Bienvenue sur le netCDF Operator (NCO) site

Current stable NCO version is 4.6.3 released

News & Milestones What is NCO? Contributing NCO→SDO Project Publications Release Highlights Executables Documentation FAQ Help/Support/Contacts ANNOUNCE/ChangeLog/README/TODO Source Code Compiling Supercomputers Known Problems People

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:

• ncap2 netCDF Arithmetic Processor (examples)
• ncatted netCDF ATTribute EDitor (examples)
• ncbo netCDF Binary Operator (addition, multiplication...) (examples)
• ncclimo netCDF CLIMatOlogy Generator (examples)
• nces netCDF Ensemble Statistics (examples)
• ncecat netCDF Ensemble conCATenator (examples)
• ncflint netCDF FiLe INTerpolator (examples)
• ncks netCDF Kitchen Sink (examples)
• ncpdq netCDF Permute Dimensions Quickly, Pack Data Quietly (examples)
• ncra netCDF Record Averager (examples)
• ncrcat netCDF Record conCATenator (examples)
• ncremap netCDF REMAPer (examples)
• ncrename netCDF RENAMEer (examples)
• ncwa netCDF Weighted Averager (examples)

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.

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

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

• 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 (): Executables AIX 5.3-compatible (last updated ). 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

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.

Debian and Ubuntu GNU/Linux

Debian NCO and Ubuntu NCO homepages. ‘aptitude install nco’ installs the standard NCO for your Debian-compatible OS. NCO packages in the Debian/Ubuntu repositories (e.g., Sid and Raring) generally lag the packages distributed here by 6–12 months. Newer (beta- or pre-release) packages are often available for intrepid Debian/Ubuntu users as described here.
Debian package for most recent NCO release (install with, e.g., ‘dpkg --install nco_4.6.3-1_i386.deb’):
• nco_4.6.3-1_amd64.deb : Executables AMD64-compatible
Thanks to Daniel Baumann, Sebastian Couwenberg, Barry deFreese, Francesco Lovergine, Brian Mays, Rorik Peterson, and Matej Vela for their help packaging NCO for Debian over the years.

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.

Gentoo GNU/Linux

Gentoo GNU/Linux homepage for NCO. Portage packages by George Shapavalov and Patrick Kursawe:
• nco-3.9.4: Latest(?) Gentoo package

Mac OS X/Darwin

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 (): Executables MacOSX 10.12-compatible (last updated ). (NB: These executables require the MacPorts dependencies for NCO). Maintained by NCO Project.
• nco-4.0.7_x86_10.6.dmg (): For Mac OS 10.6 (last updated ). 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.

Microsoft Windows (native build, compiled with Visual Studio 2015, use this if unsure)

• nco-4.6.3.windows.mvs.exe () : Windows Self-Extracting Installer (last updated ). Maintained by Pedro Vicente.

Microsoft Windows (running Cygwin environment, compiled with GNU-toolchain)

• nco-4.4.4.win32.cygwin.tar.gz (): Executables Cygwin-compatible (last updated ). Maintained by NCO Project.

Python Bindings Source and Documentation

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Documentation and Users Guide

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)

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

• nco-4.6.3.tar.gz ( 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

git clone https://github.com/nco/nco.git ~/nco

git clone git@github.com:/nco/nco.git

cd nco;git pull

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.

• Source documentation for NCO and netCDF4(alpha13)

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

Using NCO at UCI, NCAR, and other High Performance Computing Centers (HPCCs)

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.

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:

• Dr. Scott Capps, earned Earth System Science Ph.D. (2009) with Zender at UCI, then postdoc at UCLA, now at Vertum Partners.
• Stephen Jenks, former Assistant Professor of Electrical Engineering and Computer Science (EECS).
• Pedro Vicente, software engineer, 201206—201405.
• Dr. Daniel Wang: earned EECS Ph.D. (2008) with Jenks and Zender at UCI, now at SLAC.

Thanks also to past NCO contributors.