Parallel I/O with HDF5: Overview, Tuning, and New Features HPC Best Practices Webinar Quincey Koziol & Suren Byna Lawrence Berkeley National Laboratory (LBNL) March 13, 2019 exascaleproject.org ExaHDF5 Team Members • LBNL • The HDF Group – Suren Byna, Quincey – Scot Breitenfeld, John Koziol, Houjun Tang, Bin Mainzer, Dana Robinson, Dong, Junmin Gu, Jialin Liu, Jerome Soumagne, Richard Alex Sim Warren, Neelam Bagha, Elena Pourmal • ANL – Venkat Vishwanath, Rick Zamora, Paul Coffman, Todd Munson 2 WHAT IS HDF5? 4 HDF5 is like … 5 HDF5 is designed … • for high volume and / or complex data • for every size and type of system – from cell phones to supercomputers • for flexible, efficient storage and I/O • to enable applications to evolve in their use of HDF5 and to accommodate new models • to support long-term data preservation 6 7 HDF5 Ecosystem HDF5 … Too ls ers Support File Format Libra ry Data DocumentatiModel on … What is HDF5? • HDF5 Hierarchical Data Format, v5 • Open file format – Designed for high volume and complex data • Open source software – Works with data in the format • An extensible data model – Structures for data organization and specification 8 HDF5 DATA MODEL 9 HDF5 File lat | lon | temp ----|-----|----- 12 | 23 | 3.1 15 | 24 | 4.2 An HDF5 file is a 17 | 21 | 3.6 container that holds data objects. 10 HDF5 Data Model Dataset Link Group HDF5 Datatype Objects Attribute Dataspace File 11 HDF5 Dataset HDF5 Datatype Integer: 32-bit, LE HDF5 Dataspace Rank Dimensions 3 Dim[0] = 4 Dim[1] = 5 Dim[2] = 7 Specifications for single data Multi-dimensional array of element and array dimensions identically typed data elements • HDF5 datasets organize and contain data elements. • HDF5 datatype describes individual data elements. • HDF5 dataspace describes the logical layout of the data elements. 12 HDF5 Dataspace • Describes the logical layout of the elements in an HDF5 dataset – NULL • no elements – Scalar • single element – Simple array (most common) • multiple elements organized in a rectangular array – rank = number of dimensions – dimension sizes = number of elements in each dimension – maximum number of elements in each dimension » may be fixed or unlimited 13 Extreme Scale Computing Argonne HDF5 Dataspace Two roles: Spatial information for Datasets and Attributes – Rank and dimensions – Permanent part of object definition Rank = 2 Dimensions = 4x6 Partial I/O: Dataspace and selection describe application’s data buffer and data elements participating in I/O Rank = 1 Dimension = 10 Start = 5 14 Count = 3 HDF5 Datatypes • Describe individual data elements in an HDF5 dataset • Wide range of datatypes supported – Integer – Float – Enum – Array – User-defined (e.g., 13-bit integer) – Variable-length types (e.g., strings, vectors) – Compound (similar to C structs) – More … 15 Extreme Scale Computing HDF5 HDF5 Datatypes • Describe individual data elements in an HDF5 dataset • Wide range of datatypes supported – Integer – Float – Enum – Array (similar to matrix) – User-defined (e.g., 12-bit integer, 16-bit float) – Variable-length types (e.g., strings, vectors) – Compound (similar to C structs) – More … 16 Extreme Scale Computing HDF5 HDF5 Dataset 3 5 12 Datatype: 32-bit Integer Dataspace: Rank = 2 Dimensions = 5 x 3 17 HDF5 Dataset with Compound Datatype 3 5 V V V V V V V V V uint16 char int32 2x3x2 array of float32 Compound Datatype: Dataspace: Rank = 2 Dimensions = 5 x 3 18 How are data elements stored? (1/2) Buffer in memory Data in the file Data elements Contiguous stored physically (default) adjacent to each other Better access time Chunked for subsets; extendible Improves storage Chunked & efficiency, Compressed transmission speed 19 How are data elements stored? (2/2) Buffer in memory Data in the file Data elements Compact Dataset stored directly Object Header within object’s metadata Data elements stored outside the External Dataset Object Header HDF5 file, possibly in another file format Data elements actually stored in Virtual “source datasets”, using selections to map 20 HDF5 Groups and Links HDF5 groups and links Every HDF5 file Experiment Notes: / up Serial Number: 99378920 has a root gro organize Date: 3/13/09 data objects. Configuration: Standard 3 Parameters 10;100;1000 Viz SimOut lat | lon | temp ----|-----|----- 12 | 23 | 3.1 15 | 24 | 4.2 17 | 21 | 3.6 Timestep 36,000 21 HDF5 Attributes • Attributes “decorate” HDF5 objects • Typically contain user metadata • Similar to Key-Values: – Have a