DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: Massively scalable workflows for quantum chemistry: BigChem and ChemCloud

Journal Article · · Journal of Chemical Physics
DOI: https://doi.org/10.1063/5.0190834 · OSTI ID:2371584
ORCiD logo [1]; ORCiD logo [2]
  1. SLAC National Accelerator Laboratory (SLAC), Menlo Park, CA (United States). Photon Ultrafast Laser Science and Engineering Institute (PULSE); Stanford Univ., CA (United States); SLAC
  2. SLAC National Accelerator Laboratory (SLAC), Menlo Park, CA (United States). Photon Ultrafast Laser Science and Engineering Institute (PULSE); Stanford Univ., CA (United States)

Electronic structure theory, i.e., quantum chemistry, is the fundamental building block for many problems in computational chemistry. Here we present a new distributed computing framework (BigChem), which allows for an efficient solution of many quantum chemistry problems in parallel. BigChem is designed to be easily composable and leverages industry-standard middleware (e.g., Celery, RabbitMQ, and Redis) for distributed approaches to large scale problems. BigChem can harness any collection of worker nodes, including ones on cloud providers (such as AWS or Azure), local clusters, or supercomputer centers (and any mixture of these). BigChem builds upon MolSSI packages, such as QCEngine to standardize the operation of numerous computational chemistry programs, demonstrated here with Psi4, xtb, geomeTRIC, and TeraChem. BigChem delivers full utilization of compute resources at scale, offers a programable canvas for designing sophisticated quantum chemistry workflows, and is fault tolerant to node failures and network disruptions. We demonstrate linear scalability of BigChem running computational chemistry workloads on up to 125 GPUs. Finally, we present ChemCloud, a web API to BigChem and successor to TeraChem Cloud. ChemCloud delivers scalable and secure access to BigChem over the Internet.

Research Organization:
SLAC National Accelerator Laboratory (SLAC), Menlo Park, CA (United States)
Sponsoring Organization:
USDOE Office of Science (SC); US Department of the Navy, Office of Naval Research (ONR)
Grant/Contract Number:
AC02-76SF00515
OSTI ID:
2371584
Journal Information:
Journal of Chemical Physics, Journal Name: Journal of Chemical Physics Journal Issue: 14 Vol. 160; ISSN 0021-9606
Publisher:
American Institute of Physics (AIP)Copyright Statement
Country of Publication:
United States
Language:
English

References (92)

