Evidence map›Paper›PMID 41170299›Full record

ArticleFrontiers in high performance computing2024

ExaFEL: extreme-scale real-time data processing for X-ray free electron laser science.

Johannes P Blaschke, Robert Bolotovsky, Aaron S Brewster, Jeffrey Donatelli, Antoine DuJardin, Wu-Chun Feng, Vidya Ganapati, Wilko Kroeger, Derek Mendez, Peter McCorquodale and 17 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Frontiers in high performance computing, 2024. 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. Review
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

27 authors.

Johannes P BlaschkeNational Energy Research Scientific Computing Center (NERSC), Lawrence Berkeley National Laboratory, Berkeley, CA, United States.
Robert BolotovskyMolecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States.
Aaron S BrewsterMolecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States.
Jeffrey DonatelliCenter for Advanced Mathematics for Energy Research Applications (CAMERA), Lawrence Berkeley National Laboratory, Berkeley, CA, United States.
Antoine DuJardinSLAC National Accelerator Laboratory, Menlo Park, CA, United States.
Wu-Chun FengDepartment of Computer Science, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States.
Vidya GanapatiMolecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States.
Wilko KroegerSLAC National Accelerator Laboratory, Menlo Park, CA, United States.
Derek MendezMolecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States.
Peter McCorquodaleApplied Numerical Algorithms Group (ANAG), Lawrence Berkeley National Laboratory, Berkeley, CA, United States.
Seema MirchandaneySLAC National Accelerator Laboratory, Menlo Park, CA, United States.
Christopher P O'GradySLAC National Accelerator Laboratory, Menlo Park, CA, United States.
Daniel W PaleyMolecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States.
Amedeo PerazzoSLAC National Accelerator Laboratory, Menlo Park, CA, United States.
Frederic P PoitevinSLAC National Accelerator Laboratory, Menlo Park, CA, United States.
Billy K PoonMolecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States.
Vinay B RamakrishnaiahComputer, Computational and Statistical Sciences Division, Los Alamos National Laboratory, Los Alamos, NM, United States.
Nicholas K SauterMolecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States.
Niteya ShahComputer, Computational and Statistical Sciences Division, Los Alamos National Laboratory, Los Alamos, NM, United States.
Elliott SlaughterSLAC National Accelerator Laboratory, Menlo Park, CA, United States.
Christine SweeneyComputer, Computational and Statistical Sciences Division, Los Alamos National Laboratory, Los Alamos, NM, United States.
Daniel TchońMolecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States.
Monarin UervirojnangkoornSLAC National Accelerator Laboratory, Menlo Park, CA, United States.
Felix WittwerNational Energy Research Scientific Computing Center (NERSC), Lawrence Berkeley National Laboratory, Berkeley, CA, United States.
Michael E WallComputer, Computational and Statistical Sciences Division, Los Alamos National Laboratory, Los Alamos, NM, United States.
Chun Hong YoonSLAC National Accelerator Laboratory, Menlo Park, CA, United States.
Iris D YoungMolecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States.

Funding

A Synchrotron Radiation Structural Biology ResourcesP30GM133894 · NIGMS · STANFORD UNIVERSITY · PI Aina E. Cohen, KEITH O HODGSON · 2020 to 2026
$43.3M
Cctbx.xfel: Serial crystallography computational methods aimed at biomolecular functionR35GM151988 · NIGMS · UNIVERSITY OF CALIF-LAWRENC BERKELEY LAB · PI NICHOLAS K SAUTER · 2024 to 2026
$2.2M
NIGMS NIH HHS P30 GM133894NIGMS NIH HHS R35 GM151988
6 · The paper itself

Abstract

ExaFEL is an HPC-capable X-ray Free Electron Laser (XFEL) data analysis software suite for both Serial Femtosecond Crystallography (SFX) and Single Particle Imaging (SPI) developed in collaboration with the Linac Coherent Lightsource (LCLS), Lawrence Berkeley National Laboratory (LBNL) and Los Alamos National Laboratory. ExaFEL supports real-time data analysis via a cross-facility workflow spanning LCLS and HPC centers such as NERSC and OLCF. Our work therefore constitutes initial path-finding for the US Department of Energy's (DOE) Integrated Research Infrastructure (IRI) program. We present the ExaFEL team's 7 years of experience in developing real-time XFEL data analysis software for the DOE's exascale supercomputers. We present our experiences and lessons learned with the Perlmutter and Frontier supercomputers. Furthermore we outline essential data center services (and the implications for institutional policy) required for real-time data analysis. Finally we summarize our software and performance engineering approaches and our experiences with NERSC's Perlmutter and OLCF's Frontier systems. This work is intended to be a practical blueprint for similar efforts in integrating exascale compute resources into other cross-facility workflows.

Indexed as

data-intensiveexascalehardware accelerationhigh-performance computinginterfacilityreal-time processingSerial Femtosecond CrystallographySingle Particle Imaging

Identifiers

PMID41170299
PMCPMC12570208

What OpenQuestion holds

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Registered trials

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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.