Unidata NetCDF

About

The Unidata network Common Data Form (netCDF) is an interface for scientific data access and a freely-distributed software library that provides an implementation of the interface. 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. The current netCDF software provides C interfaces for applications and data. Separate software distributions available from Unidata provide Java, Fortran, Python, and C++ interfaces. They have been tested on various common platforms.

Properties

NetCDF files are self-describing, network-transparent, directly accessible, and extendible. Self-describing means that a netCDF file includes information about the data it contains. Network-transparent means that a netCDF file is represented in a form that can be accessed by computers with different ways of storing integers, characters, and floating-point numbers. Direct-access means that a small subset of a large dataset may be accessed efficiently, without first reading through all the preceding data. Extendible means that data can be appended to a netCDF dataset without copying it or redefining its structure.

Use

NetCDF is useful for supporting access to diverse kinds of scientific data in heterogeneous networking environments and for writing application software that does not depend on application-specific formats. For information about a variety of analysis and display packages that have been developed to analyze and display data in netCDF form, see

• Software for Manipulating or Displaying NetCDF Data

More information

For more information about netCDF, see

• Unidata Network Common Data Form (NetCDF)

Latest releases

You can obtain a copy of the latest released version of netCDF software for various languages:

• C library and utilities
• Fortran
• Java
• Python
• C++

Copyright

Copyright and licensing information can be found here, as well as in the COPYRIGHT file accompanying the software

Installation

netCDF-C

To install the netCDF-C software, please see the file INSTALL in the netCDF-C distribution, or the (usually more up-to-date) document:

• Building NetCDF

ESDM-NetCDF

Compiling

To compile and install ESDM-NetCDF, first install a working build system:

$ autoreconf --install --force

After this, the project can be configured with these options:

$ ./configure --prefix=<esdm-netcdf-path> --with-esdm=<esdm-path> --with-hdf5=<hdf5-path> LDFLAGS=-L<hdf5-path>/lib CFLAGS=-I<hdf5-path>/include CC=mpicc --enable-parallel-tests --disable-dap

is an installation location of your choice, is the installation location of a previously built ESDM version, and <hdf5_path> is the installation location of an HDF5 version. Building, testing, and installing is then done with the usual

$ make -j8
$ make check
$ make install

Currently, not all tests run successfully.

Using ESDM-NetCDF

The steps above install a NetCDF library at /lib/libnetcdf.so. As such, any program that was linked against NetCDF can be executed with ESDM-NetCDF. There are two main ways to do this:

1. Use an environment where /lib/libnetcdf.so is the only NetCDF library available.

2. Override the environment's NetCDF library with

   $ LD_PRELOAD=<esdm-netcdf-path>/lib/libnetcdf.so <command>
   

As a quick test, nccopy <somefile>.nc <copy>.nc can be used as . This should result in the following output by default:

$ nccopy <somefile>.nc <copy>.nc
[ESDM] [POSIX] /mnt/lustre01/pf/k/k203053/private/repositories/esiwace/esdm/src/utils/auxiliary.c:148 ea_read_file(): WARN cannot open esdm.conf No such file or directory

ESDM has not been shutdown correctly. Stacktrace:
3: /lib64/libc.so.6(__libc_start_main+0x100) [0x7f30f72d9d20]
4: nccopy() [0x402a29]

The error message about shutdown can safely be ignored for now (this should be fixed in a future version of ESDM/ESDM-NetCDF). The other message means that no ESDM configuration could be loaded, and as such, that the ESDM features are not usable.

To actually use ESDM, an esdm.conf file needs to be provided and a file system needs to be created. ESDM comes with a few sample esdm.conf file which can be used to create an ESDM file system for first tests:

$ cp /src/test/esdm-posix.conf esdm.conf

The file esdm.conf is already linked to esdm-posix.conf in the directory

$ cp <esdm-source-path>/src/test/esdm.conf <esdm-path>/install/bin/

$ /bin/mkfs.esdm -g -v --create --config=esdm.conf

$ <esdm-path>/install/bin/mkfs.esdm -g -v --create --config=esdm.conf
[mkfs] Creating ./_metadummy
[mkfs] Creating ./_posix1
[mkfs] OK

After this, the warning should go away, and it should be possbile to perform a copy into ESDM:

$ nccopy <somefile>.nc esdm://test

ESDM has not been shutdown correctly. Stacktrace:
3: /lib64/libc.so.6(__libc_start_main+0x100) [0x7f3aefb35d20]
4: nccopy() [0x402a29]

The error can still be safely ignored. This creates a container named "test" and copies all NetCDF variables into corresponding ESDM datasets within this container.

Documentation

A language-independent User's Guide for netCDF, and some other language-specific user-level documents are available from:

• Language-independent User's Guide
• NetCDF-C Tutorial
• Fortran-90 User's Guide
• Fortran-77 User's Guide
• netCDF-Java/Common Data Model library
• netCDF4-python

A mailing list, [email protected], exists for discussion of the netCDF interface and announcements about netCDF bugs, fixes, and enhancements. For information about how to subscribe, see the URL

• Unidata netCDF Mailing-Lists

Feedback

We appreciate feedback from users of this package. Please send comments, suggestions, and bug reports to [email protected].