NetCDF: Difference between revisions

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[[Category:Software]]

NetCDF (Network Common Data Form) is:

* an interface for array-oriented data access, and  

The NetCDF library also defines a machine-independent format for representing scientific data. Together, the interface, library, and format support the creation, access, and sharing of scientific data.

There were significant changes to the library with the release of version 4.0. NetCDF 4.x is backwards compatible - it can read files produced by an earlier version but the opposite isn't true. Since 4.0 was released in 2008, we will not discuss earlier versions here.

* Project web site : https://www.unidata.ucar.edu/software/netcdf

* Manual: https://www.unidata.ucar.edu/software/netcdf/docs

* FAQ: https://www.unidata.ucar.edu/software/netcdf/docs/faq.html

* The data are independent of the processor architecture ([https://en.wikipedia.org/wiki/Endianness endianness]).

* The data are structured in a way that keeps track of all the pertinent information, e.g. physical units.

* It's free software for most platforms.

* The Python interface doesn't support parallelism (version 1.0.5)

* Certain files produced with [[HDF5]] cannot be read using NetCDF

This section summarizes configuration details.

The following [[Utiliser des modules/en|modules]] providing NetCDF are available on Compute Canada systems via CVMFS:

* '''netcdf'''

** for linking with programs containing Fortran instructions

There is also a set of NetCDF modules compiled with [[MPI]] support for parallel I/O:

* '''netcdf-mpi'''

** for linking with programs containing Fortran instructions and calling MPI

Run <code>module avail netcdf</code> to see what versions are currently available with the compiler and MPI modules you have loaded. For a comprehensive list of NetCDF modules, run <code>module -r spider '.*netcdf.*'</code>.

Use <code>module load netcdf/version</code> to set your environment to use your chosen version. For example, to load the NetCDF version 4.1.3 C-based library, do:

{{Command|module load netcdf/4.1.3}}

Please refer to the page "[[Running_jobs|Running jobs]]" for examples of job scripts for the Slurm workload manager. We recommend you include the <code>module load ...</code> command in your job script.

Below are a few examples showing how to link NetCDF libraries to C and Fortran code:

For C code,

{{Commands

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For Fortran code, notice that two libraries are required and their order matters:

{{Commands

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For C code which calls MPI,

{{Commands

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An example demonstrating the use of the NetCDF can be found at the following [https://www.unidata.ucar.edu/software/netcdf/netcdf-4/newdocs/netcdf-tutorial/simple_005fxy_005fwr_002ec.html#simple_005fxy_005fwr_002ec link]. The example program creates a NetCDF file containing a single two-dimensional variable called "data", and labels the two dimensions "x" and "y".  

   

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There are several utilities that read or write files in different formats.

* ncdump

: Copies a netCDF file and can change binary format, chunk sizes, compression, and other storage settings. See [https://www.unidata.ucar.edu/software/netcdf/workshops/2011/utilities/Nccopy.html nccopy] for more.

PnetCDF is another library for reading and writing NetCDF-format files. It uses different procedure names than NetCDF and provides non-blocking procedures. See the [https://trac.mcs.anl.gov/projects/parallel-netcdf PnetCDF web site] for a detailed discussion.

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