Performance characterization of global address space applications: a case study with nwchem
Abstract not provided
Hammond, J R↗
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Combined quantum‐mechanical molecular mechanics calculations with NWChem and AMBER: Excited state properties of green fluorescent protein chromophore analogue in aqueous solution
Combined quantum mechanical molecular mechanics (QM/MM) calculations have become a popular methodology for efficient and accurate description of large molecular systems. In this work we introduce our development of a QM/MM framework based on two well‐known codes—NWChem and AMBER. As an initial application area we are focused on excited state properties of small molecules in an aqueous phase using an analogue of the green fluorescent protein (GFP) chromophore as a particular test case. Our approach incorporates high level coupled cluster theory for the analysis of excited states providing a reliable theoretical analysis of effects of an aqueous solvation environment on the photochemical properties of the GFP chromophore. Using a systematic approach, which involves comparison of gas phase and aqueous phase results for different protonation states and conformations, we resolve existing uncertainties regarding the theoretical interpretation of experimental data. We observe that the impact of aqueous environment on charged states generally results in blue shifts of the absorption spectra, but the magnitude of the effect is sensitive to both protonation state and conformation and can be rationalized based on charge movement into the area of higher/lower external electrostatic potentials. At neutral pH levels the experimentally observed absorption signal is most likely coming from the phenol protonated form. Our results also show that the high level electron correlated method is essential for a proper description of excited states of GFP. © 2017 Wiley Periodicals, Inc.
Pirojsirikul, Teerapong↗
NWChem: scalable parallel computational chemistry
NWChem is a general purpose computational chemistry code specifically designed to run on distributed memory parallel computers. The core functionality of the code focuses on molecular dynamics, Hartree-Fock and density functional theory methods for both plane-wave basis sets as well as Gaussian basis sets, tensor contraction engine based coupled cluster capabilities and combined quantum mechanics/molecular mechanics descriptions. It was realized from the beginning that scalable implementations of these methods required a programming paradigm inherently different from what message passing approaches could offer. In response a global address space library, the Global Array Toolkit, was developed. The programming model it offers is based on using predominantly one-sided communication. This model underpins most of the functionality in NWChem and the power of it is exemplified by the fact that the code scales to tens of thousands of processors. In this paper the core capabilities of NWChem are described as well as their implementation to achieve an efficient computational chemistry code with high parallel scalability. NWChem is a modern, open source, computational chemistry code1 specifically designed for large scale parallel applications2. To meet the challenges of developing efficient, scalable and portable programs of this nature a particular code design was adopted. This code design involved two main features. First of all, the code is build up in a modular fashion so that a large variety of functionality can be integrated easily. Secondly, to facilitate writing complex parallel algorithms the Global Array toolkit was developed. This toolkit allows one to write parallel applications in a shared memory like approach, but offers additional mechanisms to exploit data locality to lower communication overheads. This framework has proven to be very successful in computational chemistry but is applicable to any engineering domain. Within the context created by the features above NWChem has grown into a general purpose computational chemistry code that supports a wide variety of energy expressions and capabilities to calculate properties based there upon. The main energy expressions are classical mechanics force fields, Hartree-Fock and DFT both for finite systems and condensed phase systems, coupled cluster, as well as QM/MM. For most energy expressions single point calculations, geometry optimizations, excited states, and other properties are available. Below we briefly discuss each of the main energy expressions and the critical points involved in scalable implementations thereof.
