\input texinfo @c -*-texinfo-*- 
@c 1998/08/17: texi2html and makeinfo do not require texinfo.tex anymore
@c Unfortunately, texi2dvi does seem to need it

@ignore

$Header: /home/zender/cvs/nco/doc/nco.texi,v 1.38 1999/12/15 03:53:14 zender Exp $

Purpose: TeXinfo documentation for NCO suite

After editing any hyperlink locations, use 
C-c C-u C-a	texinfo-all-menus-update
C-c C-u C-e	texinfo-every-node-update

Usage: 
cd ~/nc/nco/doc;texi2dvi nco.texi; texi2html -monolithic -verbose nco.texi; makeinfo nco.texi; dvips -o $DATA/ps/nco.ps nco.dvi; scp -p nco.html www.cgd.ucar.edu:/web/web-data/cms/nco;cd -
texi2html -monolithic -verbose nco.texi; scp -p nco.html www.cgd.ucar.edu:/web/web-data/cms/nco
cd $DATA/ps;gzip --force nco.ps;scp -p nco.ps.gz www.cgd.ucar.edu:/web/web-data/cms/nco;cd -
texi2dvi nco.texi 
makeinfo nco.texi 
texi2html -monolithic -verbose nco.texi 
dvips -o nco.ps nco.dvi 

Example TeXinfo files: 

@end ignore

@c start of header
@setfilename nco.info
@settitle NCO @value{nco-edition} User's Guide
@smallbook
@c Merge the function index into the concept index
@syncodeindex fn cp
@c end of header

@ignore
@ifinfo
@format
START-INFO-DIR-ENTRY
* NCO: (nco.info).           User's Guide for the netCDF Operator suite
END-INFO-DIR-ENTRY
@end format
@end ifinfo
@end ignore

@c Set smallbook if printing in smallbook format so the example of the
@c smallbook font is actually written using smallbook; in bigbook, a kludge
@c is used for TeX output.
@c set smallbook
@clear smallbook

@set nco-edition 1.1.43
@set doc-edition 1.1.43
@set NCAR-copyright-years 1995, 1996, 1997, 1998, 1999
@set UC-copyright-years 1999
@set update-year 1999
@set update-date 6 December 1999
@set update-month December 1999

@c Experiment with smaller amounts of whitespace between chapters and sections.
@tex
\global\chapheadingskip = 15pt plus 4pt minus 2pt 
\global\secheadingskip = 12pt plus 3pt minus 2pt
\global\subsecheadingskip = 9pt plus 2pt minus 2pt
@end tex

@c Experiment with smaller amounts of whitespace between paragraphs in the 8.5 by 11 inch format.
@ifclear smallbook
@tex
\global\parskip 6pt plus 1pt
@end tex
@end ifclear

@finalout

@ifinfo
This file documents NCO, a collection of utilities to manipulate and 
analyze netCDF files.

Copyright (c) @value{copyright_years} University Corporation for
Atmospheric Research. 

This is the first edition of the @cite{NCO User's Guide},@*
and is consistent with version 2 of @file{texinfo.tex}.

Permission is granted to make and distribute verbatim copies of
this manual provided the copyright notice and this permission notice
are preserved on all copies.

@ignore
Permission is granted to process this file through TeX and print the
results, provided the printed document carries copying permission
notice identical to this one except for the removal of this paragraph
(this paragraph not being relevant to the printed manual).

@end ignore
Permission is granted to copy and distribute modified versions of this
manual under the conditions for verbatim copying, provided that the entire
resulting derived work is distributed under the terms of a permission
notice identical to this one.

Permission is granted to copy and distribute translations of this manual
into another language, under the above conditions for modified versions,
except that this permission notice may be stated in a translation approved
by the Free Software Foundation.

Portions of this document were extracted verbatim from Unidata netCDF
documentation, particularly ``NetCDF Operators and Utilities'' by Russ
Rew and Steve Emmerson. 
@end ifinfo

@setchapternewpage odd

@titlepage
@ifhtml
<META NAME="Author" CONTENT="Charles S. Zender">
<META NAME="Keywords" CONTENT="NCO documentation, NCO User's Guide,
netCDF, operator, GCM, CCM, scientific data, ncdiff, ncea, ncecat,
ncflint, ncks, ncra, ncrcat, ncrename, ncwa">
@end ifhtml
@title NCO User's Guide
@subtitle A suite of netCDF operators
@subtitle Edition @value{doc-edition}, for NCO Version @value{nco-edition}
@subtitle @value{update-month}

@author by Charles S. Zender
@author NCAR ACD & CGD
@author Department of Earth System Science
@author University of California at Irvine
@ifhtml
<P>WWW readers: Having trouble finding the section you want?</P> 
<P>Search for keywords in the (hyper) index at the end of this page</P> 
@end ifhtml

@c Include the Distribution inside the titlepage so that headings are turned off. 
@page
@vskip 0pt plus 1filll
Copyright @copyright{} @value{NCAR-copyright-years} University
Corporation for Atmospheric Research. 

Portions copyright @copyright{} @value{UC-copyright-years} Regents of
the University of California.

@sp 2
This is the first edition of the @cite{NCO User's Guide},@*
and is consistent with version 2 of @file{texinfo.tex}.
@sp 2

Published by the National Center for Atmospheric Research@*
Climate and Global Dynamics Division@*
P.O. Box 3000@*
Boulder, CO 80307-3000 USA@*

Permission is granted to make and distribute verbatim copies of
this manual provided the copyright notice and this permission notice
are preserved on all copies.

Permission is granted to copy and distribute modified versions of this
manual under the conditions for verbatim copying, provided that the entire
resulting derived work is distributed under the terms of a permission
notice identical to this one.

Permission is granted to copy and distribute translations of this manual
into another language, under the above conditions for modified versions,
except that this permission notice may be stated in a translation approved
by the Free Software Foundation.
@sp 2
@c Cover art by Robynn Rudel.
@end titlepage

@node  Top, Foreword, (dir), (dir)
@comment node-name, next,     previous, up

@menu
* Foreword::                    Foreword
* Summary::                     What is NCO?
* Introduction::                Overview of NCO operators
* Strategies::                  Operator Strategies
* Common features::             Common Operator Features
* Operators::                   Description of all NCO operators
* General Index::               Index of concepts

@detailmenu
 --- The Detailed Node Listing ---

Introduction

* Availability::                
* Compatability::               
* Libraries::                   
* netCDF 2.x vs. 3.x::          
* Reporting bugs::              

Operating systems compatible with NCO

* Windows NT::                  

Operator Strategies

* Philosophy::                  
* Climate model paradigm::      
* Output files::                
* Appending::                   
* Averaging vs. Concatenating::  
* Large numbers of input files::  
* Large files and Memory::      
* Memory usage::                
* Operator limitations::        

Averagers vs. Concatenators

* Concatenation::               
* Averaging::                   

Features common to most operators

* Specifying input files::      
* Remote storage::              
* File retention::              
* Variable subsetting::         
* Coordinate variables::        
* Fortran indexing::            
* Hyperslabs::                  
* Wrapped coordinates::         
* Stride::                      
* Missing values::              
* Suppressing interactive prompts::  
* Operator version::            
* History attribute::           
* NCAR CSM Conventions::        
* ARM Conventions::             

Reference manual for all operators

* ncatted netCDF Attribute Editor::  
* ncdiff netCDF Differencer::   
* ncea netCDF Ensemble Averager::  
* ncecat netCDF Ensemble Concatenator::  
* ncflint netCDF File Interpolator::  
* ncks netCDF Kitchen Sink::    
* ncra netCDF Record Averager::  
* ncrcat netCDF Record Concatenator::  
* ncrename netCDF Renamer::     
* ncwa netCDF Weighted Averager  ::  

@code{ncwa} netCDF Weighted Averager

* Masking condition::           
* Normalization::               

@end detailmenu
@end menu

@node Foreword, Summary, Top, Top
@unnumbered Foreword
@cindex foreword
@ifhtml
<BODY TEXT="#000000" BGCOLOR="#FFF8DC" LINK="#0000EF" VLINK="#008080" ALINK="#FF0000">
@end ifhtml
NCO is the result of software needs that arose while I worked on
projects funded by NCAR, NASA, and ARM.
Thinking they might prove useful as tools or templates to others,  
it is my pleasure to provide them freely to the scientific community.  
Many users (most of whom I have never met) have encouraged the
development of NCO.  
Thanks espcially to Jan Polcher, Arlindo da Silva, John Sheldon, and
William Weibel for stimulating suggestions and correspondence.
Your encouragment motivated me to complete the @cite{NCO User's Guide}.
So if you like NCO, send me a note!
I should mention that NCO is not connected to or officially endorsed by
Unidata, ACD, ASP, CGD, or Nike.
@sp 1
@noindent
Charlie Zender
@sp 1
@noindent
May 1997@*
Boulder, Colorado@*

@node Summary, Introduction, Foreword, Top
@unnumbered Summary
@cindex operators
@cindex summary
This manual describes NCO, which stands for netCDF Operators.
NCO is a suite of programs known as @dfn{operators}.
Each operator is a standalone, command line program which is executed at
the UNIX (or NT) shell-level like, e.g., @code{ls} or @code{mkdir}.
The operators take netCDF file(s) as input, perform an operation (e.g.,
averaging or hyperslabbing), and produce a netCDF file as output.
The operators are primarily designed to aid manipulation and analysis of
data.
The examples in this documentation are typical applications of the
operators for processing climate model output. 
This reflects their origin, but the operators are as general as netCDF
itself.

@node Introduction, Strategies, Summary, Top
@chapter Introduction
@cindex introduction

@menu
* Availability::                
* Compatability::               
* Libraries::                   
* netCDF 2.x vs. 3.x::          
* Reporting bugs::              
@end menu

@node Availability, Compatability, Introduction, Introduction
@section Availability
@cindex NCO availability
@cindex source code
The complete NCO source distribution is currently distributed as a
@dfn{compressed tarfile} from
@ifhtml
<a href="ftp://ftp.cgd.ucar.edu/pub/zender/nco/nco.tar.gz"> ftp://ftp.cgd.ucar.edu/pub/zender/nco/nco.tar.gz</a>.
@end ifhtml
@ifclear html
@code{ftp://ftp.cgd.ucar.edu/@-pub/@-zender/@-nco/@-nco.@-tar.@-gz}.
@end ifclear
The compressed tarfile must be uncompressed and untarred before building
NCO.
Uncompress the file with @samp{gunzip nco.tar.gz}. 
Extract the source files from the resulting tarfile with @samp{tar -xvf
nco.tar}.    
GNU @code{tar} lets you perform both operations in one step with
@samp{tar -xvzf nco.tar.gz}. 

@cindex documentation 
@cindex WWW documentation
@cindex on-line documentation
@cindex HTML
@cindex @TeX{}info
@cindex Info
@cindex @cite{User's Guide}
@cindex @cite{NCO User's Guide}
The documentation for NCO is called the @cite{NCO User's Guide}.
The @cite{User's Guide} is available in Postscript, HTML, DVI,
@TeX{}info, and Info formats.
These formats are included in the source distribution in the files
@file{nco.ps}, @file{nco.html}, @file{nco.dvi}, @file{nco.texi}, and
@file{nco.info*}, respectively.
All the documentation descends from a single source file,
@file{nco.texi}
@footnote{   
To produce these formats, @file{nco.texi} was simply run through the
freely available programs @code{texi2dvi}, @code{dvips},
@code{texi2html}, and @code{makeinfo}.    
Due to a bug in @TeX{}, the resulting Postscript file, @file{nco.ps},
contains the Table of Contents as the final pages. 
Thus if you print @file{nco.ps}, remember to insert the Table of
Contents after the cover sheet before you staple the manual.
}.
Hence the documentation in every format is very similar.
However, some of the complex mathematical expressions needed to describe
@code{ncwa} can only be displayed in the Postscript and DVI formats.

@cindex NCO homepage
If you want to quickly see what the latest improvements in NCO are
(without downloading the entire source distribution), visit the NCO
homepage at URL
@ifhtml
<a href="http://www.cgd.ucar.edu/cms/nco"> http://www.cgd.ucar.edu/cms/nco</a>.
@end ifhtml
@ifclear html
@code{http://www.cgd.ucar.edu/cms/nco}.
@end ifclear
The HTML version of the @cite{User's Guide} is also available online through
the World Wide Web at URL
@ifhtml
<a href="http://www.cgd.ucar.edu/cms/nco/nco.html"> http://www.cgd.ucar.edu/cms/nco/nco.html</a>.
@end ifhtml
@ifclear html
@code{http://www.cgd.ucar.edu/cms/nco/nco.html}.
@end ifclear
@cindex netCDF
To build and use NCO, you must have netCDF installed.
The netCDF homepage is
@ifhtml
<a href="http://www.unidata.ucar.edu/packages/netcdf"> http://www.unidata.ucar.edu/packages/netcdf</a>.
@end ifhtml
@ifclear html
@code{http://www.unidata.ucar.edu/packages/netcdf}.
@end ifclear

@node Compatability, Libraries, Availability, Introduction
@section Operating systems compatible with NCO
@cindex OS
@cindex Windows NT
@cindex compatability
@cindex portability
@cindex installation
NCO has been successfully ported and tested on the following platforms: 
GNU/Linux, SunOS 4.1.x, Solaris 2.x, IRIX 5.x and 6.x (including 64-bit
architectures), UNICOS 8.x--10.x, AIX 4.x, DEC OSF, and Windows NT4.
If you port the code to a new operating system, please send me a note
and any patches you required.

@cindex UNIX
The major prerequisite for installing NCO on a particular platform is
the successful, prior installation of the netCDF libraries themselves.
Unidata has shown a commitment to maintaining netCDF on all popular UNIX
platforms, and is moving towards full support for Windows NT.
Given this, the only difficulty in implementing NCO on a particular
platform is standardization of various C and Fortran interface and
system calls.
The C-code has been tested for ANSI compliance by compiling with GNU 
@code{gcc -ansi -pedantic}. 
@cindex ANSI C
Certain branches in the code were required to satisfy the native SGI and
SunOS @code{cc} compilers, which are strictly ANSI compliant and do not
allow variable-size arrays, a nice feature supported by GNU, UNICOS,
Solaris, and AIX compilers. 

The most time-intensive portion of NCO execution is spent in
arithmetic operations, e.g., multiplication, averaging, subtraction.
Until August, 1999, these operations were performed in Fortran by
default.  
This was a design decision based on the speed of Fortran-based object
code vs. C-based object code in late 1994.
Since 1994 native C compilers have improved their vectorization
capabilities and it has become advantageous to replace all Fortran 
subroutines with C subroutines.
Furthermore, this greatly simplifies the task of compiling on nominally 
unsupported platforms. 
As of August 1999, NCO is built entirely in C by default.
This allows NCO to compile on any machine with an ANSI C compiler.
Furthermore, NCO automatically takes advantage of extensions to ANSI C  
when compiled with the GNU compiler collection, GNU CC.

It is still possible to request Fortran routines to perform arithmetic
operations, however.
@cindex preprocessor tokens
@cindex @code{USE_FORTRAN_ARITHMETIC}
This can be accomplished by defining the preprocessor token
@code{USE_FORTRAN_ARITHMETIC} and rebuilding NCO.
@cindex performance
As its name suggests, the @code{USE_FORTRAN_ARITHMETIC} token instructs NCO to
attempts to interface the C routines with Fortran arithmetic.
Although using Fortran calls instead of C reduces the portability and
and increases the maintenance of the NCO operators, it may also increase 
the performance of the numeric operators.
Presumably this will depend on your machine type, the quality of the C
and Fortran compilers, and the size of the data files
@footnote{If you decide to test the efficiency of the averagers compiled
with @code{USE_FORTRAN_ARITHMETIC} versus the default C averagers I would be most
interested to hear the results.
Please E-mail me the results including the size of the datasets, the
platform, and the change in the wallclock time for execution.}.

@menu
* Windows NT::                  
@end menu

@node Windows NT,  , Compatability, Compatability
@subsection Compiling NCO for Windows NT
@cindex Windows NT

@cindex @code{USE_FORTRAN_ARITHMETIC}
NCO has been successfully ported and tested on the Microsoft Windows NT
4.0 operating system.
The switches necessary to accomplish this are included in the standard
distribution of NCO.
Using the freely available Cygwin (formerly gnu-win32) development
environment  
@footnote{The Cygwin package is available from@*
@code{http://sourceware.cygnus.com/cygwin}@*
Currently, Cygwin 20.x comes with the GNU C/C++/Fortran compilers (gcc,
g++, g77).
These GNU compilers may be used to build the netCDF distribution
itself.}, the compilation process is very similar to installing NCO on a
UNIX system.  
@cindex preprocessor tokens
@cindex @code{USE_FORTRAN_ARITHMETIC}
@cindex @code{Cygwin}
@cindex @code{WIN32}
@cindex @file{GNUmakefile}
The preprocessor token @code{PVM_ARCH} should be set to @code{WIN32}.  
Note that defining @code{WIN32} has the side effect of disabling
Internet features of NCO (see below). 
Unless you have a Fortran compiler (like g77 or f90) available, no other
tokens are required. 
Users with fast Fortran compilers may wish to activate the Fortran
arithmetic routines.
To do this, define the preprocessor token @code{USE_FORTRAN_ARITHMETIC}
in the makefile which comes with NCO, @file{Makefile}, or in the
compilation shell. 

@cindex @code{UNIX}
The least portable section of the code is the use of standard UNIX and
Internet protocols (e.g., @code{ftp}, @code{rcp}, @code{scp},
@code{getuid}, @code{gethostname}, and header files
@file{<arpa/nameser.h>} and 
@file{<resolv.h>}). 
@cindex @code{ftp}
@cindex @code{rcp}
@cindex @code{scp}
@cindex remote files
Fortunately, these UNIXy calls are only invoked by the single NCO
subroutine which is responsible for retrieving files stored on remote
systems (@pxref{Remote storage}).
In order to support NCO on the Windows NT platforms, this single feature
was disabled (on Windows NT only).
This was required by Cygwin 18.x---newer versions of Cygwin may support
these protocols (let me know if this is the case).
The NCO operators should behave identically on Windows NT and UNIX
platforms in all other respects.

