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AMReX

AMReX is a software framework for massively parallel, block-structured adaptive mesh refinement (AMR) applications.

You can find more information in AMReX-Codes GitHub repository.

Configuration

You can configure the AMReX 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
ncells Domain size
max_grid_size The maximum allowable size of each subdomain (used for parallel decomposal)
nlevs Number of levels
ncomp Number of components in the multifabs
nppc Number of particles per cell
nplotfile Number of plot files to write
nparticlefile Number of particle files to write
sleeptime Time to sleep before each write
restart_check Whether to check the correctness of checkpoint/restart
grids_from_file Enable AMReX to read grids from file
ref_ratio_file Refinement ratios for different AMReX refinement levels
hdf5compression Define the HDF5 compression algorithm to use

JSON Configuration (recomended)

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

{
    "benchmark": "amrex",
    "file": "amrex.h5",
    "configuration": {
        "ncells": "64",
        "max_grid_size": "8",
        "nlevs": "1",
        "ncomp": "6",
        "nppc": "2",
        "nplotfile": "2",
        "nparticlefile": "2",
        "sleeptime": "2",
        "restart_check": "1",
        "hdf5compression": "ZFP_ACCURACY#0.001",
        "mode": "SYNC"
    }
}

To read grids from file you need to set: grids_from_file, nlevels, and ref_ratio_file.

{
    "benchmark": "amrex",
    "file": "amrex.h5",
    "configuration": {
        "ncells": "64",
        "max_grid_size": "8",
        "nlevs": "1",
        "ncomp": "6",
        "nppc": "2",
        "nplotfile": "2",
        "nparticlefile": "2",
        "sleeptime": "2",
        "restart_check": "1",
        "hdf5compression": "ZFP_ACCURACY#0.001",
        "mode": "SYNC",
        "nlevs": "3",
        "grids_from_file": "1",
        "ref_ratio_file": "4 2"
    }
}

HDF5 ASYNC VOL Connector

AMReX supports the HDF5 ASYNC VOL connector. To enable it, you should specify in the vol property of you configuration.json file: the required library paths, the VOL ASYNC source path, and the connector setup.

"vol": {
    "library": "/vol-async/src:/hdf5-async-vol-register-install/lib:/argobots/install/lib:/hdf5-install/install:",
    "path": "/vol-async/src",
    "connector": "async under_vol=0;under_info={}"
}

Standalone Configuration

For standalone usage of this benchmark, this is the observed input configuration you should provide to the h5bench_amrex executable.

ncells = 64
max_grid_size = 8
nlevs = 1
ncomp = 6
nppc = 2
nplotfile = 2
nparticlefile = 2
sleeptime = 2
restart_check = 1

# Uncomment to read grids from file
# nlevs = 3
# grids_from_file = 1
# ref_ratio_file = 4 2

# Uncomment to enable compression
# hdf5compression=ZFP_ACCURACY#0.001

directory = .