NetCDF

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Contents


Authors/Maintainers

  • Also origin, if the software comes from a specific project.

Summary

NetCDF (network Common Data Form) is a set of software libraries and machine- independent data formats that support the creation, access, and sharing of array- oriented scientific data. This package is sufficiently generic and is used by many other software packages, not only in Computational Chemistry domain, but also in Environmental modeling and others. Thus NetCDF is a pre-requisite for installing these packages. It should be noted that NetCDF must be compiled with the same compiler suite as the final application, which means that in some situations more than one installations of the same version of NetCDF must be maintained. NetCDF is an interface to a library of data access functions for storing and retrieving data in the form of arrays. An array is an n-dimensional (where n is 0, 1, 2,...) rectangular structure containing items which all have the same data type (e.g., 8-bit character, 32-bit integer). NetCDF is an abstraction that supports a view of data as a collection of self-describing, portable objects that can be accessed through a simple interface. Array values may be accessed directly, without knowing details of how the data are stored. Auxiliary information about the data, such as what units are used, may be stored with the data. Generic utilities and application programs can access netCDF datasets and transform, combine, analyze, or display specified fields of the data. The development of such applications has led to improved accessibility of data and improved re-usability of software for array-oriented data management, analysis, and display. The netCDF libraries support 3 different binary formats for netCDF files: the classic netCDF format, 64-bit offset format (version 3.6.0), and netCDF-4/HDF5 (version 4.0). An extension of netCDF for parallel I/O called Parallel-NetCDF (or PnetCDF) has been developed, built upon MPI-IO. Using the high-level netCDF data structures, the Parallel- NetCDF libraries can make use of optimizations to efficiently distribute the file read and write applications between multiple processors. In many cases some of the software packages that we have to install for the needs of the project require NetCDF. Some of them even provide a tested and sometimes patched version of NetCDF as part of their own distribution.

Features

  • Listed features

Architectural/Functional Overview

  • high level design info, how it works, performance - may be a link, or several links

Usage Overview

  • If possible with small example - may be a link

Dependacies

  • list of all relevant dependencies on other libraries

HP-SEE Applications

  • PCACIC
  • FMD-PA

Resource Centers

  • RCs supporting it (with version number if not the same as above)

Usage by Other Projects and Communities

  • If any

Recommendations for Configuration and Usage

Please describe here any common settings, configurations or conventions that would make the usage of this resource (library or tool) more interoperable or scalable across the HP-SEE resources. These recommendations should include anything that is related to the resource and is agreed upon by administrators and users, or across sites and applications. These recommendations should emerge from questions or discussions opened by site administrators or application developers, at any stage, including installation, development, usage, or adaptation for another HPC centre.

Provided descriptions should describe general or site specific aspects of resource installation, configuration and usage, or describe the guidelines or convention for deploying or using the resource within the local (user/site) or temporary environment (job). Examples are:

  • Common configuration settings of execution environment
  • Filesystem path or local access string
  • Environment variables to be set or used by applications
  • Options (e.g. additional modules) that are needed or required by applications and should be present
  • Minimum quantitative values (e.g. quotas) offered by the site
  • Location and format of some configuration or usage hint instructing applications on proper use of the resource or site specific policy
  • Key installation or configuration settings that should be set to a common value, or locally tweaked by local site admins
  • Conventions for application or job bound installation and usage of the resource
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