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Integrating HDF5 with SRB

Integrating HDF5 with SRB. Object-level Access to Remote Files. P eter Cao, NCSA Mike Wan, SDSC. Sponsored by NLADR, NFS PACI Project in Support of NCSA-SDSC Collaboration. Outline. Introduction to HDF5 The HDF-SRB model SRB Support in HDFView. Matter & universe. Life & nature.

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Integrating HDF5 with SRB

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  1. Integrating HDF5 with SRB Object-level Access to Remote Files Peter Cao, NCSA Mike Wan, SDSC Sponsored by NLADR, NFS PACI Project in Support of NCSA-SDSC Collaboration SRB Workshop, San Diego

  2. Outline • Introduction to HDF5 • The HDF-SRB model • SRB Support in HDFView SRB Workshop, San Diego

  3. Matter & universe Life & nature Weather & climate August 24, 2001 August 24, 2002 Total Column Ozone (Dobson) 60 385 610 Overview of HDF5Answeringbig questions … SRB Workshop, San Diego

  4. Overview of HDF5Involves big data … SRB Workshop, San Diego

  5. Overview of HDF5On big computers … SRB Workshop, San Diego

  6. Commonmodels extensions Overview of HDF5HDF solution … File format for all kinds of data Efficiency storage & IO Software & tools open source & multiple platform Standard APIs conventions & easy use SRB Workshop, San Diego

  7. Overview of HDF5Exmaple HDF5 SRB Workshop, San Diego

  8. Overview of HDF5HDF Software Tools & Applications HDF I/O Library HDF File SRB Workshop, San Diego

  9. Overview of HDF5Object model • Primary Objects • Groups • Datasets • Additional ways to organize data • Attributes • Sharable objects • Storage and access properties SRB Workshop, San Diego

  10. “/” tom harry dick temp Overview of HDF5Groups • A mechanism for collections of related objects • Every file starts with a root group • Similar to UNIXdirectories • Can have attributes SRB Workshop, San Diego

  11. Metadata Data Dataspace Rank Dimensions 3 Dim_1 = 4 Dim_2 = 5 Dim_3 = 7 Datatype IEEE 32-bit float Attributes Storage info time = 32.4 Chunked pressure = 987 compressed temp = 56 Overview of HDF5Datasets SRB Workshop, San Diego

  12. (a) Hyperslab from a 2D array to the corner of a smaller 2D array (b) Regular series of blocks from a 2D array to a contiguous sequence at a certain offset in a 1D array (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. Overview of HDF5Data subsetting SRB Workshop, San Diego

  13. Project DescriptionMotivation High performance distributed data system SRB Workshop, San Diego

  14. Project DescriptionGoals • 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 Working prototype of client/server system for object-level access to HDF5 stored in the SRB SRB Workshop, San Diego

  15. Remote Data Access on SRBMethods • 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 SRB Workshop, San Diego

  16. HDF5 Normal SRB File AccessArchitecture client HDF5 File (whole file or a sequence of bytes) SRB Server MCAT SRB Workshop, San Diego

  17. Object-level File AccessArchitecture Client Server HDF5 Library Client Application HDF5 file HDF5 Object (File, Group, Dataset, Subset, Attribute) HDF5 Object (File, Group, Dataset, Subset, Attribute) MCAT SRB Server HDF5-SRB Module (pack/unpack messages) HDF5-SRB Module (pack/unpack messages) SRB Workshop, San Diego

  18. HDF5 Examples of File Access I need to see the eye of Hurricane Bob! SRB Workshop, San Diego

  19. Get the file HDF5 Examples of File AccessWhole file transfer client Transfer large image – slow! SRB Workshop, San Diego

  20. Open file file’s open find image image found open image image open Examples of File AccessSRB POSIX API client HDF5 Many small messages – slow and complex! SRB Workshop, San Diego

  21. Get me the eye of hurricane Bob HDF5 Examples of File AccessObject level client 1 request, small transfer – fast! SRB Workshop, San Diego

  22. 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 SRB Workshop, San Diego

  23. HDF5-SRB Model Data Flow Client API srbObjRequest(void *obj, int objID) Server API srbObjProcess(void *obj, int objID) 5. H5Object 3. H5Obj::op() 7. unpackMsg() 6. packMsg() 1. packMsg() 2. unpackMsg() HDF5 Library 4. Access file srbGenProxyFunct HDF5 file SRB Server SRB Workshop, San Diego

  24. 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 SRB Workshop, San Diego

  25. Short DemoHDFView • Support Windows and Linux SRB Workshop, San Diego

  26. Question / Comments? SRB Workshop, San Diego

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