99 GENERAL AND MISCELLANEOUS↗
NWChem: Recent and Ongoing Developments
In this paper we summarize developments in the NWChem computational chemistry suite since the last major release (NWChem 7.0). Specifically, we focus on functionalities, along with input blocks, that are currently accessible in the current stable release (NWChem 7.2) and master branches, interfaces to quantum computing simulators, interfaces to external libraries, the NWChem GitHub repository, and containerization of NWChem executable images. In conclusion, some of the ongoing developments that will be available in the near future are also discussed.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
From data to analysis: linking NWChem and Avogadro with the syntax and semantics of Chemical Markup Language
Background Multidisciplinary integrated research requires the ability to couple the diverse sets of data obtained from a range of complex experiments and computer simulations. Integrating data requires semantically rich information. In this paper the generation of semantically rich data from the NWChem computational chemistry software is discussed within the Chemical Markup Language (CML) framework. Results The NWChem computational chemistry software has been modified and coupled to the FoX library to write CML compliant XML data files. The FoX library was expanded to represent the lexical input files used by the computational chemistry software. Conclusions The production of CML compliant XML files for the computational chemistry software NWChem can be relatively easily accomplished using the FoX library. A unified computational chemistry or CompChem convention and dictionary needs to be developed through a community-based effort. The long-term goal is to enable a researcher to do Google-style chemistry and physics searches.
Chemical Markup Language, FoX, NWChem, computation↗
NWChem
Computational atomistic modeling has emerged as a powerful approach for fundamental studies in chemistry, materials science, geosciences, and biology. It has the ability to provide detailed insights into complex phenomena and over the years has grown into a powerful tool not only to validate experiment, but also to predict new phenomena. In order to harness computational modeling to the fullest, superior computational tools are required that not only offer a broad spectrum of capabilities, but are also capable of taking advantage of modern massively parallel computer architectures efficiently to solve real world problems. The NWChem program suite is an example along these lines. It offers a range of capabilities to perform first-principles electronic structure calculations on molecular and periodic systems, classical molecular dynamics simulations and hybrid QM/MM simulations that permits one to combine quantum and classical methods within a calculation. The code is designed to run on high-performance parallel supercomputers as well as conventional workstation clusters with the goal to provide scalable solutions for large scale atomistic simulations. It has been ported to almost all high-performance computing platforms, workstations, PCs running LINUX, as well as clusters of desktop platforms or workgroup servers. The package is scalable, both in its ability to treat large problems efficiently, and in its utilization of available parallel computing resources. The parallel framework for NWChem is provided by the Global Array (GA) toolkit developed at PNNL. NWChem is developed and maintained by the Environmental Molecular Sciences Laboratory (EMSL) located at the Pacific Northwest National Laboratory (PNNL) in Washington State. The latest release (version 6.0) of the code is distributed under the terms of the Educational Community License (ECL) version 2.0.
99 GENERAL AND MISCELLANEOUS↗
Recent Improvements to the NWChem COSMO Module
This work presents recent developments in the COSMO solvation model implementation in NWChem. A new cavity construction approach, based on the solvent-excluding surface (SES) and utilizing the well-established GEPOL algorithm, has been introduced. Additionally, a straightforward procedure to merge surface segments that are too close─often a source of numerical artifacts─has been implemented. The available methods for correcting outlying surface charges have also been reviewed and improved. To validate the new implementation, we computed dielectric solvation energies for a chemically diverse set of approximately 100 molecules, including neutral species, small ions, and common ionic liquid components. Results were compared to those from GAMESS using the double-cavity method as a reference. Although the double-cavity approach can be regarded as more accurate, the simpler correction schemes available in NWChem─based on scaling factors or Lagrange multipliers─can achieve excellent agreement if the potential is also properly corrected, with mean unsigned deviations of around 0.15 kcal/mol. Predictions of typical vapor–liquid and liquid–liquid equilibria using a COSMO-SAC variant based on NWChem also showed very promising results.
Cavities↗
Scaling NWChem with Efficient and Portable Asychronous Communication in MPI RMA
NWChem is one of the most widely used computational chemistry application suites for chemical and biological systems. Despite its vast success, the computational efficiency of NWChem is still low. This is especially true in higher accuracy methods such as the CCSD(T) coupled cluster method, where it currently achieves a mere 50% computational efficiency when run at large scales. In this paper, we demonstrate the most computationally efficient scaling of NWChem CCSD(T) to date, and use it to solve large water clusters. We use our recently proposed process-based asynchronous progress framework for MPI RMA, called Casper, to scale the computation on water clusters at near-100% computational efficiency on up to 12288 cores.
