netcdf-c/ncdump/nccopy.1

.\" $Id: nccopy.1 400 2010-08-27 21:02:52Z russ $
.TH NCCOPY 1 "2012-03-08" "Release 4.2" "UNIDATA UTILITIES"
.SH NAME
nccopy \- Copy a netCDF file to specified variant of netCDF format,
optionally compressing or chunking data in the output copy.
.SH SYNOPSIS
.ft B
.HP
nccopy
.nh
\%[-k \fI kind \fP]
\%[-d \fI n \fP]
\%[-s]
\%[-c \fI chunkspec \fP]
\%[-u]
\%[-w]
\%[-[v|V] var1,...]
\%[-[g|G] grp1,...]
\%[-m \fI bufsize \fP]
\%[-h \fI chunk_cache \fP]
\%[-e \fI cache_elems \fP]
\%[-r]
\%\fI infile \fP
\%\fI outfile \fP
.hy
.ft
.SH DESCRIPTION
.LP
The \fBnccopy\fP utility copies an input netCDF file in any supported
format variant to an output netCDF file, optionally converting the
output to any compatible netCDF format variant, compressing the data,
or rechunking the data.  For example, if built with the netCDF-3
library, a netCDF classic file may be copied to a netCDF 64-bit offset
file, permitting larger variables.  If built with the netCDF-4
library, a netCDF classic file may be copied to a netCDF-4 file or to
a netCDF-4 classic model file as well, permitting data compression,
efficient schema changes, larger variable sizes, and use of other
netCDF-4 features.
.LP
\fBnccopy\fP also serves as an example of a generic netCDF-4 program,
with its ability to read any valid netCDF file and handle nested
groups, strings, and user-defined types, including arbitrarily
nested compound types, variable-length types, and data of any valid
netCDF-4 type.
.LP
If DAP support was enabled when \fBnccopy\fP was built, the file name may
specify a DAP URL. This may be used to convert data on DAP servers to
local netCDF files.
.SH OPTIONS
.IP "\fB -k \fP \fI kind \fP"
Specifies the kind of file to be created (that is, the format variant)
and, by inference, the data model (i.e. netcdf-3 (classic) versus
netcdf-4 (enhanced)).  The possible arguments are as follows.
.RS
.RS
.IP "'1' or 'classic' => netcdf classic format"
.IP "'2', '64-bit-offset', or '64-bit offset' => netCDF 64-bit format"
.IP "'3', 'hdf5', 'netCDF-4', or 'enhanced' => netCDF-4 format (enhanced data model)"
.IP "'4', 'hdf5-nc3', 'netCDF-4 classic model', or 'enhanced-nc3' => netCDF-4 classic model format"
.RE
.RE
.IP 
If no value for -k is specified, then the output will use the same
format as the input, except if the input is classic or 64-bit offset
and either chunking or compression is specified, in which case the
output will be netCDF-4 classic model format.  Note that attempting
some kinds of format conversion will result in an error, if the
conversion is not possible.  For example, an attempt to copy a
netCDF-4 file that uses features of the enhanced model, such as
groups or variable-length strings, to any of the other kinds of netCDF
formats that use the classic model will result in an error.
.IP "\fB -d \fP \fI n \fP"
For netCDF-4 output, including netCDF-4 classic model, specify
deflation level (level of compression) for variable data output.  0
corresponds to no compression and 9 to maximum compression, with
higher levels of compression requiring marginally more time to
compress or uncompress than lower levels.  Compression achieved may
also depend on output chunking parameters.  If this option is
specified for a classic format or 64-bit offset format input file, it
is not necessary to also specify that the output should be netCDF-4
classic model, as that will be the default.  If this option is not
specified and the input file has compressed variables, the compression
will still be preserved in the output, using the same chunking as in
the input by default.
.IP
Note that specifying output deflation level with \fBnccopy\fP results in
all output variables compressed using 
the same compression level, but the API has no such restriction.  With
a program you can customize compression for each variable independently.
.IP "\fB -s \fP"
For netCDF-4 output, including netCDF-4 classic model, specify
shuffling of variable data bytes before compression or after
decompression.  This option is ignored unless a non-zero deflation
level is specified.  Turning shuffling on sometimes improves
compression.
.IP "\fB -u \fP"
Convert any unlimited size dimensions in the input to fixed size
dimensions in the output.  This can speed up variable-at-a-time
access, but slow down record-at-a-time access to multiple variables
along an unlimited dimension.
