Hdf5 parallel

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The HDF Group
Parallel HDF5
March 4, 2015 HPC Oil & Gas Workshop
Quincey Koziol
Director of Core Software & HPC
The HDF Group
koziol@hdfgroup.org
http://bit.ly/QuinceyKoziol
1

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Recent Parallel HDF5 Success Story
• Performance of VPIC-IO on Bluewaters
• I/O Kernel of a Plasma Physics application
• 56 GB/s I/O rate in writing 5TB data using 5K
cores with multi-dataset write optimization
• VPIC-IO kernel running on 298,048 cores
• ~10 Trillion particles
• 291 TB, single file
• 1 GB stripe size and 160 Lustre OSTs
• 52 GB/s
• 53% of the peak performance
March 4, 2015 HPC Oil & Gas Workshop 3

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Outline
• Quick Intro to HDF5
• Overview of Parallel HDF5 design
• Parallel Consistency Semantics
• PHDF5 Programming Model
• Examples
• Performance Analysis
• Parallel Tools
• Details of upcoming features of HDF5
http://bit.ly/ParallelHDF5-HPCOGW-2015

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QUICK INTRO TO HDF5

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What is HDF5?
• HDF5 == Hierarchical Data Format, v5
• A flexible data model
• Structures for data organization and specification
• Open source software
• Works with data in the format
• Open file format
• Designed for high volume or complex data

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What is HDF5, in detail?
• A versatile data model that can represent very complex
data objects and a wide variety of metadata.
• An open source software library that runs on a wide
range of computational platforms, from cell phones to
massively parallel systems, and implements a high-level
API with C, C++, Fortran, and Java interfaces.
• A rich set of integrated performance features that allow
for access time and storage space optimizations.
• Tools and applications for managing, manipulating,
viewing, and analyzing the data in the collection.
• A completely portable file format with no limit on the
number or size of data objects stored.
March 4, 2015 7HPC Oil & Gas Workshop

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HDF5 is like …

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Why use HDF5?
• Challenging data:
• Application data that pushes the limits of what can be
addressed by traditional database systems, XML
documents, or in-house data formats.
• Software solutions:
• For very large datasets, very fast access requirements,
or very complex datasets.
• To easily share data across a wide variety of
computational platforms using applications written in
different programming languages.
• That take advantage of the many open-source and
commercial tools that understand HDF5.
• Enabling long-term preservation of data.

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Who uses HDF5?
• Examples of HDF5 user communities
• Astrophysics
• Astronomers
• NASA Earth Science Enterprise
• Dept. of Energy Labs
• Supercomputing Centers in US, Europe and Asia
• Synchrotrons and Light Sources in US and Europe
• Financial Institutions
• NOAA
• Engineering & Manufacturing Industries
• Many others
• For a more detailed list, visit
• http://www.hdfgroup.org/HDF5/users5.html

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The HDF Group
• Established in 1988
• 18 years at University of Illinois’ National Center for
Supercomputing Applications
• 8 years as independent non-profit company:
“The HDF Group”
• The HDF Group owns HDF4 and HDF5
• HDF4 & HDF5 formats, libraries, and tools are open
source and freely available with BSD-style license
• Currently employ 37 people
• Always looking for more developers!

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HDF5 Technology Platform
• HDF5 Abstract Data Model
• Defines the “building blocks” for data organization and
specification
• Files, Groups, Links, Datasets, Attributes, Datatypes,
Dataspaces
• HDF5 Software
• Tools
• Language Interfaces
• HDF5 Library
• HDF5 Binary File Format
• Bit-level organization of HDF5 file
• Defined by HDF5 File Format Specification
12March 4, 2015 HPC Oil & Gas Workshop

www.hdfgroup.orgMarch 4, 2015 13
HDF5 Data Model
• File – Container for objects
• Groups – provide structure among objects
• Datasets – where the primary data goes
• Data arrays
• Rich set of datatype options
• Flexible, efficient storage and I/O
• Attributes, for metadata
Everything else is built essentially from
these parts.
HPC Oil & Gas Workshop

www.hdfgroup.orgMarch 4, 2015 14
Structures to organize objects
palette
Raster image
3-D array
2-D arrayRaster image
lat | lon | temp
----|-----|-----
12 | 23 | 3.1
15 | 24 | 4.2
17 | 21 | 3.6
Table
“/” (root)
“/TestData”
“Groups”
“Datasets”

