OpenPMD

OpenPMD is an open meta-data schema that provides meaning and self-description for data sets in science and engineering.

The openPMD-api library provides a reference API for openPMD data handling. In the h5bench Benchmarking Suite we provide support for the write and read parallel benchmarks with HDF5 backend. You can find more information in OpenPMD documentation.

Configuration

You can configure the openPMD write HDF5 benchmark with the following options. Notice that if you use the configuration.json approach to define the runs for h5bench, we will automatically generate the final configuration file based on the options you provide in the JSON file. For standalone usage of this benchmark, you can check the input format at the end of this document and refer to its documentation.

Parameter	Description
operation	Operation: write or read
fileLocation	Directory where the file will be written to or read from

When running with the write operation, you have to define the following options:

dim Number of dimensions (1, 2, or 3) balanced Should it use a balanced load? (true or false) ratio Particle to mesh ratio steps Number of iteration steps minBlock Meshes are viewed as grid of mini blocks grid Grid based on the mini block

When running with the read operation, you have to define the pattern:

pattern Read access pattern

The minBlock and grid parameters must include the values for each of the dim dimensions. For example, if "dim": "3" (for a 3D mesh) minBlock should contain three values, one for each dimension "16 32 32" and grid (which is based on the mini block) should also contain three values, one for each dimension "32 32 16".

For the pattern attribute for read you can chose:

• m: metadata only

• sx: slice of the ‘rho’ mesh in the x-axis (eg. x=0)

• sy: slice of the ‘rho’ mesh in the y-axis (eg. y=0)

• sz: slice of the ‘rho’ mesh in the z-axis (eg. z=0)

• fx: slice of the 3D magnetic field in the x-axis (eg. x=0)

• fy: slice of the 3D magnetic field in the y-axis (eg. y=0)

• fz: slice of the 3D magnetic field in the z-axis (eg. z=0)

JSON Configuration (recomended)

To run an instance of openPMD HDF5 benchmark you need to include the following in the benchmarks property of your configuration.json file:

{
    "benchmark": "openpmd",
    "configuration": {
        "operation": "write",
        "dim": "3",
        "balanced": "true",
        "ratio": "1",
        "steps": "1",
        "minBlock": "8 16 16",
        "grid": "16 16 8"
    }
},
{
    "benchmark": "openpmd",
    "configuration": {
        "operation": "read",
        "pattern": "sy"
    }
}

Standalone Configuration

For standalone usage of this benchmark, this is the observed input configuration you should provide to the h5bench_openpmd_write.

dim=3
balanced=true
ratio=1
steps=10
minBlock=16 32 32
grid=32 32 16

For the h5bench_openpmd_read, you need to provide two arguments: the file prefix and the pattern.