October 15-17, 2008 HDF and HDF-EOS Workshop XII, Denver, CO 1

HDF5-iRODSPeter Cao

The HDF Group

Mike Wan

San Diego Supercomputer Center

HDF and HDF-EOS Workshop XII

October 16, 2008

October 15-17, 2008 HDF and HDF-EOS Workshop XII, Denver, CO 2

Imagine

1 GB

100 Frames x 1 GB = 100 GB

HPSSHPSS

DBDBHPCHPC

October 15-17, 2008 HDF and HDF-EOS Workshop XII, Denver, CO 3

Outline

• HDF5-iRODS module• Applications• Demo (if time permits)

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What is iRODS?

• Stands for i Rule Oriented Data Systems.• Developed by the Storage Resource Broker

(SRB) team at the San Diego Supercomputer Center (SDSC).

• A data grid software system that enables a customizable architecture for sharing data distributed across heterogeneous resources.

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What is iRODS?

Distributed Storage Database System Rule System

For more information and download, visit

www.irods.org

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Motivation

iRODS HDF5

Distributed data system

Indexing and searching

Access control, etc.

Large and diverse data

High-performance I/O

Subsetting, etc.

High-performance distributed data system

October 15-17, 2008 HDF and HDF-EOS Workshop XII, Denver, CO 7

Whole File Access

clientclient

Get the file

Transfer large file – slow!

HDF5HDF5

serverserverI need to see the eye of

Hurricane Bob!

HDF5HDF5

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HDF5 Object or Subset Level Access

clientclient

HDF5HDF5

Get me the eye of hurricane Bob

Small transfer – fast!

serverserverI need to see the eye of

Hurricane Bob!

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HDF5-iRODS Module

Distributed Storage

Database SystemRule System

HDF5 iRODS Module

Micro-services

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HDF5-iRODS Data Flow

iRODS message(pack/unpack)

clientclient serverserver

HDF5 Object or Subset

(File, Group, Dataset,

Subset of Dataset, Attribute)

HDF5 LibraryHDF5 Library

iRODS message(pack/unpack)

HDF5 Object or Subset

(File, Group, Dataset, Subset of Dataset,

Attribute)

HDF5HDF5

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New iRODS Micro-services

• Five iRODS micro-services msiH5File_open msiH5File_close msiH5Dataset_read

• reads entire dataset or subset of dataset msiH5Dataset_read_attribute msiH5Group_read_attribute

File

Rule Engine msiH5Dataset_read H5Dataset.read()

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HDF5-Enabled iRODS Server

• HDF5 library • Other external libraries (SZIP, ZLIB)• iRODS version 1.1 or later from

https://www.irods.org/index.php/Downloads/

Follow the README instruction at module/hdf5

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Client Application Requirements

• HDF5 object header files and client handlers• iRODS client library and header files• HDF5-iRODS JNI for Java applications only• $HOME/.irods/.irodsEnv

For more information and download, visit

http://www.hdfgroup.org/projects/irods

irodsHost 'kagiso.hdfgroup.uiuc.edu'irodsPort 1247irodsUserName 'rods‘…

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Example: HDFView

Client Application HDF5-EnablediRODS Server

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Example: HDFView

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Example: islice

For more information, visit

flash.uchicago.edu

• Command-line tool to visualize data produced by FLASH simulation runs

• Data is huge (~ 100 GB)• Interesting part is small

adaptive mesh16*16*16*47531

FLASH is an adaptive-mesh simulation code for astrophysical hydrodynamics problemsFLASH is an adaptive-mesh simulation code for astrophysical hydrodynamics problems

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Example: islice

Breakout point Ash Flow

Star

A slice from a 3D simulation of The Detonation of a White Dwarf Star

Collision focus point

“./islice -t flash.pal -m rpv1 -p 2 rundir_055_8km_hdf5_plt_cnt_0424”

2048*2048*8(32MB)

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This project is sponsored by CIP/NLADR, NSF PACI Project in Support of the Collaboration between the National Center for Supercomputing Applications (NCSA) and the San Diego Supercomputer Center (SDSC). The project is managed under the CyberInfrastructure Partnership (CIP), a joint effort led by NCSA and SDSC to help scientists and engineers take full advantage of the high-end CyberInfrastructure resources funded by the National Science Foundation (NSF).

Thank You!

Questions/comments?

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