A reproducible massively parallel IO library for hierarchical data
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README.rst

bigfile

A reproducible massively parallel IO library for large, hierarchical datasets.

Python 2 and 3 binding is available via pip.

bigfile was originally developed for the BlueTides simulation on BlueWaters at NCSA. The library is currently under investigation under the BW-PAID program with NCSA.

The current implementation works on a true POSIX compliant file system, e.g. Lustre. BigFile makes two assumptions

  1. mkdir() is durable -- it shall propagate the directory to all clients.
  2. Allowing non-overlapping write from different clients. This less strict than POSIX.

Be aware NFS is not a true POSIX compliant file system.

To cite bigfile, use DOI at

Build status

Build Status Coverity Scan Build Status

Install

Usually one only needs the Python binding in order to read a BigFile.

To install the Python binding

pip install [--user] bigfile

The C-API of bigfile can be embedded into a project, by dropping in four files : bigfile.c bigfile-mpi.c, bigfile.h bigfile-mpi.h.

However, if installation is preferred, the library and executables can be compiled and installed using CMake:

mkdir build
cd build
cmake ..
make install

This will install the project in the default path (probalby /usr/local), to select an alternative installation destination, replace the cmake call by:

cmake -DCMAKE_INSTALL_PREFIX:PATH=<PREFIX> ..

where <PREFIX> is the desired destination.

Compilation is also possible using the legacy build system:

make install

However, you need to manually override CC MPICC, PREFIX as needed. Take a look at the Makefile is always recommended.

Description

bigfile provides a hierarchical structure of data columns via File, Dataset and Column.

A Column stores a two dimesional table of nmemb columns and size rows. Numerical typed columns are supported.

Attributes can be attached to a Column. Numerical attributes and string attributes are supported.

Type casting is performed on-the-fly if read/write operation requests a different data type than the file has stored.

bigfile.Dataset works with dask.from_array.

The Anatomy of a BigFile

A BigFile maps to a directory hierarchy on the file system.

This is the directroy structure of an example file:

/scratch1/scratchdirs/sd/yfeng1/example-bigfile
  block0
    header
    attrs-v2
    000000
  group1
    block1.1
      header
      attrs-v2
      000000
      000001
    block1.2
      header
      attrs-v2
      000000
      000001
  group2
    block2.1
      header
      attrs-v2
      000000
      000001

A BigFile consists of blocks (BigBlock) and groups of blocks. Files, groups and blocks are mapped to directories of the hosting file system.

A BigBlock consists of two special plain text files and a sequence of binary data files.

  • Text file header, which stores the data type and size of the block,
  • Text file attrs-v2, which stores the attributes attached to the block.
  • Binary files 000000, 000001, .... which store the binary data of for the blocks. The format of the data (endianess, data type, vector length per row) is described in header. The number of files used by a block, as well as the size (number of rows) of a block is fixed at the creation of a block.

The performance of bigfile is insulated from the configurations of the Lustre file system due to the explicit striping.

Comparision with HDF5

Good

  • bigfile is simpler. The core library of bigfile consists of 2 source files, 2 header files, and 1 Makefile, a total of less than 3000 lines of code, easily maintained by one person or dropped into a project. HDF5 is much more complicated.
  • bigfile is closer to the data. The raw data on disk is stored as binary files that can be directly accessed by any application. The meta data (block descriptions and attributes) is stored in plain text, easily understood by human. In a sense, the bigfile library is no more than a helper for reading and writing these files under the bigfile protocal. In contrast, once your data goes into HDF5 it is trapped, the HDF5 library is required to make sense of the data from that point on.

Bad

  • bigfile is limited -- for example, bigfile has no API for output streaming, and only 2-dimensional tables are supported. HDF5 is much richer in functionality and more powerful in data description. The designated use-case of bigfile is to store a large amount of static / near-immutable column-wise table data.
  • bigfile is incomplete. Bugs have yet to be identified and fixed. In contrast HDF5 has been a funded research program developed for more than 20 years.

API Reference

The documentation needs to be written.

The core library is C. Refer to bigfile.h and bigfile-mpi.h for the API interface.

There are Python bindings for Python 2 and 3.

The Python binding under MPI invoked more meta-data queries to the file system than we would like to be, though for small scale applications (thousands of cores) it is usually adequate.

Examples

# This example consumes the BlueTides Simulation data.

import bigfile

f = bigfile.File('PART_018')

print (f.blocks)
# Position and Velocity of GAS particles
data = bigfile.DataSet(f["0/"], ['Position', 'Velocity'])

print (data.size)
print (data.dtype)
# just read a few particles, because there are 700 billion of them.
print data[10:30]

Shell

We provide the following shell commands for inspecting a bigfile:

  • bigfile-cat
  • bigfile-create
  • bigfile-repartition
  • bigfile-ls
  • bigfile-get-attr
  • bigfile-set-attr

Rejected Poster for SC17

We submitted a poster to describe bigfile for SC17. Although the poster was rejected, we post them here as they contain a description of the design and some benchmarks of bigfile.

https://github.com/rainwoodman/bigfile/tree/documents

Yu Feng