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HDF5 Dataset
March 4, 2015 15
• HDF5 datasets organize and contain data elements.
• HDF5 datatype describes individual data elements.
• HDF5 dataspace describes the logical layout of the data elements.
Integer: 32-bit, LE
HDF5 Datatype
Multi-dimensional array of
identically typed data elements
Specifications for single data
element and array dimensions
3
Rank
Dim[2] = 7
Dimensions
Dim[0] = 4
Dim[1] = 5
HDF5 Dataspace

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HDF5 Attributes
• Typically contain user metadata
• Have a name and a value
• Attributes “decorate” HDF5 objects
• Value is described by a datatype and a dataspace
• Analogous to a dataset, but do not support
partial I/O operations; nor can they be compressed
or extended

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HDF5 Technology Platform
• HDF5 Abstract Data Model
• Defines the “building blocks” for data organization and
specification
• Files, Groups, Links, Datasets, Attributes, Datatypes,
Dataspaces
• HDF5 Software
• Tools
• Language Interfaces
• HDF5 Library
• HDF5 Binary File Format
• Bit-level organization of HDF5 file
• Defined by HDF5 File Format Specification
17March 4, 2015 HPC Oil & Gas Workshop

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HDF5 Software Distribution
HDF5 home page: http://hdfgroup.org/HDF5/
• Latest release: HDF5 1.8.14 (1.8.15 coming in May
2015)
HDF5 source code:
• Written in C, and includes optional C++, Fortran 90
APIs, and High Level APIs
• Contains command-line utilities (h5dump, h5repack,
h5diff, ..) and compile scripts
HDF5 pre-built binaries:
• When possible, includes C, C++, F90, and High Level
libraries. Check ./lib/libhdf5.settings file.
• Built with and require the SZIP and ZLIB external
libraries

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The General HDF5 API
• C, Fortran, Java, C++, and .NET bindings
• IDL, MATLAB, Python (h5py, PyTables)
• C routines begin with prefix H5?
? is a character corresponding to the type of object the
function acts on
Example Interfaces:
H5D : Dataset interface e.g., H5Dread
H5F : File interface e.g., H5Fopen
H5S : dataSpace interface e.g., H5Sclose

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The HDF5 API
• For flexibility, the API is extensive
 300+ functions
• This can be daunting… but there is hope
 A few functions can do a lot
 Start simple
 Build up knowledge as more features are needed
Victorinox
Swiss Army
Cybertool 34

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General Programming Paradigm
• Object is opened or created
• Object is accessed, possibly many times
• Object is closed
• Properties of object are optionally defined
Creation properties (e.g., use chunking storage)
Access properties

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Basic Functions
H5Fcreate (H5Fopen) create (open) File
H5Screate_simple/H5Screate create Dataspace
H5Dcreate (H5Dopen) create (open) Dataset
H5Dread, H5Dwrite access Dataset
H5Dclose close Dataset
H5Sclose close Dataspace
H5Fclose close File

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Useful Tools For New Users
h5dump:
Tool to “dump” or display contents of HDF5 files
h5cc, h5c++, h5fc:
Scripts to compile applications
HDFView:
Java browser to view HDF5 files
http://www.hdfgroup.org/hdf-java-html/hdfview/
HDF5 Examples (C, Fortran, Java, Python, Matlab)
http://www.hdfgroup.org/ftp/HDF5/examples/

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OVERVIEW OF PARALLEL
HDF5 DESIGN

