NWChemEx: Computational Chemistry Code for the Exascale Era

By Linda Barney

April 29, 2021

A team working on biofuel research is rewriting the decades-old NWChem software program for the exascale era. The new software, NWChemEx, will enable computational chemistry software to effectively run on exascale supercomputers. The team, part of Argonne National Laboratory’s Early Science Program (ESP), estimates that the future Argonne Aurora supercomputer, along with the new NWChemEx algorithms, will provide up to a 1,000x increase in the size of the chemical systems that can be studied.

Distinguished Professor Theresa Windus, Ames Laboratory and Iowa State University, is the principal investigator on the project. Windus states, “One of the goals of our research is to find more accurate information about chemical systems to aid in developing new methods for converting biomass into biofuels. When the Aurora supercomputer comes online at Argonne, it will be one of the largest supercomputers available. Running computer simulations of our biofuel research on Aurora using the NWChemEx software will allow the team to investigate larger molecular systems and perform deeper exploration of the energy landscape for molecules and materials. That additional knowledge provides a better understanding of the fundamental chemical reactions and their properties.”

In addition to Windus, the research team involves a broad spectrum of expertise located at Ames Laboratory, Argonne National Laboratory, Brookhaven National Laboratory, Lawrence Berkeley National Laboratory, Oak Ridge National Laboratory, Pacific Northwest National Laboratory, and Virginia Tech, and frequent collaborations with Intel, AMD, HPE and Nvidia.

Updating NWChem code for Exascale computing

NWChem is a widely used open source computational chemistry package that includes both quantum chemical and molecular dynamics functionality. However, the NWChem code was designed for computer architectures that no longer exist. NWChemEx is a complete rewrite of the software – it’s modularized and flexible from its initial design and uses the power of C++ – enabling the team to move away from the megalithic design pattern that’s plagued quantum chemistry since the 70s. A primary focus of NWChemEx is designing the code so it runs on graphic processing units (GPUs) and uses dynamic methods to shift computational work to optimize performance.

“This change lets us develop methods to optimize the code over time and not force the code to run on a specific implementation. In terms of optimization, we are enabling different levels of parallelization within and across tensor contraction expressions. This allows us to tune the parallelization strategy to the specific execution,” states Sriram Krishnamoorthy, a laboratory fellow and computer scientist at Pacific Northwest National Laboratory. The change will also enable NWChemEx to run on the Intel Ponte Vecchio GPU units that will be incorporated in Aurora.

The key points are modernization of the Density Function Theory (DFT) code that is widely used in quantum chemistry, and the Coupled Cluster (CC) theory that is used to access the high accuracy required for predictive chemistry. The team is focused on implementing reduced scaling chemistry algorithms that challenge implementation on high performance, heterogeneous hardware due to nonuniform sparsity in these methods.

David William-Young, a research scientist at Lawrence Berkeley National Laboratory, states, “To aid in the implementation, the team uses modularization of the algorithmic components (grid/batch generation, load balancing, local work drivers, reduction, etc.), so they can be swapped and sandboxed individually to rapidly test new ideas and architecture-specific implementations without interfering with other components. The module approach opens the door for reuse of software written for one purpose in other parts of NWChemEx.”

Resolving computational issues in NWChemEx

“New exascale hardware requires a new software environment. The team is modifying the code to keep up with all the changes in hardware architecture by adapting to a new and unifying programming model – oneAPI. The knowledge gained from the NWChemEx project can be used and shared when Aurora is operational,” states Abhishek Bagusetty, Aurora Early Science Program Postdoctoral Appointee, Argonne Leadership Computing Facility (ALCF).

ALCF is a U.S. Department of Energy (DOE) Office of Science User Facility located at Argonne National Laboratory. The ALCF team works with researchers to help enable breakthroughs in science and engineering by providing supercomputing resources and expertise to the research community.

“The team is working to resolve issues such as load-balancing occurring on the Oak Ridge National Laboratory Summit supercomputer in preparation for Aurora. Methods used to resolve communication and load balancing will apply outside of the NWChemEx code,” indicates Ajay Panyala, computer scientist at Pacific Northwest National Laboratory.

