Publications

Fiedler, Lenz F.; Modine, N.A.; Schmerler, Steve S.; Vogel, Dayton J.; Popoola, Gabriel P.; Thompson, Aidan P.; Rajamanickam, Sivasankaran R.; Cangi, Attila C.

The long-standing problem of predicting the electronic structure of matter on ultra-large scales (beyond 100,000 atoms) is solved with machine learning.

Kelley, Brian M.; Rajamanickam, Sivasankaran R.

Artificial intelligence and machine learning (AI/ML) are becoming important tools for scientific modeling and simulation as in several other fields such as image analysis and natural language processing. ML techniques can leverage the computing power available in modern systems and reduce the human effort needed to configure experiments, interpret and visualize results, draw conclusions from huge quantities of raw data, and build surrogates for physics based models. Domain scientists in fields like fluid dynamics, microelectronics and chemistry can automate many of their most difficult and repetitive tasks or improve the design times by use of the faster ML-surrogates. However, modern ML and traditional scientific highperformance computing (HPC) tend to use completely different software ecosystems. While ML frameworks like PyTorch and TensorFlow provide Python APIs, most HPC applications and libraries are written in C++. Direct interoperability between the two languages is possible but is tedious and error-prone. In this work, we show that a compiler-based approach can bridge the gap between ML frameworks and scientific software with less developer effort and better efficiency. We use the MLIR (multi-level intermediate representation) ecosystem to compile a pre-trained convolutional neural network (CNN) in PyTorch to freestanding C++ source code in the Kokkos programming model. Kokkos is a programming model widely used in HPC to write portable, shared-memory parallel code that can natively target a variety of CPU and GPU architectures. Our compiler-generated source code can be directly integrated into any Kokkosbased application with no dependencies on Python or cross-language interfaces.

Modine, N.A.; Stephens, John A.; Swiler, Laura P.; Thompson, Aidan P.; Vogel, Dayton J.; Cangi, Attila C.; Feilder, Lenz F.; Rajamanickam, Sivasankaran R.

The focus of this project is to accelerate and transform the workflow of multiscale materials modeling by developing an integrated toolchain seamlessly combining DFT, SNAP, LAMMPS, (shown in Figure 1-1) and a machine-learning (ML) model that will more efficiently extract information from a smaller set of first-principles calculations. Our ML model enables us to accelerate first-principles data generation by interpolating existing high fidelity data, and extend the simulation scale by extrapolating high fidelity data (10² atoms) to the mesoscale (10⁴ atoms). It encodes the underlying physics of atomic interactions on the microscopic scale by adapting a variety of ML techniques such as deep neural networks (DNNs), and graph neural networks (GNNs). We developed a new surrogate model for density functional theory using deep neural networks. The developed ML surrogate is demonstrated in a workflow to generate accurate band energies, total energies, and density of the 298K and 933K Aluminum systems. Furthermore, the models can be used to predict the quantities of interest for systems with more number of atoms than the training data set. We have demonstrated that the ML model can be used to compute the quantities of interest for systems with 100,000 Al atoms. When compared with 2000 Al system the new surrogate model is as accurate as DFT, but three orders of magnitude faster. We also explored optimal experimental design techniques to choose the training data and novel Graph Neural Networks to train on smaller data sets. These are promising methods that need to be explored in the future.

IEEE Transactions on Parallel and Distributed Systems

Trott, Christian R.; Lebrun-Grandie, Damien; Arndt, Daniel; Ciesko, Jan; Dang, Vinh Q.; Ellingwood, Nathan D.; Gayatri, Rahulkumar; Harvey, Evan C.; Hollman, Daisy S.; Ibanez, Dan; Liber, Nevin; Madsen, Jonathan; Miles, Jeff; Poliakoff, David Z.; Powell, Amy J.; Rajamanickam, Sivasankaran R.; Simberg, Mikael; Sunderland, Dan; Turcksin, Bruno; Wilke, Jeremiah

As the push towards exascale hardware has increased the diversity of system architectures, performance portability has become a critical aspect for scientific software. We describe the Kokkos Performance Portable Programming Model that allows developers to write single source applications for diverse high-performance computing architectures. Kokkos provides key abstractions for both the compute and memory hierarchy of modern hardware. We describe the novel abstractions that have been added to Kokkos version 3 such as hierarchical parallelism, containers, task graphs, and arbitrary-sized atomic operations to prepare for exascale era architectures. We demonstrate the performance of these new features with reproducible benchmarks on CPUs and GPUs.