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• Parallel HDF5 should allow multiple
processes to perform I/O to an HDF5 file at
the same time
• Single file image for all processes
• Compare with one file per process design:
• Expensive post processing
• Not usable by different number of processes
• Too many files produced for file system
• Parallel HDF5 should use a standard
parallel I/O interface
• Must be portable to different platforms
Parallel HDF5 Requirements

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Design requirements, cont
• Support Message Passing Interface
(MPI) programming
• Parallel HDF5 files compatible with
serial HDF5 files
• Shareable between different serial or
parallel platforms

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Design Dependencies
• MPI with MPI-IO
• MPICH, OpenMPI
• Vendor’s MPI-IO
• Parallel file system
• IBM GPFS
• Lustre
• PVFS

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PHDF5 implementation layers
HDF5 Application
Compute node Compute node Compute node
HDF5 Library
MPI Library
HDF5 file on Parallel File System
Switch network + I/O servers
Disk architecture and layout of data on disk

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MPI-IO VS. HDF5

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MPI-IO
• MPI-IO is an Input/Output API
• It treats the data file as a “linear byte
stream” and each MPI application needs
to provide its own file and data
representations to interpret those bytes

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MPI-IO
• All data stored are machine dependent
except the “external32” representation
• External32 is defined in Big Endianness
• Little-endian machines have to do the data
conversion in both read or write operations
• 64-bit sized data types may lose
information

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MPI-IO vs. HDF5
• HDF5 is data management software
• It stores data and metadata according
to the HDF5 data format definition
• HDF5 file is self-describing
• Each machine can store the data in its own
native representation for efficient I/O
without loss of data precision
• Any necessary data representation
conversion is done by the HDF5 library
automatically

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PARALLEL HDF5
CONSISTENCY SEMANTICS

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Consistency Semantics
• Consistency Semantics: Rules that define the
outcome of multiple, possibly concurrent,
accesses to an object or data structure by one
or more processes in a computer system.

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Parallel HDF5 Consistency Semantics
• Parallel HDF5 library defines a set of
consistency semantics to let users know what
to expect when processes access data
managed by the library.
• When the changes a process makes are
actually visible to itself (if it tries to read back
that data) or to other processes that access the
same file with independent or collective I/O
operations

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• Same as MPI-I/O semantics
• Default MPI-I/O semantics doesn’t guarantee
atomicity or sequence of above calls!
• Problems may occur (although we haven’t
seen any) when writing/reading HDF5
metadata or raw data
Process 0 Process 1
MPI_File_write_at()
MPI_Barrier() MPI_Barrier()
MPI_File_read_at()

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• MPI I/O provides atomicity and sync-barrier-
sync features to address the issue
• PHDF5 follows MPI I/O
• H5Fset_mpio_atomicity function to turn on
MPI atomicity
• H5Fsync function to transfer written data to
storage device (in implementation now)

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• For more information see “Enabling a strict
consistency semantics model in parallel
HDF5” linked from the HDF5
H5Fset_mpi_atomicity Reference Manual
page1
1
http://www.hdfgroup.org/HDF5/doc/RM/Advanced/PHDF5FileConsistencySem
antics/PHDF5FileConsistencySemantics.pdf

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HDF5 PARALLEL
PROGRAMMING MODEL

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How to compile PHDF5 applications
• h5pcc – HDF5 C compiler command
• Similar to mpicc
• h5pfc – HDF5 F90 compiler command
• Similar to mpif90
• To compile:
• % h5pcc h5prog.c
• % h5pfc h5prog.f90

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Programming restrictions
• PHDF5 opens a parallel file with an MPI
communicator
• Returns a file handle
• Future access to the file via the file handle
• All processes must participate in collective
PHDF5 APIs
• Different files can be opened via different
communicators

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Collective HDF5 calls
• All HDF5 APIs that modify structural
metadata are collective!
• File operations
- H5Fcreate, H5Fopen, H5Fclose, etc
• Object creation
- H5Dcreate, H5Dclose, etc
• Object structure modification (e.g., dataset
extent modification)
- H5Dset_extent, etc
• http://www.hdfgroup.org/HDF5/doc/RM/CollectiveCalls.html

