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Accurate and scalable graph neural network force field and molecular dynamics with direct force architecture
Abstract Recently, machine learning (ML) has been used to address the computational cost that has been limiting ab initio molecular dynamics (AIMD). Here, we present GNNFF, a graph neural network framework to directly predict atomic forces from automatically extracted features of the local atomic environment that are translationally-invariant, but rotationally-covariant to the coordinate of the atoms. We demonstrate that GNNFF not only achieves high performance in terms of force prediction accuracy and computational speed on various materials systems, but also accurately predicts the forces of a large MD system after being trained on forces obtained from a smaller system. Finally, we use our framework to perform an MD simulation of Li 7 P 3 S 11 , a superionic conductor, and show that resulting Li diffusion coefficient is within 14% of that obtained directly from AIMD. The high performance exhibited by GNNFF can be easily generalized to study atomistic level dynamics of other material systems.
Scalable Learning of Independent Cascade Dynamics from Partial Observations
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Scalable HPC and AI Infrastructure for COVID-19 Therapeutics
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The Effective Fragment Molecular Orbital Method: Achieving High Scalability and Accuracy for Large Systems
The effective fragment molecular orbital (EFMO) method has been developed to predict the total energy of a very large molecular system accurately (with respect to the underlying quantum mechanical method) and efficiently by taking advantage of the locality of strong chemical interactions and employing a two-level hierarchical parallelism. The accuracy of the EFMO method is partly attributed to the accurate and robust intermolecular interaction prediction between distant fragments, in particular, the many-body polarization and dispersion effects, which require the generation of static and dynamic polarizability tensors by solving the coupled perturbed Hartree–Fock (CPHF) and time-dependent HF (TDHF) equations, respectively. Solving the CPHF and TDHF equations is the main EFMO computational bottleneck due to the inefficient (serial) and I/O-intensive implementation of the CPHF and TDHF solvers. In this work, the efficiency and scalability of the EFMO method are significantly improved with a new CPU memory-based implementation for solving the CPHF and TDHF equations that are parallelized by either message passing interface (MPI) or hybrid MPI/OpenMP. Here, the accuracy of the EFMO method is demonstrated for both covalently bonded systems and noncovalently bound molecular clusters by systematically examining the effects of basis sets and a key distance-related cutoff parameter, R cut . R cut determines whether a fragment pair (dimer) is treated by the chosen ab initio method or calculated using the effective fragment potential (EFP) method (separated dimers). Decreasing the value of Rcut increases the number of separated (EFP) dimers, thereby decreasing the computational effort. It is demonstrated that excellent accuracy (<1 kcal/mol error per fragment) can be achieved when using a sufficiently large basis set with diffuse functions coupled with a small R cut value. With the new parallel implementation, the total EFMO wall time is substantially reduced, especially with a high number of MPI ranks. Given a sufficient workload, nearly ideal strong scaling is achieved for the CPHF and TDHF parts of the calculation. For the first time, EFMO calculations with the inclusion of long-range polarization and dispersion interactions on a hydrated mesoporous silica nanoparticle with explicit water solvent molecules (more than 15k atoms) are achieved on a massively parallel supercomputer using nearly 1000 physical nodes. In addition, EFMO calculations on the carbinolamine formation step of an amine-catalyzed aldol reaction at the nanoscale with explicit solvent effects are presented.
Nonlinear structural response using adaptive dynamic relaxation on a massively-parallel-processing system
A parallel adaptive dynamic relaxation (ADR) algorithm has been developed for nonlinear structural analysis. This algorithm has minimal memory requirements, is easily parallelizable and scalable to many processors, and is generally very reliable and efficient for highly nonlinear problems. Performance evaluations on single-processor computers have shown that the ADR algorithm is reliable and highly vectorizable, and that it is competitive with direct solution methods for the highly nonlinear problems considered. The present algorithm is implemented on the 512-processor Intel Touchstone DELTA system at Caltech, and it is designed to minimize the extent and frequency of interprocessor communication. The algorithm has been used to solve for the nonlinear static response of two and three dimensional hyperelastic systems involving contact. Impressive relative speedups have been achieved and demonstrate the high scalability of the ADR algorithm. For the class of problems addressed, the ADR algorithm represents a very promising approach for parallel-vector processing.