Si, Min↗
Integral Equation Theory of Molecular Solvation Coupled with Quantum Mechanical/Molecular Mechanics Method in NWChem Package
We have developed a hybrid approach based on a combination of integral equation theory of molecular liquids and QM/MM methodology in NorthWest computational Chemistry (NWChem) software package. We have split the evaluations into conse- quent QM/MM and statistical mechanics calculations based on the one-dimensional reference interaction site model, which allows us to reduce signicantly the time of computation. The method complements QM/MM capabilities existing in the NWChem package. The accuracy of the presented method was tested through com- putation of water structure around several organic solutes and their hydration free energies. We have also evaluated the solvent effect on the conformational equilibria. The applicability and limitations of the developed approach are discussed.
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First Principles Nonadiabatic Excited-State Molecular Dynamics in NWChem
Computational simulation of non-adiabatic molecular dynamics is an indispensable tool for understanding complex photoinduced processes such as internal conversion, energy transfer, charge separation, and spatial localization of excitons, to name a few. Here, we report an implementation of the fewest-switches surface hopping algorithm in the NWChem computational chemistry program. Here the surface hopping method is combined with linear-response time-dependent density functional theory calculations of adiabatic excited state potential energy surfaces. To treat quantum transitions between arbitrary electronic Born{Oppenheimer states, we have implemented both numerical and analytical differentiation schemes for derivative non-adiabatic couplings. A numerical approach for the time-derivative non-adiabatic couplings together with an analytical method for calculating non-adiabatic coupling vectors is an efficient combination for surface hopping approaches. Additionally, electronic decoherence schemes and a state reassigned unavoided crossings algorithm are also implemented to improve the accuracy of the simulated dynamics and to handle trivial unavoided crossings. We apply our code to study the ultrafast decay of photoexcited benzene, including a detailed analysis of the potential energy surface, population decay time scales, and vibrational coordinates coupled to the excitation dynamics. The development presented in this work is a baseline for future implementations of more sophisticated frameworks for simulating of non-adiabatic molecular dynamics in NWChem.
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NWChem: Past, present, and future
Specialized computational chemistry packages have permanently reshaped the landscape of chemical sciences by providing tools to support and guide the experimental effort and for prediction of chemical and materials properties. In this regard, a special role has been played by electronic structure packages where complex chemical and materials processes can be modeled using first-principle-driven methodologies. Over the last few decades, the rapid development of computing technologies and a tremendous increase in computational power has offered a unique chance to study complex chemical transformations using sophisticated and predictive many-body techniques to describe correlated behavior of electrons in molecular and condensed phase systems at different levels of theory. In enabling these simulations, a critical role has been played by novel parallel algorithms capable of taking advantage of computational resources to address polynomial scaling of electronic structure methods. NWChem was among the first electronic structure codes that focused on delivering scalable performance for electronic structure simulations. Herein, we briefly review the NWChem suite of computational codes including its history, design principles, parallel tools, current capabilities, outreach and outlook.
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NWChem: Quantum Chemistry Simulations at Scale
Methods based on quantum mechanics equations have been developed since the 1930's with the purpose of accurately studying the electronic structure of molecules. However, it is only during the last two decades that intense development of new computational algorithms has opened the possibility of performing accurate simulations of challenging molecular processes with high-order many-body methods. A wealth of evidence indicates that the proper inclusion of instantaneous interactions between electrons (or the so-called electron correlation effects) is indispensable for the accurate characterization of chemical reactivity, molecular properties, and interactions of light with matter. The availability of reliable methods for benchmarking of medium-size molecular systems provides also a unique chance to propagate high-level accuracy across spatial scales through the multiscale methodologies. Some of these methods have potential to utilize computational resources in an effi*cient way since they are characterized by high numerical complexity and appropriate level of data granularity, which can be effi*ciently distributed over multi-processor architectures. The broad spectrum of coupled cluster (CC) methods falls into this class of methodologies. Several recent CC implementations clearly demonstrated the scalability of CC formalisms on architectures composed of hundreds thousand computational cores. In this context NWChem provides a collection of Tensor Contraction Engine (TCE) generated parallel implementations of various coupled cluster methods capable of taking advantage of many thousand of cores on leadership class parallel architectures.
