2.92 speedup
oconnell2023-aws-gpu4-somaticsniper speedup (relative to the CPU machine on AWS)
- Tested configuration
- Parabricks 3.7.0-1, 4 GPUs on AWS (O'Connell et al. 2023)
- Protocol
- SomaticSniper execution on CPU and GPU cloud and DGX machines (O'Connell et al. 2023 Table 1)
- Dataset
- Synthetic tumour BAM: HG002 30x with 198 SNVs added by SomatoSim v1.0.0
- Procedure
- model-execution-20261009-protocol-oconnell2023-somaticsniper
- Evaluation
- SomaticSniper on Parabricks 3.7.0-1, 4 GPUs on AWS (O'Connell et al. 2023)
- Coverage
- Not reported scored / Not reported eligible
- Uncertainty
- Not reported by the source: Single recorded run per cell; no repeats or intervals printed
- Evidence
- Independent external evaluation · source checkedAccelerating genomic workflows using NVIDIA Parabricks · Table 1, row 58 (AWS, GPU4, SomaticSniper), column 'Fold acceleration'
A source-checked result verifies the numerical transcription, not every model or protocol detail. Evaluation metadata: source checked. Source checked does not mean independently reproduced.
Reproduction
- Split
- Single sample
- Adaptation
- Not reported
- Scoring implementation
- Workflow wall-clock; cost from on-demand hourly price
No execution recipe has been verified for this exact configuration and evaluation. A benchmark's general instructions may use different inputs, splits or model settings.
Reproducing this published result requires matching its model configuration, data, split and scorer. Source checking or a successful smoke test does not establish score reproduction.
Evidence
Source checking verifies the cited claim or transcription. It does not establish independent reproduction.
Evidence table
Inspect claims, sources and review details
Trace each statement to its source and review. A context-only reference supports the record generally; it does not verify an individual field. Source checking does not reproduce an experiment.
One row per statement and cited source. Multiple citations are not independent evaluations. Shared locators are labelled explicitly.
1 evidence row matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Reported result 2.92 Individual claims | Accelerating genomic workflows using NVIDIA Parabricks Table 1, row 58 (AWS, GPU4, SomaticSniper), column 'Fold acceleration' Version: BMC Bioinformatics 24:221, published 2023-05-31; PMC10230726 full-text XML | source checked ["source-hash-verification","deterministic-table-parse","independent-cell-check"] · 2026-10-09T20:46:48Z independent paper Audit detailsExtracted by deterministic parse of Table 1 (table-wrap Tab1) in the pinned article XML (extract/extract_model_execution.py), with the header, platform, pipeline, VM-type and variant-caller labels asserted; blank Platform and Variant-caller cells inherit the row above, as the table layout shows. printed_value is the cell text. Independent review 2026-10-09: printed value, numeric value, metric, qualifier, unit, direction, locator and configuration and protocol identity match the source. AWS GPU model is unresolved: the Table 1 footnote says p3 (V100), the Results text attributes the Table 1 AWS savings to p4 (A100). Every AWS GPU cost equals the printed minutes times 12.24 USD per hour (2 and 4 GPUs) or 31.22 USD per hour (8 GPUs), not the 32.8 USD per hour p4d.24xlarge price in the text. The printed value is correct as transcribed. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record Extraction artifact SHA-256: |
Sources and history
Release 2026-10-09-8cc1db47c7f9 · Record review: source checked
1 source records and release history
- Accelerating genomic workflows using NVIDIA Parabricks · Original source · BMC Bioinformatics 24:221, published 2023-05-31; PMC10230726 full-text XML
Technical metadata and extraction receipts
Stable ID: model-execution-20261009-result-oconnell2023-aws-gpu4-somaticsniper-speedup
- metric
- speedup
- metric direction
- higher
- unit
- unitless
- metric qualifier
- relative to the CPU machine on AWS
- printed value
- 2.92
- numeric value
- 2.92
- source locator
- Table 1, row 58 (AWS, GPU4, SomaticSniper), column 'Fold acceleration'
- missing metadata
- uncertainty: reason: unreported; note: Single recorded run per cell; no repeats or intervals printed
- review
- method: source-hash-verification; deterministic-table-parse; independent-cell-check; method note: Re-downloaded the article XML and matched its SHA-256. Parsed table-wrap Tab1 with a separate script written for this review (the extractor's scripts were not imported or run), carrying platform and caller labels down blank cells, and asserted the header and 66 body rows. Checked printed and numeric value, metric, qualifier, unit, direction, locator, and the linked evaluation's configuration and protocol. Recomputed hours from minutes, fold acceleration from the CPU and GPU minutes, % cost-savings from the CPU and GPU costs, and the hourly rate implied by each cost.; reviewer: claude; reviewer note: Separate Claude review agent, independent of the extractor; no human review claimed; reviewed at: 2026-10-09T20:46:48Z; artifact sha256: 1d9c27beb3780a153bc6d80817bf098539e5c605107da0e88f34d6e0d56f3e4f; retrieval url: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC10230726/fullTextXML; note: Extracted by deterministic parse of Table 1 (table-wrap Tab1) in the pinned article XML (extract/extract_model_execution.py), with the header, platform, pipeline, VM-type and variant-caller labels asserted; blank Platform and Variant-caller cells inherit the row above, as the table layout shows. printed_value is the cell text. Independent review 2026-10-09: printed value, numeric value, metric, qualifier, unit, direction, locator and configuration and protocol identity match the source. AWS GPU model is unresolved: the Table 1 footnote says p3 (V100), the Results text attributes the Table 1 AWS savings to p4 (A100). Every AWS GPU cost equals the printed minutes times 12.24 USD per hour (2 and 4 GPUs) or 31.22 USD per hour (8 GPUs), not the 32.8 USD per hour p4d.24xlarge price in the text. The printed value is correct as transcribed.