IEEE Transactions on Parallel and Distributed Systems

Moon, Gordon E.; Kwon, Hyoukjun; Jeong, Geonhwa; Chatarasi, Prasanth; Rajamanickam, Sivasankaran R.; Krishna, Tushar

There is a growing interest in custom spatial accelerators for machine learning applications. These accelerators employ a spatial array of processing elements (PEs) interacting via custom buffer hierarchies and networks-on-chip. The efficiency of these accelerators comes from employing optimized dataflow (i.e., spatial/temporal partitioning of data across the PEs and fine-grained scheduling) strategies to optimize data reuse. The focus of this work is to evaluate these accelerator architectures using a tiled general matrix-matrix multiplication (GEMM) kernel. To do so, we develop a framework that finds optimized mappings (dataflow and tile sizes) for a tiled GEMM for a given spatial accelerator and workload combination, leveraging an analytical cost model for runtime and energy. Our evaluations over five spatial accelerators demonstrate that the tiled GEMM mappings systematically generated by our framework achieve high performance on various GEMM workloads and accelerators.

Fiedler, Lenz F.; Hoffmann, Nils H.; Mohammed, Parvez M.; Popoola, Gabriel A.; Yovell, Tamar Y.; Oles, Vladyslav O.; Ellis, Austin E.; Rajamanickam, Sivasankaran R.; Cangi, Attila -.

A myriad of phenomena in materials science and chemistry rely on quantum-level simulations of the electronic structure in matter. While moving to larger length and time scales has been a pressing issue for decades, such large-scale electronic structure calculations are still challenging despite modern software approaches and advances in high-performance computing. The silver lining in this regard is the use of machine learning to accelerate electronic structure calculations – this line of research has recently gained growing attention. The grand challenge therein is finding a suitable machine-learning model during a process called hyperparameter optimization. This, however, causes a massive computational overhead in addition to that of data generation. We accelerate the construction of machine-learning surrogate models by roughly two orders of magnitude by circumventing excessive training during the hyperparameter optimization phase. We demonstrate our workflow for Kohn-Sham density functional theory, the most popular computational method in materials science and chemistry.

IEEE Transactions on Parallel and Distributed Systems

Yasar, Abdurrahman; Rajamanickam, Sivasankaran R.; Berry, Jonathan W.; Catalyurek, Umit V.

Triangle counting is a fundamental building block in graph algorithms. In this article, we propose a block-based triangle counting algorithm to reduce data movement during both sequential and parallel execution. Our block-based formulation makes the algorithm naturally suitable for heterogeneous architectures. The problem of partitioning the adjacency matrix of a graph is well-studied. Our task decomposition goes one step further: it partitions the set of triangles in the graph. By streaming these small tasks to compute resources, we can solve problems that do not fit on a device. We demonstrate the effectiveness of our approach by providing an implementation on a compute node with multiple sockets, cores and GPUs. The current state-of-the-art in triangle enumeration processes the Friendster graph in 2.1 seconds, not including data copy time between CPU and GPU. Using that metric, our approach is 20 percent faster. When copy times are included, our algorithm takes 3.2 seconds. This is 5.6 times faster than the fastest published CPU-only time.

SIAM Journal on Scientific Computing

Heinlein, Alexander; Perego, Mauro P.; Rajamanickam, Sivasankaran R.

Numerical simulations of Greenland and Antarctic ice sheets involve the solution of large-scale highly nonlinear systems of equations on complex shallow geometries. This work is concerned with the construction of Schwarz preconditioners for the solution of the associated tangent problems, which are challenging for solvers mainly because of the strong anisotropy of the meshes and wildly changing boundary conditions that can lead to poorly constrained problems on large portions of the domain. Here, two-level generalized Dryja-Smith-Widlund (GDSW)-type Schwarz preconditioners are applied to different land ice problems, i.e., a velocity problem, a temperature problem, as well as the coupling of the former two problems. We employ the message passing interface (MPI)- parallel implementation of multilevel Schwarz preconditioners provided by the package FROSch (fast and robust Schwarz) from the Trilinos library. The strength of the proposed preconditioner is that it yields out-of-the-box scalable and robust preconditioners for the single physics problems. To the best of our knowledge, this is the first time two-level Schwarz preconditioners have been applied to the ice sheet problem and a scalable preconditioner has been used for the coupled problem. The preconditioner for the coupled problem differs from previous monolithic GDSW preconditioners in the sense that decoupled extension operators are used to compute the values in the interior of the subdomains. Several approaches for improving the performance, such as reuse strategies and shared memory OpenMP parallelization, are explored as well. In our numerical study we target both uniform meshes of varying resolution for the Antarctic ice sheet as well as nonuniform meshes for the Greenland ice sheet. We present several weak and strong scaling studies confirming the robustness of the approach and the parallel scalability of the FROSch implementation. Among the highlights of the numerical results are a weak scaling study for up to 32 K processor cores (8 K MPI ranks and 4 OpenMP threads) and 566 M degrees of freedom for the velocity problem as well as a strong scaling study for up to 4 K processor cores (and MPI ranks) and 68 M degrees of freedom for the coupled problem.

