.com/nco/nco/archive/4.6.3.tar.gz
- tar xvzf 4.6.3.tar.gz
- cd nco-4.6.3
- ./configure --prefix=/usr/local
- make
- sudo make install
- export PATH=/usr/local/bin\:${PATH}
- export LD_LIBRARY_PATH=/usr/local/lib\:${LD_LIBRARY_PATH}
Please post questions about building or installing NCO to the
list
only after reading and attempting to follow these instructions.
To indicate you have done this, include the word “bonobo”
in the first sentence of your post.
Yes, “bonobo”.
Otherwise we will likely redirect you here.
For more sophisticated build/install options, see the next section.
- CMake build. To build with CMake, do:
- mkdir build
- cd build
- cmake ..
- make
The CMake script tries to find header and dependency libraries in standard locations.
They can also be set manually with, e.g.,
- cmake .. -DNETCDF_INCLUDE:PATH=/my/netcdf/include/path
-DNETCDF_LIBRARY=/my/netcdf/library/file
-DHDF5_LIBRARY=/my/hdf5/library/file
-DHDF5_HL_LIBRARY=/my/hdf5 high level/library/file
-DSZIP_LIBRARY=/my/szip/library/file
-DZLIB_LIBRARY=/my/zlib/library/file
-DCURL_LIBRARY=/my/curl/library/file
Still having trouble building NCO from source? Read these
Build Hints
Using NCO at UCI, NCAR, and other High Performance Computing Centers (HPCCs)
HPCCs unfortunately do not utilize modern package systems like RPMs or
.debs, or do so on old OSs with no access to newer RPMs and .debs.
Institution-supported executables are usually available with module load nco.
These stable releases are often many versions (up to two years) old.
Thanks to funding from external grants, DOE, NCAR, and UCI HPCC
users may find more recent pre-built NCO executableses the
personal directories shown below.
These are usually built from a recent tagged-version of NCO (e.g.,
4.6.X-alphaY) not from the “bleeding-edge” of master which
is usually untagged.
One way to use these pre-built executables is to prepend them to
your executable and library search paths, e.g.,
export PATH="~zender/bin:${PATH}",
export LD_LIBRARY_PATH="~zender/lib:${LD_LIBRARY_PATH}"
- ANL ALCF Cooley cooley.alcf.anl.gov: ~zender/bin
- ANL ALCF Mira mira.alcf.anl.gov: ~zender/bin
- ANL LCRC Blues blues.lcrc.anl.gov: ~zender/bin
- LLNL aims4.llnl.gov: ~zender1/bin
- NCAR CISL yellowstone.ucar.edu: ~zender/bin
- NCAR CISL mirage0.ucar.edu: ~zender/bin
- NERSC Cori cori.nersc.gov: ~zender/bin_cori
- NERSC Edison edison.nersc.gov: ~zender/bin_edison
- ORNL OLCF Pileus pileus-login01.ornl.gov: ~zender/bin
- ORNL OLCF Rhea rhea.ccs.ornl.gov: ~zender/bin_rhea
- ORNL OLCF Titan titan.ccs.ornl.gov: ~zender/bin_titan
- UCI ESS greenplanet.ps.uci.edu: ~zender/bin
Known Problems from 2013 (version 4.2.4) Onwards
Recent Generic Run-time Problems:
- netCDF4 Strided Hyperslab bug:
Multiple users complain that access to strided hyperslabs of
netCDF4 datasets is orders of magnitude slower than expected.
This occurs with NCO and also with related software like NCL.
The cause appears to be that all recent versions of netCDF up
to 4.3.3 access strided hyperslabs via an algorithm
(in nc_get_vars()) that becomes unwieldy and error-prone
for large datasets.
We developed and implemented a transparent workaround (that avoids
the troublesome algorithm) for the most common case which is where
strides are taken in only one dimension, e.g., -d time,0,,12.
With the workaround introduced in NCO 4.4.6, strided access to
netCDF4 datasets now completes in nearly the same amount of time as
non-strided.
This workaround works transparently with any version of netCDF.
We are not yet sure that we have fully and correctly diagnosed the
cause nor that our workaround is always effective.
Comments welcome. Updates will be posted right here.
- netCDF4 Renaming bugs:
Unforunately from 2007–present (February, 2015) the netCDF
library (versions 4.0.0–4.3.3) contained bugs or limitations
that prevent ncrename (and other netCDF4-based software)
from correctly renaming coordinate variables, dimensions, groups,
and attributes in netCDF4 files.
(To our knowledge the netCDF library calls for renaming always work
well on netCDF3 files so one workaround to netCDF4 bugs is convert to
netCDF3, rename, then convert back).
A summary of renaming limitations associated with particular versions
of netCDF4 is maintained in the online manual
here.
Important updates will also be posted here on the homepage.
There are no known bugs with renaming features as of netCDF library
version 4.3.3.1 (March, 2015).
Recent Operator-specific Run-time Problems:
- Minimization/maximization of packed variables bug:
Versions 4.3.y—4.4.5 of ncwa
incorrectly handled packed variables during these operations.