Scalable optimal Bayesian classification of single-cell trajectories under regulatory model uncertainty
Single-cell gene expression measurements offer opportunities in deriving mechanistic understanding of complex diseases, including cancer. However, due to the complex regulatory machinery of the cell, gene regulatory network (GRN) model inference based on such data still manifests significant uncertainty. The goal of this paper is to develop optimal classification of single-cell trajectories accounting for potential model uncertainty. Partially-observed Boolean dynamical systems (POBDS) are used for modeling gene regulatory networks observed through noisy gene-expression data. We derive the exact optimal Bayesian classifier (OBC) for binary classification of single-cell trajectories. The application of the OBC becomes impractical for large GRNs, due to computational and memory requirements. To address this, we introduce a particle-based single-cell classification method that is highly scalable for large GRNs with much lower complexity than the optimal solution. The performance of the proposed particle-based method is demonstrated through numerical experiments using a POBDS model of the well-known T-cell large granular lymphocyte (T-LGL) leukemia network with noisy time-series gene-expression data.
Experimental evaluation of a flexible I/O architecture for accelerating workflow engines in ultrascale environments
The increasing volume of scientific data and the limited scalability and performance of storage systems are currently presenting a significant limitation for the productivity of the scientific workflows running on both high-performance computing (HPC) and cloud platforms. Clearly needed is better integration of storage systems and workflow engines to address this problem. This paper presents and evaluates a novel solution that leverages codesign principles for integrating Hercules—an in-memory data store—with a workflow management system. We consider four main aspects: workflow representation, task scheduling, task placement, and task termination. As a result, the experimental evaluation on both cloud and HPC systems demonstrates significant performance and scalability improvements over existing state-of-the-art approaches.
20 petaflops simulation of proteins suspensions in crowding conditions, In: SC '13 Proceedings of the International Conference on High Performance Computing, Networking, Storage and Analysis
We present performance results for the simulation of proteins suspensions in crowding conditions obtained with MUPHY, a computational platform for multi-scale simulations of real-life biofluidic problems. Previous versions of MUPHY have been used in the past for the simulation of blood flow through the human coronary arteries and DNA translocation across nanopores. The simulation exhibits excellent scalability up to 18, 000 K20X Nvidia GPUs and achieves almost 20 Petaflops of aggregate sustained performance with a peak performance of 27.5 Petaflops for the most intensive computing component. Those figures demonstrate once again the flexibility of MUPHY in simulating biofluidic phenomena, exploiting at their best the features of the architecture in use. Preliminary results were obtained in the present case on a completely different platform, the IBM Blue Gene/Q. The combination of novel mathematical models, computational algorithms, hardware technology, code tuning and parallelization techniques required to achieve these results are presented.
Fault Survivability of Lightweight Operating Systems for exascale
Concern is growing in the High-Performance Computing community regarding the reliability of proposed exascale systems. Current research has shown that the expected reliability of these machines will greatly reduce their scalability. In constrast to current fault tolerance methods whose reliability focus is only the application, this project investigates the benefits integrating reliability mechcanisms in the operating system and runtime, as well as the appli- cation. More specifically, this project has three broad contributions in the field: First, using failure logs from current leadership-class high-performance computing systems, we outline the failures common on these large-scale systems. Second, we describe a novel memory pro- tection mechcanism capable of protecting common observed failures that uses the similarity inherrant in many OS and applications state, thereby reducing overheads. Finally, using an analogy with OS jitter, we develop a highly effecient simulator capable predicting the performance of resilience methods at the scales expected for future extreme-scale systems.
Alternating Anderson–Richardson method: An efficient alternative to preconditioned Krylov methods for large, sparse linear systems
Here, we present the Alternating Anderson–Richardson (AAR) method: an efficient and scalable alternative to preconditioned Krylov solvers for the solution of large, sparse linear systems on high performance computing platforms. Specifically, we generalize the recently proposed Alternating Anderson–Jacobi (AAJ) method (Pratapa et al., 2016) to include preconditioning, discuss efficient parallel implementation, and provide serial MATLAB and parallel C/C++ implementations. In serial applications to nonsymmetric systems, we find that AAR is comparably robust to GMRES, using the same preconditioning, while often outperforming it in time to solution; and find AAR to be more robust than Bi-CGSTAB for the problems considered. In parallel applications to the Helmholtz and Poisson equations, we find that AAR shows superior strong and weak scaling to GMRES, Bi-CGSTAB, and Conjugate Gradient (CG) methods, using the same preconditioning, with consistently shorter times to solution at larger processor counts. Finally, in massively parallel applications to the Poisson equation, on up to 110,592 processors, we find that AAR shows superior strong and weak scaling to CG, with shorter minimum time to solution. We thus find that AAR offers a robust and efficient alternative to current state-of-the-art solvers, with increasing advantages as the number of processors grows.