.IP "\fB -w \fP"
Keep output in memory (as a diskless netCDF file) until output is
closed, at which time output file is written to disk.  This can
greatly speedup operations such as converting unlimited dimension to
fixed size (-u option), chunking, rechunking, or compressing the
input.  It requires that available memory is large enough to hold the
output file.  This option may provide a larger speedup than careful
tuning of the -m, -h, or -e options, and it's certainly a lot simpler.
.IP "\fB -c \fP \fIchunkspec\fP"
For netCDF-4 output, including netCDF-4 classic model, specify
chunking (multidimensional tiling) for variable data in the output.
This is useful to specify the units of disk access, compression, or
other filters such as checksums.  Changing the chunking in a netCDF
file can also greatly speedup access, by choosing chunk shapes that
are appropriate for the most common access patterns.
.IP
The \fIchunkspec\fP argument is a string of comma-separated
associations, each specifying a dimension name, a '/' character, and
optionally the corresponding chunk length for that dimension.  No
blanks should appear in the chunkspec string, except possibly escaped
blanks that are part of a dimension name.  A chunkspec must name at
least one dimension, and may omit dimensions which are not to be
chunked or for which the default chunk length is desired.  If a
dimension name is followed by a '/' character but no subsequent chunk
length, the actual dimension length is assumed.  If copying a classic
model file to a netCDF-4 output file and not naming all dimensions in
the chunkspec, unnamed dimensions will also use the actual dimension
length for the chunk length.  An example of a chunkspec for variables
that use 'm' and 'n' dimensions might be 'm/100,n/200' to specify
100 by 200 chunks.  To see the chunking resulting from copying with a
chunkspec, use the '-s' option of ncdump on the output file.
.IP
As an I/O optimization, \fBnccopy\fP has a threshold for the minimum size of
non-record variables that get chunked, currently 8192 bytes.  In the future,
use of this threshold and its size may be settable in an option.
.IP
Note that \fBnccopy\fP requires variables that share a dimension to
also share the chunk size associated with that dimension, but the
programming interface has no such restriction.  If you need to
customize chunking for variables independently, you will need to use
the library API in a custom utility program.
.IP "\fB -v \fP \fI var1,... \fP"
The output will include data values for the specified variables, in
addition to the declarations of all dimensions, variables, and
attributes. One or more variables must be specified by name in the
comma-delimited list following this option. The list must be a single
argument to the command, hence cannot contain unescaped blanks or
other white space characters. The named variables must be valid netCDF
variables in the input-file. A variable within a group in a netCDF-4
file may be specified with an absolute path name, such as
'/GroupA/GroupA2/var'.  Use of a relative path name such as 'var' or
'grp/var' specifies all matching variable names in the file.  The
default, without this option, is to include data values for \fI all \fP variables
in the output.
.IP "\fB -V \fP \fI var1,... \fP"
The output will include the specified variables only but all dimensions and
global or group attributes. One or more variables must be specified by name in the
comma-delimited list following this option. The list must be a single argument
to the command, hence cannot contain unescaped blanks or other white space
characters. The named variables must be valid netCDF variables in the
input-file. A variable within a group in a netCDF-4 file may be specified with
an absolute path name, such as '/GroupA/GroupA2/var'.  Use of a relative path
name such as 'var' or 'grp/var' specifies all matching variable names in the
file.  The default, without this option, is to include \fI all \fP variables in the
output.
.IP "\fB -g \fP \fI grp1,... \fP"
The output will include data values only for the specified groups.
One or more groups must be specified by name in the comma-delimited
list following this option. The list must be a single argument to the
command. The named groups must be valid netCDF groups in the
input-file. The default, without this option, is to include data values for all
groups in the output.
.IP "\fB -G \fP \fI grp1,... \fP"
The output will include only the specified groups.
One or more groups must be specified by name in the comma-delimited
list following this option. The list must be a single argument to the
command. The named groups must be valid netCDF groups in the
input-file. The default, without this option, is to include all groups in the
output.
.IP "\fB -m \fP \fI bufsize \fP"
An integer or floating-point number that specifies the size, in bytes,
of the copy buffer used to copy large variables.  A suffix of K, M, G,
or T multiplies the copy buffer size by one thousand, million,
billion, or trillion, respectively.  The default is 5 Mbytes,
but will be increased if necessary to hold at least one chunk of
netCDF-4 chunked variables in the input file.  You may want to specify
a value larger than the default for copying large files over high
latency networks.  Using the '-w' option may provide better
performance, if the output fits in memory.
.IP "\fB -h \fP \fI chunk_cache \fP"
For netCDF-4 output, including netCDF-4 classic model, an integer or
floating-point number that specifies the size in bytes of chunk cache
for each chunked variable.  This is not a property of the file, but merely
a performance tuning parameter for avoiding compressing or
decompressing the same data multiple times while copying and changing
chunk shapes.  A suffix of K, M, G, or T multiplies the chunk cache
size by one thousand, million, billion, or trillion, respectively.