chemistry↗
From NWChem to NWChemEx: Evolving with the Computational Chemistry Landscape
Since the advent of the first computers, chemists have been at the forefront of using computers to understand and solve complex chemical problems. As the hardware and software have evolved, so have the theoretical and computational chemistry methods and algorithms. Parallel computers clearly changed the common computing paradigm in the late 1970s and 80s, and the field has again seen a paradigm shift with the advent of graphical processing units. This review explores the challenges and some of the solutions in transforming software from the terascale to the petascale and now to the upcoming exascale computers. While discussing the field in general, NWChem and its redesign, NWChemEx, will be highlighted as one of the early codesign projects to take advantage of massively parallel computers and emerging software standards to enable large scientific challenges to be tackled.
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Optimization of the Coupled Cluster Implementation in NWChem on Petascale Parallel Architectures
Coupled cluster singles and doubles (CCSD) algorithm has been optimized in NWChem software package. This modification alleviated the communication bottleneck and provided from 2- to 5-fold speedup in the CCSD iteration time depending on the problem size and available memory. Sustained 0.60 petaflop/sec performance on CCSD(T) calculation has been obtained on NCSA Blue Waters. This number included all stages of the calculation from initialization till termination, iterative computation of single and double excitations, and perturbative accounting for triple excitations. In the section of perturbative triples alone, the computation maintained 1.18 petaflop/sec performance level. CCSD computations have been performed on Guanine-Cytosine deoxydinucleotide monophosphate (GC-dDMP) to probe the conformational energy difference in DNA single strand in A- and B-conformations. The computation revealed significant discrepancy between CCSD and classical force fields in prediction of relative energy of A- and B-conformations of GC-dDMP.
calculations↗
Thread-level parallelization and optimization of NWChem for the Intel MIC architecture
In the multicore era it was possible to exploit the increase in on-chip parallelism by simply running multiple MPI processes per chip. Unfortunately, manycore processors' greatly increased thread- and data-level parallelism coupled with a reduced memory capacity demand an altogether different approach. In this paper we explore augmenting two NWChem modules, triples correction of the CCSD(T) and Fock matrix construction, with OpenMP in order that they might run efficiently on future manycore architectures. As the next NERSC machine will be a self-hosted Intel MIC (Xeon Phi) based supercomputer, we leverage an existing MIC testbed at NERSC to evaluate our experiments. In order to proxy the fact that future MIC machines will not have a host processor, we run all of our experiments in native mode. We found that while straightforward application of OpenMP to the deep loop nests associated with the tensor contractions of CCSD(T) was sufficient in attaining high performance, significant e ort was required to safely and efeciently thread the TEXAS integral package when constructing the Fock matrix. Ultimately, our new MPI+OpenMP hybrid implementations attain up to 65× better performance for the triples part of the CCSD(T) due in large part to the fact that the limited on-card memory limits the existing MPI implementation to a single process per card. Additionally, we obtain up to 1.6× better performance on Fock matrix constructions when compared with the best MPI implementations running multiple processes per card.