Hardware-accelerated inference for real-time gravitational-wave astronomy
The field of transient astronomy has seen a revolution with the first gravitational-wave detections and the arrival of multi-messenger observations they enabled. Transformed by the first detection of binary black hole and binary neutron star mergers, computational demands in gravitational-wave astronomy are expected to grow by at least a factor of two over the next five years as the global network of kilometer-scale interferometers are brought to design sensitivity. With the increase in detector sensitivity, real-time delivery of gravitational-wave alerts will become increasingly important as an enabler of multi-messenger followup. In this work, we report a novel implementation and deployment of deep learning inference for real-time gravitational-wave data denoising and astrophysical source identification. This is accomplished using a generic Inference-as-a-Service model that is capable of adapting to the future needs of gravitational-wave data analysis. Overall, our implementation allows seamless incorporation of hardware accelerators and also enables the use of commercial or private (dedicated) as-a-service computing. Based on our results, we propose a paradigm shift in low-latency and offline computing in gravitational-wave astronomy. Such a shift can address key challenges in peak-usage, scalability and reliability, and provide a data analysis platform particularly optimized for deep learning applications. The achieved sub-millisecond scale latency will also be relevant for any machine learning-based real-time control systems that may be invoked in the operation of near-future and next generation ground-based laser interferometers, as well as the front-end collection, distribution and processing of data from such instruments.
Application of the Denovo Discrete Ordinates Radiation Transport Code to Large-Scale Fusion Neutronics
Fusion energy systems pose unique challenges to the modeling and simulation community. These challenges must be met to ensure the success of the ITER experimental fusion reactor. ITER’s complex systems require detailed modeling that goes beyond the scale of comparable simulations to date. In this work, the Denovo radiation transport code was used to calculate neutron fluence and kerma for the JET streaming benchmark. This work was performed on the Titan supercomputer at the Oak Ridge Leadership Computing Facility. Denovo is a novel three-dimensional discrete ordinates transport code designed to be highly scalable. Sensitivity studies have been completed to examine the impact of several deterministic parameters. Furthermore, results were compared against experiment as well as the MCNP and Shift Monte Carlo codes.
Model-based, in-situ, non-destructive qualification and certification of parts made by autonomous additive manufacturing
To address the significant productivity challenges associated with the qualification and certification (Q&C) tasks of additively manufactured (AM) parts, which have traditionally relied on rigorous post‐build inspection and testing, we propose an integrated framework that combines model‐based qualification and certification (MBQ&C) with autonomous additive manufacturing (AAM). MBQ&C employs high‐fidelity predictive models, developed within the Integrated Computational Materials Engineering (ICME) paradigm, to simulate process–structure–property–performance relationships for assessing a part’s fitness for use. Since predictive models are commonly machine learning (ML)-based or reduced-order surrogates of validated physics models, they run efficiently, enabling timely inference. In parallel, the self-driving AAM utilises ML-based adaptive, closed‐loop control strategies to avoid, mitigate, or repair defects and anomalies during fabrication, thereby increasing the likelihood of producing acceptable parts. A key feature of the combined AAM-MBQ&C framework is that predictive models explicitly incorporate defects or anomalies that persist after the build, using instance-specific data captured via in-situ sensing. This customisation enables a build‐specific assessment of fitness for use, rather than relying on nominal or generic parameters. Such individualised evaluation provides a robust basis for Q&C-related acceptance decisions relating to each build. Additionally, the rapid solution capabilities of ML or reduced-order models enable the determination of a part’s suitability for service shortly after build completion. As the framework matures, it has the potential to substantially reduce reliance on conventional point‐design approaches—such as time‐consuming post‐build computed tomography scanning and costly destructive testing. Thus, the AAM-MBQ&C framework represents a transformative, scalable strategy for quality assurance of AM components, as parts produced within a stable, validated, and certified envelope can be certified with reduced testing. Key benefits include: (1) significant gains in Q&C productivity through efficient, model-centric assessment; (2) performance-based classification of defects into critical and non-critical categories; (3) the ability to predict potential deviations in the performance of parts affected by real-time, adaptive process control interventions relative to those produced under a certified process, and (4) the enabling of virtual Q&C for service environments that are difficult, hazardous, or impractical to access or reproduce experimentally. Collectively, these capabilities strengthen the business case for AM, particularly for high‐consequence and mission‐critical applications. Finally, although this work focuses on powder-based AM, the proposed techniques could be extended to AM processes employing alternative feedstock forms.