@node Libraries, netCDF 2.x vs. 3.x, Compatability, Introduction
@section Libraries
@cindex libraries
@cindex @code{LD_LIBRARY_PATH}
@cindex dynamic linking
@cindex static linking
Like all executables, the NCO operators can be built using dynamic
linking. 
@cindex performance
@cindex operator speed
@cindex speed
@cindex execution time
This reduces the size of the executable and can result in significant
performance enhancements on multiuser systems.
Unfortunately, if your library search path (usually the
@code{LD_LIBRARY_PATH} environment variable) is not set correctly, or if
the system libraries have been moved, renamed, or deleted since NCO was
installed, it is possible an NCO operator will fail with a message that
it cannot find a dynamically loaded (aka @dfn{shared object} or
@samp{.so}) library. 
This usually produces a distinctive error message, such as
@samp{ld.so.1:@- /usr/local/bin/ncea:@- fatal:@- libsunmath.@-so.1:@- can't
open@- file:@- errno@-=2}.   
If you received an error message like this, ask your system 
administrator to diagnose whether the library is truly missing
@footnote{The @code{ldd} command, if it is available on your system,
will tell you where the executable is looking for each dynamically
loaded library. Use, e.g., @code{ldd `which ncea`}.}, or whether you
simply need to alter your library search path.
As a final remedy, you can reinstall NCO with all operators statically
linked.  

@node netCDF 2.x vs. 3.x, Reporting bugs, Libraries, Introduction
@section netCDF 2.x vs. 3.x
@cindex netCDF 2.x
@cindex netCDF 3.x
NCO began with netCDF 2.x in 1994.
netCDF 3.0 was released in 1996, and we are eager to reap the
performance advantages of the newer netCDF implementation.
One netCDF 3.x interface call (@code{nc_inq_libvers}) was added to NCO in
January, 1998, to aid in maintainance and debugging. 
To support this call, NCO must be built with netCDF 3.x releases.
Currently, the rest of NCO still uses the netCDF 2.x interface, but,
because of the single @code{nc_inq_libvers} call, NCO no longer builds
with netCDF 2.x releases. 

@cindex HDF
@cindex Hierarchical Data Format
However, the ability to compile NCO with only netCDF 2.x calls is worth 
maintaining because HDF
@footnote{The Hierarchical Data Format, or HDF, is another
self-describing data format similar to, but more elaborate than, netCDF.}
(available from 
@ifhtml
<a href="http://hdf.ncsa.uiuc.edu">HDF</a>
@end ifhtml
@ifclear html
@code{http://hdf.ncsa.uiuc.edu}
@end ifclear
) supports only the netCDF 2.x library calls.  
If NCO is built with only netCDF 2.x calls then some NCO operators will
work with HDF files as well as netCDF files 
@footnote{I have never tried this but other NCO users have confirmed
this is true---it has something to do with linking to the MFHDF
library in addition to or instead of the usual netCDF library. 
Apparently MFHDF only supports netCDF 2.x calls.
Thus I will try to keep this capability in NCO as long as it is not too
much trouble.
If you know which NCO operations should/should not work with HDF files,
please let me know.}.
@cindex @code{NETCDF2_ONLY}
Therefore, the preprocessor token @code{NETCDF2_ONLY} has been
implemented in NCO to eliminate all netCDF 3.x calls. 
If, at compilation time, @code{NETCDF2_ONLY} is defined, then NCO will
not use any netCDF 3.x calls and the resulting NCO operators should work
with HDF files. 
Note that there are multiple versions of HDF.
Currently HDF version 4.x supports netCDF 2.x and thus NCO.
HDF version 5.x became available in 1999, but did not support netCDF
(or, for that matter, Fortran) as of December 1999.
Support for netCDF 3.x in HDF 5.x is being worked on and we will attempt
to convert NCO to netCDF 3.x once this is complete.

@node Reporting bugs,  , netCDF 2.x vs. 3.x, Introduction
@section Reporting bugs
@cindex reporting bugs
@cindex bugs, reporting
Please read the manual before sending me any bug reports. 
Sending me questions whose answers are not in the manual is the best
way to motivate me to write more documentation.  
I would also like to accentuate the contrapositive of this statement.  
If you think you have found a real bug: simplify the problem 
to a manageable size, document your run-time environment, and send me  
the exact error messages (and run the operator with @samp{-D 5} 
to increase the verbosity of the debugging output). 
Write a bug report based on the latest version of NCO. 
Send the bug report to @code{zender@@ncar.ucar.edu}.

@node Strategies, Common features, Introduction, Top
@chapter Operator Strategies

@menu
* Philosophy::                  
* Climate model paradigm::      
* Output files::                
* Appending::                   
* Averaging vs. Concatenating::  
* Large numbers of input files::  
* Large files and Memory::      
* Memory usage::                
* Operator limitations::        
@end menu

@node Philosophy, Climate model paradigm, Strategies, Strategies
@section NCO operator philosophy
@cindex philosophy

The main design goal has been to produce operators that can be invoked
from the command line to perform useful operations on netCDF files. 
Many scientists work with models and observations which produce too much
data to analyze in tabular format.
Thus, it is often natural to reduce and massage this raw or primary
level data into summary, or second level data, e.g., temporal or spatial
averages. 
These second level data may become the inputs to graphical and
statistical packages, and are often more suitable for archival and
dissemination to the scientific community.
NCO performs a suite of operations useful in manipulating data from the
primary to the second level state.
@cindex NCL
@cindex Perl
@cindex Yorick
Higher level interpretive languages (e.g., IDL, Yorick, Matlab, NCL,
Perl, Python),
and lower level compiled languages (e.g., C, Fortran) can always perform
any task performed by NCO, but often with more overhead.
NCO, on the other hand, is limited to a much smaller set of arithmetic
and metadata operations than these full blown languages.

Another goal has been to implement enough command line switches so that
frequently used sequences of these operators can be executed from a
shell script or batch file.
Finally, NCO was written to consume the absolute minimum amount of
system memory required to perform a given job.
The arithmetic operators are extremely efficient; their exact memory
usage is detailed in @ref{Memory usage}.

@node Climate model paradigm, Output files, Philosophy, Strategies
@section Climate model paradigm
@cindex climate modeling
@cindex NCAR
@cindex GCM

NCO was developed at NCAR to aid analysis and manipulation of
datasets produced by General Circulation Models (GCMs). 
Datasets produced by GCMs share many features with all gridded
scientific datasets and so provide a useful paradigm for the explication
of the NCO operator set.
Examples in this manual use a GCM paradigm because latitude, longitude,
time, temperature and other fields related to our natural environment
are as easy to visualize for the layman as the expert.

@node Output files, Appending, Climate model paradigm, Strategies
@section Temporary output files 
@cindex data safety
@cindex error tolerance
@cindex safeguards
@cindex temporary output files
NCO operators are designed to be reasonably fault tolerant, so that
if there is a system failure or the user aborts the operation (e.g.,
with @kbd{C-c}), then no data is lost. 
The user-specified @var{output-file} is only created upon successful
completion of the operation  
@footnote{The @code{ncrename} operator is an exception to this rule.
@xref{ncrename netCDF Renamer}.}.
This is accomplished by performing all operations in a temporary copy
of @var{output-file}.
The name of the temporary output file is constructed by appending
@code{@var{<process ID>}.@var{<operator name>}.tmp} to the
user-specified @var{output-file} name.  
When the operator completes its task with no fatal errors, the temporary
output file is moved to the user-specified @var{output-file}.
Note the construction of a temporary output file uses more disk space
than just overwriting existing files ``in place'' (because there may be
two copies of the same file on disk until the NCO operation successfully
concludes and the temporary output file overwrites the existing
@var{output-file}).  
@cindex performance
@cindex operator speed
@cindex speed
@cindex execution time
Also, note this feature increases the execution time of the operator
by approximately the time it takes to copy the @var{output-file}.
Finally, note this feature allows the @var{output-file} to be the same
as the @var{input-file} without any danger of ``overlap''.

@cindex overwriting files
@cindex appending to files
Other safeguards exist to protect the user from inadvertently
overwriting data.
If the @var{output-file} specified for a command is a pre-existing file,
then the operator will prompt the user whether to overwrite (erase) the
existing @var{output-file}, attempt to append to it, or abort the
operation. 
However, in processing large amounts of data, too many interactive
questions can be a curse to productivity.
Therefore NCO also implements two ways to override its own safety
features, the @samp{-O} and @samp{-A} switches.
Specifying @samp{-O} tells the operator to overwrite any existing
@var{output-file} without prompting the user interactively.
Specifying @samp{-A} tells the operator to attempt to append to any
existing @var{output-file} without prompting the user interactively.
These switches are useful in batch environments because they suppress
interactive keyboard input.

@node Appending, Averaging vs. Concatenating, Output files, Strategies
@section Appending variables to a file
A frequently useful operation is adding variables from one file to
another. 
@cindex concatenation
@cindex appending variables
@cindex merging files
@cindex pasting variables
This is referred to as @dfn{appending}, although some prefer the
terminology @dfn{merging} @footnote{The terminology @dfn{merging} is
reserved for an (unwritten) operator which replaces hyperslabs of a
variable in one file with hyperslabs of the same variable from another 
file} or @dfn{pasting}. 
Appending is often confused with what NCO calls @dfn{concatenation}.
In NCO, concatenation refers to splicing a variable along the record
dimension. 
Appending, on the other hand, refers to adding variables from one file
to another
@footnote{Yes, the terminology is confusing. 
By all means mail me if you think of a better nomenclature.
Should NCO use @dfn{paste} instead of @dfn{append}?
}. 
In this sense, @code{ncks} can append variables from one file to another
file. 
This capability is invoked by naming two files on the command line,
@var{input-file} and @var{output-file}. 
When @var{output-file} already exists, the user is prompted whether to
@dfn{overwrite}, @dfn{append/replace}, or @dfn{exit} from the command.
Selecting @dfn{overwrite} tells the operator to erase the existing
@var{output-file} and replace it with the results of the operation.
Selecting @dfn{exit} causes the operator to exit---the @var{output-file}
will not be touched in this case.
Selecting @dfn{append/replace} causes the operator to attempt to place
the results of the operation in the existing @var{output-file}, 
@xref{ncks netCDF Kitchen Sink}.

@node Averaging vs. Concatenating, Large numbers of input files, Appending, Strategies
@section Averagers vs. Concatenators

The most frequently used operators of NCO are probably the averagers and
concatenators.
Because there are so many permutations of averaging (e.g., across files,
within a file, over the record dimension, over other dimensions, with or
without weights and masks) and of concatenating (across files, along the
record dimension, along other dimensions), there are currently no fewer
than five operators which tackle these two purposes: @code{ncra},
@code{ncea}, @code{ncwa}, @code{ncrcat}, and @code{ncecat}. 
These operators do share many capabilities @footnote{Currently
@code{ncea} and @code{ncrcat} are symbolically linked to the @code{ncra}
executable, which behaves slightly differently based on its invocation
name (i.e., @samp{argv[0]}). 
These three operators share the same source code, but merely have
different inner loops.}, but each has its unique specialty.
Two of these operators, @code{ncrcat} and @code{ncecat}, are for
concatenating hyperslabs across files. 
The other two operators, @code{ncra} and @code{ncea}, are for averaging
hyperslabs across files 
@footnote{The third averaging operator, @code{ncwa}, is the most
sophisticated averager in NCO. 
However, @code{ncwa} is in a different class than @code{ncra} and
@code{ncea} because it can only operate on a single file per invocation
(as opposed to multiple files).   
On that single file, however, @code{ncwa} provides a richer set of 
averaging options---including weighting, masking, and broadcasting.}.  
First, let's describe the concatenators, then the averagers. 

@menu
* Concatenation::               
* Averaging::                   
@end menu

@node Concatenation, Averaging, Averaging vs. Concatenating, Averaging vs. Concatenating
@subsection Concatenators @code{ncrcat} and @code{ncecat}
@cindex @code{ncecat}
@cindex @code{ncrcat}

Joining independent files together along a record coordinate is called
@dfn{concatenation}.    
@code{ncrcat} is designed for concatenating record variables, while
@code{ncecat} is designed for concatenating fixed length variables.
Consider 5 files, @file{85.nc}, @file{86.nc}, @dots{}
@file{89.nc} each containing a year's worth of data. 
Say you wish to create from them a single file, @file{8589.nc}
containing all the data, i.e., spanning all 5 years.
If the annual files make use of the same record variable, then
@code{ncrcat} will do the job nicely with, e.g., @code{ncrcat 8?.nc
8589.nc}. 
The number of records in the input files is arbitrary and can vary from
file to file. 
@xref{ncrcat netCDF Record Concatenator}, for a complete description of
@code{ncrcat}. 

However, suppose the annual files have no record variable, and thus
their data is all fixed length. 
@cindex ensemble
For example, the files may not be conceptually sequential, but rather
members of the same group, or @dfn{ensemble}. 
Members of an ensemble may have no reason to contain a record dimension.
@code{ncecat} will create a new record dimension (named @var{record} by
default) with which to glue together the individual files into the single
ensemble file.
If @code{ncecat} is used on files which contain an existing record
dimension, that record dimension will be converted into a fixed length
dimension of the same name and a new record dimension will be created. 
Consider five realizations, @file{85a.nc}, @file{85b.nc}, @dots{}
@file{85e.nc} of 1985 predictions from the same climate model.
Then @code{ncecat 85?.nc 85_ens.nc} glues the individual realizations
together into the single file, @file{85_ens.nc}. 
If an input variable was dimensioned [@code{lat},@code{lon}], it will have
dimensions [@code{record},@code{lat},@code{lon}] in the output file.
A restriction of @code{ncecat} is that the hyperslabs of the processed
variables must be the same from file to file.
Normally this means all the input files are the same size, and contain
data on different realizations of the same variables.
@xref{ncecat netCDF Ensemble Concatenator}, for a complete description of
@code{ncecat}. 

Note that @code{ncrcat} cannot concatenate fixed-length variables,
whereas @code{ncecat} can concatenate both fixed-length and record
variables.
To conserve system memory, use @code{ncrcat} rather than
@code{ncecat} when concatenating record variables.

@node Averaging,  , Concatenation, Averaging vs. Concatenating
@subsection Averagers @code{ncea}, @code{ncra}, and @code{ncwa} 
@cindex @code{ncea}
@cindex @code{ncra}
@cindex @code{ncwa}

The differences between the averagers @code{ncra} and @code{ncea} are
analogous to the differences between the concatenators.
@code{ncra} is designed for averaging record variables from at least one
file, while @code{ncea} is designed for averaging fixed length variables
from multiple files.
@code{ncra} performs a simple arithmetic average over the record
dimension of all the input files, with each record having an equal
weight in the average. 
@code{ncea} performs a simple arithmetic average of all the input files,
with each file having an equal weight in the average. 
Note that @code{ncra} cannot average fixed-length variables,
but @code{ncea} can average both fixed-length and record variables.  
To conserve system memory, use @code{ncra} rather than
@code{ncea} where possible (e.g., if each @var{input-file} is one record
long). 
The file output from @code{ncea} will have the same dimensions (meaning 
dimension names as well as sizes) as the input hyperslabs  
(@pxref{ncea netCDF Ensemble Averager}, for a complete description of
@code{ncea}).  
The file output from @code{ncra} will have the same dimensions as
the input hyperslabs except for the record dimension, which will have a 
size of 1 (@pxref{ncra netCDF Record Averager}, for a complete
description of @code{ncra}). 

@node Large numbers of input files, Large files and Memory, Averaging vs. Concatenating, Strategies
@section Working with large numbers of input files
@cindex files, numerous input
@cindex @code{-n @var{loop}}

Occasionally one desires to digest (i.e., concatenate or average)
hundreds or thousands of input files.
One brave user, for example, recently created a five year timeseries of
satellite observations by using @code{ncecat} to join thousands of daily
data files together.
Unfotunately, data archives (e.g., NASA EOSDIS) are unlikely to
distribute netCDF files conveniently named in a format the @samp{-n
@var{loop}} switch (which automatically generates arbitrary numbers of
input filenames) understands. 
If there is not a simple, arithmetic pattern to the input filenames
(e.g., @file{h00001.nc}, @file{h00002.nc}, @dots{} @file{h90210.nc}) 
then the @samp{-n @var{loop}} switch is useless.
Moreover, when the input files are so numerous that the input filenames
are too lengthy (when strung together as a single argument) to be passed
by the calling shell to the NCO operator 
@footnote{The exact length which exceeds the operating system internal
limit for command line lengths varies from OS to OS and from shell to
shell.  
GNU @code{bash} may not have any arbitrary fixed limits to the size of
command line arguments. 
Many OSs cannot handle command line arguments longer than a few thousand
characters.
When this occurs, the ANSI C-standard @code{argc}-@code{argv} method of
passing arguments from the calling shell to a C-program (i.e., an NCO
operator) breaks down.},  
then the following strategy has proven useful to specify the input
filenames to NCO. 
Write a script that creates symbolic links between the irregular input
filenames and a set of regular, arithmetic filenames that @samp{-n
@var{loop}} switch understands.
The NCO operator will then succeed at automatically generating the
filnames with the @samp{-n @var{loop}} option (which circumvents any OS
and shell limits on command line size).
You can remove the symbolic links once the operator completes its task. 

@node Large files and Memory, Memory usage, Large numbers of input files, Strategies
@section Working with large files
@cindex large files

@dfn{Large files} are those files that are comparable in size to the
amount of memory (RAM) in your computer.
Many users of NCO work with files larger than 100 Mb.
Files this large not only push the current edge of storage technology, 
they present special problems for programs which attempt to access the  
entire file at once, such as @code{ncea}, and @code{ncecat}.
@cindex swap space
If you need to work with a 300 Mb file on a machine with only 32 Mb of
memory then you will need large amounts of swap space (virtual
memory on disk) and NCO will work slowly, or else NCO will fail.
There is no easy solution for this and the best strategy is to work on a
machine with massive amounts of memory and swap space.
@cindex server
@cindex UNICOS
@cindex Cray
That is, if your local machine has problems working with large files,
try running NCO from a more powerful machine, such as a network server. 
Certain machine architectures, e.g., Cray UNICOS, have special commands
which allow one to increase the amount of interactive memory.
@cindex @code{ilimit}
If you get a core dump on a Cray system (e.g., @samp{Error exit (core
dumped)}), try increasing the available memory by using the
@code{ilimit} command. 

@cindex speed
The speed of the NCO operators also depends on file size.
When processing large files the operators may appear to hang, or do
nothing, for large periods of time.
In order to see what the operator is actually doing, it is useful to
activate a more verbose output mode.
This is accomplished by supplying a number greater than 0 to the
@samp{-D @var{debug_level}} switch.
@cindex @var{debug_level}
@cindex debugging
When the @var{debug_level} is nonzero, the operators report their
current status to the terminal through the @var{stderr} facility.
Using @samp{-D} does not slow the operators down. 
Choose a @var{debug_level} between 1 and 3 for most situations, e.g.,
@code{ncea -D 2 85.nc 86.nc 8586.nc}.
A full description of how to estimate the actual amount of memory the
multi-file NCO operators consume is given in @ref{Memory usage}. 

@node Memory usage, Operator limitations, Large files and Memory, Strategies
@section Approximate NCO memory requirements
@cindex memory requirements

The multi-file operators currently comprise the record operators,
@code{ncra} and @code{ncrcat}, and the ensemble operators, @code{ncea}
and @code{ncecat}, 
The record operators require @emph{much less} memory than the ensemble
operators. 
This is because the record operators are designed to operate on a single
record of a file at a time, while the ensemble operators must retrieve
an entire variable at a time into memory.
Let @math{MS} be the peak sustained memory demand of an operator,
@math{FT} be the memory required to store the entire contents of the
variables to be processed in an input file,
@math{FR} be the memory required to store the entire contents of a
single record of the variables to be processed in an input file, 
@math{VR} be the memory required to store a single record of the
largest record variable to be processed in an input file, 
@math{VT} be the memory required to store the largest variable 
to be processed in an input file,
@math{VI} be the memory required to store the largest variable 
which is not processed, but is copied from the initial file to the
output file. 
All operators require @math{MI = VI} during the initial copying of
variables from the first input file to the output file. 
This is the @emph{initial} (and transient) memory demand.
The @emph{sustained} memory demand is that memory required by the
operators during the processing (i.e., averaging, concatenation)
phase which lasts until all the input files have been processed.
The operators have the following memory requirements: 
@code{ncrcat} requires @math{MS <= VR}. 
@code{ncecat} requires @math{MS <= VT}. 
@code{ncra} requires @math{MS = 2FR + VR}. 
@code{ncea} requires @math{MS = 2FT + VT}. 
Note that only variables which are processed, i.e., averaged or
concatenated, contribute to @math{MS}.
Memory is never allocated to hold variables which do not appear in the
output file (@pxref{Variable subsetting}). 

@node Operator limitations,  , Memory usage, Strategies
@section Performance limitations of the operators

@enumerate
@item 
@cindex buffering
No buffering of data is performed during @code{ncvarget} and
@code{ncvarput} operations.  
@cindex performance
@cindex operator speed
@cindex speed
@cindex execution time
Hyperslabs too large too hold in core memory will suffer substantial
performance penalties because of this. 

@item 
@cindex monotonic coordinates
Since coordinate variables are assumed to be monotonic, the search for
bracketing the user-specified limits should employ a quicker algorithm,
like bisection, than the two-sided incremental search currently
implemented.  

@item 
@cindex @var{C_format}
@cindex @var{FORTRAN_format}
@cindex @var{signedness}
@cindex @var{scale_format} 
@cindex @var{add_offset} 
@var{C_format}, @var{FORTRAN_format}, @var{signedness},
@var{scale_format} and @var{add_offset} attributes are ignored by
@code{ncks} when printing variables to screen. 

@item
@cindex Yorick
Some random access operations on large files on certain architectures
(e.g., 400 Mb on UNICOS) are @emph{much} slower with these operators
than with similar operations performed using languages that bypass the
netCDF interface (e.g., Yorick).  
The cause for this is not understood at present.
@end enumerate

@node Common features, Operators, Strategies, Top
@chapter Features common to most operators

Many features have been implemented in more than one operator and are
described here for brevity. 
The description of each feature is preceded by a box listing the
operators for which the feature is implemented. 
Command line switches for a given feature are consistent across all
operators wherever possible. 
If no ``key switches'' are listed for a feature, then that particular
feature is automatic and cannot be controlled by the user. 

@menu
* Specifying input files::      
* Remote storage::              
* File retention::              
* Variable subsetting::         
* Coordinate variables::        
* Fortran indexing::            
* Hyperslabs::                  
* Wrapped coordinates::         
* Stride::                      
* Missing values::              
* Suppressing interactive prompts::  
* Operator version::            
* History attribute::           
* NCAR CSM Conventions::        
* ARM Conventions::             
@end menu

@node Specifying input files, Remote storage, Common features, Common features
@section Specifying input files
@cindex globbing
@cindex regular expressions
@cindex @code{NINTAP}
@cindex Processor, CCM
@cindex CCM Processor
@cindex @code{-n @var{loop}}
@cindex @code{-p @var{input-path}}
@cindex @var{input-path}
@cartouche
@noindent
Availability: All operators@*
Key switches: @samp{-n}, @samp{-p}@*
@end cartouche
It is important that the user be able to specify multiple input files
without tediously typing in each by its full name. 
@cindex UNIX
There are four different ways of specifying input files to NCO:
explicitly typing each, using UNIX shell wildcards, and using the NCO
@samp{-n} and @samp{-p} switches.
To illustrate these methods, consider the simple problem of using
@code{ncra} to average five input files, @file{85.nc}, @file{86.nc},
@dots{} @file{89.nc}, and store the results in @file{8589.nc}.
Here are the four methods in order.
They produce identical answers.
@example
ncra 85.nc 86.nc 87.nc 88.nc 89.nc 8589.nc
ncra 8[56789].nc 8589.nc
ncra -p @var{input-path} 85.nc 86.nc 87.nc 88.nc 89.nc 8589.nc
ncra -n 5,2,1 85.nc 8589.nc
@end example
The first method (explicitly specifying all filenames) works by brute
force. 
The second method relies on the operating system shell to @dfn{glob}
(expand) the @dfn{regular expression} @code{8[56789].nc}.
The shell passes valid filenames which match the expansion to
@code{ncra}.
The third method uses the @samp{-p @var{input-path}} argument to specify
the directory where all the input files reside.
NCO prepends @var{input-path} (e.g., @file{/data/usrname/model}) to all
@var{input-files} (but not to @var{output-file}). 
Thus, using @samp{-p}, the path to any number of input files need only
be specified once.
Note @var{input-path} need not end with @samp{/}; the @samp{/} is
automatically generated if necessary. 

The last method passes (with @samp{-n}) syntax concisely describing 
the entire set of filenames
@footnote{The @samp{-n} option is a backward compatible superset of the
@code{NINTAP} option from the NCAR CCM Processor.}. 
@cindex multi-file operators
@cindex files, multiple
This option is only available with the @dfn{multi-file operators}:
@code{ncra}, @code{ncrcat}, @code{ncea}, and @code{ncecat}.
By definition, multi-file operators are able to process an arbitrary
number of @var{input-files}.
This option is very useful for abbreviating lists of filenames
representable as
@var{alphanumeric_prefix}+@var{numeric_suffix}+@file{.}+@var{filetype}
where @var{alphanumeric_prefix} is a string of arbitrary length and
composition, @var{numeric_suffix} is a fixed width field of digits, and
@var{filetype} is a standard filetype indicator. 
For example, in the file @file{ccm3_h0001.nc}, we have
@var{alphanumeric_prefix} = @file{ccm3_h}, @var{numeric_suffix} =
@file{0001}, and @var{filetype} = @file{nc}.

NCO is able to decode lists of such filenames encoded using the
@samp{-n} option. 
The simpler (3-argument) @samp{-n} usage takes the form 
@code{-n @var{file_number},@var{digit_number},@var{numeric_increment}}
where @var{file_number} is the number of files, @var{digit_number} is
the fixed number of numeric digits comprising the @var{numeric_suffix},
and @var{numeric_increment} is the constant, integer-valued difference
between the @var{numeric_suffix} of any two consecutive files.
The value of @var{alphanumeric_prefix} is taken from the input file,
which serves as a template for decoding the filenames.
In the example above, the encoding @code{-n 5,2,1} along with the input
file name @file{85.nc} tells NCO to
construct five (5) filenames identical to the template @file{85.nc}
except that the final two (2) digits are a numeric suffix to be
incremented by one (1) for each successive file.
Currently @var{filetype} may be either be empty, @file{nc},
@file{cdf}, @file{hdf}, or @file{hd5}. 
If present, these @var{filetype} suffixes (and the preceding @file{.})
are ignored by NCO as it uses the @samp{-n} arguments to locate,
evaluate, and compute the @var{numeric_suffix} component of filenames.  

@cindex wrapped filenames
Recently the @samp{-n} option has been extended to allow convenient
specification of filenames with ``circular'' characteristics.
This means it is now possible for NCO to automatically generate
filenames which increment regularly until a specified maximum value, and
then wrap back to begin again at a specified minimum value. 
The corresponding @samp{-n} usage becomes more complex, taking one or
two additional arguments for a total of four or five, respectively: 
@code{-n
@var{file_number},@var{digit_number},@var{numeric_increment}[,@var{numeric_max}[,@var{numeric_min}]]}
where @var{numeric_max}, if present, is the maximum integer-value of 
@var{numeric_suffix} and @var{numeric_min}, if present, is the minimum
integer-value of @var{numeric_suffix}.
Consider, for example, the problem of specifying non-consecutive input
files where the filename suffixes end with the month index.  
In climate modeling it is common to create summertime and wintertime
averages which contain the averages of the months June--July--August,
and December--January--February, respectively:
@example
ncra -n 3,2,1 85_06.nc 85_0608.nc
ncra -n 3,2,1,12 85_12.nc 85_1202.nc
ncra -n 3,2,1,12,1 85_12.nc 85_1202.nc
@end example
The first example shows that three arguments to the @samp{-n} option
suffice to specify consecutive months (@code{06, 07, 08}) which do not
``wrap'' back to a minimum value.
The second example shows how to use the optional fourth and fifth
elements of the @samp{-n} option to specify a wrap value to NCO.
The fourth argument to @samp{-n}, if present, specifies the maximum
integer value of @var{numeric_suffix}.
In this case the maximum value is 12, and will be formatted as @file{12}
in the filename string. 
The fifth argument to @samp{-n}, if present, specifies the minimum
integer value of @var{numeric_suffix}.
The default minimum filename suffix is 1, which is formatted as
@file{01} in this case.   
Thus the second and third examples have the same effect, that is, they
automatically generate, in order, the filenames @file{85_12.nc},
@file{85_01.nc}, and @file{85_02.nc} as input to NCO.

@node Remote storage, File retention, Specifying input files, Common features
@section Accessing files stored remotely
@cindex @code{rcp}
@cindex @code{scp}
@cindex @file{.rhosts}
@cindex NCAR MSS
@cindex MSS
@cindex Mass Store System
@cindex URL
@cindex @code{ftp}
@cindex remote files
@cindex synchronous file access
@cindex asynchronous file access
@cartouche
@noindent
Availability: All operators@*
Key switches: @samp{-p}, @samp{-l}, @samp{-R}@*
@end cartouche
All NCO operators can retrieve files from remote sites as well as the
local file system.
A remote site can be an anonymous FTP server, a machine on which the
user has @code{rcp(1)} or @code{scp(1)} privileges, or NCAR's Mass
Storage System (MSS).  
To access a file via an anonymous FTP server, supply the remote file's
URL.
To access a file using @code{rcp(1)} or @code{scp(1)}, specify the
Internet address of the remote file.
Of course in this case you must have @code{rcp(1)} or @code{scp(1)}
privileges which allow transparent (no password entry required) access
to the remote machine. 
This means that @file{~/.rhosts} or @file{~/ssh/authorized_keys} must
be set accordingly on both local and remote machines.   

@cindex @code{msrcp}
@cindex @code{msread}
@cindex @code{nrnet}
To access a file on NCAR's MSS, specify the full MSS pathname of the
remote file. 
NCO will attempt to detect whether the local machine has direct
(synchronous) MSS access. 
In this case, NCO attempts to use the NCAR @code{msrcp} command
@footnote{The @code{msrcp} command must be in the user's path and
located in one of the following directories: @code{/usr/local/bin},
@code{/usr/bin}, @code{/opt/local/bin}, or @code{/usr/local/dcs/bin}.
}, or, failing that, @code{/usr/local/bin/msread}.
Otherwise NCO attempts to retrieve the MSS file through the
(asynchronous) Masnet Interface Gateway System (MIGS) using the
@code{nrnet} command. 

The following examples show how one might analyzed files stored on  
remote systems.
@example
ncks -H -l ./ ftp://ftp.cgd.ucar.edu/pub/zender/nc/in.nc
ncks -H -l ./ dust.ps.uci.edu:/home/zender/nc/in.nc
ncks -H -l ./ /ZENDER/nc/in.nc 
@end example
@noindent
The first example should work verbatim on your system if your system is
connected to the Internet and is not behind a firewall.
The second example should fail on your system unless you have @code{rcp}
or @code{scp} priveleges on the machine @code{dust.ps.uci.edu}.
The third example should work from NCAR computers with local access to 
the @code{msrcp}, @code{msread}, or @code{nrnet} commands.
The above commands can be rewritten using the @samp{-p @var{input-path}}
option as follows: 
@cindex @code{-p @var{input-path}}
@cindex @var{input-path}
@cindex @code{-l @var{output-path}}
@cindex @var{output-path}
@example
ncks -H -p ftp://ftp.cgd.ucar.edu/pub/zender/nc -l ./ in.nc
ncks -H -p dust.ps.uci.edu:/home/zender/nc -l ./ in.nc
ncks -H -p /ZENDER/nc -l ./ in.nc 
@end example
@noindent
Using @samp{-p} is recommended because it clearly separates the
@var{input-path} from the filename itself, sometimes called the
@dfn{stub}. 
@cindex stub
When @var{input-path} is not explicitly specified using @samp{-p}, NCO
internally generates an @var{input-path} from the first input filename. 
The automatically generated @var{input-path} is constructed by stripping
the input filename of everything following the final @samp{/} character
(i.e., removing the stub).
The @samp{-l @var{output-path}} option tells NCO where to store the
remotely retrieved file and the output file.
Often the path to a remotely retrieved file is quite different than the
path on the local machine where you would like to store the file.
If @samp{-l} is not specified then NCO internally generates an
@var{output-path} by simply setting @var{output-path} equal to
@var{input-path} stripped of any machine names.
If @samp{-l} is not specified and the remote file resides on the NCAR 
MSS system, then the leading character of @var{input-path}, @samp{/}, is
also stripped from @var{output-path}.
Specifying @var{output-path} as @samp{-l ./} tells NCO to store the
remotely retrieved file and the output file in the current directory.
Note that @samp{-l .} is equivalent to @samp{-l ./} though the latter is
syntactically more clear.

Note that this remote retrieval feature can easily be used to retrieve
@emph{any} file, including non-netCDF files, via anonymous FTP.
Often this method is quicker than using a browser, or running an FTP
session from a shell window yourself.
For example, say you want to obtain a JPEG file from a weather server.
@example
ncks -p ftp://weather.edu/pub/pix/jpeg -l ./ storm.jpg
@end example
@noindent
In this example, @code{ncks} automatically performs an anonymous FTP
login to the remote machine and retrieves the specified file.
When @code{ncks} attempts to read the local copy of @file{storm.nc}
as a netCDF file, it fails and exits, leaving  @file{storm.nc} in
the current directory.

@node File retention, Variable subsetting, Remote storage, Common features
@section Retention of remotely retrieved files
@cindex file deletion
@cindex file removal
@cindex file retention
@cindex @code{-R}
@cartouche
@noindent
Availability: All operators@*
Key switches: @samp{-R}@*
@end cartouche
In order to conserve local file system space, files retrieved from
remote locations are automatically deleted from the local file system
once they have been processed.
Many NCO operators were constructed to work with numerous large (e.g.,
200 Mb) files. 
Retrieval of multiple files from remote locations is done serially. 
Each file is retrieved, processed, then deleted before the cycle
repeats.  
In cases where it is useful to keep the remotely-retrieved files on the
local file system after processing, the automatic removal feature may be
disabled by specifying @samp{-R} on the command line.

@node Variable subsetting, Coordinate variables, File retention, Common features
@section Including/Excluding specific variables
@cindex @code{-v @var{var}}
@cindex @code{-x}
@cartouche
@noindent
Availability: @code{ncdiff}, @code{ncea}, @code{ncecat}, @code{ncflint},
@code{ncks},  @code{ncra}, @code{ncrcat}, @code{ncwa}@*
Key switches: @samp{-v}, @samp{-x}@*
@end cartouche
Variable subsetting is implemented with the @samp{-v @var{var}[,@dots{}]} and
@samp{-x} options. 
A list of variables to extract is specified following the @samp{-v}
option, e.g., @samp{-v time,lat,lon}.
Not using the @samp{-v} option is equivalent to specifying all
variables.  
The @samp{-x} option causes the list of variables specified with
@samp{-v} to be excluded rather than extracted.
Thus @samp{-x} saves typing when you only want to extract fewer than
half of the variables in a file.
@cindex memory requirements
Remember, if you are stretching the limits of your system's memory by
averaging or concatenating large files, then the easiest solution is
often to use the @samp{-v} option to retain only the variables you
really need (@pxref{Memory usage}).

@node Coordinate variables, Fortran indexing, Variable subsetting, Common features
@section Including/Excluding coordinate variables
@cindex @code{-C}
@cindex @code{-c}
@cartouche
@noindent
Availability: @code{ncdiff}, @code{ncea}, @code{ncecat}, @code{ncflint},
@code{ncks},  @code{ncra}, @code{ncrcat}, @code{ncwa}@*
Key switches: @samp{-C}, @samp{-c}@*
@end cartouche
By default, coordinates variables associated with any variable appearing
in the @var{output-file} will also appear in the @var{output-file}, even
if they are not explicitly specified, e.g., with the @samp{-v} switch.
Thus variables with a latitude coordinate @code{lat} always carry the
values of @code{lat} with them into the @var{output-file}.
This feature can be disabled with @samp{-C}, which causes NCO to not
automatically add coordinates to the variables appearing in the
@var{output-file}. 
However, using @samp{-C} does not preclude the user from including some
coordinates in the output files simply by explicitly selecting the
coordinates with the @var{-v} option.
The @samp{-c} option, on the other hand, is a shorthand way of
automatically specifying that @emph{all} coordinate variables in the
@var{input-files} should appear in the @var{output-file}.
Thus @samp{-c} allows the user to select all the coordinate variables
without having to know their names.

@node Fortran indexing, Hyperslabs, Coordinate variables, Common features
@section C & Fortran index conventions
@cindex index conventions
@cindex Fortran index convention
@cindex C index convention
@cindex @code{-F}
@cartouche
@noindent
Availability: @code{ncdiff}, @code{ncea}, @code{ncecat}, @code{ncflint},
@code{ncks},  @code{ncra}, @code{ncrcat}, @code{ncwa}@*
Key switches: @samp{-F}@*
@end cartouche
By default, NCO uses C-style (0-based) indices for all I/O.
The @samp{-F} switch tells NCO to switch to reading and writing with
Fortran index conventions.
In Fortran, indices begin counting from 1 (rather than 0), and
dimensions are ordered from fastest varying to slowest varying.
Consider a file @file{85.nc} containing 12 months of data in the record
dimension @code{time}.
The following hyperslab operations produce identical results, a
June-July-August average of the data:
@example
ncra -d time,5,7 85.nc 85_JJA.nc
ncra -F -d time,6,8 85.nc 85_JJA.nc
@end example

Printing variable @var{three_dim_var} in file @file{in.nc} first with C 
indexing conventions, then with Fortran indexing conventions results in
the following output formats: 
@example
% ncks -H -v three_dim_var in.nc
% lat[0]=-90 lev[0]=1000 lon[0]=-180 three_dim_var[0]=0 
@dots{}
% ncks -F -H -v three_dim_var in.nc
% lon(1)=-180 lev(1)=1000 lat(1)=-90 three_dim_var(1)=0 
@end example

@node Hyperslabs, Wrapped coordinates, Fortran indexing, Common features
@section Hyperslabs 
@cindex hyperslab
@cindex dimension limits
@cindex coordinate limits
@cindex @code{-d @var{dim},[@var{min}][,[@var{max}]]}
@cartouche
@noindent
Availability: @code{ncdiff}, @code{ncea}, @code{ncecat}, @code{ncflint},
@code{ncks},  @code{ncra}, @code{ncrcat}, @code{ncwa}@*
Key switches: @samp{-d}@*
@end cartouche
A @dfn{hyperslab} is a subset of a variable's data.
The coordinates of a hyperslab are specified with the @code{-d
@var{dim},[@var{min}][,[@var{max}]]} option.
The bounds of the hyperslab to be extracted are specified by the
associated @var{min} and @var{max} values. 
A half-open range is specified by omitting either the @var{min} or
@var{max} parameter but including the separating comma. 
The unspecified limit is interpreted as the maximum or minimum value in
the unspecified direction.  
A cross-section at a specific coordinate is extracted by specifying only
the @var{min} limit and omitting a trailing comma. 
Dimensions not mentioned are passed with no reduction in range.
The dimensionality of variables is not reduced (in the case of a
cross-section, the size of the constant dimension will be one). 
If values of a coordinate-variable are used to specify a range or
cross-section, then the coordinate variable must be monotonic (values
either increasing or decreasing). 
In this case, command-line values need not exactly match coordinate
values for the specified dimension. 
Ranges are determined by seeking the first coordinate value to occur in
the closed range [@var{min},@var{max}] and including all subsequent values until one
falls outside the range. 
The coordinate value for a cross-section is the coordinate-variable
value closest to the specified value and must lie within the range or
coordinate-variable values. 

Coordinate values should be specified using real notation with a decimal
point required in the value, whereas dimension indices are specified
using integer notation without a decimal point. 
Note that this convention is only to differentiate coordinate values
from dimension indices, and is independent of the actual type of netCDF
coordinate variables, if any. 
For a given dimension, the specified limits must both be coordinate
values (with decimal points) or dimension indices (no decimal points).

@cindex @code{NC_BYTE}
@cindex @code{NC_CHAR}
User-specified coordinate limits are promoted to double precision values
while searching for the indices which bracket the range. 
Thus, hyperslabs on coordinates of type @code{NC_BYTE} and
@code{NC_CHAR} are computed numerically rather than lexically, so the
results are unpredictable. 

@cindex wrapped coordinates
The relative magnitude of @var{min} and @var{max} indicate to the
operator whether to expect a @dfn{wrapped coordinate}
(@pxref{Wrapped coordinates}), such as longitude.
When @math{@var{min} > @var{max}} NCO expects the coordinate to be
wrapped, and a warning message will be printed.
When this occurs, NCO selects all values outside the domain
[@math{@var{max} < @var{min}}], i.e., all the values exclusive of the
values which would have been selected if @var{min} and @var{max} were
swapped. 
If this seems confusing, test your command on just the coordinate
variables with @code{ncks}, and then examine the output (also with
@code{ncks}) to ensure NCO selected the hyperslab you expected.

Because of the way wrapped coordinates are interpreted, it is very
important to make sure you always specify hyperslabs in the
monotonically increasing sense, i.e., @math{@var{min} < @var{max}}
(even if the underlying coordinate variable is monotonically
decreasing). 
The only exception to this is when you are indeed specifying a wrapped
coordinate.  
The distinction is crucial to understand because the points selected by,
e.g., @code{-d longitude,50.,340.} are exactly the complement of the
points selected by @code{-d longitude,340.,50.}.

Not specifying this option is equivalent to specifying full ranges of
all dimensions. 
This option may be specified more than once.

@node Wrapped coordinates, Stride, Hyperslabs, Common features
@section Wrapped coordinates
@cindex wrapped coordinates
@cindex longitude
@cindex @code{-d @var{dim},[@var{min}][,[@var{max}]]}
@cartouche
@noindent
Availability: @code{ncks}@*
Key switches: @samp{-d}@*
@end cartouche
A @dfn{wrapped coordinate} is a coordinate whose values increase or
decrease monotonically (nothing unusual so far), but which represents a
dimension that ends where it begins (i.e., wraps around on itself).
Longitude (i.e., degrees on a circle) is a familiar example of a wrapped
coordinate.
Longitude increases to the East of Greenwich, England, where it is
defined to be zero.
Halfway around the globe, the longitude is 180 degrees East (or West). 
Continuing eastward, longitude increases to 360 degrees East at
Greenwich. 
The longitude values of most geophysical data is either in the range
[0,360), or [-180,180).
In either case, the Westernmost and Easternmost longitudes are
numerically separated by 360 degrees, but represent contiguous regions
on the globe.
For example, the Saharan desert stretches from roughly 340 to 50 degrees
East.
Extracting the hyperslab of data representing the Sahara from a global
dataset presents special problems when the global dataset is stored
consecutively in longitude from 0 to 360 degrees.
This is because the data for the Sahara will not be contiguous in the
@var{input-file} but is expected by the user to be contiguous in the
@var{output-file}. 
In this case, @code{ncks} must invoke special software routines to assemble
the desired output hyperslab from multiple reads of the @var{input-file}.

Assume the domain of the monotonically increasing longitude coordinate
@code{lon} is @math{0 < @var{lon} < 360}. 
@code{ncks} will extract a hyperslab which crosses the Greenwich
meridian simply by specifying the westernmost longitude as @var{min} and
the easternmost longitude as @var{max}.
Thus, the following commands extract a hyperslab containing the Saharan desert:
@example
ncks -d lon,340.,50. in.nc out.nc
ncks -d lon,340.,50. -d lat,10.,35. in.nc out.nc
@end example
@noindent
The first example selects data in the same longitude range as the Sahara. 
The second example further constrains the data to having the same
latitude as the Sahara.
The coordinate @code{lon} in the @var{output-file}, @file{out.nc}, will
no longer be monotonic! 
The values of @code{lon} will be, e.g., @samp{340, 350, 0, 10, 20, 30,
40, 50}. 
This can have serious implications should you run @file{out.nc} through
another operation which expects the @code{lon} coordinate to be
monotonically increasing.
Fortunately, the chances of this happening are slim, since @code{lon}
has already been hyperslabbed, there should be no reason to hyperslab
@code{lon} again.
Should you need to hyperslab @code{lon} again, be sure to give
dimensional indices as the hyperslab arguments, rather than coordinate
values (@pxref{Hyperslabs}).

@node Stride, Missing values, Wrapped coordinates, Common features
@section Stride 
@cindex stride
@cindex @code{-d @var{dim},[@var{min}][,[@var{max}]]}
@cartouche
@noindent
Availability: @code{ncks}@*
Key switches: @samp{-d}@*
@end cartouche
@code{ncks} offers support for specifying a @dfn{stride} for any
hyperslab 
@footnote{Actually, the @var{stride} argument is valid for all operators
which accept the @samp{-d} hyperslab option.
However, using @var{stride} with operators besides @code{ncks} is not 
supported, and may never be.
This limitation is largely due to the complicated bookkeeping required
to keep track of strides across multi-file input data sets.}.  
The @var{stride} is the spacing between consecutive points in a
hyperslab. 
A @var{stride} of 1 means pick all the elements of the hyperslab, but a
@var{stride} of 2 means skip every other element, etc.

The @var{stride} is specified as the optional fourth argument to the
@samp{-d} hyperslab specification:  
@code{-d @var{dim},[@var{min}][,[@var{max}]][,[@var{stride}]]}.
Specify @var{stride} as an integer (i.e., no decimal point) following
the third comma in the @samp{-d} argument.  
There is no default value for @var{stride}. 
Thus using @samp{-d time,,,2} is valid but @samp{-d time,,,2.0} and
@samp{-d time,,,} are not.
When @var{stride} is specified but @var{min} is not, there is an
ambiguity as to whether the extracted hyperslab should begin with (using
C-style, 0-based indexes) element 0 or element @samp{stride-1}.
NCO resolves this by alway choosing element 0 to be the first element of
the hyperslab.
Thus @samp{-d time,,,@var{stride}} is syntactically equivalent to
@samp{-d time,0,,@var{stride}}.
This means, for example, that specifying the operation @samp{-d
time,,,2} on the array @samp{1,2,3,4,5} selects the hyperslab @samp{1,3,5}.
To obtain the hyperslab @samp{2,4} instead, simply explicitly specify
the starting index as 1, i.e., @samp{-d time,1,,2}. 

For example, consider a file @file{8501_8912.nc} which contains 60
consecutive months of data. 
Say you wish to obtain just the March data from this file.
Using 0-based subscripts (@pxref{Fortran indexing}) these
data are stored in records 2, 14, @dots{} 50 so the desired @var{stride}
is 12.  
Without the @var{stride} option, the procedure is very awkward.
One could use @code{ncks} five times and then use @code{ncrcat} to
concatenate the resulting files together:
@example
foreach idx (02 14 26 38 50) 
ncks -d time,$idx 8501_8912.nc foo.$idx
end
ncrcat foo.?? 8589_03.nc
rm foo.??
@end example
With the @var{stride} option, @code{ncks} performs this hyperslab
extraction in one operation:
@example
ncks -d time,2,,12 8501_8912.nc 8589_03.nc
@end example
For more information on @code{ncks} @xref{ncks netCDF Kitchen Sink}.

@node Missing values, Suppressing interactive prompts, Stride, Common features
@section Missing values
@cindex missing values
@cindex data, missing 
@cindex averaging data
@cindex @code{missing_value} attribute
@cartouche
@noindent
Availability: @code{ncdiff}, @code{ncea}, @code{ncflint}, @code{ncra},
@code{ncwa}@* 
Key switches: None@*
@end cartouche

The phrase @dfn{missing data} refers to data points that are missing,
invalid, or for any reason not intended to be arithmetically processed
in the same fashion as valid data.  
@cindex arithmetic operators
The NCO arithmetic operators attempt to handle missing data in an
intelligent fashion. 
There are four steps in the NCO treatment of missing data:
@enumerate
@item 
Identifying variables which may contain missing data. 

NCO follows the convention that missing data should be stored
with the @var{missing_value} specified in the variable's
@code{missing_value} attribute.  
The @emph{only} way NCO recognizes that a variable @emph{may} contain
missing data is if the variable has a @code{missing_value} attribute.
In this case, any elements of the variable which are numerically equal
to the @var{missing_value} are treated as missing data.

@item 
Converting the @var{missing_value} to the type of the variable, if
neccessary. 

Consider a variable @var{var} of type @var{var_type} with a
@code{missing_value} attribute of type @var{att_type} containing the
value @var{missing_value}.  
As a guideline, the type of the @code{missing_value} attribute should be
the same as the type of the variable it is attached to.
If @var{var_type} equals @var{att_type} then NCO straightforwardly 
compares each value of @var{var} to @var{missing_value} to determine
which elements of @var{var} are to be treated as missing data.
If not, then NCO will internally convert @var{att_type} to
@var{var_type} by using the implicit conversion rules of C, or, if  
@var{att_type} is @code{NC_CHAR}
@footnote{For example, the DOE ARM program often uses @var{att_type} = 
@code{NC_CHAR} and @var{missing_value} = @samp{-99999.}.
}, by typecasting the results of the C function
@code{strtod(@var{missing_value})}. 
@cindex @code{ncatted}
You may use the NCO operator @code{ncatted} to change the
@code{missing_value} attribute and all data whose data is
@var{missing_value} to a new value
(@pxref{ncatted netCDF Attribute Editor}).

@item 
Identifying missing data during arithmetic operations.

@cindex performance
@cindex operator speed
@cindex speed
@cindex execution time
@cindex arithmetic operators
When an NCO arithmetic operator is processing a variable @var{var} with
a @code{missing_value} attribute, it compares each value of @var{var}
to @var{missing_value} before performing an operation.
Note the @var{missing_value} comparison inflicts a performance penalty
on the operator.
Arithmetic processing of variables which contain the
@code{missing_value} attribute always incurs this penalty, even when
none of the data is missing.
Conversely, arithmetic processing of variables which do not contain the
@code{missing_value} attribute never incurs this penalty.
In other words, do not attach a @code{missing_value} attribute to a
variable which does not contain missing data.
This exhortation can usually be obeyed for model generated data, but it
may be harder to know in advance whether all observational data will be
valid or not.

@item 
Treatment of any data identified as missing in arithmetic operators.

@cindex @code{ncea}
@cindex @code{ncra}
@cindex @code{ncwa}
@cindex @code{ncdiff}
@cindex @code{ncflint}
NCO averagers (@code{ncra}, @code{ncea}, @code{ncwa}) do not count any
element with the value @var{missing_value} towards the average.
@code{ncdiff} and @code{ncflint} define a @var{missing_value} result
when either of the input values is a @var{missing_value}.
Sometimes the @var{missing_value} may change from file to file in a
multi-file operator, e.g., @code{ncra}.
NCO is written to account for this (it always compares a variable to the
@var{missing_value} assigned to that variable in the current file).
Suffice it to say that, in all known cases, NCO does ``the right thing''.

@end enumerate

@node  Suppressing interactive prompts, Operator version, Missing values, Common features
@section Suppressing interactive prompts
@cindex overwriting files
@cindex appending to files
@cindex force overwrite
@cindex force append
@cindex @code{-O}
@cindex @code{-A}
@cartouche
@noindent
Availability: All operators@*
Key switches: @samp{-O}, @samp{-A}@*
@end cartouche
If the @var{output-file} specified for a command is a pre-existing file,
then the operator will prompt the user whether to overwrite (erase) the
existing @var{output-file}, attempt to append to it, or abort the
operation. 
However, in processing large amounts of data, too many interactive
questions can be a curse to productivity.
Therefore NCO also implements two ways to override its own safety
features, the @samp{-O} and @samp{-A} switches.
Specifying @samp{-O} tells the operator to overwrite any existing
@var{output-file} without prompting the user interactively.
Specifying @samp{-A} tells the operator to attempt to append to any
existing @var{output-file} without prompting the user interactively.
These switches are useful in batch environments because they suppress
interactive keyboard input.

@node Operator version, History attribute, Suppressing interactive prompts, Common features
@section Operator version
@cindex version
@cindex RCS
@cindex @code{-r}
@cartouche
@noindent
Availability: All operators@*
Key switches: @samp{-r}@*
@end cartouche
All operators can be told to print their internal version number and
copyright notice and then quit with the @samp{-r} switch.
The internal version number varies between operators, and indicates the
most recent change to a particular operator's source code.
This is useful in making sure you are working with the most recent
operators.
The version of NCO you are using might be, e.g., 1.0.
However using @samp{-r} on, say, @code{ncks}, will produce something
like @samp{ncks 3.24 (1997/05/06) Copyright 1995--1997 University
Corporation for Atmospheric Research}.
This tells you @code{ncks} contains all patches up to version 3.24,
which dates from May 6, 1997. 

@node History attribute, NCAR CSM Conventions, Operator version, Common features
@section History attribute
@cindex @code{history} attribute
@cindex timestamp
@cindex global attributes
@cindex attributes, global
@cindex @code{-h}
@cartouche
@noindent
Availability: All operators@*
Key switches: @samp{-h}@*
@end cartouche
All operators automatically append a @code{history} global attribute to
any file they modify or create.
The @code{history} attribute consists of a timestamp and the full string
of the invocation command to the operator, e.g., @samp{Mon May 26 20:10:24
1997: ncks in.nc foo.nc}.
The full contents of an existing @code{history} attribute are copied
from the first @var{input-file} to the @var{output-file}.
The timestamps appear in reverse chronological order, with the most
recent timestamp appearing first in the @code{history} attribute.
Since NCO and many other netCDF operators adhere to the @code{history}
convention, the entire data processing path of a given netCDF file may
often be deduced from examination of its @code{history} attribute.
@cindex @code{ncatted}
To avoid information overkill, all operators have an optional switch
(@samp{-h}) to override automatically appending the @code{history}
attribute (@pxref{ncatted netCDF Attribute Editor}).  

@node NCAR CSM Conventions, ARM Conventions, History attribute, Common features
@section NCAR CSM Conventions
@cindex NCAR CSM conventions
@cindex CSM conventions
@cindex @code{gw}
@cindex @code{ORO}
@cindex @code{date}
@cindex @code{datesec}
@cindex @code{time}
@cartouche
@noindent
Availability: @code{ncdiff}, @code{ncea}, @code{ncecat}, @code{ncflint},
@code{ncra}, @code{ncwa}@*
Key switches: None@*
@end cartouche
NCO has been programmed to recognize NCAR CSM history tapes.
If you do not work with NCAR CSM data then you may skip this section.
The CSM netCDF convention is described at
@ifhtml
<a href="http://www.cgd.ucar.edu/csm/experiments/output.format.html"> http://www.cgd.ucar.edu/csm/experiments/output.format.html</a>.
@end ifhtml
@ifclear html
@c DBG XXX: printed manual is not hyphenating this long web-page name.
@code{http://@-www.cgd.ucar.edu/@-csm/@-experiments/@-output.@-format.@-html}.
@end ifclear
Most of the CSM netCDF convention is transparent to NCO
@footnote{
The exception is appending/altering the attributes @code{x_op},
@code{y_op}, @code{z_op}, and @code{t_op} for variables which have been
averaged across space and time dimensions.
This feature is scheduled for future inclusion in NCO.
}.
There are no known pitfalls associated with using any NCO operator on
files adhering to this convention
@footnote{
The CSM convention recommends @code{time} be stored in the format
@var{time} since @var{base_time}, e.g., the @code{units} attribute of
@code{time} might be @samp{days since 1992-10-8 15:15:42.5 -6:00}. 
A problem with this format occurs when using @code{ncrcat} to
concatenate multiple files together, each with a different
@var{base_time}. 
That is, any @code{time} values from files following the first file to
be concatenated should be corrected to the @var{base_time} offset
specified in the @code{units} attribute of @code{time} from the first
file. 
The analogous problem has been fixed in ARM files (@pxref{ARM Conventions})
and could be fixed for CSM files if there is sufficient lobbying, and if
Unidata fixes the UDUNITS package to build out of the box on Linux.
}.
However, to facilitate maximum user friendliness, NCO does treat certain
variables in some CSM files specially. 
The special functions are not required by the CSM netCDF convention,
but experience has shown they do make life easier.

Currently, NCO determines whether a datafile is a CSM output datafile
simply by checking whether value of the global attribute
@code{convention} (if it exists) equals @samp{NCAR-CSM}.  
Should @code{convention} equal @samp{NCAR-CSM} in the (first)
@var{input-file}, NCO will attempt to treat certain variables specially,
because of their meaning in CSM files. 
NCO will not average the following variables often found in CSM files:
@code{ntrm}, @code{ntrn}, @code{ntrk}, @code{ndbase}, @code{nsbase},
@code{nbdate}, @code{nbsec}, @code{mdt}, @code{mhisf}.
These variables contain scalar metadata such as the resolution of the
host CSM model and it makes no sense to change their values.
Furthermore, the @code{ncdiff} operator will not attempt to difference
the following variables: @code{gw}, @code{ORO}, @code{date},
@code{datesec}, @code{hyam}, @code{hybm}, @code{hyai}, @code{hybi}.
These variables represent the Gaussian weights, the orography field,
time fields, and hybrid pressure coefficients.
These are fields which you want to remain unaltered in the differenced
file 99% of the time.
If you decide you would like any of the above CSM fields processed, you
must use @code{ncrename} to rename them first.

@node ARM Conventions,  , NCAR CSM Conventions, Common features
@section ARM Conventions
@cindex ARM conventions
@cindex @code{time_offset}
@cindex @code{base_time}
@cindex @code{time}
@cartouche
@noindent
Availability: @code{ncrcat}@*
Key switches: None@*
@end cartouche
@code{ncrcat} has been programmed to recognize ARM (Atmospheric
Radiation Measurement Program) data files.
If you do not work with ARM data then you may skip this section.
ARM data files store time information in two variables, a scalar,
@code{base_time}, and a record variable, @code{time_offset}.
Subtle but serious problems can arise when these type of files are
just blindly concatenated.
Therefore @code{ncrcat} has been specially programmed to be able to
chain together consecutive ARM @var{input-files} and produce and
an @var{output-file} which contains the correct time information.
Currently, @code{ncrcat} determines whether a datafile is an ARM
datafile simply by testing for the existence of the variables
@code{base_time}, @code{time_offset}, and the dimension @code{time}. 
If these are found in the @var{input-file} then @code{ncrcat} will 
automatically perform two non-standard, but hopefully useful,
procedures. 
First, @code{ncrcat} will ensure that values of @code{time_offset}
appearing in the @var{output-file} are relative to the @code{base_time}
appearing in the first @var{input-file} (and presumably, though not
necessarily, also appearing in the @var{output-file}).
Second, if a coordinate variable named @code{time} is not found in the
@var{input-files}, then @code{ncrcat} automatically creates the
@code{time} coordinate in the @var{output-file}.  
The values of @code{time} are defined by the ARM convention
@math{@var{time} = @var{base_time} + @var{time_offset}}.
Thus, if @var{output-file} contains the @code{time_offset}
variable, it will also contain the @code{time} coordinate.
@cindex @code{history} attribute
@cindex global attributes
@cindex attributes, global
A short message is added to the @code{history} global attribute whenever
these ARM-specific procedures are executed.

@node Operators, General Index, Common features, Top
@chapter Reference manual for all operators

This chapter presents reference pages for each of the operators
individually. 
The operators are presented in alphabetical order.
All valid command line switches are included in the syntax statement.
Recall that descriptions of many of these command line switches are
provided only in @ref{Common features}, to avoid redundancy.
Only options specific to, or most useful with, a particular operator are
described in any detail in the sections below.  

@menu
* ncatted netCDF Attribute Editor::  
* ncdiff netCDF Differencer::   
* ncea netCDF Ensemble Averager::  
* ncecat netCDF Ensemble Concatenator::  
* ncflint netCDF File Interpolator::  
* ncks netCDF Kitchen Sink::    
* ncra netCDF Record Averager::  
* ncrcat netCDF Record Concatenator::  
* ncrename netCDF Renamer::     
* ncwa netCDF Weighted Averager  ::  
@end menu

@page
@node ncatted netCDF Attribute Editor, ncdiff netCDF Differencer, Operators, Operators
@section @code{ncatted} netCDF Attribute Editor
@cindex attributes
@cindex attribute names
@cindex editing attributes
@findex ncatted

@noindent
SYNTAX
@example
ncatted [-a @var{att_dsc}] [-a @dots{}] [-D] [-h]
[-l path] [-O] [-p path] [-R] [-r] 
@var{input-file} [@var{output-file}]  
@end example
 
@noindent
DESCRIPTION

@code{ncatted} edits attributes in a netCDF file.  
If you are editing attributes then you are spending too much time in the
world of metadata, and @code{ncatted} was written to get you back out as
quickly and painlessly as possible.
@code{ncatted} can @dfn{append}, @dfn{create}, @dfn{delete},
@dfn{modify}, and @dfn{overwrite} attributes (all explained below).  
Furthermore, @code{ncatted} allows each editing operation to be applied
to every variable in a file, thus saving you time when you want to
change attribute conventions throughout a file.
@code{ncatted} interprets character attributes as strings.

@cindex @code{history} attribute
@cindex @code{-h}
Because repeated use of @code{ncatted} can considerably increase the size
of the @code{history} global attribute (@pxref{History attribute}), the
@samp{-h} switch is provided to override automatically appending the
command to the @code{history} global attribute in the @var{output-file}.

@cindex missing values
@cindex data, missing 
@cindex @code{missing_value} attribute
When @code{ncatted} is used to change the @code{missing_value} attribute,
it changes the associated missing data self-consistently.
If the internal floating point representation of a missing value, 
e.g., 1.0e36, differs between two machines then netCDF files produced 
on those machines will have incompatible missing values.
This allows @code{ncatted} to change the missing values in files from 
different machines to a single value so that the files may then be 
concatenated together, e.g., by @code{ncrcat}, without losing any
information.   
For more information @xref{Missing values}. 

The key to mastering @code{ncatted} is understanding the meaning of the
structure describing the attribute modification, @var{att_dsc}.
Each @var{att_dsc} contains five elements, which makes using
@code{ncatted} somewhat complicated, but powerful.
The @var{att_dsc} argument structure contains five arguments in the
following order:@* 

@var{att_dsc} = @var{att_nm}, @var{var_nm}, @var{mode}, @var{att_type},
@var{att_val}@*

@table @var
@item att_nm
Attribute name. 
Example: @code{units}
@item var_nm
Variable name. 
Example: @code{pressure}
@item mode
Edit mode abbreviation. 
Example: @code{a}. 
See below for complete listing of valid values of @var{mode}.
@item att_type
Attribute type abbreviation. Example: @code{c}. 
See below for complete listing of valid values of @var{att_type}.
@item att_val
Attribute value. Example: @code{pascal}. 
@end table
@noindent
There should be no empty space between these five consecutive
arguments. 
The description of these arguments follows in their order of
appearance. 

The value of @var{att_nm} is the name of the attribute you want to edit.
This meaning of this should be clear to all users of the @code{ncatted}
operator. 

@cindex global attributes
@cindex attributes, global
The value of @var{var_nm} is the name of the variable containing the
attribute (named @var{att_nm}) that you want to edit.
There are two very important and useful exceptions to this rule.
The value of @var{var_nm} can also be used to direct @code{ncatted} to
edit global attributes, or to repeat the editing operation for every
variable in a file.
A value of @var{var_nm} of ``global'' indicates that @var{att_nm} refers
to a global attribute, rather than a particular variable's attribute.
This is the method @code{ncatted} supports for editing global
attributes.
If @var{var_nm} is left blank, on the other hand, then @code{ncatted} 
attempts to perform the editing operation on every variable in the file.
This option may be convenient to use if you decide to change the
conventions you use for describing the data.

The value of @var{mode} is a single character abbreviation (@code{a},
@code{c}, @code{d}, @code{m}, or @code{o}) standing for one of
five editing modes:@*
@cindex attributes, appending
@cindex attributes, creating
@cindex attributes, deleting
@cindex attributes, modifying
@cindex attributes, editing
@cindex attributes, overwriting
@table @code
@item a 
@dfn{Append}.
Append value @var{att_val} to current @var{var_nm} attribute
@var{att_nm} value @var{att_val}, if any.  
If @var{var_nm} does not have an attribute @var{att_nm}, there is no
effect.
@item c
@dfn{Create}.
Create variable @var{var_nm} attribute @var{att_nm} with @var{att_val}
if @var{att_nm} does not yet exist.  
If @var{var_nm} already has an attribute @var{att_nm}, there is no
effect. 
@item d
@dfn{Delete}.
Delete current @var{var_nm} attribute @var{att_nm}.
If @var{var_nm} does not have an attribute @var{att_nm}, there is no
effect. 
When @dfn{Delete} mode is selected, the @var{att_type} and @var{att_val}
arguments are superfluous and may be left blank.
@item m
@dfn{Modify}.
Change value of current @var{var_nm} attribute @var{att_nm} to value
@var{att_val}. 
If @var{var_nm} does not have an attribute @var{att_nm}, there is no
effect. 
@item o
@dfn{Overwrite}.
Write attribute @var{att_nm} with value @var{att_val} to variable
@var{var_nm}, overwriting existing attribute @var{att_nm}, if any. 
This is the default mode.
@end table

The value of @var{att_type} is a single character abbreviation (@code{f},
@code{d}, @code{l}, @code{s}, @code{c}, or @code{b}) standing for one of
the six primitive netCDF data types:@* 
@table @code
@item f
@dfn{Float}.
Value(s) specified in @var{att_val} will be stored as netCDF intrinsic
type NC_FLOAT. 
@item d
@dfn{Double}.
Value(s) specified in @var{att_val} will be stored as netCDF intrinsic
type NC_DOUBLE.
@item l
@dfn{Long}.
Value(s) specified in @var{att_val} will be stored as netCDF intrinsic
type NC_LONG.
@item s
@dfn{Short}.
Value(s) specified in @var{att_val} will be stored as netCDF intrinsic
type NC_SHORT.
@item c
@dfn{Char.} 
Value(s) specified in @var{att_val} will be stored as netCDF intrinsic
type NC_CHAR.
@item b
@dfn{Byte}.
Value(s) specified in @var{att_val} will be stored as netCDF intrinsic
type NC_BYTE.
@end table
@noindent
The specification of @var{att_type} is optional in @dfn{Delete} mode.

The value of @var{att_val} is what you want to change attribute
@var{att_nm} to contain.
The specification of @var{att_val} is optional in @dfn{Delete} mode.
Attribute values for all types besides NC_CHAR must have an attribute
length of at least one.
Thus @var{att_val} may be a single value or one-dimensional array of
elements of type @code{att_type}.
If the @var{att_val} is not set or is set to empty space,
and the @var{att_type} is NC_CHAR, e.g., @code{-a units,T,o,c,""} or 
@code{-a units,T,o,c,}, then the corresponding attribute is set to 
have zero length.
When specifying an array of values, it is safest to enclose
@var{att_val} in double or single quotes, e.g., 
@code{-a levels,T,o,s,"1,2,3,4"} or   
@code{-a levels,T,o,s,'1,2,3,4'}.
The quotes are strictly unnecessary around @var{att_val} except 
when @var{att_val} contains characters which would confuse the calling
shell, such as spaces, commas, and wildcard characters. 

@cindex Perl
NCO processing of NC_CHAR attributes is a bit like Perl in that
it attempts to do you want by default (but this sometimes causes
unexpected results if you want unusual data storage).
@cindex @code{printf()}
@cindex @code{\n} (ASCII LF, linefeed)
@cindex characters, special
@cindex @code{\t} (ASCII HT, horizontal tab)
If the @var{att_type} is NC_CHAR then the argument is interpreted as a
string and it may contain C-language escape sequences, e.g., @code{\n},
which NCO will interpret before writing anything to disk.
NCO translates valid escape sequences and stores the appropriate ASCII
code instead.
Since two byte escape sequences, e.g., @code{\n}, represent one byte
ASCII codes, e.g., ASCII 10 (decimal), the stored string attribute is
one byte shorter than the input string length for each embedded escape
sequence. 
The most frequently used C-language escape sequences are @code{\n} (for
linefeed) and @code{\t} (for horizontal tab).
These sequences in particular allow convenient editing of formatted text
attributes. 
@cindex @code{\a} (ASCII BEL, bell)
@cindex @code{\b} (ASCII BS, backspace)
@cindex @code{\f} (ASCII FF, formfeed)
@cindex @code{\r} (ASCII CR, carriage return)
@cindex @code{\v} (ASCII VT, vertical tab)
@cindex @code{\\} (ASCII \, backslash)
The other valid ASCII codes are @code{\a}, @code{\b}, @code{\f},
@code{\r}, @code{\v}, and @code{\\}. 
@xref{ncks netCDF Kitchen Sink}, for more examples of string formatting
(with the @code{ncks} @samp{-s} option) with special characters. 

@cindex @code{\'} (protected end quote)
@cindex @code{\"} (protected double quote)
@cindex @code{\?} (protected question mark)
@cindex @code{\\} (protected backslash)
@cindex @code{'} (end quote)
@cindex @code{"} (double quote)
@cindex @code{?} (question mark)
@cindex @code{\} (backslash)
@cindex special characters
@cindex ASCII
Analogous to @code{printf}, other special characters are also allowed by
@code{ncatted} if they are "protected" by a backslash.
The characters @code{"}, @code{'}, @code{?}, and @code{\} may be 
input to the shell as @code{\"}, @code{\'}, @code{\?}, and @code{\\}.
NCO simply strips away the leading backslash from these characters
before editing the attribute.
No other characters require protection by a backslash.
Backslashes which precede any other character (e.g., @code{3}, @code{m},
@code{$}, @code{|}, @code{&}, @code{@@}, @code{%}, @code{@{}, and
@code{@}}) will not be filtered and will be included in the attribute.

@cindex strings
@cindex NUL-termination
@cindex NUL
@cindex @code{0} (NUL)
Note that the NUL character @code{\0} which terminates C language
strings is assumed and need not be explicitly specified.
If @code{\0} is input, it will not be translated (because it would
terminate the string in an additional location).
Because of these context-sensitive rules, if wish to use an attribute of
type NC_CHAR to store data, rather than text strings, you should use
@code{ncatted} with care.

@noindent
EXAMPLES

Append the string "Data version 2.0.\n" to the global attribute
@code{history}: 
@example
ncatted -O -a history,global,a,c,"Data version 2.0\n" in.nc 
@end example
Note the use of embedded C language @code{printf()}-style escape sequences.

Change the value of the @code{long_name} attribute for variable @code{T}
from whatever it currently is to "temperature":
@example
ncatted -O -a long_name,T,o,c,temperature in.nc
@end example

Delete all existing @code{units} attributes:
@example
ncatted -O -a units,,d,, in.nc
@end example
@noindent
The value of @var{var_nm} was left blank in order to select all
variables in the file.
The values of @var{att_type} and @var{att_val} were left blank because
they are superfluous in @dfn{Delete} mode. 

Modify all existing @code{units} attributes to "meter second-1"
@example
ncatted -O -a units,,m,c,"meter second-1" in.nc
@end example

Overwrite the @code{quanta} attribute of variable
@code{energy} to an array of four integers. 
@example
ncatted -O -a quanta,energy,o,s,"010,101,111,121" in.nc
@end example

Demonstrate input of C-language escape sequences (e.g., @code{\n}) and
other special characters (e.g., @code{\"}) 
@example
ncatted -h -a special,global,o,c,
'\nDouble quote: \"\nTwo consecutive double quotes: \"\"\n
Single quote: Beyond my shell abilities!\nBackslash: \\\n
Two consecutive backslashes: \\\\\nQuestion mark: \?\n' in.nc
@end example
Note that the entire attribute is protected from the shell by single
quotes. 
These outer single quotes are necessary for interactive use, but may be
omitted in batch scripts.

@page
@node ncdiff netCDF Differencer, ncea netCDF Ensemble Averager, ncatted netCDF Attribute Editor, Operators
@section @code{ncdiff} netCDF Differencer
@cindex subtraction
@cindex differencing data
@cindex anomalies
@findex ncdiff

@noindent
SYNTAX
@example 
ncdiff [-A] [-C] [-c] [-D @var{dbg}] 
[-d @var{dim},[@var{min}][,[@var{max}]]] [-F] [-h] [-l @var{path}] 
[-O] [-p @var{path}] [-R] [-r] [-v @var{var}[,@dots{}]] 
[-x] @var{file_1} @var{file_2} @var{file_3}
@end example

@noindent
DESCRIPTION

@code{ncdiff} subtracts variables in @var{file_2} from the corresponding
variables (those with the same name) in @var{file_1} and stores the
results in @var{file_3}. 
@cindex broadcasting variables
Variables in @var{file_2} are @dfn{broadcast} to conform to the
corresponding variable in @var{file_1} if necessary.  
Broadcasting a variable means creating data in non-existing dimensions
from the data in existing dimensions.
For example, a two dimensional variable in @var{file_2} can be
subtracted from a four, three, or two (but not one or zero)
dimensional variable (of the same name) in @code{file_1}. 
This functionality allows the user to compute anomalies from the mean.
Note that variables in @var{file_1} are @emph{not} broadcast to conform
to the dimensions in @var{file_2}. 
@cindex rank
Thus, @code{ncdiff}, the number of dimensions, or @dfn{rank}, of any
processed variable in @var{file_1} must be greater than or equal to the
rank of the same variable in @var{file_2}. 
Furthermore, the size of all dimensions common to both @var{file_1} and
@var{file_2} must be equal. 

When computing anomalies from the mean it is often the case that
@var{file_2} was created by applying an averaging operator to a file
with the same dimensions as @var{file_1}, if not @var{file_1} itself.
In these cases, creating @var{file_2} with @code{ncra} rather than
@code{ncwa} will cause the @code{ncdiff} operation to fail.
For concreteness say the record dimension in @code{file_1} is
@code{time}.  
If @var{file_2} were created by averaging @var{file_1} over the
@code{time} dimension with the @code{ncra} operator rather than with the
@code{ncwa} operator, then @var{file_2} will have a @code{time}
dimension of size 1 rather than having no @code{time} dimension at all 
@cindex degenerate dimensions
@footnote{This is because @code{ncra} collapses the record dimension
to a size of 1 (making it a @dfn{degenerate} dimension), but does not
remove it, while @code{ncwa} removes all dimensions it averages over. 
In other words, @code{ncra} changes the size but not the rank of
variables, while @code{ncwa} changes both the size and the rank of
variables.}.   
In this case the input files to @code{ncdiff}, @var{file_1} and
@var{file_2}, will have unequally sized @code{time} dimensions which
causes @code{ncdiff} to fail.
To prevent this from occuring, use @code{ncwa} to remove the @code{time}
dimension from @var{file_2}.
An example is given below.

@code{ncdiff} will never difference coordinate variables or variables of
type @code{NC_CHAR} or @code{NC_BYTE}. 
This ensures that coordinates like (e.g., latitude and longitude) are
physically meaningful in the output file, @var{file_3}. 
This behavior is hardcoded.
@cindex NCAR CSM conventions
@cindex CSM conventions
@code{ncdiff} applies special rules to some NCAR CSM fields (e.g.,
@code{ORO}).
See @ref{NCAR CSM Conventions} for a complete description.

@noindent
EXAMPLES

Say files @file{85_0112.nc} and @file{86_0112.nc} each contain 12 months
of data.
Compute the change in the monthly averages from 1985 to 1986:
@example
ncdiff 86_0112.nc 85_0112.nc 86m85_0112.nc
@end example

The following examples demonstrate the broadcasting feature of
@code{ncdiff}.  
Say we wish to compute the monthly anomalies of @code{T} from the yearly
average of @code{T} for the year 1985.
First we create the 1985 average from the monthly data, which is stored
with the record dimension @code{time}.
@example
ncra 85_0112.nc 85.nc
ncwa -O -a time 85.nc 85.nc
@end example
@noindent
The second command, @code{ncwa}, gets rid of the @code{time} dimension
of size 1 that @code{ncra} left in @file{85.nc}. 
Now none of the variables in @file{85.nc} has a @code{time} dimension.
A quicker way to accomplish this is to use @code{ncwa} from the
beginning:  
@example
ncwa -a time 85_0112.nc 85.nc
@end example
@noindent
We are now ready to use @code{ncdiff} to compute the anomalies for 1985:
@example
ncdiff -v T 85_0112.nc 85.nc t_anm_85_0112.nc
@end example
@noindent
Each of the 12 records in @file{t_anm_85_0112.nc} now contains the
monthly deviation of @code{T} from the annual mean of @code{T} for each
gridpoint. 

Say we wish to compute the monthly gridpoint anomalies from the zonal
annual mean. 
A @dfn{zonal mean} is a quantity that has been averaged over the
longitudinal (or @var{x}) direction.
First we use @code{ncwa} to average over longitudinal direction
@code{lon}, creating @file{xavg_85.nc}, the zonal mean of @file{85.nc}. 
Then we use @code{ncdiff} to subtract the zonal annual means from the
monthly gridpoint data:
@example
ncwa -a lon 85.nc xavg_85.nc
ncdiff 85_0112.nc xavg_85.nc tx_anm_85_0112.nc
@end example
@noindent
Assuming @file{85_0112.nc} has dimensions @code{time} and @code{lon}, 
this example only works if @file{xavg_85.nc} has no @code{time} or
@code{lon} dimension.

As a final example, say we have five years of monthly data (i.e., 60 
months) stored in @file{8501_8912.nc} and we wish to create a file
which contains the twelve month seasonal cycle of the average monthly
anomaly from the five-year mean of this data. 
The following method is just one permutation of many which will
accomplish the same result.
First use @code{ncwa} to create the file containing the five-year mean:
@example
ncwa -a time 8501_8912.nc 8589.nc
@end example
@noindent
Next use @code{ncdiff} to create a file containing the difference of
each month's data from the five-year mean:
@example
ncdiff 8501_8912.nc 8589.nc t_anm_8501_8912.nc
@end example
@noindent
Now use @code{ncks} to group the five January anomalies together in one 
file, and use @code{ncra} to create the average anomaly for all five
Januarys. 
These commands are embedded in a shell loop so they are repeated for all
twelve months:
@example
foreach idx (01 02 03 04 05 06 07 08 09 10 11 12) 
ncks -F -d time,$idx,,12 t_anm_8501_8912.nc foo.$idx
ncra foo.$idx t_anm_8589_$idx.nc
end
@end example
@noindent
Finally, use @code{ncrcat} to concatenate the 12 average monthly anomaly
files into one file which then contains the entire seasonal cycle of the
monthly anomalies:
@example
ncrcat t_anm_8589_??.nc t_anm_8589_0112.nc
@end example
@noindent

@page
@node ncea netCDF Ensemble Averager, ncecat netCDF Ensemble Concatenator, ncdiff netCDF Differencer, Operators
@section @code{ncea} netCDF Ensemble Averager
@cindex averaging data
@cindex ensemble average
@findex ncea

@noindent
SYNTAX
@example
ncea [-A] [-C] [-c] [-D @var{dbg}] 
[-d @var{dim},[@var{min}][,[@var{max}]]] [-F] [-h] [-l @var{path}] 
[-n @var{loop}] [-O] [-p @var{path}] [-R] [-r] [-v @var{var}[,@dots{}]]
[-x] @var{input-files} @var{output-file}   
@end example

@noindent
DESCRIPTION

@code{ncea} performs gridpoint averages of variables across an arbitrary
number (an @dfn{ensemble}) of input files, with each file receiving an
equal weight in the average.
@cindex ensemble
Each variable in the @var{output-file} will be the same size as the same
variable in any one of the in the @var{input-files}, and all
@var{input-files} must be the same size. 
Whereas @code{ncra} only performs averages over the record dimension
(e.g., time), and weights each record in the record dimension evenly, 
@code{ncea} averages entire files, and weights each file evenly.
All dimensions, including the record dimension, are treated identically
and preserved in the @var{output-file}.
@xref{Averaging vs. Concatenating}, for a description of the
distinctions between the various averagers and concatenators. 

The file is the logical unit of organization for the results of many
scientific studies.
Often one wishes to generate a file which is the gridpoint average of
many separate files. 
This may be to reduce statistical noise by combining the results of a
large number of experiments, or it may simply be a step in a procedure
whose goal is to compute anomalies from a mean state. 
In any case, when one desires to generate a file whose properties are
the mean of all the input files, then @code{ncea} is the operator to
use. 
@code{ncea} assumes coordinate variable are properties common to all of
the experiments and so does not average them across files.
Instead, @code{ncea} copies the values of the coordinate variables from
the first input file to the output file.

@noindent
EXAMPLES

Consider a model experiment which generated five realizations of one
year of data, say 1985.
You can imagine that the experimenter slightly perturbs the
initial conditions of the problem before generating each new solution.  
Assume each file contains all twelve months (a seasonal cycle) of data
and we want to produce a single file containing the ensemble average
(mean) seasonal cycle.  
Here the numeric filename suffix denotes the experiment number
(@emph{not} the month):
@example
ncea 85_01.nc 85_02.nc 85_03.nc 85_04.nc 85_05.nc 85.nc
ncea 85_0[1-5].nc 85.nc
ncea -n 5,2,1 85_01.nc 85.nc
@end example
@noindent
These three commands produce identical answers.
@xref{Specifying input files}, for an explanation of the distinctions
between these methods.
The output file, @file{85.nc}, is the same size as the inputs files.
It contains 12 months of data (which might or might not be stored in the
record dimension, depending on the input files), but each value in the
output file is the average of the five values in the input files.

In the previous example, the user could have obtained the ensemble
average values in a particular spatio-temporal region by adding a 
hyperslab argument to the command, e.g.,
@example
ncea -d time,0,2 -d lat,-23.5,23.5 85_??.nc 85.nc
@end example
@noindent
In this case the output file would contain only three slices of data in
the @var{time} dimension. 
These three slices are the average of the first three slices from the
input files.
Additionally, only data inside the tropics is included.

@page
@node ncecat netCDF Ensemble Concatenator, ncflint netCDF File Interpolator, ncea netCDF Ensemble Averager, Operators
@section @code{ncecat} netCDF Ensemble Concatenator
@cindex concatenation
@cindex ensemble concatenation
@findex ncecat

@noindent
SYNTAX
@example
ncecat [-A] [-C] [-c] [-D @var{dbg}] 
[-d @var{dim},[@var{min}][,[@var{max}]]] [-F] [-h] [-l @var{path}] 
[-n @var{loop}] [-O] [-p @var{path}] [-R] [-r] [-v @var{var}[,@dots{}]]
[-x] @var{input-files} @var{output-file}   
@end example

@noindent
DESCRIPTION

@code{ncecat} concatenates an arbitrary number of input files into a
single output file.
Input files are glued together by creating a record dimension in the
output file. 
Input files must be the same size.
Each input file is stored consecutively as a single record in the output
file.
Thus, the size of the output file is the sum of the sizes of the input
files. 
@xref{Averaging vs. Concatenating}, for a description of the
distinctions between the various averagers and concatenators. 

Consider five realizations, @file{85a.nc}, @file{85b.nc}, @dots{}
@file{85e.nc} of 1985 predictions from the same climate model.
Then @code{ncecat 85?.nc 85_ens.nc} glues the individual realizations
together into the single file, @file{85_ens.nc}. 
If an input variable was dimensioned [@code{lat},@code{lon}], it will have
dimensions [@code{record},@code{lat},@code{lon}] in the output file.
A restriction of @code{ncecat} is that the hyperslabs of the processed
variables must be the same from file to file.
Normally this means all the input files are the same size, and contain
data on different realizations of the same variables.

@noindent
EXAMPLES

Consider a model experiment which generated five realizations of one
year of data, say 1985.
You can imagine that the experimenter slightly perturbs the
initial conditions of the problem before generating each new solution.  
Assume each file contains all twelve months (a seasonal cycle) of data
and we want to produce a single file containing all the seasonal cycles.
Here the numeric filename suffix denotes the experiment number
(@emph{not} the month):
@example
ncecat 85_01.nc 85_02.nc 85_03.nc 85_04.nc 85_05.nc 85.nc
ncecat 85_0[1-5].nc 85.nc
ncecat -n 5,2,1 85_01.nc 85.nc
@end example
@noindent
These three commands produce identical answers.
@xref{Specifying input files}, for an explanation of the distinctions
between these methods.
The output file, @file{85.nc}, is five times the size as a single
@var{input-file}. 
It contains 60 months of data (which might or might not be stored in the
record dimension, depending on the input files).

@page
@node ncflint netCDF File Interpolator, ncks netCDF Kitchen Sink, ncecat netCDF Ensemble Concatenator, Operators
@section @code{ncflint} netCDF File Interpolator
@cindex interpolation
@findex ncflint

@noindent
SYNTAX
@example
ncflint [-A] [-C] [-c] [-D @var{dbg}] 
[-d @var{dim},[@var{min}][,[@var{max}]]] [-F] [-h]
[-i @var{var,val3}]  
[-l @var{path}] [-O] [-p @var{path}] [-R] [-r] [-v @var{var}[,@dots{}]]  
[-w @var{wgt1}[,@var{wgt2}]] [-x] @var{file_1} @var{file_2} @var{file_3}
@end example

@noindent
DESCRIPTION

@code{ncflint} creates an output file that is a linear combination of 
the input files.
This linear combination can be a weighted average, a normalized weighted
average average, or an interpolation of the input files.
Coordinate variables are not acted upon in any case, they are simply
copied from @var{file_1}.

There are two conceptually distinct methods of using @code{ncflint}.
The first method is to specify the weight each input file is to have in 
the output file.
In this method, the value @var{val3} of a variable in the output file
@var{file_3} is determined from its values @var{val1} and @var{val2} in the
two input files according to 
@set flg
@tex
$val3 = wgt1 \times val1 + wgt2 \times val2$
@clear flg
@end tex
@ifinfo
@math{@var{val3} = @var{wgt1}*@var{val1} + @var{wgt2}*@var{val2}} 
@clear flg
@end ifinfo
@ifset flg
@c texi2html doesn't like @math{}
@var{val3} = @var{wgt1}*@var{val1} + @var{wgt2}*@var{val2} 
@clear flg
@end ifset
.
Here at least @var{wgt1}, and, optionally, @var{wgt2}, are specified on
the command line with the @samp{-w} switch.
If only @var{wgt1} is specified then @var{wgt2} is automatically
computed as @math{@var{wgt2} = 1 - @var{wgt1}}.
Note that weights larger than 1 are allowed. 
Thus it is possible to specify @math{@var{wgt1} = 2} and
@math{@var{wgt2} = -3}.

The second method of using @code{ncflint} is specifying the
interpolation option with @samp{-i}.
This is really the inverse of the first method in the following sense.
When the user specifies the weights directly, @code{ncflint} has no
work to do besides multiplying the input values by their respective
weights and adding the results together to produce the output values.  
This assumes it is the weights that are known a priori.
@cindex arrival value 
In another class of cases it is the @dfn{arrival value} (i.e.,
@var{val3}) of a particular variable @var{var} that is known a priori.
In this case, the implied weights can always be inferred by examining
the values of @var{var} in the input files. 
This results in one equation in two unknowns, @var{wgt1} and @var{wgt2}:
@set flg
@tex
$val3 = wgt1 \times val1 + wgt2 \times val2$
@clear flg
@end tex
@ifinfo
@math{@var{val3} = @var{wgt1}*@var{val1} + @var{wgt2}*@var{val2}} 
@clear flg
@end ifinfo
@ifset flg
@c texi2html doesn't like @math{}
@var{val3} = @var{wgt1}*@var{val1} + @var{wgt2}*@var{val2} 
@clear flg
@end ifset
.
Unique determination of the weights requires imposing the additional
constraint of normalization on the weights:
@math{@var{wgt1} + @var{wgt2} = 1}.
Thus, to use the interpolation option, the user specifies @var{var}
and @var{val3} with the @samp{-i} option.
@code{ncflint} will compute @var{wgt1} and @var{wgt2}, and use these
weights on all variables to generate the output file.
Although @var{var} may have any number of dimensions in the input
files, it must represent a single, scalar value.  
@cindex degenerate dimensions
Thus any dimensions associated with @var{var} must be @dfn{degenerate},
i.e., of size one.

If neither @samp{-i} nor @samp{-w} is specified on the command line,
@code{ncflint} defaults to weighting each input file equally in the
output file.
This is equivalent to specifying @samp{-w .5} or @samp{-w .5,.5}.
Note that attempting to specify both methods with @samp{-i} and
@samp{-w} will result in an error.

@code{ncflint} is programmed not to interpolate variables of type
@code{NC_CHAR} and @code{NC_BYTE}.
This behavior is hardcoded.