CCSD(T)↗
Thread-Level Parallelization and Optimization of NWChem for the Intel MIC Architecture
In the multicore era it was possible to exploit the increase in on-chip parallelism by simply running multiple MPI processes per chip. Unfortunately, manycore processors' greatly increased thread- and data-level parallelism coupled with a reduced memory capacity demand an altogether different approach. In this paper we explore augmenting two NWChem modules, triples correction of the CCSD(T) and Fock matrix construction, with OpenMP in order that they might run efficiently on future manycore architectures. As the next NERSC machine will be a self-hosted Intel MIC (Xeon Phi) based supercomputer, we leverage an existing MIC testbed at NERSC to evaluate our experiments. In order to proxy the fact that future MIC machines will not have a host processor, we run all of our experiments in tt native mode. We found that while straightforward application of OpenMP to the deep loop nests associated with the tensor contractions of CCSD(T) was sufficient in attaining high performance, significant effort was required to safely and efficiently thread the TEXAS integral package when constructing the Fock matrix. Ultimately, our new MPI OpenMP hybrid implementations attain up to 65x better performance for the triples part of the CCSD(T) due in large part to the fact that the limited on-card memory limits the existing MPI implementation to a single process per card. Additionally, we obtain up to 1.6x better performance on Fock matrix constructions when compared with the best MPI implementations running multiple processes per card.
97 MATHEMATICS AND COMPUTING↗
Performance Evaluation of NWChem Ab-Initio Molecular Dynamics (AIMD) Simulations on the Intel® Xeon Phi™ Processor
Ab-initio Molecular Dynamics (AIMD) methods are an important class of algorithms, as they enable scientists to understand the chemistry and dynamics of molecular and condensed phase systems while retaining a first-principles-based description of their interactions. Many-core architectures such as the Intel® Xeon Phi™ processor are an interesting and promising target for these algorithms, as they can provide the computational power that is needed to solve interesting problems in chemistry. In this paper, we describe the efforts of refactoring the existing AIMD plane-wave method of NWChem from an MPI-only implementation to a scalable, hybrid code that employs MPI and OpenMP to exploit the capabilities of current and future many-core architectures. We describe the optimizations required to get close to optimal performance for the multiplication of the tall-and-skinny matrices that form the core of the computational algorithm. We present strong scaling results on the complete AIMD simulation for a test case that simulates 256 water molecules and that strong-scales well on a cluster of 1024 nodes of Intel Xeon Phi processors. We compare the performance obtained with a cluster of dual-socket Intel® Xeon® E5–2698v3 processors.
Environmental Molecular Sciences Laboratory↗
An Ab Initio Multiple Cloning Method for Non-Adiabatic Excited-State Molecular Dynamics in NWChem
The recently developed ab-initio multiple cloning (AIMC) approach based on the multicongurational Ehrenfest (MCE) method provides a powerful and accurate way of describing the excited-state dynamics of molecular systems. The AIMC method is a controlled approximation to non-adiabatic dynamics with a particular strength in the proper description of decoherence effects due to branching of vibrational wavepackets at a level crossing. In this work, we report a new implementation of the AIMC algorithm in the open source NWChem computational chemistry program. The framework combines linear-response time-dependent density functional theory with Ehrenfest mean-eld theory to determine the equations of motion for classical trajectories. The multi-dimensional wave function is decomposed into a superposition of Gaussian coherent states guided by Ehrenfest trajectories (i.e., MCE approach), which can clone with fully quantum mechanical amplitudes and phases. By using an efficient time-derivative based non-adiabatic coupling approach within the AIMC method, all observable are calculated on-the-y in the non-adiabatic molecular dynamics process. As a representative example, we apply our implementation to study the ultrafast photoinduced electronic and vibrational energy transfer in a pyridine molecule. The effects of the cloning procedure on electronic and vibrational coherence, relaxation and unidirectional energy transfer are discussed. This new AIMC implementation provides a high-level non-adiabatic molecular dynamics framework for simulating photoexcited dynamics in complex molecular systems and experimentally relevant ultrafast spectroscopic probes, such as nonlinear coherent optical and X-ray signals.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