unique name (for that object) and a value • Analogous to a dataset – “Value” is an array described by a datatype and a dataspace – Do not support partial I/O operations; nor can they be compressed or extended 22 HDF5 SOFTWARE 24 HDF5 Home Page HDF5 home page: http://www.hdfgroup.org/solutions/hdf5/ – Latest release: HDF5 1.10.5 (1.10.6 coming soon) HDF5 source code: – Written in C, and includes optional C++, Fortran, and Java APIs • Along with “High Level” APIs – Contains command-line utilities (h5dump, h5repack, h5diff, ..) and compile scripts HDF5 pre-built binaries: – When possible, include C, C++, Fortran, Java and High Level libraries. • Check ./lib/libhdf5.settings file. – Built with and require the SZIP and ZLIB external libraries 25 Useful Tools For New Users h5dump: Tool to “dump” or display contents of HDF5 files h5cc, h5c++, h5fc: Scripts to compile applications (like mpicc, …) HDFView: Java browser to view HDF5 files http://support.hdfgroup.org/products/java/hdfview/ HDF5 Examples (C, Fortran, Java, Python, Matlab, …) http://support.hdfgroup.org/HDF5/examples/ 26 HDF5 PROGRAMMING MODEL AND API 27 HDF5 Software Layers & Storage API High Level H5Part netCDF-4 … h5dump HDFview … VPIC … Apps APIs Language Interfaces HDF5 Data Model Objects Tunable Properties Groups, Datasets, Attributes, … Chunk Size, I/O Driver, … C, Fortran, C++ Memory Datatype Chunked Version and so on… Internals Filters Mgmt Conversion Storage Compatibility HDF5 Library HDF5 Virtual File Posix Split Layer MPI I/O Custom I/O Files I/O Drivers HDF5 File File on Split Format File Parallel Other Files Storage Filesystem 28 The General HDF5 API • C, Fortran, Java, C++, and .NET bindings – Also: IDL, MATLAB, Python (H5Py, PyTables), Perl, ADA, Ruby, … • C routines begin with prefix: H5? ? is a character corresponding to the type of object the function acts on Example Functions: H5D : Dataset interface e.g., H5Dread H5F : File interface e.g., H5Fopen H5S : dataSpace interface e.g., H5Sclose 29 The HDF5 API • For flexibility, the API is extensive Victorinox Swiss Army Cybertool 300+ functions 34 • 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 30 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 31 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 32 Other Common Functions DataSpaces: H5Sselect_hyperslab (Partial I/O) H5Sselect_elements (Partial I/O) H5Dget_space DataTypes: H5Tcreate, H5Tcommit, H5Tclose H5Tequal, H5Tget_native_type Groups: H5Gcreate, H5Gopen, H5Gclose Attributes: H5Acreate, H5Aopen_name, H5Aclose H5Aread, H5Awrite Property lists: H5Pcreate, H5Pclose H5Pset_chunk, H5Pset_deflate 33 PARALLEL HDF5 34 (MPI-)Parallel vs. Serial HDF5 • PHDF5 allows multiple MPI processes in an MPI application to perform I/O to a single HDF5 file • Uses a standard parallel I/O interface (MPI-IO) • Portable to different platforms • PHDF5 files ARE HDF5 files conforming to the HDF5 file format specification • The PHDF5 API consists of: – The standard HDF5 API – A few extra knobs and calls – A parallel “etiquette” 39 Standard HDF5 “Skeleton” 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 40 Example of a PHDF5 C Program A parallel HDF5 program has a few extra calls … file_id = H5Fcreate(FNAME, …, H5P_DEFAULT); space_id = H5Screate_simple(…); dset_id = H5Dcreate(file_id, DNAME, H5T_NATIVE_INT, space_id, …); status = H5Dwrite(dset_id, H5T_NATIVE_INT, …, H5P_DEFAULT, …); … 41 Example of a PHDF5 C Program A parallel HDF5 program has a few extra calls MPI_Init(&argc, &argv); … fapl_id = H5Pcreate(H5P_FILE_ACCESS); H5Pset_fapl_mpio(fapl_id, comm, info); file_id = H5Fcreate(FNAME, …, fapl_id); space_id = H5Screate_simple(…); dset_id = H5Dcreate(file_id, DNAME, H5T_NATIVE_INT, space_id, …); xf_id = H5Pcreate(H5P_DATASET_XFER); H5Pset_dxpl_mpio(xf_id, H5FD_MPIO_COLLECTIVE); status = H5Dwrite(dset_id, H5T_NATIVE_INT, …, xf_id, …); … MPI_Finalize(); 42 PHDF5 Implementation Layers Science Application Compute node Compute node Compute node HDF5 Library MPI Library HDF5 file on Parallel File System Interconnect network + I/O servers Disk architecture and layout of data on disk 43 PHDF5 Etiquette • PHDF5 opens a shared file with an MPI communicator – Returns a file handle – All future access to the file via that file handle • All processes must participate in collective PHDF5 APIs • Different files can be opened via different communicators • All HDF5 APIs that modify file structure are collective! – Object create / delete, attribute and group