sdrbench

The SDRBench scientific datasets as numpy arrays, served from the Hugging Face mirror (byte-for-byte copies of the original archives, pinned and sha256-verified), with automatic fallback to the original Globus archives at Argonne.

pip install sdrbench            # or "sdrbench[sz3]" to also get pysz (SZ3)

import sdrbench

sdrbench.list()                          # ['basilisk-turbulence', 'cesm-atm', 'exaalt', ...]
sdrbench.list(variants=True)             # ['basilisk-turbulence/small', ..., 'nyx/original', 'nyx/log', ...]

nyx = sdrbench.dataset("nyx")            # default variant; sdrbench.dataset("nyx", "log")
nyx.fields                               # ['baryon_density', 'dark_matter_density', 'temperature', ...]
t = nyx["temperature"]                   # numpy memmap, float32, shape (512, 512, 512), C order
sdrbench.load("cesm-atm", "CLDHGH")      # one-liner

# time series: fields are "var/step"
hur = sdrbench.dataset("hurricane-isabel", "P")
hur.steps                                # ['01', ..., '48']
p = hur.series("P")                      # ordered sequence of fields
x = hur["P", "07"]                       # one step
block = p.stack(slice(0, 4))             # (4, 100, 500, 500) copy

# stacked files are split into zero-copy views per variable
T = sdrbench.dataset("s3d")["T/1.1000E-03"]      # (500, 500, 500), component 6 of the stored file

# raw files to a directory (original SDRBench names, downloaded in parallel)
nyx.download("data/")                    # -> data/512x512x512/*.f32
sdrbench.dataset("nyx", root="data/")    # later: use local files first (also $SDRBENCH_DATA)

print(nyx.citation())                    # BibTeX + provider request + exact data version

Compress with SZ3 through pysz:

import numpy as np
from pysz import sz, szConfig, szErrorBoundMode

x = sdrbench.dataset("scale-letkf")["T"]
conf = szConfig()
conf.errorBoundMode = szErrorBoundMode.REL
conf.relErrorBound = 1e-3
compressed, ratio = sz.compress(np.ascontiguousarray(x), conf)
y, _ = sz.decompress(compressed, x.dtype.type, x.shape)
print(ratio, sz.verify(np.asarray(x), y))  # ratio, (max error, PSNR, NRMSE)

Command line:

sdrbench list                                   # every dataset/variant with field count and size
sdrbench info hurricane-isabel/P                # description, fields, dtype, shape, files
sdrbench download nyx temperature -o data/      # plain files under data/<repo path>, -j parallel
sdrbench path cesm-atm CLDHGH                   # local path (downloads if needed), e.g. for `sz3 -i`
sdrbench cite qmcpack

How it works

• Datasets, variants, fields. A dataset (nyx) has variants with descriptive names (original, log; cesm-atm: 2d, 2d-cleared, 3d; hacc: medium, big, sbig, region1...; hurricane-isabel: snapshot, P, QCLOUD, ...). The first is the default. The SDRBench / Hugging Face folder name also works as a variant name (dataset("nyx", "512x512x512")).
• Field names are physical variables (CLDHGH, T, temperature), or var/step for time series and slabs (P/07, xx/00042, density/31); ds.variables, ds.steps and ds.series(var) expose the structure. The original SDRBench file name also works (ds["CLDHGH_1_1800_3600.f32"]), lookups are case-insensitive, and errors suggest close matches. Non-array files are in ds.extra_files.
• dtype and shape come from the catalog, never from names. Shapes are C order (slowest first; the convention of the SZ3 test-suite table): np.fromfile(path, dtype).reshape(field.stored_shape) reads any stored file. field.shape_fastest_first is the order command-line compressors expect.
• Views, no copies of the data. QMCPACK's default variant preconditioned (288 x 115 x 69 x 69, the layout of the SDRBench examples) is computed on load by transposing the stored native file (variant original); S3D's stacked files are split into per-variable memmap views. field.save(path) writes the array exactly as loaded.
• Downloads come from Hugging Face, pinned to the commit this release's catalog was built from and checked against the catalog sha256, and are cached (SDRBENCH_CACHE moves the cache). Local copies are used first when root= / $SDRBENCH_DATA is given (an untarred SDRBench directory works). If Hugging Face cannot deliver, the package falls back to the original archive on Globus (whole archive, md5 and sha256 verified, size shown in a warning; resumes dropped connections). source="globus" forces it.
• Arrays are read-only memmaps; np.array(x) (or load(mmap=False)) gives a writable copy, e.g. for torch.from_numpy.