The default is 4.194304 Mbytes (or whatever was specified for the
configure-time constant CHUNK_CACHE_SIZE when the netCDF library was
built).  Ideally, the \fBnccopy\fP utility should accept only one
memory buffer size and divide it optimally between a copy buffer and
chunk cache, but no general algorithm for computing the optimum chunk
cache size has been implemented yet.  Using the '-w' option may
provide better performance, if the output fits in memory.
.IP "\fB -e \fP \fI cache_elems \fP"
For netCDF-4 output, including netCDF-4 classic model, specifies
number of chunkss that the chunk cache can hold. A suffix of K, M, G,
or T multiplies the number of chunks that can be held in the cache
by one thousand, million, billion, or trillion, respectively.  This is not a
property of the file, but merely a performance tuning parameter for
avoiding compressing or decompressing the same data multiple times
while copying and changing chunk shapes.  The default is 1009 (or
whatever was specified for the configure-time constant
CHUNK_CACHE_NELEMS when the netCDF library was built).  Ideally, the
\fBnccopy\fP utility should determine an optimum value for this
parameter, but no general algorithm for computing the optimum number
of chunk cache elements has been implemented yet.
.IP "\fB -r \fP"
Read netCDF classic or 64-bit offset input file into a diskless netCDF
file in memory before copying.  Requires that input file be small
enough to fit into memory.  For nccopy, this doesn't seem to provide
any significant speedup, so may not be a useful option.
.SH EXAMPLES
.LP
Make a copy of foo1.nc, a netCDF file of any type, to foo2.nc, a
netCDF file of the same type:
.RS
.HP
nccopy foo1.nc foo2.nc
.RE
.LP
Note that the above copy will not be as fast as use of cp or other
simple copy utility, because the file is copied using
only the netCDF
API.  If the input file has extra bytes
after the end of the
netCDF data, those will not be copied, because they are not accessible
through the netCDF interface.  If the original file was generated in
'No fill' mode so that fill values are not stored for padding for data
alignment, the output file may have different padding bytes.
.LP
Convert a netCDF-4 classic model file, compressed.nc, that uses compression,
to a netCDF-3 file classic.nc:
.RS
.HP
nccopy -k classic compressed.nc classic.nc
.RE
.LP
Note that '1' could be used instead of 'classic'.
.LP
Download the variable 'time_bnds' and its associated attributes from
an OPeNDAP server and copy the result to a netCDF file named 'tb.nc':
.RS
.HP
nccopy 'http://test.opendap.org/opendap/data/nc/sst.mnmean.nc.gz?time_bnds' tb.nc
.RE
.LP
Note that URLs that name specific variables as command-line arguments
should generally be quoted, to avoid the shell interpreting special
characters such as '?'.
.LP
Compress all the variables in the input file foo.nc, a netCDF file of any
type, to the output file bar.nc:
.RS
.HP
nccopy -d1 foo.nc bar.nc
.RE
.LP
If foo.nc was a classic or 64-bit offset netCDF file, bar.nc will be a
netCDF-4 classic model netCDF file, because the classic and 64-bit
offset format variants don't support compression.  If foo.nc was a
netCDF-4 file with some variables compressed using various deflation
levels, the output will also be a netCDF-4 file of the same type, but
all the variables, including any uncompressed variables in the input,
will now use deflation level 1.
.LP
Assume the input data includes gridded variables that use time, lat,
lon dimensions, with 1000 times by 1000 latitudes by 1000 longitudes,
and that the time dimension varies most slowly.  Also assume that
users want quick access to data at all times for a small set of
lat-lon points.  Accessing data for 1000 times would typically require
accessing 1000 disk blocks, which may be slow.
.LP
Reorganizing the data into chunks on disk that have all the time in
each chunk for a few lat and lon coordinates would greatly speed up
such access.  To chunk the data in the input file slow.nc, a netCDF
file of any type, to the output file fast.nc, you could use;
.RS
.HP
nccopy -c time/1000,lat/40,lon/40 slow.nc fast.nc
.RE
.LP
to specify data chunks of 1000 times, 40 latitudes, and 40 longitudes.
If you had enough memory to contain the output file, you could speed
up the rechunking operation significantly by creating the output in
memory before writing it to disk on close:
.RS
.HP
nccopy -w -c time/1000,lat/40,lon/40 slow.nc fast.nc
.RE
.SH "SEE ALSO"
.LP
.BR ncdump(1), ncgen(1), netcdf(3)