What will be new in HDF5?

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HDF5 Road Map

Performance Ease of use Robustness Innovation October 15, 2008 HDF and HDF-EOS Workshop XII 2

Outline

• Performance improvements • Fortran 2003 features • HDF5 file recover (metadata journaling)

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Performance Improvements

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Performance Improvements in HDF5

• Examples of completed work: • New implementation of metadata cache to improve I/O performance and memory usage when accessing many objects (HDF5 1.8.0) • Faster, more scalable storage and access for large groups (HDF5 1.8.0)

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Performance Improvements in HDF5

• Work in progress • New implementation of free-space management • Affects “dynamic” applications that add/delete/modify existing objects • When creating HDF5 objects, space is allocated from available space tracked by the free-space manager • When deleting objects, unused space is added to the free-space pool via free-space manager • Current implementation uses O(N 2 ) operations for each N allocations or freeing space • New implementation O(log 2 N)

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Free-space Management

• Test: creating/deleting attributes • Create first set of attributes • Delete odd-numbered attributes from the first set • Create second set of attributes • Delete all attributes from the second set

Number of attributes

500 1000

Old implementation New implementation Improvement ratio

786.5 sec 11000 sec 68.2 sec 289 sec 11.5x

38x

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Performance Improvements in HDF5

• Work in progress • Fast data append (along slowest changing dimension) • Future areas of interest • Efficient chunking cache implementation (NetCDF4) • Efficient handling of the variable-length data including compression (will affect sizes of NPOESS files)

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Fortran 2003 features

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Status of the HDF5 Fortran Library

• HDF5 Fortran library is a part of standard HDF5 distribution • First release goes back to 1999 • Implemented as Fortran90 wrappers on top of the HDF5 C library • Supported on Linux, Windows, Mac Intel, Solaris, VMS, clusters, etc.

• Compilers • Open source gfortran, g95 • Vendors (SUN, Intel, PGI, Absoft) • 32 and 64-bit versions

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HDF5 Fortran Library

• Mimics HDF5 C APIs • Fortran 90 features used • Modules • Function overloading • Function interfaces • Dynamic memory allocation • Optional parameters • Many Fortran APIs are simpler than their C counterparts

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Current Limitations

• Supports only “native” Fortran types such as • INTEGER • REAL • CHARACTER • DOUBLE PRECISION (obsolete Fortran feature) • No support for INTEGER*1, INTEGER*2, INTEGER*8, INTEGER*16, REAL*8, REAL*16 • Cannot write/read buffers of those types • Fortran types have to match C types • No support for –r8 and –r16 flags (Fortran real =/= C float)

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Current Limitations

• No support for INTEGER(KIND=n) and REAL(KIND=m) • Integers n and m are called KIND parameters • Returned by selected _int_kind (r) -10 r < n < 10 r selected_real_kind(p,r) p – precision r – decimal exponent range

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Current Limitations

• Limited support for derived types (compare with C structures and HDF5 compound datatypes) • Supports derived types with “native” fields only • Doesn’t support complex HDF5 datatypes (e.g., with array member, or nested compound) • Writes/reads HDF5 compound datasets by fields only • Cannot be used in parallel applications • No support for enum types • No support for callback functions

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Current Limitations - Summary

• Any application written according to Fortran 95/2003 standard will struggle using HDF5 Fortran Library • Many HDF5 features are not available to Fortran applications

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Fortran 2003 Features

• Fortran 2003 provides a standardized mechanism for interoperating with C • Module ISO_C_BINDING for interoperability of intrinsic types • C_PTR and C_FUNCPTR for interoperability with C pointers • C_LOC(x) and C_FUNLOC(x) inquiry functions for getting addresses of variables and procedures • BIND attribute for interoperability of derived types and C structures and enumerated types

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Fortran 2003 Features and HDF5