FireWorks: a dynamic workflow system designed for high-throughput applications: FireWorks: A Dynamic Workflow System Designed for High-Throughput Applications journal May 2015
cclib: A library for package-independent computational chemistry algorithms journal January 2008
The performance of low-cost commercial cloud computing as an alternative in computational chemistry journal March 2015
Cuby: An integrative framework for computational chemistry journal February 2016
pysisyphus: Exploring potential energy surfaces in ground and excited states journal August 2020
Turbomole
  • Furche, Filipp; Ahlrichs, Reinhart; Hättig, Christof
  • Wiley Interdisciplinary Reviews: Computational Molecular Science, Vol. 4, Issue 2 https://doi.org/10.1002/wcms.1162
journal July 2013
adcc: A versatile toolkit for rapid development of algebraic‐diagrammatic construction methods journal January 2020
The MolSSI QCA rchive project: An open‐source platform to compute, organize, and share quantum chemistry data journal July 2020
TeraChem : A graphical processing unit ‐accelerated electronic structure package for large‐scale ab initio molecular dynamics journal July 2020
WebMO : Web‐based computational chemistry calculations in education and research journal June 2021
Molpro: a general-purpose quantum chemistry program package: Molpro
  • Werner, Hans-Joachim; Knowles, Peter J.; Knizia, Gerald
  • Wiley Interdisciplinary Reviews: Computational Molecular Science, Vol. 2, Issue 2 https://doi.org/10.1002/wcms.82
journal July 2011
Car-Parrinello molecular dynamics: Car-Parrinello molecular dynamics journal September 2011
MOPAC: A semiempirical molecular orbital program journal March 1990
Parallel direct SCF for large-scale calculations journal January 1993
Network supercomputing: A distributed-concurrent direct SCF scheme journal January 1993
Exploring the quantum mechanical/molecular mechanical replica path method: a pathway optimization of the chorismate to prephenate Claisen rearrangement catalyzed by chorismate mutase
  • Lee Woodcock, H.; Hodošček, Milan; Sherwood, Paul
  • Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta), Vol. 109, Issue 3 https://doi.org/10.1007/s00214-002-0421-3
journal April 2003
Spectrum simulation and decomposition with nuclear ensemble: formal derivation and application to benzene, furan and 2-phenylfuran journal June 2012
Pseudospectral correlation methods on distributed memory parallel architectures journal August 1995
Excited state direct dynamics of benzene with reparameterized multi-reference semiempirical configuration interaction methods journal September 2004
Implementation of ab initio multiple spawning in the Molpro quantum chemistry package journal May 2008
AFLOW: An automatic framework for high-throughput materials discovery journal June 2012
AiiDA: automated interactive infrastructure and database for computational science journal January 2016
Simple data and workflow management with the signac framework journal April 2018
NWChem: A comprehensive and scalable open-source solution for large scale molecular simulations journal September 2010
The on-the-fly surface-hopping program system Newton-X: Application to ab initio simulation of the nonadiabatic photodynamics of benchmark systems journal August 2007
FPGA acceleration of a quantum Monte Carlo application journal May 2008
Parallelization of SCF calculations within Q-Chem journal June 2000
Multi-threading: A new dimension to massively parallel scientific computation journal June 2000
Ab Initio Direct Dynamics journal September 2021
Ab Initio Nonadiabatic Quantum Molecular Dynamics journal February 2018
TorchANI: A Free and Open Source PyTorch-Based Deep Learning Implementation of the ANI Neural Network Potentials journal June 2020
QMflows: A Tool Kit for Interoperable Parallel Workflows in Quantum Chemistry journal June 2019
TeraChem Cloud: A High-Performance Computing Service for Scalable Distributed GPU-Accelerated Electronic Structure Calculations journal April 2020
PySpawn: Software for Nonadiabatic Quantum Molecular Dynamics journal July 2020
Harnessing the Power of Multi-GPU Acceleration into the Quantum Interaction Computational Kernel Program journal June 2021
Faster Self-Consistent Field (SCF) Calculations on GPU Clusters journal November 2021
Efficient Treatment of Large Active Spaces through Multi-GPU Parallel Implementation of Direct Configuration Interaction journal January 2020
Novel Computer Architectures and Quantum Chemistry journal May 2020
The Blue Obelisk—Interoperability in Chemical Informatics journal May 2006
Chemical Markup, XML, and the Worldwide Web. 1. Basic Principles journal September 1999
OpenMM 4: A Reusable, Extensible, Hardware Independent Library for High Performance Molecular Simulation journal November 2012
Quantum Chemistry on Graphical Processing Units. 1. Strategies for Two-Electron Integral Evaluation journal January 2008
Accelerating Density Functional Calculations with Graphics Processing Unit journal July 2008
Quantum Chemistry on Graphical Processing Units. 2. Direct Self-Consistent-Field Implementation journal March 2009
Quantum Chemistry on Graphical Processing Units. 3. Analytical Energy Gradients, Geometry Optimization, and First Principles Molecular Dynamics journal August 2009
Accelerating Resolution-of-the-Identity Second-Order Møller−Plesset Quantum Chemistry Calculations with Graphical Processing Units journal March 2008
Interfacing the Ab Initio Multiple Spawning Method with Electronic Structure Methods in GAMESS: Photodecay of trans- Azomethane journal October 2014
Charge Transfer and Polarization in Solvated Proteins from Ab Initio Molecular Dynamics journal June 2011
Harnessing cloud computing with Galaxy Cloud journal November 2011
Nextflow enables reproducible computational workflows journal April 2017
Quantum chemistry structures and properties of 134 kilo molecules journal August 2014
Utilizing high performance computing for chemistry: parallel computational chemistry journal January 2010
Atomistic non-adiabatic dynamics of the LH2 complex with a GPU-accelerated ab initio exciton model journal January 2017
Improved tangent estimate in the nudged elastic band method for finding minimum energy paths and saddle points journal December 2000
A growing string method for determining transition states: Comparison to the nudged elastic band and string methods journal May 2004
Nested Markov chain Monte Carlo sampling of a density functional theory potential: Equilibrium thermodynamics of dense fluid nitrogen journal August 2009
Parallel algorithms for quantum chemistry. I. Integral transformations on a hypercube multiprocessor journal February 1987
A method for two‐electron Gaussian integral and integral derivative evaluation using recurrence relations journal November 1988
Geometry optimization made simple with translation and rotation coordinates journal June 2016
Coupled-cluster techniques for computational chemistry: The CFOUR program package journal June 2020
NWChem: Past, present, and future journal May 2020
P si4 1.4: Open-source software for high-throughput quantum chemistry journal May 2020
Software for the frontiers of quantum chemistry: An overview of developments in the Q-Chem 5 package journal August 2021
Quantum Chemistry Common Driver and Databases (QCDB) and Quantum Chemistry Engine (QCEngine): Automation and interoperability among computational chemistry programs journal November 2021
The atomic simulation environment—a Python library for working with atoms journal June 2017
Taverna: a tool for building and running workflows of services journal July 2006
String method for the study of rare events journal August 2002
Amdahl's Law in the Multicore Era journal July 2008
Cloud Technologies for Bioinformatics Applications journal June 2011
MapReduce: simplified data processing on large clusters journal January 2008
Cassandra: a decentralized structured storage system journal April 2010
Middleware journal February 1996
Borg, Omega, and Kubernetes: Lessons learned from three container-management systems over a decade journal January 2016
Apache Spark: a unified engine for big data processing journal October 2016
Reevaluating Amdahl's law journal May 1988
Interactive Quantum Chemistry Enabled by Machine Learning, Graphical Processing Units, and Cloud Computing journal April 2023
Vibronic and Environmental Effects in Simulations of Optical Spectroscopy journal January 2021
AB Initio Molecular Electronic Structure on Parallel Computers journal October 1994
Cloud Computing Enabled Big Multi-Omics Data Analytics journal January 2021
Cloud computing for comparative genomics journal May 2010
Cloud BioLinux: pre-configured and on-demand bioinformatics computing for the genomics community journal March 2012
The case for cloud computing in genome informatics journal January 2010
Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences journal January 2010
Biomedical Cloud Computing With Amazon Web Services journal August 2011
Cloud computing applications for biomedical science: A perspective journal June 2018
Singularity: Scientific containers for mobility of compute journal May 2017
Big Data Analysis: Apache Storm Perspective [English] journal January 2015
Dremel: interactive analysis of web-scale datasets journal September 2010
The OAuth 2.0 Authorization Framework report October 2012
From Laptop to Benchtop to Bedside: Structure-based Drug Design on Protein Targets journal March 2012
Cloud Computing for Comparative Genomics with Windows Azure Platform journal January 2012
The Digital Universe Rich Data and the Increasing Value of the Internet of Things journal October 2014