Rajamanickam, Sivasankaran R.

Abstract not provided.

Rajamanickam, Sivasankaran R.; Berger-Vergiat, Luc B.; Boman, Erik G.; Yamazaki, Ichitaro Y.

Abstract not provided.

Rajamanickam, Sivasankaran R.; Rajamanickam, Sivasankaran R.

Abstract not provided.

Loe, Jennifer A.; Rajamanickam, Sivasankaran R.

Abstract not provided.

Rajamanickam, Sivasankaran R.; Heinlein, Alexander H.; Thornquist, Heidi K.; Yamazaki, Ichitaro Y.

Abstract not provided.

Heinlein, Alexander H.; Perego, Mauro P.; Rajamanickam, Sivasankaran R.; Yamazaki, Ichitaro Y.

Abstract not provided.

Hughes, Clayton H.; Ashraf, Rizwan A.; Gioiosa, Roberto G.; Phillips, Cynthia A.; Berry, Jonathan W.; Hart, William E.; Laird, Carl L.; Rajamanickam, Sivasankaran R.

Abstract not provided.

Rajamanickam, Sivasankaran R.

Abstract not provided.

Kelley, Brian M.; Rajamanickam, Sivasankaran R.

Abstract not provided.

Rajamanickam, Sivasankaran R.

Abstract not provided.

Littlewood, David J.; Wood, Mitchell A.; Montes de Oca Zapiain, David M.; Rajamanickam, Sivasankaran R.; Trask, Nathaniel A.

This report includes a compilation of several slide presentations: 1) Interatomic Potentials for Materials Science and Beyond–Advances in Machine Learned Spectral Neighborhood Analysis Potentials (Wood); 2) Agile Materials Science and Advanced Manufacturing through AI/ML (de Oca Zapiain); 3) Machine Learning for DFT Calculations (Rajamanickam); 4) Structure-preserving ML discovery of a quantum-to-continuum codesign stack (Trask); and 5) IBM Overview of Accelerated Discovery Technology (Pitera)

Garg, Raveesh G.; Qin, Eric Q.; Martinez, Francisco M.; Guirado, Robert G.; Jain, Akshay J.; Abadal, Sergi A.; Abellan, Jose L.; Acacio, Manuel E.; Alarcon, Eduard A.; Rajamanickam, Sivasankaran R.; Krishna, Tushar K.

Graph Neural Networks (GNNs) have garnered a lot of recent interest because of their success in learning representations from graph-structured data across several critical applications in cloud and HPC. Owing to their unique compute and memory characteristics that come from an interplay between dense and sparse phases of computations, the emergence of reconfigurable dataflow (aka spatial) accelerators offers promise for acceleration by mapping optimized dataflows (i.e., computation order and parallelism) for both phases. The goal of this work is to characterize and understand the design-space of dataflow choices for running GNNs on spatial accelerators in order for the compilers to optimize the dataflow based on the workload. Specifically, we propose a taxonomy to describe all possible choices for mapping the dense and sparse phases of GNNs spatially and temporally over a spatial accelerator, capturing both the intra-phase dataflow and the inter-phase (pipelined) dataflow. Using this taxonomy, we do deep-dives into the cost and benefits of several dataflows and perform case studies on implications of hardware parameters for dataflows and value of flexibility to support pipelined execution.

Parallel Computing

Acer, Seher A.; Boman, Erik G.; Glusa, Christian A.; Rajamanickam, Sivasankaran R.