Using NWChemEx to find catalytic materials for conversion of biomass into biofuels

The development of advanced biofuels is driven by both energy security and climate change considerations. The Department of Energy (DOE) has an advanced biofuels program to develop fuels that can use the existing infrastructure and replace existing fuels with biofuels on a gallon-for-gallon basis. Windus states, “Producing high-quality biofuels in a sustainable and economically competitive way is technically challenging, especially in a changing global climate. The NWChemEx project directly addresses one of DOE’s priority goals to develop high-performance computational models demonstrating that biomass can be a viable, sustainable feedstock for the production of biofuels and other bioproducts. Of particular interest in this project is the prediction of specific, selective and low-temperature catalytic conversion of biomass to fuels and other products.”

Zeolites, such as H-ZSM-5, offer great promise for the catalytic conversion of renewable biomass-derived alcohols into fuels and chemicals. Compared to metal oxides with diverse surface and acid properties, acidic zeolites are solid structures that have relatively well-defined and uniform acid site structures. This makes it easy to perform rigorous kinetic and theoretical investigations of the effect of acid strength and solvation environment and confinement on the chemical reaction energies. Although there have been a number of prior atomic-scale computational studies of these systems, unraveling the true complexity of the conversion process and identifying means of achieving conversions at lower temperatures and pressures is an unsolved problem.

To illustrate the capability of NWChemEx for chemical reactions, the project will examine a number of elementary chemical transformations that have been postulated for the conversion of propanol to propene in the H-ZSM-5 zeolite (basic unit cell: Si96O192). The team will run calculations using computer simulations to predict the binding energy of water and propanol and their reactions in the zeolite cavity to help identify appropriate biofuels.

“By running the millions of simulations on Aurora, and then identifying a smaller subset of possible chemical solutions, the task of conducting physical experiments will be facilitated and therefore speed the discovery of real solutions,” states Windus.

Figure 1. Example of H-ZSM5 with 2-propanol and water. Image curtesy of Peter Sushko (PNNL).

Intel solutions used in developing NWChemEx

NWChemEx uses Data Parallel C++ (DPC++) as one of its programming models. DPC++ is a cross-architecture programming language, based on C++ and SYCL and part of oneAPI – an industry initiative to unify and simplify application development across diverse computing architectures. To facilitate porting of any existing CUDA code, Intel’s DPC++ Compatibility Tool helps migrate that code to create new DPC++ code. Further performance analysis and tuning uses Intel VTune Profiler and Intel Advisor. The compilers (C, C++, Fortran), Intel oneAPI Math Kernel Library (oneMKL) and Intel oneAPI DPC++ Library (oneDPL) – all part of Intel’s oneAPI Base Toolkit, are also employed.

Future benefits of NWChemEx and exascale supercomputers

The impact of the team’s biofuel research and rewriting NWChemEx software will have benefits outside the Argonne ESP project. “Chemistry simulations need to be able to model more complex, realistic systems. With current hardware and software, we can only simulate simplistic systems by removing impurities, getting rid of defects, and simplifying the solvent environments. In the future, researchers must be able to do real-life simulations that bring in all the complexities of the chemical system to have confidence the research results show the real-life issues, and the research findings will have comparable results to experimental conditions,” states Windus.

“Quantum chemistry research methods have become ubiquitous in hard science and engineering and are used in a variety of fields. What makes molecular dynamics and quantum chemistry tools such as NWChemEx so valuable is that they provide predictive results that are accurate when compared with many other research algorithms. Tools such as NWChemEx and access to hardware such as the future Argonne Aurora supercomputer will be critical to finding future solutions,” states Eric Bylaska, chemist at Pacific Northwest National Laboratory.

NWChemEx research was supported by the Exascale Computing Project, a collaborative effort of the U.S. Department of Energy Office of Science and the National Nuclear Security Administration.

Linda Barney is the founder and owner of Barney and Associates, a technical/marketing writing, training, and web design firm in Beaverton, Oregon.

Subscribe to HPCwire's Weekly Update!

Be the most informed person in the room! Stay ahead of the tech trends with industy updates delivered to you every week!

IBM Research Debuts 2nm Test Chip with 50 Billion Transistors

May 6, 2021

IBM Research today announced the successful prototyping of the world's first 2 nanometer chip, fabricated with silicon nanosheet technology on a standard 300mm bulk wafer. With ~50 billion transistors, the chip will enab Read more…

Supercomputer-Powered CRISPR Simulation Lights Path to Better DNA Editing

May 5, 2021

CRISPR-Cas9 – mostly just known as CRISPR – is a powerful genome editing tool that uses an enzyme (Cas9) to slice off sections of DNA and a guide RNA to repair and modify the DNA as desired, opening the door for cure Read more…

LRZ Announces New Phase of SuperMUC-NG Supercomputer with Intel’s ‘Ponte Vecchio’ GPU

May 5, 2021

At the Leibniz Supercomputing Centre (LRZ) in München, Germany – one of the constituent centers of the Gauss Centre for Supercomputing (GCS) – the SuperMUC-NG system has stood tall for several years, placing 15th on Read more…

HPC Simulations Show How Antibodies Quash SARS-CoV-2

May 5, 2021

Following more than a year of rapid-fire research and pharmaceutical development, nearly a billion COVID-19 vaccine doses have been administered around the world, with many of those vaccines proving remarkably effective Read more…

Crystal Ball Gazing at Nvidia: R&D Chief Bill Dally Talks Targets and Approach

May 4, 2021

There’s no quibbling with Nvidia’s success. Entrenched atop the GPU market, Nvidia has ridden its own inventiveness and growing demand for accelerated computing to meet the needs of HPC and AI. Recently it embarked o Read more…

AWS Solution Channel

FLYING WHALES runs CFD workloads 15 times faster on AWS

FLYING WHALES is a French startup that is developing a 60-ton payload cargo airship for the heavy lift and outsize cargo market. The project was born out of France’s ambition to provide efficient, environmentally friendly transportation for collecting wood in remote areas. Read more…

2021 Winter Classic – Coaches Chat

May 4, 2021

The Winter Classic Invitational Student Cluster Competition raged for all last week and now we’re into the week of judging interviews. Time has been flying. So as we wait for results, let’s dive a bit deeper into t Read more…

IBM Research Debuts 2nm Test Chip with 50 Billion Transistors

May 6, 2021

IBM Research today announced the successful prototyping of the world's first 2 nanometer chip, fabricated with silicon nanosheet technology on a standard 300mm Read more…

Crystal Ball Gazing at Nvidia: R&D Chief Bill Dally Talks Targets and Approach

May 4, 2021

There’s no quibbling with Nvidia’s success. Entrenched atop the GPU market, Nvidia has ridden its own inventiveness and growing demand for accelerated compu Read more…

Intel Invests $3.5 Billion in New Mexico Fab to Focus on Foveros Packaging Technology

May 3, 2021

Intel announced it is investing $3.5 billion in its Rio Rancho, New Mexico, facility to support its advanced 3D manufacturing and packaging technology, Foveros. Read more…

Supercomputer Research Shows Standard Model May Withstand Muon Discrepancy

May 3, 2021

Big news recently struck the physics world: researchers at the Fermi National Accelerator Laboratory (FNAL), in the midst of their Muon g-2 experiment, publishe Read more…

HPC Career Notes: May 2021 Edition

May 3, 2021

In this monthly feature, we’ll keep you up-to-date on the latest career developments for individuals in the high-performance computing community. Whether it Read more…

NWChemEx: Computational Chemistry Code for the Exascale Era

April 29, 2021

A team working on biofuel research is rewriting the decades-old NWChem software program for the exascale era. The new software, NWChemEx, will enable computatio Read more…

HPE Will Build Singapore’s New National Supercomputer

April 28, 2021

More than two years ago, Singapore’s National Supercomputing Centre (NSCC) announced a $200 million SGD (~$151 million USD) investment to boost its supercomputing power by an order of magnitude. Today, those plans come closer to fruition with the announcement that Hewlett Packard Enterprise (HPE) has been awarded... Read more…

Arm Details Neoverse V1, N2 Platforms with New Mesh Interconnect, Advances Partner Ecosystem

April 27, 2021

Chip designer Arm Holdings is sharing details about its Neoverse V1 and N2 cores, introducing its new CMN-700 interconnect, and showcasing its partners' plans t Read more…

Julia Update: Adoption Keeps Climbing; Is It a Python Challenger?

January 13, 2021

The rapid adoption of Julia, the open source, high level programing language with roots at MIT, shows no sign of slowing according to data from Julialang.org. I Read more…

Intel Launches 10nm ‘Ice Lake’ Datacenter CPU with Up to 40 Cores

April 6, 2021

The wait is over. Today Intel officially launched its 10nm datacenter CPU, the third-generation Intel Xeon Scalable processor, codenamed Ice Lake. With up to 40 Read more…

CERN Is Betting Big on Exascale

April 1, 2021

The European Organization for Nuclear Research (CERN) involves 23 countries, 15,000 researchers, billions of dollars a year, and the biggest machine in the worl Read more…

HPE Launches Storage Line Loaded with IBM’s Spectrum Scale File System

April 6, 2021

HPE today launched a new family of storage solutions bundled with IBM’s Spectrum Scale Erasure Code Edition parallel file system (description below) and featu Read more…

10nm, 7nm, 5nm…. Should the Chip Nanometer Metric Be Replaced?

June 1, 2020

The biggest cool factor in server chips is the nanometer. AMD beating Intel to a CPU built on a 7nm process node* – with 5nm and 3nm on the way – has been i Read more…

Saudi Aramco Unveils Dammam 7, Its New Top Ten Supercomputer

January 21, 2021

By revenue, oil and gas giant Saudi Aramco is one of the largest companies in the world, and it has historically employed commensurate amounts of supercomputing Read more…

Quantum Computer Start-up IonQ Plans IPO via SPAC

March 8, 2021

IonQ, a Maryland-based quantum computing start-up working with ion trap technology, plans to go public via a Special Purpose Acquisition Company (SPAC) merger a Read more…

Can Deep Learning Replace Numerical Weather Prediction?

March 3, 2021

Numerical weather prediction (NWP) is a mainstay of supercomputing. Some of the first applications of the first supercomputers dealt with climate modeling, and Read more…

Leading Solution Providers


Livermore’s El Capitan Supercomputer to Debut HPE ‘Rabbit’ Near Node Local Storage

February 18, 2021

A near node local storage innovation called Rabbit factored heavily into Lawrence Livermore National Laboratory’s decision to select Cray’s proposal for its CORAL-2 machine, the lab’s first exascale-class supercomputer, El Capitan. Details of this new storage technology were revealed... Read more…

AMD Launches Epyc ‘Milan’ with 19 SKUs for HPC, Enterprise and Hyperscale

March 15, 2021

At a virtual launch event held today (Monday), AMD revealed its third-generation Epyc “Milan” CPU lineup: a set of 19 SKUs -- including the flagship 64-core, 280-watt 7763 part --  aimed at HPC, enterprise and cloud workloads. Notably, the third-gen Epyc Milan chips achieve 19 percent... Read more…

Programming the Soon-to-Be World’s Fastest Supercomputer, Frontier

January 5, 2021

What’s it like designing an app for the world’s fastest supercomputer, set to come online in the United States in 2021? The University of Delaware’s Sunita Chandrasekaran is leading an elite international team in just that task. Chandrasekaran, assistant professor of computer and information sciences, recently was named... Read more…

New Deep Learning Algorithm Solves Rubik’s Cube

July 25, 2018

Solving (and attempting to solve) Rubik’s Cube has delighted millions of puzzle lovers since 1974 when the cube was invented by Hungarian sculptor and archite Read more…

African Supercomputing Center Inaugurates ‘Toubkal,’ Most Powerful Supercomputer on the Continent

February 25, 2021

Historically, Africa hasn’t exactly been synonymous with supercomputing. There are only a handful of supercomputers on the continent, with few ranking on the Read more…

GTC21: Nvidia Launches cuQuantum; Dips a Toe in Quantum Computing

April 13, 2021

Yesterday Nvidia officially dipped a toe into quantum computing with the launch of cuQuantum SDK, a development platform for simulating quantum circuits on GPU-accelerated systems. As Nvidia CEO Jensen Huang emphasized in his keynote, Nvidia doesn’t plan to build... Read more…

The History of Supercomputing vs. COVID-19

March 9, 2021

The COVID-19 pandemic poses a greater challenge to the high-performance computing community than any before. HPCwire's coverage of the supercomputing response t Read more…

HPE Names Justin Hotard New HPC Chief as Pete Ungaro Departs

March 2, 2021

HPE CEO Antonio Neri announced today (March 2, 2021) the appointment of Justin Hotard as general manager of HPC, mission critical solutions and labs, effective Read more…

  • arrow
  • Click Here for More Headlines
  • arrow