High Performance Netcdf-4 Proposal

This documents outlines a proposal to create an alternate Netcdf-4 file format targeted to high-performance, READ-ONLY, access.

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NetCDF Compression

The steady state of disks is full. --Ken Thompson

Introduction

From our support questions, it appears that the major feature of netCDF-4 attracting users to upgrade their libraries from netCDF-3 is compression. The netCDF-4 libraries inherit the capability for data compression from the HDF5 storage layer underneath the netCDF-4 interface. Linking a program that uses netCDF to a netCDF-4 library allows the program to read compressed data without changing a single line of the program source code. Writing netCDF compressed data only requires a few extra statements. And the nccopy utility program supports converting classic netCDF format data to or from compressed data without any programming.

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Accessing netCDF Data by Coordinates

Library software like netCDF or HDF5 provides access to multidimensional data by array indices, but we would often rather access data by coordinates, such as points on the Earth's surface or space-time bounding boxes.  This blog, with an accompanying iPython notebook, explores some issues with correctness and efficiency in accessing data by coordinates instead of array indices in a real-world example.

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Chunking Data: Choosing Shapes

In part 1, we explained what data chunking is about in the context of scientific data access libraries such as netCDF-4 and HDF5, presented a 38 GB 3-dimensional dataset as a motivating example, discussed benefits of chunking, and showed with some benchmarks what a huge difference chunk shapes can make in balancing read times for data that will be accessed in multiple ways.

In this post, I'll continue looking at that example dataset to see how we can derive good chunk shapes, generalize to other datasets, look at how long it can take to rechunk a multidimensional dataset, and look at the use of Solid State Disk (SSD) for both accessing and rechunking data.

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Chunking Data: Why it Matters

What is data chunking? How can chunking help to organize large multidimensional datasets for both fast and flexible data access?  How should chunk shapes and sizes be chosen?  Can software such as netCDF-4 or HDF5 provide better defaults for chunking? If you're interested in those questions and some of the issues they raise, read on ...

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