Graph partitioning has been an important tool to partition the work among several processors to minimize the communication cost and balance the workload. While accelerator-based supercomputers are emerging to be the standard, the use of graph partitioning becomes even more important as applications are rapidly moving to these architectures. However, there is no distributed-memory-parallel, multi-GPU graph partitioner available for applications. We developed a spectral graph partitioner, Sphynx, using the portable, accelerator-friendly stack of the Trilinos framework. In Sphynx, we allow using different preconditioners and exploit their unique advantages. We use Sphynx to systematically evaluate the various algorithmic choices in spectral partitioning with a focus on the GPU performance. We perform those evaluations on two distinct classes of graphs: regular (such as meshes, matrices from finite element methods) and irregular (such as social networks and web graphs), and show that different settings and preconditioners are needed for these graph classes. The experimental results on the Summit supercomputer show that Sphynx is the fastest alternative on irregular graphs in an application-friendly setting and obtains a partitioning quality close to ParMETIS on regular graphs. When compared to nvGRAPH on a single GPU, Sphynx is faster and obtains better balance and better quality partitions. Sphynx provides a good and robust partitioning method across a wide range of graphs for applications looking for a GPU-based partitioner.

Jeong, Geonhwa J.; Kestor, Gokcen K.; Chatarsi, Prasanth C.; Parashar, Angshuman P.; Tsai, Po-An T.; Rajamanickam, Sivasankaran R.; Gioiosa, Roberto G.; Krishna, Tushar K.

Abstract not provided.

Abdelfattah, Ahmad A.; Anzt, Hartwig A.; Ayala, Alan A.; Boman, Erik G.; Carson, Erin C.; Cayrols, Sebastien C.; Cojean, Terry C.; Dongarra, Jack D.; Falgout, Rob F.; Gates, Mark G.; Gr\"{u}tzmacher, Thomas G.; Higham, Nicholas J.; Kruger, Scott E.; Li, Sherry L.; Lindquist, Neil L.; Liu, Yang L.; Loe, Jennifer A.; Nayak, Pratik N.; Osei-Kuffuor, Daniel O.; Pranesh, Sri P.; Rajamanickam, Sivasankaran R.; Ribizel, Tobias R.; Smith, Bryce B.; Swirydowicz, Kasia S.; Thomas, Stephen T.; Tomov, Stanimire T.; M. Tsai, Yaohung M.; Yamazaki, Ichitaro Y.; Yang, Urike M.

Over the last year, the ECP xSDK-multiprecision effort has made tremendous progress in developing and deploying new mixed precision technology and customizing the algorithms for the hardware deployed in the ECP flagship supercomputers. The effort also has succeeded in creating a cross-laboratory community of scientists interested in mixed precision technology and now working together in deploying this technology for ECP applications. In this report, we highlight some of the most promising and impactful achievements of the last year. Among the highlights we present are: Mixed precision IR using a dense LU factorization and achieving a 1.8× speedup on Spock; results and strategies for mixed precision IR using a sparse LU factorization; a mixed precision eigenvalue solver; Mixed Precision GMRES-IR being deployed in Trilinos, and achieving a speedup of 1.4× over standard GMRES; compressed Basis (CB) GMRES being deployed in Ginkgo and achieving an average 1.4× speedup over standard GMRES; preparing hypre for mixed precision execution; mixed precision sparse approximate inverse preconditioners achieving an average speedup of 1.2×; and detailed description of the memory accessor separating the arithmetic precision from the memory precision, and enabling memory-bound low precision BLAS 1/2 operations to increase the accuracy by using high precision in the computations without degrading the performance. We emphasize that many of the highlights presented here have also been submitted to peer-reviewed journals or established conferences, and are under peer-review or have already been published.

Acer, Seher A.; Boman, Erik G.; Glusa, Christian A.; Rajamanickam, Sivasankaran R.

Abstract not provided.

Physical Review B

Ellis, J.A.; Fiedler, L.; Popoola, G.A.; Modine, N.A.; Stephens, John A.; Thompson, Aidan P.; Cangi, A.; Rajamanickam, Sivasankaran R.

We present a numerical modeling workflow based on machine learning which reproduces the total energies produced by Kohn-Sham density functional theory (DFT) at finite electronic temperature to within chemical accuracy at negligible computational cost. Based on deep neural networks, our workflow yields the local density of states (LDOS) for a given atomic configuration. From the LDOS, spatially resolved, energy-resolved, and integrated quantities can be calculated, including the DFT total free energy, which serves as the Born-Oppenheimer potential energy surface for the atoms. We demonstrate the efficacy of this approach for both solid and liquid metals and compare results between independent and unified machine-learning models for solid and liquid aluminum. Our machine-learning density functional theory framework opens up the path towards multiscale materials modeling for matter under ambient and extreme conditions at a computational scale and cost that is unattainable with current algorithms.