The two workarounds are to unpack first or to perform the
statistics in single precision with the --flt option.
The solution is to upgrade to NCO 4.4.6.
- Promoting packed records with missing values bug:
Versions 4.3.X—4.4.5 of ncra could produce (wildly)
inaccurate statistics when promoting (e.g., to double- from
single-precision) variables that are packed and that have missing
values.
The two workarounds are to unpack first or to perform the
statistics in single precision with the --flt option.
The solution is to upgrade to NCO 4.4.6.
- Chunking while hyperslabbing bug:
Versions 4.3.X—4.4.4 of most operators could send incorrect
chunking requests to the netCDF library, resulting in failures.
This occurred only while simultaneously hyperslabbing.
The solution is to upgrade to NCO 4.4.5.
- ncwa mask condition bug:
All versions through 4.4.3 of ncwa could return incorrect
mask values for negative numbers.
Thanks to Keith Lindsay for report, and to Henry Butowsky for fix.
Prior to this fix, the ncwa lexer would drop the negative
sign, if any, from the comparators appearing in the mask condition,
e.g., ncwa --mask_condition "lat < -20" was parsed as
"lat < 20" not "lat < -20".
Hence, users of ncwa --mask_condition (or of -B)
should upgrade. NB: The -m -M -T form of ncwa
masking is/was not buggy.
Thus the workaround is to use the -m -M -T form
of ncwa masking, while the long-term solution is to upgrade
to NCO 4.4.4+.
- ncra, ncea, and ncrcat file close bug:
Versions 4.3.9—4.4.0 of ncra, ncea,
and ncrcat failed to correctly close and optionally remove
input files.
This could cause NCO to exceed system limits on the maximum number of
open files when hundreds-to-thousands of input files were specified
per NCO invocation.
The exact failure point is OS-dependent (NCO commands on Mac OS X 10.9
would fail when processing more than 256 files at a time).
This is embarassing because NCO has always been designed to work with
arbitrary numbers of input files and we want power users to be
comfortable running it on hundreds of thousands of input files.
The workaround is to avoid versions 4.3.9—4.4.0, while the
long-term solution is to upgrade to NCO 4.4.1+.
- ncra MRO missing value bug:
Versions 4.3.6—4.3.9 of ncra could treat missing values
incorrectly during double-precision arithmetic.
A symptom was that missing values could be replaced by strange numbers
like, well, infinity or zero.
This mainly affects ncra in MRO (multi-record output) mode,
and the symptoms should be noticeable.
The workaround is to run the affected versions of ncra using the
--flt switch, so that single-precision floating point numbers
are not promoted prior to arithmetic.
The solution is to upgrade to NCO 4.4.0+.
- ncwa hyperslabbing while averaging bug:
Versions 4.3.3—4.3.5 of ncwa could return incorrect
answers when user-specified hyperslabs were simultaneously extracted.
In such cases, hyperslab limits were not consistently applied.
This could produce incorrect answers that look correct.
This bug only affected hyperslabbed statistics (those produced
by simultaneously invoking -a and -d switches);
“global averages” were unaffected.
We urge all ncwa users to upgrade to NCO 4.3.6+.
- ncpdq unpacking bug with auxiliary coordinates:
Versions 4.3.2–4.3.3 of ncpdq did not correctly
store unpacked variables.
These versions unpacked (when specified with -U or -P
upk) the values, but inadvertently stored their original packing
attributes with the unpacked values.
This would lead further operators to assume that the values were still
packed.
Hence consecutive operations could lead to incorrect values.
Fixed in version 4.3.4.
All ncpdq users are encouraged to upgrade.
NB: this bug did not affect the other arithmetic operators which
unpack data prior to arithmetic.
Recent Platform-specific Run-time Problems:
No known platform-specific problems with recent releases.
Known Problems through 2012 (version 4.2.3)
People:
Current Developers (please contact us via the project forums not via email):
-
Charlie Zender,
Professor of Earth System Science
(ESS) and of
Computer Science
(CS).
Role: Project PI.
Contributions: Core library, porting, release manager
Related Research:
1. Group-Oriented Data Analysis and Distribution
(GODAD).
2. Extend empirically verified analytic model
(described here)
for terascale data reduction of gridded datasets to account for
cluster- and network-effects.
3. Enable and optimize NCO for intra-file-level parallelism using
netCDF4/HDF5 parallel filesystem features.
Other Interests: Atmospheric Physics, Climate Change.
-
Henry Butowsky,
software engineer.
Roles: Scientific programmer
Current Research:
1. Efficient complex data analysis with storage-layer constraints.
2. Develop and thread the ncap2 interpreter.
Other Interests: Compilers and interpreters.
-
Wenshan Wang,
Roles: PhD Candidate
Current Research:
1. Causes and implications of Greenland snowmelt.
2. Rapid evaluation and exploitation of multi-model datasets.
Other Interests: Advancing to candidacy.
Alumni Developers: