ncdiff hgt300.mon.mean.nc hgt850.mon.mean.nc thickness300850.mon.mean.nc
Subtract hgt850 from hgt300, and write it out to thickness...

With the exception of ncrcat, there are always only one input and one output file in a NCO operation. One way to include two or more input variables in a calculation is to append additional variable files to a file. The reanalysis daily-average data is stored as one year per file. Append vwnd to the uwnd file:
ncks -A vwnd.1948.nc uwnd.1948.nc

Calculate the product uv for a year of daily-average data.
ncap -s "uv=uwnd*vwnd" uwnd.1948.nc product.nc
where product.nc will contain uv, uwnd, and vwnd.

Beginning of pentad loop:
Calculate the pentad means of uv.
ncra -O -F -d time,day1,day2 product.nc product.pentad.nc
where day1 and day2 are the first and last Julian days of the pentad, respectively.

Calculate u'v'.
ncap -s "upvp=uv-uwnd*vwnd" -v product.pentad.nc upvp.pentad.nc
where -v forces only upvp (and not uv, uwnd, or vwnd) to be output to upvp.pentad.nc
End of pentad loop

Concatenate the pentad files in a single file for the year.
ncrcat -h -O upvp.pentad.nc upvp.1948.nc

For air temperature the add_offset and scale_factor are 512.81 and 0.01, respectively:

ncap -O -s "air=(air-512.81)/0.01" filename.nc temp.nc
ncap -O -s "air=short(air);air@add_offset=512.81;air@scale_factor=0.01" temp.nc filename.nc

ncatted -O -a units,air,c,c,"units goes here" filename.nc
where "-a" is followed by "attribute name, variable name, mode (append, create, delete, modify, overwrite), attribute variable type (float, character, ...), attribute value"
ncatted -O -a long_name,air,c,c,"long_name goes here" filename.nc
ncatted -O -h -a title,global,o,c,"title goes here" filename.nc
ncatted -O -h -a history,global,o,c,'history goes here' filename.nc
"\n" (no quotes) can be used to put in a carriage return.

ncrename -h -O -v old_variable_name,new_variable_name filename.nc
-h: do not add to the history variable
-O: (upper case) overwrite the file.
will make the Live Access Server software happy.

If you want to put two variables with the same time dimension into the same file, use
ncap -h -A file_a file_b
will put variables a and b into file file_b

If you have yearly files that you want to concatenate, use
ncrcat -h file_1979 file_1980 file_1981 file_197919801981
ncrcat -h file_1979 file_198[01] file_197919801981
should do the same thing.
-h: do not add to the history variable.*

* There is a special problem that can arise with the time dimension in the concatenated files. I write time as "so many units since some reference time" where the reference time is the first time period present in a file. ncrcat, at present, doesn't calculate the time correctly for files written with the above time prescription, and it provides a non-fatal error. I have come up with a matlab5 work-around where I write correct time values into the time variable inside a matlab session. For example,

f = netcdf( filename, 'write' )
f{'time'}(:) = correct_time_values;
f{'time'}(penultimate:last) = (penultimate and last correct_time_values);
% For reasons that make no sense to me I had to do the previous line.
ncclose( filename ) % You have to "ncclose" the file to write the changes.

Sometimes the file has a time variable that has a value that you want to use in the fixed file. Consider the header and time value of the following file. As with Part I, you need to make time a "record dimension" so that NCOs will concatenate files.

netcdf filename {
dimensions:
        time = 1 ;
        lat = 89 ;
        lon = 180 ;
variables:
        float time(time) ;
                time:units = "days since 1854-01-15" ;
        float data(time,lat,lon)
        ...
data:
 time = 15 ;
}

set str1 = 'time = 1 ;'
set str2 = 'time = UNLIMITED ; // (1 currently)'
ncdump in.nc  | sed -e "s#^.$str1# $str2#" | ncgen -o out.nc

Subsetting a region of an array is handled differently than subsetting time.

i) Subsetting a region

Say you have a global dataset, and you only want the data for the northeast portion of the Pacific Ocean.

ncea -d lat,minimum_lat,maximum_lat -d lon,minimum_lon,maximum_lon in.nc out.nc