skip to main content
OSTI.GOV title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: A lightweight method for evaluating in situ workflow efficiency

Journal Article · · Journal of Computational Science
ORCiD logo [1];  [1];  [2]; ORCiD logo [1]; ORCiD logo [3];  [3];  [4];  [2];  [1]
  1. Univ. of Southern California, Los Angeles, CA (United States). Information Sciences Institute
  2. Univ. of Tennessee, Knoxville, TN (United States)
  3. Cornell Univ., Ithaca, NY (United States). Weill Medical College
  4. Univ. of New Mexico, Albuquerque, NM (United States)
+ Show Author Affiliations

Performance evaluation is crucial to understanding the behavior of scientific workflows. In this study, we target an emerging type of workflow, called in situ workflows. These workflows tightly couple components such as simulation and analysis to improve overall workflow performance. To understand the tradeoffs of various configurable parameters for coupling these heterogeneous tasks, namely simulation stride, and component placement, separately monitoring each component is insufficient to gain insights into the entire workflow behavior. Through an analysis of the state-of-the-art research, we propose a lightweight metric, derived from a defined in situ step, for assessing resource usage efficiency of an in situ workflow execution. By applying this metric to a synthetic workflow, which is parameterized to emulate behaviors of a molecular dynamics simulation, we explore two possible scenarios (Idle Simulation and Idle Analyzer) for the characterization of in situ workflow execution. In addition to preliminary results from a recently published study [11], we further exploit the proposed metric to evaluate a practical in situ workflow with a real molecular dynamics application, i.e., GROMACS. Here, experimental results show that the in transit placement (analytics on dedicated nodes) sustains a higher frequency for performing in situ analysis compared to the helper-core configuration (analytics co-allocated with simulation).

Research Organization:
Univ. of Southern California, Los Angeles, CA (United States)
Sponsoring Organization:
USDOE Office of Science (SC), Advanced Scientific Computing Research (ASCR); National Science Foundation (NSF)
Grant/Contract Number:
SC0012636; AC05-00OR22725; 1741040; 1740990; 1741057
OSTI ID:
1787006
Alternate ID(s):
OSTI ID: 1780268
Journal Information:
Journal of Computational Science, Vol. 48; ISSN 1877-7503
Publisher:
ElsevierCopyright Statement
Country of Publication:
United States
Language:
English

References (17)

Transport domain unlocking sets the uptake rate of an aspartate transporter journal February 2015
Optimization of the Additive CHARMM All-Atom Protein Force Field Targeting Improved Sampling of the Backbone ϕ, ψ and Side-Chain χ 1 and χ 2 Dihedral Angles journal August 2012
Implementation of the CHARMM Force Field in GROMACS: Analysis of Protein Stability Effects from Correction Maps, Virtual Interaction Sites, and Water Models journal January 2010
Coupling substrate and ion binding to extracellular gate of a sodium-dependent aspartate transporter journal January 2007
Coupling Exascale Multiphysics Applications: Methods and Lessons Learned conference October 2018
DataSpaces: an interaction and coordination framework for coupled simulation workflows journal February 2011
MaDaTS: Managing Data on Tiered Storage for Scientific Workflows
  • Ghoshal, Devarshi; Ramakrishnan, Lavanya
  • Proceedings of the 26th International Symposium on High-Performance Parallel and Distributed Computing - HPDC '17 https://doi.org/10.1145/3078597.3078611
conference January 2017
In situ data analytics and indexing of protein trajectories journal January 2017
Flexible IO and integration for scientific codes through the adaptable IO system (ADIOS)
  • Lofstead, Jay F.; Klasky, Scott; Schwan, Karsten
  • Proceedings of the 6th international workshop on Challenges of large applications in distributed environments - CLADE '08 https://doi.org/10.1145/1383529.1383533
conference January 2008
The Tau Parallel Performance System journal May 2006
A characterization of workflow management systems for extreme-scale applications journal October 2017
On the use of burst buffers for accelerating data-intensive scientific workflows conference January 2017
PLUMED 2: New feathers for an old bird journal February 2014
A Scalable Observation System for Introspection and In Situ Analytics conference November 2016
Big Data Staging with MPI-IO for Interactive X-ray Science conference December 2014
WOWMON: A Machine Learning-based Profiler for Self-adaptive Instrumentation of Scientific Workflows journal January 2016
FlexAnalytics: A Flexible Data Analytics Framework for Big Data Applications with I/O Performance Improvement journal August 2014

Similar Records

Performance assessment of ensembles of in situ workflows under resource constraints
Journal Article · Wed Jun 08 00:00:00 EDT 2022 · Concurrency and Computation. Practice and Experience · OSTI ID:1787006
+3 more
PANORAMA: An approach to performance modeling and diagnosis of extreme-scale workflows
Journal Article · Tue Jul 14 00:00:00 EDT 2015 · International Journal of High Performance Computing Applications · OSTI ID:1787006
+12 more
Enabling In-situ Execution of Coupled Scientific Workflow on Multi-core Platform
Conference · Thu Aug 16 00:00:00 EDT 2012 · 2012 IEEE 26TH INTERNATIONAL PARALLEL AND DISTRIBUTED PROCESSING SYMPOSIUM (IPDPS) · OSTI ID:1787006
+3 more

Related Subjects

97 MATHEMATICS AND COMPUTING
Scientific workflow
In situ model
Molecular dynamics
High-performance computing