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Other HDF5 calls
• Array data transfer can be collective or
independent
- Dataset operations: H5Dwrite, H5Dread
• Collectiveness is indicated by function
parameters, not by function names as in MPI API

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What does PHDF5 support ?
• After a file is opened by the processes of a
communicator
• All parts of file are accessible by all processes
• All objects in the file are accessible by all
processes
• Multiple processes may write to the same data
array
• Each process may write to individual data array

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PHDF5 API languages
• C and F90, 2003 language interfaces
• Most platforms with MPI-IO supported. e.g.,
• IBM BG/x
• Linux clusters
• Cray

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Programming model
• HDF5 uses access property list to control
the file access mechanism
• General model to access HDF5 file in
parallel:
- Set up MPI-IO file access property list
- Open File
- Access Data
- Close File

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Example of Serial HDF5 C program
1.
2.
3. file_id = H5Fcreate(FNAME,…, H5P_DEFAULT);
4. space_id = H5Screate_simple(…);
5. dset_id = H5Dcreate(file_id, DNAME, H5T_NATIVE_INT,
space_id,…);
6.
7.
8. status = H5Dwrite(dset_id, H5T_NATIVE_INT, …, H5P_DEFAULT,
…);

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Example of Parallel HDF5 C program
Parallel HDF5 program has extra calls:
MPI_Init(&argc, &argv);
1. fapl_id = H5Pcreate(H5P_FILE_ACCESS);
2. H5Pset_fapl_mpio(fapl_id, comm, info);
3. file_id = H5Fcreate(FNAME,…, fapl_id);
4. space_id = H5Screate_simple(…);
5. dset_id = H5Dcreate(file_id, DNAME, H5T_NATIVE_INT,
space_id,…);
6. xf_id = H5Pcreate(H5P_DATASET_XFER);
7. H5Pset_dxpl_mpio(xf_id, H5FD_MPIO_COLLECTIVE);
8. status = H5Dwrite(dset_id, H5T_NATIVE_INT, …, xf_id…);
MPI_Finalize();

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WRITING PATTERNS -
EXAMPLE

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Parallel HDF5 tutorial examples
• For sample programs of how to write different
data patterns see:
http://www.hdfgroup.org/HDF5/Tutor/parallel.html

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Programming model
• Each process defines memory and file
hyperslabs using H5Sselect_hyperslab
• Each process executes a write/read call using
hyperslabs defined, which can be either
collective or independent
• The hyperslab parameters define the portion of
the dataset to write to:
- Contiguous hyperslab
- Regularly spaced data (column or row)
- Pattern
- Blocks

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Four processes writing by rows
HDF5 "SDS_row.h5" {
GROUP "/" {
DATASET "IntArray" {
DATATYPE H5T_STD_I32BE
DATASPACE SIMPLE { ( 8, 5 ) / ( 8, 5 ) }
DATA {
10, 10, 10, 10, 10,
10, 10, 10, 10, 10,
11, 11, 11, 11, 11,
11, 11, 11, 11, 11,
12, 12, 12, 12, 12,
12, 12, 12, 12, 12,
13, 13, 13, 13, 13,
13, 13, 13, 13, 13

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Parallel HDF5 example code
71 /*
72 * Each process defines dataset in memory and writes it to the
73 * hyperslab in the file.
74 */
75 count[0] = dims[0] / mpi_size;
76 count[1] = dims[1];
77 offset[0] = mpi_rank * count[0];
78 offset[1] = 0;
79 memspace = H5Screate_simple(RANK, count, NULL);
80
81 /*
82 * Select hyperslab in the file.
83 */
84 filespace = H5Dget_space(dset_id);
85 H5Sselect_hyperslab(filespace, H5S_SELECT_SET, offset, NULL,
count, NULL);