@noindent
EXAMPLES

Although it has other uses, the interpolation feature was designed 
to interpolate @var{file_3} to a time between existing files.
Consider input files @file{85.nc} and @file{87.nc} containing variables
describing the state of a physical system at times @math{@code{time} =
85} and @math{@code{time} = 87}.
Assume each file contains its timestamp in the scalar variable
@code{time}.  
Then, to linearly interpolate to a file @file{86.nc} which describes
the state of the system at time at @code{time} = 86, we would use
@example
ncflint -i time,86 85.nc 87.nc 86.nc
@end example

Say you have observational data covering January and April 1985 in two
files named @file{85_01.nc} and @file{85_04.nc}, respectively.
Then you can estimate the values for February and March by interpolating
the existing data as follows.
Combine @file{85_01.nc} and @file{85_04.nc} in a 2:1 ratio to make
@file{85_02.nc}:  
@example
ncflint -w .667 85_01.nc 85_04.nc 85_02.nc
ncflint -w .667,.333 85_01.nc 85_04.nc 85_02.nc
@end example

Multiply @file{85.nc} by 3 and by @minus{}2 and add them together to
make @file{tst.nc}: 
@example
ncflint -w 3,-2 85.nc 85.nc tst.nc
@end example
@noindent
This is an example of a null operation, so @file{tst.nc} should be
identical (within machine precision) to @file{85.nc}.

@page
@node ncks netCDF Kitchen Sink, ncra netCDF Record Averager, ncflint netCDF File Interpolator, Operators
@section @code{ncks} netCDF Kitchen Sink
@cindex kitchen sink
@cindex printing files contents
@cindex printing variables
@findex ncks

@noindent
SYNTAX
@example
ncks [-A] [-a] [-C] [-c] [-D] 
[-d @var{dim},[@var{min}][,[@var{max}]][,[@var{stride}]]]
[-F] [-H] [-h] [-l @var{path}] [-M] [-m] [-O] [-p @var{path}] [-R] 
[-r] [-s @var{format}] [-u] [-v @var{var}[,@dots{}]] [-x]
@var{input-file} [@var{output-file}] 
@end example

@noindent
DESCRIPTION

@code{ncks} combines selected features of @code{ncdump(1)},
@code{ncextr(1)}, and the nccut and ncpaste specifications into one
versatile utility. 
@code{ncks} extracts a subset of the data from @var{input-file} and
either prints it as ASCII text to stdout, or writes (or pastes) it to
@var{output-file}, or both. 

@code{ncks} will print netCDF data in ASCII format to @code{stdout},
like @code{ncdump(1)}, but with these differences: 
@code{ncks} prints data in a tabular format intended to be easy to
search for the data you want, one datum per screen line, with all
dimension subscripts and coordinate values (if any) preceding the datum.
Option @samp{-s} allows the user the format the data using C-style
format strings.

Options @samp{-a}, @samp{-M}, @samp{-m}, @samp{-H}, @samp{-F}, @samp{-s},
and @samp{-u} control the formatted appearance of the data. 

@cindex global attributes
@cindex attributes, global
@code{ncks} will extract (and optionally create a new netCDF file
comprised of) only selected variable from the input file, like
@code{ncextr(1)} but with these differences: Only variables and
coordinates may be specifically included or excluded---all global
attributes and any attribute associated with an extracted variable will
be copied to the screen and/or output netCDF file. 
Options @samp{-c}, @samp{-C}, @samp{-v}, and @samp{-x} control which
variables are extracted.

@code{ncks} will extract hyperslabs from the specified variables.
In fact @code{ncks} implements the nccut specification exactly.
Option @samp{-d} controls the hyperslab specification.

Input dimensions that are not associated with any output variable will
not appear in the output netCDF.
This feature removes superfluous dimensions from a netCDF file. 

@cindex appending data
@cindex merging files
@code{ncks} will append variables and attributes from the
@var{input-file} to @var{output-file} if @var{output-file} is a
pre-existing netCDF file whose relevant dimensions conform to dimension
sizes of @var{input-file}. 
The append features of @code{ncks} are intended to provide a rudimentary
means of adding data from one netCDF file to another, conforming, netCDF
file. 
When naming conflicts exists between the two files, data in
@var{output-file} is usually overwritten by the corresponding data from
@var{input-file}.  
Thus it is recommended that the user backup @var{output-file} in case
valuable data is accidentally overwritten.

If @var{output-file} exists, the user will be queried whether to
@dfn{overwrite}, @dfn{append}, or @dfn{exit} the @code{ncks} call
completely.  
Choosing @dfn{overwrite} destroys the existing @var{output-file} and
create an entirely new one from the output of the @code{ncks} call.  
Append has differing effects depending on the uniqueness of the
variables and attributes output by @code{ncks}: If a variable or
attribute extracted from @var{input-file} does not have a name conflict with
the members of @var{output-file} then it will be added to @var{output-file}
without overwriting any of the existing contents of @var{output-file}. 
In this case the relevant dimensions must agree (conform) between the
two files; new dimensions are created in @var{output-file} as required. 
@cindex global attributes
@cindex attributes, global
When a name conflict occurs, a global attribute from @var{input-file}
will overwrite the corresponding global attribute from
@var{output-file}.  
If the name conflict occurs for a non-record variable, then the
dimensions and type of the variable (and of its coordinate dimensions,
if any) must agree (conform) in both files. 
Then the variable values (and any coordinate dimension values)
from @var{input-file} will overwrite the corresponding variable values (and
coordinate dimension values, if any) in @var{output-file} 
@footnote{
Those familiar with netCDF mechanics might wish to know what is
happening here: @code{ncks} does not attempt to redefine the variable in
@var{output-file} to match its definition in @var{input-file}, @code{ncks} merely
copies the values of the variable and its coordinate dimensions, if any,
from @var{input-file} to @var{output-file}.
}.

Since there can only be one record dimension in a file, the record
dimension must have the same name (but not necessarily the same size) in
both files if a record dimension variable is to be appended. 
If the record dimensions are of differing sizes, the record dimension of
@var{output-file} will become the greater of the two record dimension sizes,
the record variable from @var{input-file} will overwrite any counterpart in
@var{output-file} and fill values will be written to any gaps left in the
rest of the record variables (I think). 
In all cases variable attributes in @var{output-file} are superseded by
attributes of the same name from @var{input-file}, and left alone if
there is no name conflict. 

Some users may wish to avoid interactive @code{ncks} queries about
whether to overwrite existing data.
For example, batch scripts will fail if @code{ncks} does not receive
responses to its queries. 
Options @samp{-O} and @samp{-A} are available to force overwriting
existing files and variables, respectively. 

@unnumberedsubsec Options specific to @code{ncks}:

The following list provides a short summary of the features unique to
@code{ncks}.  
Features common to many operators are described in 
@ref{Common features}. 

@table @samp

@cindex alphabetize output
@cindex sort alphabetically
@cindex @code{-a}
@item -a 
Do not alphabetize extracted fields. 
By default, the specified output variables are extracted, printed, and
written to disk in alphabetical order.
This tends to make long output lists easier to search for particular
variables. 
Specifying @code{-a} results in the variables being extracted, printed,
and written to disk in the order in which they were saved in the input
file.
Thus @code{-a} retains the original ordering of the variables.

@cindex stride
@item -d @var{dim},[@var{min}][,[@var{max}]][,[@var{stride}]]
Add @dfn{stride} argument to hyperslabber. 
For a complete description of the @var{stride} argument, @xref{Stride}.

@cindex @code{-H}
@item -H 
Print data to screen.

@cindex @code{-M}
@item -M
Print to screen the global metadata describing the file.
This includes file summary information and global attributes. 

@cindex @code{-m}
@item -m
Print variable metadata to screen (similar to @code{ncdump -h}). 
This displays all the metadata pertaining to each variable, one variable
at at time.

@cindex @code{-s}
@cindex @code{printf()}
@item -s @var{format}
String format for text output. Accepts C language escape sequences and
@code{printf()} formats. 

@cindex @code{-u}
@item -u 
Accompany the printing of a variable's values with its units attribute,
if it exists.  

@end table

@noindent
EXAMPLES

View all data in netCDF @file{in.nc}, printed with Fortran indexing
conventions: 
@example
ncks -H -F in.nc
@end example

Copy the netCDF file @file{in.nc} to file @file{out.nc}.
@example
ncks -O in.nc out.nc
@end example
Now the file @file{out.nc} contains all the data from @file{in.nc}.
There are, however, two differences between @file{in.nc} and
@file{out.nc}.
@cindex @code{history} attribute
First, the @code{history} global attribute (@pxref{History attribute})
will contain the command used to create @file{out.nc}.
@cindex alphabetize output
@cindex sort alphabetically
@cindex @code{-a}
Second, the variables in @file{out.nc} will be defined in alphabetical
order.
Of course the internal storage of variable in a netCDF file should be
transparent to the user, but there are cases when alphabetizing a file 
is useful (see description of @code{-a} switch).

@cindex @code{printf()}
@cindex @code{\n} (linefeed)
@cindex @code{\t} (horizontal tab)
Print variable @code{three_dim_var} from file @file{in.nc} with
default notations. 
Next print @code{three_dim_var} as an un-annotated text column.
Then print @code{three_dim_var} signed with very high precision.
Finally, print @code{three_dim_var} as a comma-separated list.
@example
ncks -H -C -v three_dim_var in.nc
ncks -s "%f\n" -H -C -v three_dim_var in.nc
ncks -s "%+16.10f\n" -H -C -v three_dim_var in.nc
ncks -s "%f, " -H -C -v three_dim_var in.nc
@end example
@noindent
The second and third options are useful when pasting data into text
files like reports or papers.  
@xref{ncatted netCDF Attribute Editor}, for more details on string
formatting and special characters. 

Create netCDF @file{out.nc} containing all variables, and any associated
coordinates, except variable @code{time}, from netCDF @file{in.nc}:
@example
ncks -x -v time in.nc out.nc
@end example

Extract variables @code{time} and @code{pressure} from netCDF @file{in.nc}. 
If @file{out.nc} does not exist it will be created.
Otherwise the you will be prompted whether to append to or to
overwrite @file{out.nc}: 
@example
ncks -v time,pressure in.nc out.nc
ncks -C -v time,pressure in.nc out.nc
@end example
@noindent
The first version of the command creates an @file{out.nc} which contains
@code{time}, @code{pressure}, and any coordinate variables associated
with @var{pressure}. 
The @file{out.nc} from the second version is guaranteed to contain only
two variables @code{time} and @code{pressure}.  

Create netCDF @file{out.nc} containing all variables from file @file{in.nc}. 
Restrict the dimensions of these variables to a hyperslab. 
Print (with @code{-H}) the hyperslabs to the screen for good measure.  
The specified hyperslab is: the fifth value in dimension @code{time}; the
half-open range @math{@var{lat} > 0.} in coordinate @code{lat}; the
half-open range @math{@var{lon} < 330.} in coordinate @code{lon}; the
closed interval @math{.3 < @var{band} < .5} in coordinate @code{band}; and
cross-section closest to 1000. in coordinate @code{lev}.  
Note that limits applied to coordinate values are specified with a
decimal point, and limits applied to dimension indices do not have a
decimal point @xref{Hyperslabs}.
@example
ncks -H -d time,5 -d lat,,0. -d lon,330., -d band,.3,.5 
-d lev,1000. in.nc out.nc 
@end example

@cindex wrapped coordinates
Assume the domain of the monotonically increasing longitude coordinate
@code{lon} is @math{0 < @var{lon} < 360}. 
Here, @code{lon} is an example of a wrapped coordinate.
@code{ncks} will extract a hyperslab which crosses the Greenwich
meridian simply by specifying the westernmost longitude as @var{min} and
the easternmost longitude as @var{max}, as follows:
@example
ncks -d lon,260.,45. in.nc out.nc
@end example
For more details @xref{Wrapped coordinates}.

@page
@node ncra netCDF Record Averager, ncrcat netCDF Record Concatenator, ncks netCDF Kitchen Sink, Operators
@section @code{ncra} netCDF Record Averager
@cindex averaging data
@cindex record average
@cindex running average
@findex ncra

@noindent
SYNTAX
@example
ncra [-A] [-C] [-c] [-D @var{dbg}] 
[-d @var{dim},[@var{min}][,[@var{max}]]] [-F] [-h] [-l @var{path}] 
[-n @var{loop}] [-O] [-p @var{path}] [-R] [-r] [-v @var{var}[,@dots{}]]
[-x] @var{input-files} @var{output-file}   
@end example

@noindent
DESCRIPTION

@code{ncra} averages record variables across an arbitrary number of
input files.
@cindex degenerate dimensions
The record dimension is retained as a degenerate (size 1) dimension in
the output variables.
Input files may vary in size, but each must have a record dimension.
The record coordinate, if any, should be monotonic (or else non-fatal
warnings may be generated).
@code{ncra} weights each record (e.g., time slice) in the
@var{input-files} equally.
@code{ncra} does not attempt to see if, say, the @code{time} coordinate
is irregularly spaced and thus would require a weighted average in order
to be a true time average.

Hyperslabs of the record dimension which include more than one file are
handled correctly.
@xref{Averaging vs. Concatenating}, for a description of the
distinctions between the various averagers and concatenators. 

@noindent
EXAMPLES

Average files @file{85.nc}, @file{86.nc}, @dots{} @file{89.nc}
along the record dimension, and store the results in @file{8589.nc}: 
@cindex globbing
@cindex @code{NINTAP}
@cindex Processor
@cindex CCM Processor
@example
ncra 85.nc 86.nc 87.nc 88.nc 89.nc 8589.nc
ncra 8[56789].nc 8589.nc
ncra -n 5,2,1 85.nc 8589.nc
@end example
These three methods produce identical answers.
@xref{Specifying input files}, for an explanation of the distinctions
between these methods.

@cindex fortran
Assume the files @file{85.nc}, @file{86.nc}, @dots{} @file{89.nc} each
contain a record coordinate @var{time} of length 12 defined such that
the third record in @file{86.nc} contains data from March 1986, etc.
NCO knows how to hyperslab the record dimension across files.
Thus, to average data from December, 1985 through February, 1986:
@example
ncra -d time,11,13 85.nc 86.nc 87.nc 8512_8602.nc
ncra -F -d time,12,14 85.nc 86.nc 87.nc 8512_8602.nc
@end example
@noindent
The file @file{87.nc} is superfluous, but does not cause an error.
The @samp{-F} turns on the Fortran (1-based) indexing convention.

Assume the @var{time} coordinate is incrementally numbered such that
January, 1985 = 1 and December, 1989 = 60.
Assuming @samp{??} only expands to the five desired files, the following
averages June, 1985--June, 1989: 
@example
ncra -d time,6.,54. ??.nc 8506_8906.nc
@end example

@page
@node ncrcat netCDF Record Concatenator, ncrename netCDF Renamer, ncra netCDF Record Averager, Operators
@section @code{ncrcat} netCDF Record Concatenator
@cindex concatenation
@cindex record concatenation
@findex ncrcat

@noindent
SYNTAX
@example
ncrcat [-A] [-C] [-c] [-D @var{dbg}] 
[-d @var{dim},[@var{min}][,[@var{max}]]] [-F] [-h] [-l @var{path}] 
[-n @var{loop}] [-O] [-p @var{path}] [-R] [-r] [-v @var{var}[,@dots{}]]
[-x] @var{input-files} @var{output-file}   
@end example

@noindent
DESCRIPTION

@code{ncrcat} concatenates record variables across an arbitrary number
of input files.
The final record dimension is by default the sum of the lengths of the
record dimensions in the input files.
@xref{Averaging vs. Concatenating}, for a description of the
distinctions between the various averagers and concatenators. 

Input files may vary in size, but each must have a record dimension.
The record coordinate, if any, should be monotonic (or else non-fatal
warnings may be generated).
Hyperslabs of the record dimension which include more than one file are 
handled correctly.
@cindex ARM conventions
@code{ncrcat} applies special rules to ARM convention time fields (e.g.,
@code{time_offset}).
See @ref{ARM Conventions} for a complete description.

@noindent
EXAMPLES

Concatenate files @file{85.nc}, @file{86.nc}, @dots{} @file{89.nc}
along the record dimension, and store the results in @file{8589.nc}: 
@cindex globbing
@cindex @code{NINTAP}
@cindex Processor
@cindex CCM Processor
@example
ncrcat 85.nc 86.nc 87.nc 88.nc 89.nc 8589.nc
ncrcat 8[56789].nc 8589.nc
ncrcat -n 5,2,1 85.nc 8589.nc
@end example
@noindent
These three methods produce identical answers.
@xref{Specifying input files}, for an explanation of the distinctions
between these methods.

@cindex fortran
Assume the files @file{85.nc}, @file{86.nc}, @dots{} @file{89.nc} each
contain a record coordinate @var{time} of length 12 defined such that
the third record in @file{86.nc} contains data from March 1986, etc.
NCO knows how to hyperslab the record dimension across files.
Thus, to concatenate data from December, 1985--February, 1986:
@example
ncrcat -d time,11,13 85.nc 86.nc 87.nc 8512_8602.nc
ncrcat -F -d time,12,14 85.nc 86.nc 87.nc 8512_8602.nc
@end example
@noindent
The file @file{87.nc} is superfluous, but does not cause an error.
The @samp{-F} turns on the Fortran (1-based) indexing convention.

Assume the @var{time} coordinate is incrementally numbered such that
January, 1985 = 1 and December, 1989 = 60.
Assuming @code{??} only expands to the five desired files, the following
concatenates June, 1985--June, 1989: 
@example
ncrcat -d time,6.,54. ??.nc 8506_8906.nc
@end example

@page
@node ncrename netCDF Renamer, ncwa netCDF Weighted Averager  , ncrcat netCDF Record Concatenator, Operators
@section @code{ncrename} netCDF Renamer
@cindex renaming variables
@cindex renaming dimensions
@cindex renaming attributes
@cindex variable names
@cindex dimension names
@cindex attribute names
@findex ncrename

@noindent
SYNTAX
@example
ncrename [-a @var{old_name},@var{new_name}] [-a @dots{}] [-D] 
[-d @var{old_name},@var{new_name}] [-d @dots{}] [-h] [-l path] [-O] [-p path]
[-R] [-r] [-v @var{old_name},@var{new_name}] [-v @dots{}]
@var{input-file} [@var{output-file}]  
@end example
 
@noindent
DESCRIPTION

@code{ncrename} renames dimensions, variables, and attributes in a
netCDF file.  
Each object that has a name in the list of old names is renamed using
the corresponding name in the list of new names. 
All the new names must be unique. 
Every old name must exist in the input file, unless the name is preceded
by the character @samp{.}. 
The validity of the old names is not checked prior to the renaming. 
Thus, if an old name is specified without the the @samp{.} prefix and is
not present in @var{input-file}, @code{ncrename} will abort. 

