February 2-3, 2006 SRB Workshop, San Diego

Peter Cao, NCSA

Mike Wan, SDSC

Sponsored by NLADR, NFS PACI Project in Support of NCSA-SDSC Collaboration

Object-level Access to Remote Files

Integrating HDF5 with SRB

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Outline

Introduction to HDF5

The HDF-SRB model

SRB Support in HDFView

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Overview of HDF5 Answering big

questions …

Matter & universe

Weather & climate

August 24, 2001 August 24, 2002Total Column Ozone (Dobson)

60 385 610

Life & nature

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Overview of HDF5 Involves big

data …

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Overview of HDF5 On big

computers …

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Overview of HDF5 HDF solution

…

Software & tools

open source & multiple platform

Commonmodels

extensions Standard

APIsconventions & easy use

File formatfor all kinds of data

Efficiencystorage & IO

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Overview of HDF5 Exmaple HDF5

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Overview of HDF5 HDF Software

HDF I/O Library

Tools & ApplicationsTools & Applications

HDF FileHDF File

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Overview of HDF5 Object

model

Primary ObjectsGroupsDatasets

Additional ways to organize dataAttributesSharable objectsStorage and access properties

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Overview of HDF5 Groups

“/”

tom dick harry

temp

A mechanism for collections of related objectsEvery file starts with a root groupSimilar to UNIXdirectoriesCan have attributes

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Overview of HDF5

Datasets

DataMetadataDataspace

3

RankRank

Dim_2 = 5Dim_1 = 4

DimensionsDimensions

time = 32.4

pressure = 987

temp = 56

AttributesAttributes

Chunked

compressed

Dim_3 = 7

Storage infoStorage info

IEEE 32-bit float

DatatypeDatatype

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Overview of HDF5 Data

subsetting

(c) A sequence of points from a 2D array to a sequence of points in a 3D array.

(d) Union of hyperslabs in file to union of hyperslabs in memory.

(b) Regular series of blocks from a 2D array to a contiguous sequence at a certain offset in a 1D array

(a) Hyperslab from a 2D array to the corner of a smaller 2D array

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Project Description

Motivation

SRB HDF5

Indexing and searching Distributed data system Access control

Large and diverse data High performance access Interactive and subsetting

High performance distributed data system

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Project Description Goals

Working prototype of client/server system forobject-level access to HDF5 stored in the SRB

Use SRB as middleware to transfer data between the server and client Use Object-level access for interactive and efficient access to part of the file

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Remote Data Access on SRB

Methods

Normal ways to access SRB:Get the whole file: large files (100TB

SCEC)Use POSIX low level calls: low

performance

New way: Implement proxy operations to access

objects or parts of objects in one request

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Normal SRB File Access Architecture

SRB ServerSRB Server

HDF5HDF5

MCAT

clientclient

HDF5 File(whole file or a

sequence of bytes)

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Object-level File Access Architecture

SRB ServerSRB Server

MCAT

HDF5 LibraryHDF5 Library

HDF5-SRB Module(pack/unpack messages)

HDF5 Object(File, Group, Dataset,

Subset, Attribute)

HDF5-SRB Module(pack/unpack messages)

ClientClient ServerServer

HDF5 Object(File, Group, Dataset,

Subset, Attribute)

Client Application HDF5 file

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Examples of File Access

HDF5HDF5

I need to see the eye of Hurricane Bob!

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Examples of File Access Whole file

transfer

clientclient

Get the file

Transfer large image – slow!

HDF5HDF5

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Examples of File Access SRB POSIX

API

HDF5HDF5

clientclient

image foundimage open

open image

find imagefile’s open

Open file

Many small messages – slow and complex!

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Examples of File Access Object

level

clientclient

HDF5HDF5

Get me the eye of hurricane Bob

1 request, small transfer – fast!

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HDF5-SRB Model New

objects/APIs

A new set data objects H5File, H5Group, H5Dataset, H5Datatype, etc Encapsulated client requests and server results

Enhanced SRB APIs Pack/Unpack routines (exchange data between

byte stream and structure) to handle complicated struct – string, pointers, pointers to arrays, arrays of pointers, etc

New srbGenProxyFunct (general Proxy Function) handles other types of request besides HDF5

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HDF5-SRB Model Data Flow

Client APIsrbObjRequest(void *obj, int objID)

Server APIsrbObjProcess(void *obj, int objID)

srbGenProxyFunct

1. packMsg()

2. u

npac

kMsg

()

HDF5 Library

HDF5 file

3. H5Obj::op()

4. Access file

5. H5Object

6. p

ackM

sg()

7. unpackMsg()

SRB Server

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Running Server/Client

A SRB server that supports HDF5 HDF5 library and other external libraries (SZIP, ZLIB) A SRB version 3.4 or later from

http://www.sdsc.edu/srb/ Follow instruction on how to run SRB server from UG

packed with SRB source release or online at http://hdf.ncsa.uiuc.edu/hdf-srb-html/HDF-SRB-UG.html

Any client application that implements HDF5-SRB Objects No HDF5 library is required on the client Example client application: HDFView 2.3 or above

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Short Demo HDFViewSupport Windows and Linux

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Question / Comments?