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Two processes writing by columns
HDF5 "SDS_col.h5" {
GROUP "/" {
DATA {
1, 2, 10, 20, 100, 200,
1, 2, 10, 20, 100, 200,
1, 2, 10, 20, 100, 200,
1, 2, 10, 20, 100, 200,
1, 2, 10, 20, 100, 200,
1, 2, 10, 20, 100, 200,
1, 2, 10, 20, 100, 200,
1, 2, 10, 20, 100, 200

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Four processes writing by pattern
HDF5 "SDS_pat.h5" {
GROUP "/" {
DATA {
1, 3, 1, 3,
2, 4, 2, 4,
1, 3, 1, 3,
2, 4, 2, 4,
1, 3, 1, 3,
2, 4, 2, 4,
1, 3, 1, 3,
2, 4, 2, 4

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Four processes writing by blocks
HDF5 "SDS_blk.h5" {
GROUP "/" {
DATA {
1, 1, 2, 2,
1, 1, 2, 2,
1, 1, 2, 2,
1, 1, 2, 2,
3, 3, 4, 4,
3, 3, 4, 4,
3, 3, 4, 4,
3, 3, 4, 4

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Complex data patterns
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HDF5 doesn’t have restrictions on data patterns and data balance

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Examples of irregular selection
• Internally, the HDF5 library creates an MPI
datatype for each lower dimension in the
selection and then combines those types into
one giant structured MPI datatype

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PERFORMANCE ANALYSIS

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Performance analysis
• Some common causes of poor performance
• Possible solutions

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My PHDF5 application I/O is slow
“Tuning HDF5 for Lustre File Systems” by
Howison, Koziol, Knaak, Mainzer, and
Shalf1
 Chunking and hyperslab selection
 HDF5 metadata cache
 Specific I/O system hints
1http://www.hdfgroup.org/pubs/papers/howison_hdf5_lustre_iasds2010.pdf

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Collective vs. independent calls
• MPI definition of collective calls:
• All processes of the communicator must participate
in calls in the right order. E.g.,
• Process1 Process2
• call A(); call B(); call A(); call B(); **right**
• call A(); call B(); call B(); call A(); **wrong**
• Independent means not collective 
• Collective is not necessarily synchronous, nor
must require communication

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Independent vs. collective access
• User reported
independent data
transfer mode was
much slower than
the collective data
transfer mode
• Data array was tall
and thin: 230,000
rows by 6 columns
:
:
:
230,000 rows
:
:
:

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Debug Slow Parallel I/O Speed(1)
• Writing to one dataset
- Using 4 processes == 4 columns
- HDF5 datatype is 8-byte doubles
- 4 processes, 1000 rows == 4x1000x8 = 32,000
bytes
• % mpirun -np 4 ./a.out 1000
- Execution time: 1.783798 s.
• % mpirun -np 4 ./a.out 2000
- Execution time: 3.838858 s.
• Difference of 2 seconds for 1000 more rows =
32,000 bytes.
• Speed of 16KB/sec!!! Way too slow.

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Debug slow parallel I/O speed(2)
• Build a version of PHDF5 with
• ./configure --enable-debug --enable-parallel …
• This allows the tracing of MPIO I/O calls in the
HDF5 library.
• E.g., to trace
• MPI_File_read_xx and MPI_File_write_xx calls
• % setenv H5FD_mpio_Debug “rw”

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Debug slow parallel I/O speed(3)
% setenv H5FD_mpio_Debug ’rw’
% mpirun -np 4 ./a.out 1000 # Indep.; contiguous.
in H5FD_mpio_write mpi_off=0 size_i=96
…
• Total of 4000 of these little 8 bytes writes == 32,000 bytes.

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Independent calls are many and small
• Each process writes
one element of one
row, skips to next
row, write one
element, so on.
• Each process issues
230,000 writes of 8
bytes each.
:
:
:
230,000 rows
:
:
:

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Debug slow parallel I/O speed (4)
% setenv H5FD_mpio_Debug ’rw’
% mpirun -np 4 ./a.out 1000 # Indep., Chunked by column.
…
Execution time: 0.011599 s.