@cindex data safety
@cindex safeguards
@cindex temporary output files
@code{ncrename} is the exception to the normal rules that the user will
be interactively prompted before an existing file is changed, and that a
temporary copy of an output file is constructed during the operation.
If only @var{input-file} is specified, then @code{ncrename} will change
the names of the @var{input-file} in place without prompting and without
creating a temporary copy of @code{input-file}.
This is because the renaming operation is considered reversible, i.e.,
the @var{new_name} can easily be changed back to @var{old_name} by using
@code{ncrename} one more time.

Note that renaming a dimension to the name of a dependent variable can
be used to invert the relationship between an independent coordinate
variable and a dependent variable. 
In this case, the named dependent variable must be one-dimensional and
should have no missing values. 
Such a variable will become a coordinate variable.

@cindex performance
@cindex operator speed
@cindex speed
@cindex execution time
According to the @cite{netCDF User's Guide}, renaming properties in
netCDF files does not incur the penalty of recopying the entire file
when the @var{new_name} is shorter than the @var{old_name}.

@noindent
OPTIONS

@table @samp
@item -a @var{old_name},@var{new_name}
Attribute renaming. 
The old and new names of the attribute are specified by the associated
@var{old_name} and @var{new_name} values. 
@cindex global attributes
@cindex attributes, global
Global attributes are treated no differently than variable attributes.
This option may be specified more than once.

@item -d @var{old_name},@var{new_name}
Dimension renaming. 
The old and new names of the dimension are specified by the associated
@var{old_name} and @var{new_name} values. 
This option may be specified more than once.
 
@item -v @var{old_name},@var{new_name}
Variable renaming. 
The old and new names of the variable are specified by the associated
@var{old_name} and @var{new_name} values. 
This option may be specified more than once.

@c @cindex interactive prompting
@c @item -i 
@c Interactive. 
@c @code{ncrename} will prompt for confirmation before overwriting an
@c existing file. 
@end table

@noindent
EXAMPLES

Rename the variable @code{p} to @code{pressure} and @code{t} to
@code{temperature} in netCDF @file{in.nc}. 
In this case @code{p} must exist in the input file (or @code{ncrename} will
abort), but the presence of @code{t} is optional:
@example
ncrename -v p,pressure -v .t,temperature in.nc
@end example
 
@cindex global attributes
@cindex attributes, global
@cindex @code{_FillValue} attribute
@cindex @code{missing_value} attribute
Create netCDF @file{out.nc} identical to @file{in.nc} except the attribute
@code{_FillValue} is changed to @code{missing_value} (in all variables
which possess it) and the global attribute @code{Zaire} is changed to
@code{Congo}:  
@example
ncrename -a _FillValue,missing_value -a Zaire,Congo in.nc out.nc 
@end example

@page
@node ncwa netCDF Weighted Averager  ,  , ncrename netCDF Renamer, Operators
@section @code{ncwa} netCDF Weighted Averager
@cindex averaging data
@cindex weighted average
@cindex masked average
@cindex broadcasting variables
@findex ncwa

@noindent
SYNTAX
@example
ncwa [-A] [-a @var{dim}[,@dots{}]] [-C] [-c] [-D @var{dbg}] 
[-d @var{dim},[@var{min}][,[@var{max}]]] [-F] [-h] [-I] [-l @var{path}] 
[-M @var{val}] [-m @var{var}] [-N] [-n] [-O] [-o @var{condition}] 
[-p @var{path}] [-R] [-r] [-v @var{var}[,@dots{}]] [-W] [-w @var{weight}]
[-x] @var{input-file} @var{output-file} 
@end example

@noindent
DESCRIPTION

@code{ncwa} averages variables in a single file over arbitrary
dimensions, with options to specify weights, masks, and normalization.   
@xref{Averaging vs. Concatenating}, for a description of the
distinctions between the various averagers and concatenators. 
The default behavior of @code{ncwa} is to arithmetically average every
numerical variable over all dimensions and produce a scalar result.
To average variables over only a subset of their dimensions, specify
these dimensions in a comma-separated list following @samp{-a}, e.g.,
@samp{-a time,lat,lon}. 
@cindex arithmetic operators
@cindex hyperslab
@cindex @code{-d @var{dim},[@var{min}][,[@var{max}]]}
As with all arithmetic operators, the operation may be restricted to
an arbitrary hypserslab by employing the @samp{-d} option
(@pxref{Hyperslabs}). 
@code{ncwa} also handles values matching the variable's
@code{missing_value} attribute correctly. 
Moreover, @code{ncwa} understands how to manipulate user-specified
weights, masks, and normalization options.
With these options, @code{ncwa} can compute sophisticated averages (and
integrals) from the command line. 

@var{mask} and @var{weight}, if specified, are broadcast to conform to
the variables being averaged. 
@cindex rank
The rank of variables is reduced by the number of dimensions which they
are averaged over.  
Thus arrays which are one dimensional in the @var{input-file} and are
averaged by @code{ncwa} appear in the @var{output-file} as scalars.
This allows the user to infer which dimensions may have been averaged.
Note that that it is impossible for @code{ncwa} to make make a
@var{weight} or @var{mask} of rank @var{W} conform to a @var{var} of
rank @var{V} if @var{W > V}.
This situation often arises when coordinate variables (which, by
definition, are one dimensional) are weighted and averaged.
@code{ncwa} assumes you know this is impossible and so @code{ncwa} does
not attempt to broadcast @var{weight} or @var{mask} to conform to
@var{var} in this case, nor does @code{ncwa} print a warning message
telling you this, because it is so common.  
Specifying @var{dbg > 2} does cause @code{ncwa} to emit warnings in
these situations, however.

Non-coordinate variables are always masked and weighted if specified.
Coordinate variables, however, may be treated specially.
By default, an averaged coordinate variable, e.g., @code{latitude},
appears in @var{output-file} averaged the same way as any other variable
containing an averaged dimension.
In other words, by default @code{ncwa} weights and masks
coordinate variables like all other variables.  
This design decision was intended to be helpful but for some
applications it may be preferable not to weight or mask coordinate
variables just like all other variables.   
Consider the following arguments to @code{ncwa}:  @code{-a latitude -w
lat_wgt -d latitude,0.,90.} where @code{lat_wgt} is a weight in the
@code{latitude} dimension.
Since, by default @code{ncwa} weights coordinate variables, the
value of @code{latitude} in the @var{output-file} depends on the weights 
in @var{lat_wgt} and is not likely to be 45.---the midpoint latitude of
the hyperslab.
@cindex coordinate variable
@cindex @code{-I}
Option @samp{-I} overrides this default behavior and causes @code{ncwa}
not to weight or mask coordinate variables.
In the above case, this causes the value of @code{latitude} in the
@var{output-file} to be 45.---which is a somewhat appealing result.
Thus, @samp{-I} specifies simple arithmetic averages for the coordinate
variables. 
In the case of latitude, @samp{-I} specifies that you prefer to archive
the central latitude of the hyperslab over which variables were averaged 
rather than the area weighted centroid of the hyperslab
@footnote{If @code{lat_wgt} contains Gaussian weights then the value of 
@code{latitude} in the @var{output-file} will be the area-weighted
centroid of the hyperslab. For the example given, this is about 30
degrees.}. 
Note that the default behavior of (@samp{-I}) changed on
1998/12/01---before this date the default was not to weight or mask
coordinate variables.

@ifhtml
Note for HTML user's: The documentation for <CODE>ncwa</CODE> relies
heavily on mathematical expressions which cannot be easily represented
in HTML.
The printed manual contains much better documentation on
<CODE>ncwa</CODE>. 
@end ifhtml
@ifinfo
Note for Info user's: The documentation for @code{ncwa} relies heavily
on mathematical expressions which cannot be easily represented in
Info. 
The printed manual contains much better documentation on @code{ncwa}.
@end ifinfo

@tex
@code{ncwa} defines the generic average of the variable $x$ to be
$$
\bar x_j = {\sum_{i = 1}^{i = N} \mu_i m_i w_i x_i \over \sum_{i =
1}^{i = N} \mu_i m_i w_i} 
$$
where $\bar x_j$ is the $j$'th element of the output hyperslab, $x_i$ is
the $i$'th element of the input hyperslab, $\mu_i$ is 1 unless $x_i$
equals the missing value, $m_i$ is 1 unless $x_i$ is masked, and $w_i$
is the weight.  
This formiddable looking formula represents a simple weighted average
whose bells and whistles are all explained below. 
It is not early to note, however, that when $\mu_i = m_i = w_i = 1$, the
generic averaging expression above reduces to a simple arithmetic
average. 
The size $J$ of the output hyperslab for a given variable is the product
of all the dimensions of the input variable which are not averaged over.
The size $N$ of the input hyperslab contributing to each $\bar x_j$ is
simply the product of the sizes of all dimensions which are averaged
over (i.e., dimensions specified with @samp{-a}). 
Thus $N$ is the number of input elements which @emph{potentially}
contribute to each output element.
An input element $x_i$ contributes to the output element $x_j$ except
in two conditions:  
@cindex missing values
@enumerate
@item $x_i$ equals the @var{missing value} (@pxref{Missing values}) for the
variable. 
@item $x_i$ is located at a point where the masking condition
(@pxref{Masking condition}) is false.
@end enumerate
Points $x_i$ in either of these two categories do not contribute to
$x_j$, they are ignored.
We now define these criteria more rigorously.

Each $x_i$ has an associated Boolean weight $\mu_i$ whose value is 0 or
1 (false or true).
The value of $\mu_i$ is 1 (true) unless $x_i$ equals the @var{missing
value} (@pxref{Missing values}) for the variable.
Thus, for a variable with no @code{missing_value} attribute, $\mu_i$ is
always 1.
All other NCO arithmetic operators (@code{ncdiff}, @code{ncra},
@code{ncea}, @code{ncflint}) treat missing values analogously.
@end tex

@menu
* Masking condition::           
* Normalization::               
@end menu

@node Masking condition, Normalization, ncwa netCDF Weighted Averager  , ncwa netCDF Weighted Averager
@unnumberedsubsec Masking condition
@cindex masking condition
@tex
Each $x_i$ also has an associated masking weight $m_i$ whose value is 0
or 1 (false or true).
The value of $m_i$ is always 1 unless a @var{mask} is specified (with
@samp{-m}).
As noted above, @var{mask} is broadcast, if possible, to conform 
to the variable being averaged.  
In this case, the value of $m_i$ depends on the @dfn{masking
condition}. 
As expected, $m_i = 1$ when the masking condition is @dfn{true} and $m_i
= 0$ otherwise.   
@end tex

The masking condition has the syntax @math{@var{mask}}
@math{@var{condition}} @math{@var{val}}. 
Here @var{mask} is the name of the masking variable (specified with
@samp{-m}). 
The @var{condition} argument to @samp{-o} may be any one of the six
arithmetic comparatives: @kbd{eq}, @kbd{ne}, @kbd{gt}, @kbd{lt},
@kbd{ge}, @kbd{le}. 
@set flg
@tex
These are the Fortran-style character abbreviations for the logical 
operations $=$, $\neq$, $>$, $<$, $\ge$, $\le$. 
@clear flg
@end tex
@ifinfo
These are the Fortran-style character abbreviations for the logical 
operations @math{==}, @math{!=}, @math{>}, @math{<}, @math{>=},
@math{<=}. 
@clear flg
@end ifinfo
@ifset flg
@c texi2html doesn't like @math{}
These are the Fortran-style character abbreviations for the logical 
operations @kbd{==}, @kbd{!=}, @kbd{>}, @kbd{<}, @kbd{>=},
@clear flg
@end ifset
The masking condition defaults to @kbd{eq} (equality).
The @var{val} argument to @samp{-M} is the right hand side of the
@dfn{masking condition}.
Thus for the @var{i}'th element of the hyperslab to be averaged,
the masking condition is 
@math{@var{mask_i}} @var{condition} @var{val}.

@tex
Each $x_i$ is also associated with an additional weight $w_i$ whose
value may be user-specified.
The value of $w_i$ is identically 1 unless the user specifies a
@var{weight} (with @samp{-w}).
In this case, the value of $w_i$ is determined by the @var{weight}
variable in the @var{input-files}. 
As noted above, @var{weight} is broadcast, if possible, to conform 
to the variable being averaged.  

$M$ is the number of input elements $x_i$ which @emph{actually}
contribute to the output element $x_j$.
$M$ is also known as the @dfn{tally} and is defined as 
$$
M = \sum_{i = 1}^{i = N} \mu_i m_i 
$$
$M$ is identical to the denominator of the generic averaging expression
except for the omission of the weight $w_i$.
Thus $M = N$ whenever no input points are missing values or are masked. 
Whether an element contributes to the output, and thus increments
$M$ by one, has more to do with the above two criteria (missing value
and masking) than with the numeric value of the element per se.
For example, $x_i = 0.0$ does contribute to $x_j$ (assuming the
@code{missing_value} attribute is not 0.0 and location $i$ is not
masked). 
The value $x_i = 0.0$ will not change the numerator of the generic
averaging expression, but it will change the denominator (unless its
weight $w_i =0.0$ as well).
@end tex

@node Normalization,  , Masking condition, ncwa netCDF Weighted Averager
@unnumberedsubsec Normalization
@cindex normalization
@code{ncwa} has one switch which controls the normalization of the
averages appearing in the @var{output-file}.
Option @samp{-N} prevents @code{ncwa} from dividing the weighted sum of
the variable (the numerator in the averaging expression) by the weighted
sum of the weights (the denominator in the averaging expression). 
Thus @samp{-N} tells @code{ncwa} to return just the numerator of the
above expression. 

@ignore
The second normalization option tells @code{ncwa} to multiply the
weighted average the variable (given by the averaging expression)
by the tally, @var{M}.
Thus this option is similar to integration---multiplying the mean value
of a quantity by the number of gridpoints to which it applies.

The third normalization option is equivalent to specifying the first two
options simultaneously. 
In other words this option causes @code{ncwa} to return @var{M} times
the numerator of the generic averaging expression.  
With these normalization options, @code{ncwa} can compute sophisticated
averages (and integrals) from the command line.
@end ignore

@noindent
EXAMPLES

Given file @file{85_0112.nc}:
@example
netcdf 85_0112 @{
dimensions:
        lat = 64 ;
        lev = 18 ;
        lon = 128 ;
        time = UNLIMITED ; // (12 currently)
variables:
        float lat(lat) ;
        float lev(lev) ;
        float lon(lon) ;
        float time(time) ;
        float scalar_var ;
        float three_dim_var(lat, lev, lon) ;
        float two_dim_var(lat, lev) ;
        float mask(lat, lon) ;
        float gw(lat) ;
@} 
@end example

Average all variables in @file{in.nc} over all dimensions @file{out.nc}:
@example
ncwa in.nc out.nc
@end example
@noindent
Every variable in @file{in.nc} is reduced to a scalar in @file{out.nc}
because averaging was performed over all dimensions were averaged over. 

Store the zonal (longitudinal) average of @file{in.nc} in @file{out.nc}:
@example
ncwa -a lon in.nc out.nc
@end example
@noindent
Here the tally is simply the size of @code{lon}, or 128.

@cindex @code{gw}
@cindex Gaussian weights
Compute the meridional (latitudinal) average, with values weighted by
the corresponding element of @var{gw}
@footnote{@code{gw} stands for @dfn{Gaussian weight} in the NCAR climate
model.}: 
@example
ncwa -w gw -a lat in.nc out.nc
@end example
@noindent
Here the tally is simply the size of @code{lat}, or 64.
The sum of the Gaussian weights is 2.0.

Compute the area average over the tropical Pacific:
@example
ncwa -w gw -a lat,lon -d lat,-20.,20. -d lon,120.,270. 
in.nc out.nc
@end example
@noindent
Here the tally is 
@set flg
@tex
$64 \times 128 = 8192$.
@clear flg
@end tex
@ifset flg
64 times 128 = 8192.
@clear flg
@end ifset

@cindex @code{ORO}
Compute the area average over the globe, but include only points for
which 
@set flg
@tex
$ORO < 0.5$
@clear flg
@end tex
@ifset flg
@var{ORO} < 0.5
@clear flg
@end ifset
@footnote{@code{ORO} stands for @dfn{Orography} in the NCAR climate model.
@math{@var{ORO} < 0.5} selects the gridpoints which are covered by ocean.}:
@example
ncwa -m ORO -M 0.5 -o lt -w gw -a lat,lon in.nc out.nc
@end example
@noindent
Assuming 70% of the gridpoints are maritime, then here the tally is
@set flg
@tex
$0.70 \times 8192 \approx 5734$.
@clear flg
@end tex
@ifset flg
0.70 times 8192 = 5734.
@clear flg
@end ifset

Compute the global annual average over the maritime tropical Pacific:
@example
ncwa -m ORO -M 0.5 -o lt -w gw -a lat,lon,time 
-d lat,-20.,20. -d lon,120.,270. in.nc out.nc
@end example

@c @ignore
@c @node CSM Example, General Index, Operators, Top
@c @chapter Example: Analyzing a CSM run

@c This chapter presents an in depth example of using NCO to analyze the
@c results of a CSM run.
@c @end ignore

@c @node Name Index, General Index, Operators, Top
@c @unnumbered Function and Variable Index

@c @printindex fn

@node General Index,  , Operators, Top
@unnumbered General Index

@printindex cp

@c Print the tables of contents
@contents

@c That's all
@bye
