| --- |
| license: other |
| license_name: sdrbench |
| license_link: https://sdrbench.github.io/ |
| pretty_name: "SDRBench: XGC" |
| tags: |
| - scientific-data |
| - lossy-compression |
| - sdrbench |
| - hpc |
| - sz3 |
| configs: |
| - config_name: files |
| data_files: files.jsonl |
| default: true |
| --- |
| |
| # SDRBench — XGC |
|
|
| Gyrokinetic fusion plasma simulation (XGC, PPPL): fields on an unstructured mesh of 20694 nodes x 512 toroidal planes, 9 time steps, double precision. |
|
|
| > **Raw binary arrays, not an Arrow/Parquet dataset.** `datasets.load_dataset("sdrbench/xgc")` returns the table of files (`files.jsonl`: path, dtype, shape, sha256). Read the arrays with the `sdrbench` package or `hf_hub_download` + numpy as shown below. |
| |
| This repository is an **unmodified mirror** of the XGC data of [SDRBench](https://sdrbench.github.io/datasets.html), the |
| Scientific Data Reduction Benchmark. The originals are hosted by Argonne National Laboratory on Globus; |
| every archive was unpacked and its files uploaded byte-for-byte (sha256 verified) (revision `f2518596a1`). `metadata/` holds |
| the original SDRBench property and template files. Kept in sync automatically by |
| [szcompressor/sdrbench](https://github.com/szcompressor/sdrbench). |
| |
| - **Data provider:** Princeton Plasma Physics Laboratory (PPPL); https://jychoi-hpc.github.io/adios-python-docs/XGC-mesh-and-field-data.html |
| - **Size:** 3.1 GB in 2 variant(s) |
| - **Format:** raw little-endian binary, C order (slowest dimension first); dtype and shape per field below |
| |
| ## Usage |
| |
| ```bash |
| pip install "sdrbench[sz3]" # sdrbench + pysz (SZ3) |
| ``` |
| |
| ```python |
| import numpy as np |
| import sdrbench |
| from pysz import sz, szConfig, szErrorBoundMode |
| |
| ds = sdrbench.dataset("xgc") # default variant "raw" |
| print(ds.fields) |
| x = ds["mesh_coordinates-values"] # numpy array, dtype <f8, shape (20694, 2) |
| |
| # compress with SZ3 (pysz) at a 1e-3 value-range-relative error bound |
| 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) |
| max_err, psnr, nrmse = sz.verify(np.asarray(x), y) |
| print(f"ratio {ratio:.1f}x, PSNR {psnr:.1f} dB, max error {max_err:.3g}") |
| ``` |
| |
| Files are fetched on first use (in parallel with `ds.download("data/")`) and cached, pinned to the revision |
| of the installed `sdrbench` release; if Hugging Face is unreachable the package falls back to the original |
| archive on Globus. Existing local SDRBench copies can be used with `sdrbench.dataset("xgc", root="/path")`. |
| |
| Without the package, with `huggingface_hub` and numpy only: |
| |
| ```python |
| from huggingface_hub import hf_hub_download |
| import numpy as np |
| p = hf_hub_download("sdrbench/xgc", "xgc/xgc.mesh.bp_coordinates-values_20694x2_double", repo_type="dataset", revision="f2518596a116a47c2e439417e17f4d9458012ccb") |
| x = np.fromfile(p, dtype="<f8").reshape((20694, 2)) |
| ``` |
| |
| ## Variants and fields |
| |
| |
| ### `raw` (default) |
| |
| `sdrbench.dataset("xgc", "raw")` — folder `xgc/` — 45 files, 1.5 GB, from [xgc.zip](https://g-d0cd3f.fd635.8443.data.globus.org/raw-data/XGC/xgc.zip). |
| |
| Raw binary arrays extracted from the ADIOS files: per time step dpot, iden (20694 x 512), pot0, potm0 (20694); mesh arrays prefixed mesh_. |
| |
| 13 variable(s) x 9 steps (08100 ... 08900): `ds.series("dpot")`, `ds["dpot", "08100"]`. |
| |
| | Field | dtype | Shape (C order) | File | |
| |---|---|---|---| |
| | `dpot/08100` | `<f8` | 20694 x 512 | `xgc/xgc.3d.08100.bp_dpot_20694x512_double` | |
| | `iden/08100` | `<f8` | 20694 x 512 | `xgc/xgc.3d.08100.bp_iden_20694x512_double` | |
| | `pot0/08100` | `<f8` | 20694 | `xgc/xgc.3d.08100.bp_pot0_20694_double` | |
| | `potm0/08100` | `<f8` | 20694 | `xgc/xgc.3d.08100.bp_potm0_20694_double` | |
| | `dpot/08200` | `<f8` | 20694 x 512 | `xgc/xgc.3d.08200.bp_dpot_20694x512_double` | |
| | `iden/08200` | `<f8` | 20694 x 512 | `xgc/xgc.3d.08200.bp_iden_20694x512_double` | |
| | `pot0/08200` | `<f8` | 20694 | `xgc/xgc.3d.08200.bp_pot0_20694_double` | |
| | `potm0/08200` | `<f8` | 20694 | `xgc/xgc.3d.08200.bp_potm0_20694_double` | |
| | `dpot/08300` | `<f8` | 20694 x 512 | `xgc/xgc.3d.08300.bp_dpot_20694x512_double` | |
| | `iden/08300` | `<f8` | 20694 x 512 | `xgc/xgc.3d.08300.bp_iden_20694x512_double` | |
| | ... 35 more | | | | |
| |
| ### `adios` |
| |
| `sdrbench.dataset("xgc", "adios")` — folder `xgc.3d/` — 10 files, 1.5 GB, from [xgc.3d.tar.gz](https://g-d0cd3f.fd635.8443.data.globus.org/raw-data/XGC/xgc.3d.tar.gz). |
| |
| The original ADIOS BP files (not raw arrays; read them with ADIOS). |
| |
| |
| Other files: `xgc.3d/xgc.3d.08100.bp`, `xgc.3d/xgc.3d.08200.bp`, `xgc.3d/xgc.3d.08300.bp`, `xgc.3d/xgc.3d.08400.bp`, `xgc.3d/xgc.3d.08500.bp`, `xgc.3d/xgc.3d.08600.bp`, `xgc.3d/xgc.3d.08700.bp`, `xgc.3d/xgc.3d.08800.bp`, `xgc.3d/xgc.3d.08900.bp`, `xgc.3d/xgc.mesh.bp` |
| |
| ## Citation |
| |
| Please cite SDRBench; `sdrbench cite xgc` prints it: |
| |
| ```bibtex |
| @inproceedings{zhao2020sdrbench, |
| title = {{SDRBench}: Scientific Data Reduction Benchmark for Lossy Compressors}, |
| author = {Zhao, Kai and Di, Sheng and Liang, Xin and Li, Sihuan and Tao, Dingwen and Chen, Zizhong and Cappello, Franck}, |
| booktitle = {2020 IEEE International Conference on Big Data (Big Data)}, |
| pages = {2716--2724}, |
| year = {2020} |
| } |
| ``` |
| |
| ## License and terms |
| |
| The data are distributed by the SDRBench team for research use under the terms of the original |
| data providers listed above (see the [SDRBench website](https://sdrbench.github.io/datasets.html)); please acknowledge them as |
| requested. Rights remain with the data providers. |
| |