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Use collective mode or chunked storage
• Collective I/O will
combine many small
independent calls
into few but bigger
calls
• Chunks of columns
speeds up too
:
:
:
230,000 rows
:
:
:

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Collective vs. independent write
0
100
200
300
400
500
600
700
800
900
1000
0.25 0.5 1 1.88 2.29 2.75
Secondstowrite
Data size in MBs
Independent write
Collective write

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Collective I/O in HDF5
• Set up using a Data Transfer Property List
(DXPL)
• All processes must participate in the I/O call
(H5Dread/write) with a selection (which could
be a NULL selection)
• Some cases where collective I/O is not used
even when the use asks for it:
• Data conversion
• Compressed Storage
• Chunking Storage:
• When the chunk is not selected by a certain
number of processes

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Enabling Collective Parallel I/O with HDF5
/* Set up file access property list w/parallel I/O access */
fa_plist_id = H5Pcreate(H5P_FILE_ACCESS);
H5Pset_fapl_mpio(fa_plist_id, comm, info);
/* Create a new file collectively */
file_id = H5Fcreate(filename, H5F_ACC_TRUNC,
H5P_DEFAULT, fa_plist_id);
/* <omitted data decomposition for brevity> */
/* Set up data transfer property list w/collective MPI-IO */
dx_plist_id = H5Pcreate(H5P_DATASET_XFER);
H5Pset_dxpl_mpio(dx_plist_id, H5FD_MPIO_COLLECTIVE);
/* Write data elements to the dataset */
status = H5Dwrite(dset_id, H5T_NATIVE_INT,
memspace, filespace, dx_plist_id, data);

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Collective I/O in HDF5
• Can query Data Transfer Property List (DXPL)
after I/O for collective I/O status:
• H5Pget_mpio_actual_io_mode
• Retrieves the type of I/O that HDF5 actually
performed on the last parallel I/O call
• H5Pget_mpio_no_collective_cause
• Retrieves local and global causes that broke
collective I/O on the last parallel I/O call
• H5Pget_mpio_actual_chunk_opt_mode
• Retrieves the type of chunk optimization that
HDF5 actually performed on the last parallel I/O
call. This is not necessarily the type of
optimization requested

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EFFECT OF HDF5 STORAGE

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Contiguous storage
• Metadata header separate from dataset data
• Data stored in one contiguous block in HDF5 file
Application memory
Metadata cache
Dataset header
………….
Datatype
Dataspace
………….
Attributes
…
File
Dataset data
Dataset data

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On a parallel file system
File Dataset data
OST 1 OST 2 OST 3 OST 4
The file is striped over multiple OSTs depending on
the stripe size and stripe count that the file was
created with.

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Chunked storage
• Data is stored in chunks of predefined size
• Two-dimensional instance may be referred to as data
tiling
• HDF5 library writes/reads the whole chunk
Contiguous Chunked

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Chunked storage (cont.)
• Dataset data is divided into equally sized blocks (chunks).
• Each chunk is stored separately as a contiguous block in
HDF5 file.
Application memory
Metadata cache
Dataset header
………….
Datatype
Dataspace
………….
Attributes
…
File
Dataset data
A DC Bheader
Chunk
index
Chunk
index
A B C D

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On a parallel file system
File A DC B
OST 1 OST 2 OST 3 OST 4
header
Chunk
index
The file is striped over multiple OSTs depending on
the stripe size and stripe count that the file was
created with

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Which is better for performance?
• It depends!!
• Consider these selections:
• If contiguous: 2 seeks
• If chunked: 10 seeks
• If contiguous: 16 seeks
• If chunked: 4 seeks
Add to that striping over a Parallel File System, which
makes this problem very hard to solve!