• New 2003 features allowed us to support • Any Fortran INTEGER and REAL type data in HDF5 files • Fortran derived types and HDF5 compound datatypes • Fortran enumerated types and HDF5 enumerated types • HDF5 APIs with callbacks

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Intel g95 gfortran SUN compilers PGI Fortran Compilers with 2003 Features

Compiler Current versions and status of HDF5

Versions 10.1 and 11 All F2003 functionality works in HDF5

Future versions

Version 11 will have a fix that will allow us to remove common blocks

August 2008 and later; All Fortran 2003 functionality works in HDF5 Version 4.4 Limited support for C interoperability; HDF5 doesn’t work No plans from compiler developers to improve the support Express-July 2008 build; HDF5 doesn’t work Version 7.2.1; HDF5 doesn’t work No timeline for fixes; may be in a year Fixes will be available in Version 8.

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PROGRAM main USE HDF5

Example

TYPE(s1_t),

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:: s1(LENGTH)

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Example

CALL h5tarray_create_f(H5T_NATIVE_CHARACTER, 1, tdims1, …) CALL h5tinsert_f(s1_tid, "chr_name", H5OFFSETOF(C_LOC(s1(1)),C_LOC(s1(1)%chr)),tid3, hdferr) CALL h5tinsert_f(s1_tid, "a_name", H5OFFSETOF(C_LOC(s1(1)),C_LOC(s1(1)%a)), hdferr) …..

CALL h5dcreate_f(file, DATASETNAME, s1_tid, space, …) …..

CALL h5dwrite_f(dataset, s1_tid, , hdferr)

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Example

HDF5 "SDScompound.h5" { GROUP "/" { DATASET "ArrayOfStructures" { DATATYPE H5T_COMPOUND { H5T_ARRAY { [13] H5T_STRING { STRSIZE 1; STRPAD H5T_STR_SPACEPAD; CSET H5T_CSET_ASCII; CTYPE H5T_C_S1; } } "chr_name"; H5T_STD_I8LE "a_name"; H5T_IEEE_F64LE "c_name"; H5T_IEEE_F32LE "b_name"; } …..

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Information

• Source code location http://svn.hdfgroup.uiuc.edu/hdf5/branches/F2003 • See examples for new features • Send comments to [email protected]

• Documentation will be available in November 2008

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HDF5 file recovery or Surviving a System Failure through Metadata Journaling

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Surviving a System Failure in HDF5

• Problem: • Data in an opened HDF5 files susceptible to corruption in the event of an application or system crash.

• Corruption possible if an opened HDF5 file has been updated when the crash occurs.

• Initial Objective: • Guarantee an HDF5 file with consistent metadata can be reconstructed in the event of a crash.

• No guarantee on state of raw data – contains whatever made it to disk prior to crash.

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Crash Survivability in HDF5

• Approach: Metadata Journaling • When an HDF5 file is opened with Metadata Journaling enabled, a companion Journal file is created.

• When an HDF5 API function that modifies metadata is completed, a transaction is recorded in the Journal file.

• If the application crashes, a recovery program can replay the journal by applying in order all metadata writes until the end of the last completed transaction written to the journal file.

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HDF5 Metadata Journaling Recovery

Application crashed h5recover tool liFe Corrupted 5DFH Restored HDF5 File Companion Journal File

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Implementation Status

• Serial HDF5 with synchronous write mode • Alpha1 released August 2008 • User interface (API definition and h5recover tool) and file format may change

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Metadata Journaling Plans

• Serial HDF5 with synchronous write mode • Finalize User interface definitions and file format • Serial HDF5 with asynchronous write mode • To improve Journal file write speed • More features (need funding) • Make raw data operations atomic • Allow "super ‐ transactions" to be created by applications • Enable journaling for Parallel HDF5

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Questions?

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Acknowledgement

• This report is based upon work supported in part by a Cooperative Agreement with the National Aeronautics and Space Administration (NASA) under NASA Awards NNX06AC83A and NNX08AO77A. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Aeronautics and Space Administration.

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