Datasets

Dataset	Hugging Face	Variants	Source
CESM-ATM	sdrbench/cesm-atm	2d, 2d-cleared, 3d	climate (SNL)
EXAALT	sdrbench/exaalt	small, copper-1/2, helium-1/2	molecular dynamics
Hurricane ISABEL	sdrbench/hurricane-isabel	snapshot, P, U, ..., CLOUD_log10, ...	weather (NCAR, IEEE Vis 2004)
EXAFEL	sdrbench/exafel	small, large, assembled	LCLS X-ray images
HACC	sdrbench/hacc	medium, big, sbig, region1-6	cosmology particles
NYX	sdrbench/nyx	original, log	cosmology
NWChem	sdrbench/nwchem	default, f32	quantum chemistry
SCALE-LETKF	sdrbench/scale-letkf	original, log	weather (RIKEN)
QMCPACK	sdrbench/qmcpack	preconditioned, original	quantum Monte Carlo
Miranda	sdrbench/miranda	small, big	turbulence (LLNL)
S3D	sdrbench/s3d	default	combustion (SNL)
Basilisk-Turbulence	sdrbench/basilisk-turbulence	small, large	2D turbulence
XGC	sdrbench/xgc	raw, adios	fusion (PPPL)

sdrbench list and sdrbench info show fields and sizes. NSTX GPI is not mirrored (its owner asks to be contacted before results are published); HACC region 5 is not available on Globus (HTTP 404).

Please cite SDRBench and the data provider named on each dataset card (sdrbench cite <dataset>), and report the sdrbench version you used: a release always reads the same data.

Keeping the mirror in sync

Globus remains the source of truth. .github/workflows/release.yml runs weekly:

1. sync/sync.py check HEADs every archive linked from the SDRBench page and compares size, ETag and Last-Modified with sync/state.json; archives that appear on, or disappear from, the page open an issue.
2. Changed archives are re-mirrored in parallel jobs (sync.py mirror). Archives are streamed: each file is unpacked, hashed and committed to sdrbench/<dataset> in batches and then deleted, so a runner only needs room for the largest single file (~17 GB); the job frees disk like the SZ3 CI. Files removed from an archive are removed from the repo, but only if the whole archive arrived and at most 25% of a variant goes (--allow-delete overrides). The same command works on any machine: HF_TOKEN=... python sync/sync.py mirror --only <dataset>.
3. sync.py catalog regenerates src/sdrbench/catalog.json (pinned to the new Hugging Face revisions), sync.py verify checks dtypes, element counts and dimension order against the data, sync.py cards refreshes the dataset cards and file tables, and a new patch version is tagged and published to PyPI.

Adding a dataset

1. Add an entry to sync/datasets.json (see its _comment): title, provider, science description, and per variant the Hugging Face folder, Globus archive, optional select/exclude, and rules mapping file globs to dtype, C-order shape and var/step name templates.
2. python sync/sync.py mirror --only <dataset> --dry --workdir /tmp/w downloads and hashes without uploading (writes /tmp/w/state.dry.json); fix rules until sync.py catalog builds without errors (it refuses files without a rule or with a size that does not match the shape).
3. Mirror for real, then sync.py catalog, sync.py verify --only <dataset>, sync.py cards --only <dataset>, and python sync/selftest.py --only <dataset> --workdir /big/tmp (every field through the package).

Development

pip install -e ".[test,sz3]"
pytest                       # offline tests
pytest -m online             # end-to-end against Hugging Face and Globus
python sync/sync.py verify   # data-level check of every dtype/shape (network)
python sync/selftest.py --workdir /big/tmp   # every field of every dataset through the package