Evidence map›Paper›PMID 34429723›Full record

ArticleJournal of applied crystallography2021

GPU-accelerated multitiered iterative phasing algorithm for fluctuation X-ray scattering.

Pranay Reddy Kommera, Vinay Ramakrishnaiah, Christine Sweeney, Jeffrey Donatelli, Petrus H Zwart

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Journal of applied crystallography, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.

0numbers the graph read from it
0cells of the map it votes in
2citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

2 citing papers in PubMed.

  1. Article
  2. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

5 authors.

Pranay Reddy KommeraApplied Computer Science, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
Vinay RamakrishnaiahApplied Computer Science, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.ORCID https://orcid.org/0000-0002-2925-4798
Christine SweeneyApplied Computer Science, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.ORCID https://orcid.org/0000-0003-2352-490X
Jeffrey DonatelliCenter for Advanced Mathematics for Energy Research Applications, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
Petrus H ZwartCenter for Advanced Mathematics for Energy Research Applications, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.ORCID https://orcid.org/0000-0003-3315-4092

Funding

The Development of Computational Methods for Fluctuation Xray ScatteringR01GM109019 · NIGMS · UNIVERSITY OF CALIF-LAWRENC BERKELEY LAB · PI ZWART, PETRUS H · 2014 to 2018
$1.9M
NIGMS NIH HHS R01 GM109019
6 · The paper itself

Abstract

The multitiered iterative phasing (MTIP) algorithm is used to determine the biological structures of macromolecules from fluctuation scattering data. It is an iterative algorithm that reconstructs the electron density of the sample by matching the computed fluctuation X-ray scattering data to the external observations, and by simultaneously enforcing constraints in real and Fourier space. This paper presents the first ever MTIP algorithm acceleration efforts on contemporary graphics processing units (GPUs). The Compute Unified Device Architecture (CUDA) programming model is used to accelerate the MTIP algorithm on NVIDIA GPUs. The computational performance of the CUDA-based MTIP algorithm implementation outperforms the CPU-based version by an order of magnitude. Furthermore, the Heterogeneous-Compute Interface for Portability (HIP) runtime APIs are used to demonstrate portability by accelerating the MTIP algorithm across NVIDIA and AMD GPUs.

Indexed as

AMD GPUsCUDA programmingfluctuation X-ray scatteringGPU accelerationHIP programmingmultitiered iterative phasingNVIDIA GPUspolar Fourier transformspherical harmonic transform

Identifiers

PMID34429723
PMCPMC8366419

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.