Newton versus the machine: solving the chaotic three-body problem using deep neural networks
ABSTRACT Since its formulation by Sir Isaac Newton, the problem of solving the equations of motion for three bodies under their own gravitational force has remained practically unsolved. Currently, the solution for a given initialization can only be found by performing laborious iterative calculations that have unpredictable and potentially infinite computational cost, due to the system’s chaotic nature. We show that an ensemble of converged solutions for the planar chaotic three-body problem obtained using an arbitrarily precise numerical integrator can be used to train a deep artificial neural network (ANN) that, over a bounded time interval, provides accurate solutions at a fixed computational cost and up to 100 million times faster than the numerical integrator. In addition, we demonstrate the importance of training an ANN using converged solutions from an arbitrary precise integrator, relative to solutions computed by a conventional fixed precision integrator, which can introduce errors in the training data, due to numerical round-off and time discretization, that are learned by the ANN. Our results provide evidence that, for computationally challenging regions of phase space, a trained ANN can replace existing numerical solvers, enabling fast and scalable simulations of many-body systems to shed light on outstanding phenomena such as the formation of black hole binary systems or the origin of the core collapse in dense star clusters.
Scaling Ensembles of Data-Intensive Quantum Chemical Calculations for Millions of Molecules
Deep learning models are efficient computational tools that can accelerate the inverse design of molecules with desired functional properties by generating predictions at a fraction of the time required by traditional quantum chemical approaches. To ensure that a model maintains accuracy and transferability across broad regions of the chemical space explored during the inverse design, it must be trained on massively large volumes of simulation data. This requires running large-scale ensemble quantum chemical calculations on high-performance computing (HPC) systems for data collection. However, the efficient execution of such large ensemble calculations and the management of large volumes of output data require tools that can judiciously utilize computational resources and manage metadata overhead on the file system. Therefore, we present a high-performance, scalable, ensemble management framework for performing data-intensive quantum chemical electronic structure calculations for organic molecules. This framework provides abstractions to plug different ab initio, first principles, and first principles-based semi-empirical methods and executes them efficiently at large scale on HPC systems. It dynamically distributes tasks to resources and uses tiered storage for managing large collections of files. We employed this framework to process over ten million organic molecules and generate open-source datasets that provide UV-vis absorption spectra by running time-dependent density-functional tight-binding calculations. It is the largest database containing molecular optical spectra that were simulated with quantum chemical methods in a consistent manner.
A Nonrelational Data Warehouse for the Analysis of Field and Laboratory Data From Multiple Heterogeneous Photovoltaic Test Sites
A nonrelational, distributed computing, data warehouse, and analytics environment (Energy-CRADLE) was developed for the analysis of field and laboratory data from multiple heterogeneous photovoltaic (PV) test sites. This data informatics and analytics infrastructure was designed to process diverse formats of PV performance data and climatic telemetry time-series data collected from a PV outdoor test network, i.e., the Solar Durability and Lifetime Extension global SunFarm network, as well as point-in-time laboratory spectral and image measurements of PV material samples. Using Hadoop/HBase for the distributed data warehouse, Energy-CRADLE does not have a predefined data table schema, which enables ingestion of data in diverse and changing formats. For easy data ingestion and data retrieval, Energy-CRADLE utilizes Hadoop streaming to enable Python MapReduce and provides a graphical user interface, i.e., py-CRADLE. By developing the Hadoop distributed computing platform and the HBase NoSQL database schema for solar energy, Energy-CRADLE exemplifies an integrated, scalable, secure, and user-friendly data informatics and analytics system for PV researchers. Furthermore, an example of Energy-CRADLE enabled scalable, data-driven, analytics is presented, where machine learning is used for anomaly detection across 2.2 million real-world current-voltage (I–V) curves of PV modules in three distinct Koppen–Geiger climatic zones.
GenomeFace v1.0
GenomeFace is meta-genome binning software. Metagenomic binning, the process of grouping DNA sequences into taxonomic units, is critical for understanding the functions, interactions, and evolutionary dynamics of microbial communities. We propose a deep learning approach to binning using two neural networks, one based on composition and another on environmental abundance, dynamically weighting the contribution of each based on characteristics of the input data. Trained on over 43,000 prokaryotic genomes, our network for composition-based binning is inspired by metric learning techniques used for facial recognition. Using a task-specific, multi-GPU accelerated algorithm to cluster the embeddings produced by our network, our binner leverages marker genes observed to be universally present in nearly all taxa to grade and select optimal clusters of sequences from a hierarchy of candidates. We evaluate our approach on four simulated datasets with known ground truth. Our linear time integration of marker genes recovers more near complete genomes than state of the art but computationally infeasible solutions using them, while being over an order of magnitude faster. Finally, we demonstrate the scalability and acuity of our approach by testing it on three of the largest metagenome assemblies ever performed. Compared to other binners, we produced 47%-183% more near complete genomes. From these datasets, we find over the genomes of over 3000 new candidate species which have never been previously cataloged, representing a potential 4% expansion of the known bacterial tree of life.