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Integrating HDF5 with SRB

Integrating HDF5 with SRB. The HDF5-SRB Architecture Peter Cao, HDF, NCSA February 24, 2005. Project Description. Object-level access to HDF5 stored in the SRB Use SRB as middleware to transfer data between the server and client Interactive and efficient access Previous work

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Integrating HDF5 with SRB

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  1. Integrating HDF5 with SRB The HDF5-SRB Architecture Peter Cao, HDF, NCSA February 24, 2005

  2. Project Description • Object-level access to HDF5 stored in the SRB • Use SRB as middleware to transfer data between the server and client • Interactive and efficient access • Previous work • Extracting entire HDF5 files • Extracting byte-streams through the SRB’s POSIX interface

  3. The SRB Architecture SRB Client MCAT SRB Server HPSS Unitree DB2 ObjStore HDF5 FTP Distributed Storage Resources: database system, archival storage system, file system, ftp

  4. The HDF5-SRB Architecture HDF5 file HDF Application HDF5 Library HDF5 Object (File, Group, Dataset, Attribute) MCAT HDF5 Object (File, Group, Dataset, Attribute) HDF5-SRB Module (unpackMsg/packMsg) SRB Server HDF5-SRB Module (unpackMsg/packMsg)

  5. The HDF5-SRB Module Client API srbObjRequest(void *obj, int objID) Server API srbObjProcess(void *obj, int objID) 5. H5Object 3. H5Obj::op() 7. unpackMsg() 6. packMsg() HDF5 Library 1. packMsg() 2. unpackMsg() 4. Access file HDF5 file SRB Server

  6. Implementation Requirement • Object fashion • Interactive access • Data information encapsulated in structure • Easy mapping to objects in client application • Simple and efficient • No complicated packMsg()/unpackMsg() • Use one set of objects for both server and client • Minimum data to transfer between client and server • Pack only required data • No redundant member object within an object

  7. HDF5 Objects H5File H5Group H5Dataset Data operations implemented on the server side Client Side Server Side H5Datatspace H5Attribute H5Datatype

  8. H5File

  9. H5Group typedef struct H5Object_t { enum { H5GROUP, H5DATASET }t; union { struct H5Group; struct H5dataset }u; } H5Object;

  10. H5Dataset

  11. H5Datatype

  12. H5Dataspace

  13. H5Attribute

  14. Implementation Challenge • Efficiency of the packMsg/unpackMsg • Datatype conversion • The Client needs to know the datatype from server • The server have to use client datatype to load data • Life cycle of object • When to close object (dataset, group, file) • When to clean memory space • Byte stream to transfer large raw data • How to pack/unpack VL/compound data

  15. Milestone • Module specifications • RFC 02/11/05 • Tech. seminar 02/24/05 • final publication 03/04/05 • Implementation • Compile and install test SRB server 03/18/05 • Client-side module 03/31/05 • Server-side module 04/22/05 • Client application 05/20/05 • Testing and merge source with SDSC07/15/05 • Documentation and release 08/31/05

  16. Further Work • Metadata Ingest • srbObjPut() calls the HDF5 ingest program to put file information into MCAT • Datacutter • searching and filtering HDF5 data • HDF5 Indexing • store HDF5 indexing table into MCAT

  17. Questions/Comments? • [Ruth Aydt] what object can be packed in the new srbObjRequest() and srbObjProcess APIs. What are the objIDs, how they are managed • [Jae Alameda] what kind of message is transferred through SRB: objects or string message • [Mike Folk and other] How to transfer large raw dataset: byte stream or openDAP-g way • [Albert Cheng] how to accomplish complex HDF5 request: number of message vs complex message • [Elena Pourmal] Is the packMsg()/unpackMsg() part of the current SRB or new functions • [Quincey Koziol] When passing objects between client and server, how to ensure to pass fields of the object only need for the operation • [Bob Mcgrath] How to manage the life cycle of object on the server side. When client dies, how to close the object on the server (timeout?) • [Stuart Levy] Synchronization and locking issues. concurrent access to file and operations on file. File cache and physical file location • [Quincey Koziol and other] In general, there were a lot of questions about the message protocol, what parts of the structure are optional, etc.. I would say we need to document the protocol as completely as we can. • [Quincey Koziol] How will datatypes of attributes be handled, how will selection from compound datatype [fields of compound] be done. • [Joe Futrelle] How MCAT handle complex query from HDF5 or other data • [Ruth Aydt] How file access control is handled in HDF5 or SRB • Elena had some idea about precomputing some of the messages.  Notclear if this is really viable. • It would be good to add an example that shows the steps of a simple operation,e.g., open dataset.

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