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Chunking and hyperslab selection
• When writing or reading, try to use hyperslab
selections that coincide with chunk boundaries.
P2P1 P3
83

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EFFECT OF HDF5 METADATA
CACHE

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Parallel HDF5 and Metadata
• Metadata operations:
• Creating/removing a dataset, group, attribute, etc…
• Extending a dataset’s dimensions
• Modifying group hierarchy
• etc …
• All operations that modify metadata are collective,
i.e., all processes have to call that operation:
• If you have 10,000 processes running your
application, and one process needs to create a
dataset, ALL processes must call H5Dcreate to
create 1 dataset.

www.hdfgroup.org
Space allocation
• Allocating space at the file’s EOF is very simple in
serial HDF5 applications:
• The EOF value begins at offset 0 in the file
• When space is required, the EOF value is
incremented by the size of the block requested.
• Space allocation using the EOF value in parallel
HDF5 applications can result in a race condition if
processes do not synchronize with each other:
• Multiple processes believe that they are the sole
owner of a range of bytes within the HDF5 file.
• Solution: Make it Collective

www.hdfgroup.org
Metadata cache
• To handle synchronization issues, all HDF5
operations that could potentially modify the
metadata in an HDF5 file are required to be
collective
• A list of these routines is available in the HDF5
reference
manual:http://www.hdfgroup.org/HDF5/doc/RM/C
ollectiveCalls.html

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Managing the metadata cache
• All operations that modify metadata in the HDF5
file are collective:
• All processes will have the same dirty metadata
entries in their cache (i.e., metadata that is
inconsistent with what is on disk).
• Processes are not required to have the same clean
metadata entries (i.e., metadata that is in sync with
what is on disk).
• Internally, the metadata cache running on process
0 is responsible for managing changes to the
metadata in the HDF5 file.
• All the other caches must retain dirty metadata until
the process 0 cache tells them that the metadata is
clean (i.e., on disk).

www.hdfgroup.org
Flushing the cache
• Initiated when:
• The size of dirty entries in cache exceeds a
certain threshold
• The user calls a flush
• The actual flush of metadata entries to disk is
currently implemented in two ways:
• Single Process (Process 0) write
• Distributed write

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PARALLEL TOOLS

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Parallel tools
• h5perf
• Performance measuring tool showing
I/O performance for different I/O APIs

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h5perf
• An I/O performance measurement tool
• Tests 3 File I/O APIs:
• POSIX I/O (open/write/read/close…)
• MPI-I/O (MPI_File_{open,write,read,close})
• HDF5 (H5Fopen/H5Dwrite/H5Dread/H5Fclose)
• An indication of I/O speed upper limits

www.hdfgroup.org
Useful parallel HDF5 links
• Parallel HDF information site
http://www.hdfgroup.org/HDF5/PHDF5/
• Parallel HDF5 tutorial available at
http://www.hdfgroup.org/HDF5/Tutor/
• HDF Help email address
help@hdfgroup.org

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UPCOMING FEATURES IN
HDF5

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PHDF5 Improvements in Progress
• Multi-dataset read/write operations
• Allows single collective operation on multiple
datasets
• Similar to PnetCDF “write-combining” feature
• H5Dmulti_read/write(<array of datasets,
selections, etc>)
• Order of magnitude speedup

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H5Dwrite vs. H5Dwrite_multi
0
1
2
3
4
5
6
7
8
9
400 800 1600 3200 6400
Writetimeinseconds
Number of datasets
H5Dwrite
H5Dwrite_multi
Rank = 1
Dims = 200
Contiguous floating-point datasets
109

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• Avoid file truncation
• File format currently requires call to truncate
file, when closing
• Expensive in parallel (MPI_File_set_size)
• Change to file format will eliminate truncate call

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• Collective Object Open
• Currently, object open is independent
• All processes perform I/O to read metadata
from file, resulting in I/O storm at file system
• Change will allow a single process to read, then
broadcast metadata to other processes

www.hdfgroup.org
Collective Object Open Performance

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Other HDF5 Improvements in Progress
• Single-Writer/Multiple-Reader (SWMR)
• Virtual Object Layer (VOL)
• Virtual Datasets

