One of the most interesting capabilities of HDF5 is parallel I/O. Moreover, you can create lots of metadata to associate with data inside an HDF5 file.ĭata in an HDF5 file can be accessed randomly, as in a database, so you don't have to read the entire file to access the data you want (unlike XML). Chunking can result in faster access times for subsets of the data. The libraries from the HDF5 group are capable of compressing data within the file and even "chunking" the data into sub-blocks for storage. The HDF5 format can also accommodate data in row-major (C/C++, Mathematica) or column-major (Fortran, Matlab, Octave, Scilab, R, Julia, NumPy) order. For example, C, C++, Fortran, and Java are officially supported with HDF5 tools, but some third-party bindings (i.e., outside the official distribution) are also available for Python, Matlab, Octave, Scilab, Mathematica, R, Julia, Perl, Lua, Node.js, Erlang, Haskell, and others. At the bottom of the viewer, the metadata associated with that data displays when you click on a data value (the temperature).įigure 1: Example of the HDF5 data hierarchy in HDFView.Ī number of tools and libraries use HDF5 in your favorite language. Notice how the temperature data falls under a hierarchy of directories. ![]() Metadata is the key to useful data files, and attributes make HDF5 files self-describing (e.g., like XML).Īn example of how you could structure data within an HDF5 file is described in an online tutorial that shows how to use HDFView ( Figure 1) to view an HDF5 file of hyperspectral remote sensing data. HDF5 also allows metadata (attributes) to be associated with virtually any object in the data file. Files written in the HDF5 format are portable across operating systems and hardware (little endian and big endian). You can store almost any data you want in an HDF5 file, including user-defined data types integer, floating point, and string data and binary data such as images, PDFs, and Excel spreadsheets. It uses a filesystem-like data format familiar to anyone who has used a modern operating system – thus, the "hierarchical" portion of the name. HDF5 is a freely available file format standard and set of tools for storing and organizing large amounts of data. In this article, I introduce HDF5 and focus on the concepts and its strengths in performing I/O then, I look at some simple Python and Fortran code examples, before ending with an example of parallel I/O with HDF5 and Fortran. A great example of such a library is the Hierarchical Data Format (HDF), a standard library used primarily for scientific computing. One of the options mentioned was to use a high-level library to perform the I/O. In a previous article, I discussed options for improving I/O performance, focusing on parallel I/O. Therefore, applications can use a very significant portion of their total run time to perform I/O, which becomes critical in Big Data, machine learning, and high-performance computing (HPC). It can be installed from the software repositories of most major KDE Linux distributions.Input/output operations are a very important part of many applications, sometimes involving a huge amount of data and a large number of reads and writes. Multisync supports synching multiple folders into one folder. The user can switch between these sections by using the toolbar. The user interface of Synkron is divided into several sections: Synchronise, Multisync, SyncView, Scheduler, Restore, Blacklist and Filters. Synkron is distributed under the terms of the GPL v2.Īpart from carrying out synchronisations, Synkron provides other features. It is written in C++ and uses the Qt4 libraries. Synkron is an open-source multiplatform utility designed for file synchronization of two or more folders, supporting synchs across computers. ![]() English, Arabic, Portuguese, Chinese, Czech, Dutch, Finnish, French, German, Italian, Japanese, Polish, Russian, Spanish, Valencian
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