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Single-Writer/Multiple-Reader (SWMR)
• Improves HDF5 for Data Acquisition:
• Allows simultaneous data gathering and
monitoring/analysis
• Focused on storing data sequences for
high-speed data sources
• Supports ‘Ordered Updates’ to file:
• Crash-proofs accessing HDF5 file
• Possibly uses small amount of extra
space
January 21, 2015 127Computing for Light and Neutron Sources Forum

www.hdfgroup.org
Virtual Object Layer (VOL)
• Goal
- Provide an application with the HDF5 data model
and API, but allow different underlying storage
mechanisms
• New layer below HDF5 API
- Intercepts all API calls that can touch the data on
disk and routes them to a VOL plugin
• Potential VOL plugins:
- Native HDF5 driver (writes to HDF5 file)
- Raw driver (maps groups to file system directories
and datasets to files in directories)
- Remote driver (the file exists on a remote machine)

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VOL Plugins
VOL plugins

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Raw Plugin
• The flexibility of the virtual object layer
provides developers with the option to
abandon the single file, binary format like the
native HDF5 implementation.
• A “raw” file format could map HDF5 objects
(groups, datasets, etc …) to file system objects
(directories, files, etc …).
• The entire set of raw file system objects
created would represent one HDF5 container.

www.hdfgroup.org
Remote Plugin
• A remote VOL plugin would allow access to
files located on a server.
• Prototyping two implementations:
• Web-services via RESTful access:
http://www.hdfgroup.org/projects/hdfserver/
• Native HDF5 file access over sockets:
http://svn.hdfgroup.uiuc.edu/h5netvol/trunk/

www.hdfgroup.org
Virtual Datasets
• Mechanism for creating a composition of multiple
source datasets, while accessing through single
virtual dataset
• Modifications to source datasets are visible to
virtual dataset
• And writing to virtual dataset modifies source
datasets
• Can have subset within source dataset mapped to
subsets within virtual dataset
• Source and virtual datasets can have unlimited
dimensions
• Source datasets can be virtual datasets
themselves

www.hdfgroup.org
Virtual Datasets, Example 1

www.hdfgroup.org

www.hdfgroup.org
HDF5 Roadmap
March 4, 2015 149
• Concurrency
• Single-Writer/Multiple-
Reader (SWMR)
• Internal threading
• Virtual Object Layer (VOL)
• Data Analysis
• Query / View / Index APIs
• Native HDF5 client/server
• Performance
• Scalable chunk indices
• Metadata aggregation
and Page buffering
• Asynchronous I/O
• Variable-length
records
• Fault tolerance
• Parallel I/O
• I/O Autotuning
Extreme Scale Computing HDF5
“The best way to predict the
future is to invent it.”
– Alan Kay

www.hdfgroup.org
The HDF Group
Thank You!
Questions?

www.hdfgroup.org
Codename “HEXAD”
• Excel is a great frontend with a not so great rear ;-)
• We’ve fixed that with an HDF5 Excel Add-in
• Let’s you do the usual things including:
• Display content (file structure, detailed object info)
• Create/read/write datasets
• Create/read/update attributes
• Plenty of ideas for bells an whistles, e.g., HDF5
image & PyTables support
• Send in* your Must Have/Nice To Have feature list!
• Stay tuned for the beta program * help@hdfgroup.org

www.hdfgroup.org
HDF Server
• REST-based service for HDF5 data
• Reference Implementation for REST API
• Developed in Python using Tornado
Framework
• Supports Read/Write operations
• Clients can be Python/C/Fortran or Web Page
• Let us know what specific features you’d like to
see. E.g. VOL REST Client Plugin

www.hdfgroup.org
HDF Server Architecture

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Restless About HDF5/REST

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HDF Compass
• “Simple” HDF5 Viewer application
• Cross platform (Windows/Mac/Linux)
• Native look and feel
• Can display extremely large HDF5 files
• View HDF5 files and OpenDAP resources
• Plugin model enables different file
formats/remote resources to be supported
• Community-based development model

www.hdfgroup.org
Compass Architecture

Hdf5 parallel

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