Multi-Architecture Monte-Carlo (MC) Simulation of Soft Coarse-Grained Polymeric Materials: SOft coarse grained Monte-carlo Acceleration (SOMA)

Multi-component polymer systems are important for the development of new materials because of their ability to phase-separate or self-assemble into nano-structures. The Single-Chain-in-Mean-Field (SCMF) algorithm in conjunction with a soft, coarse-grained polymer model is an established technique to investigate these soft-matter systems. Here we present an im- plementation of this method: SOft coarse grained Monte-carlo Accelera- tion (SOMA). It is suitable to simulate large system sizes with up to billions of particles, yet versatile enough to study properties of different kinds of molecular architectures and interactions. We achieve efficiency of the simulations commissioning accelerators like GPUs on both workstations as well as supercomputers. The implementa- tion remains flexible and maintainable because of the implementation of the scientific programming language enhanced by OpenACC pragmas for the accelerators. We present implementation details and features of the program package, investigate the scalability of our implementation SOMA, and discuss two applications, which cover system sizes that are difficult to reach with other, common particle-based simulation methods

A Survey of Processing Systems for Phylogenetics and Population Genetics

The COVID-19 pandemic brought Bioinformatics into the spotlight, revealing that several existing methods, algorithms, and tools were not well prepared to handle large amounts of genomic data efficiently. This led to prohibitively long execution times and the need to reduce the extent of analyses to obtain results in a reasonable amount of time. In this survey, we review available high-performance computing and hardware-accelerated systems based on FPGA and GPU technology. Optimized and hardware-accelerated systems can conduct more thorough analyses considerably faster than pure software implementations, allowing to reach important conclusions in a timely manner to drive scientific discoveries. We discuss the reasons that are currently hindering high-performance solutions from being widely deployed in real-world biological analyses and describe a research direction that can pave the way to enable this

Efficient Algorithms And Optimizations For Scientific Computing On Many-Core Processors

Designing efficient algorithms for many-core and multicore architectures requires using different strategies to allow for the best exploitation of the hardware resources on those architectures. Researchers have ported many scientific applications to modern many-core and multicore parallel architectures, and by doing so they have achieved significant speedups over running on single CPU cores. While many applications have achieved significant speedups, some applications still require more effort to accelerate due to their inherently serial behavior. One class of applications that has this serial behavior is the Monte Carlo simulations. Monte Carlo simulations have been used to simulate many problems in statistical physics and statistical mechanics that were not possible to simulate using Molecular Dynamics. While there are a fair number of well-known and recognized GPU Molecular Dynamics codes, the existing Monte Carlo ensemble simulations have not been ported to the GPU, so they are relatively slow and could not run large systems in a reasonable amount of time. Due to the previously mentioned shortcomings of existing Monte Carlo ensemble codes and due to the interest of researchers to have a fast Monte Carlo simulation framework that can simulate large systems, a new GPU framework called GOMC is implemented to simulate different particle and molecular-based force fields and ensembles. GOMC simulates different Monte Carlo ensembles such as the canonical, grand canonical, and Gibbs ensembles. This work describes many challenges in developing a GPU Monte Carlo code for such ensembles and how I addressed these challenges. This work also describes efficient many-core and multicore large-scale energy calculations for Monte Carlo Gibbs ensemble using cell lists. Designing Monte Carlo molecular simulations is challenging as they have less computation and parallelism when compared to similar molecular dynamics applications. The modified cell list allows for more speedup gains for energy calculations on both many-core and multicore architectures when compared to other implementations without using the conventional cell lists. The work presents results and analysis of the cell list algorithms for each one of the parallel architectures using top of the line GPUs, CPUs, and Intel’s Phi coprocessors. In addition, the work evaluates the performance of the cell list algorithms for different problem sizes and different radial cutoffs. In addition, this work evaluates two cell list approaches, a hybrid MPI+OpenMP approach and a hybrid MPI+CUDA approach. The cell list methods are evaluated on a small cluster of multicore CPUs, Intel Phi coprocessors, and GPUs. The performance results are evaluated using different combinations of MPI processes, threads, and problem sizes. Another application presented in this dissertation involves the understanding of the properties of crystalline materials, and their design and control. Recent developments include the introduction of new models to simulate system behavior and properties that are of large experimental and theoretical interest. One of those models is the Phase-Field Crystal (PFC) model. The PFC model has enabled researchers to simulate 2D and 3D crystal structures and study defects such as dislocations and grain boundaries. In this work, GPUs are used to accelerate various dynamic properties of polycrystals in the 2D PFC model. Some properties require very intensive computation that may involve hundreds of thousands of atoms. The GPU implementation has achieved significant speedups of more than 46 times for some large systems simulations

GPU-PCC: A GPU Based Technique to Compute Pairwise Pearson’s Correlation Coefficients for Big fMRI Data

Functional Magnetic Resonance Imaging (fMRI) is a non-invasive brain imaging technique for studying the brain’s functional activities. Pearson’s Correlation Coefficient is an important measure for capturing dynamic behaviors and functional connectivity between brain components. One bottleneck in computing Correlation Coefficients is the time it takes to process big fMRI data. In this paper, we propose GPU-PCC, a GPU based algorithm based on vector dot product, which is able to compute pairwise Pearson’s Correlation Coefficients while performing computation once for each pair. Our method is able to compute Correlation Coefficients in an ordered fashion without the need to do post-processing reordering of coefficients. We evaluated GPU- PCC using synthetic and real fMRI data and compared it with sequential version of computing Correlation Coefficient on CPU and existing state-of-the-art GPU method. We show that our GPU-PCC runs 94.62× faster as compared to the CPU version and 4.28× faster than the existing GPU based technique on a real fMRI dataset of size 90k voxels. The implemented code is available as GPL license on GitHub portal of our lab at https://github.com/pcdslab/GPU-PCC

Neuromorphic Learning Systems for Supervised and Unsupervised Applications

The advancements in high performance computing (HPC) have enabled the large-scale implementation of neuromorphic learning models and pushed the research on computational intelligence into a new era. Those bio-inspired models are constructed on top of unified building blocks, i.e. neurons, and have revealed potentials for learning of complex information. Two major challenges remain in neuromorphic computing. Firstly, sophisticated structuring methods are needed to determine the connectivity of the neurons in order to model various problems accurately. Secondly, the models need to adapt to non-traditional architectures for improved computation speed and energy efficiency. In this thesis, we address these two problems and apply our techniques to different cognitive applications. This thesis first presents the self-structured confabulation network for anomaly detection. Among the machine learning applications, unsupervised detection of the anomalous streams is especially challenging because it requires both detection accuracy and real-time performance. Designing a computing framework that harnesses the growing computing power of the multicore systems while maintaining high sensitivity and specificity to the anomalies is an urgent research need. We present AnRAD (Anomaly Recognition And Detection), a bio-inspired detection framework that performs probabilistic inferences. We leverage the mutual information between the features and develop a self-structuring procedure that learns a succinct confabulation network from the unlabeled data. This network is capable of fast incremental learning, which continuously refines the knowledge base from the data streams. Compared to several existing anomaly detection methods, the proposed approach provides competitive detection accuracy as well as the insight to reason the decision making. Furthermore, we exploit the massive parallel structure of the AnRAD framework. Our implementation of the recall algorithms on the graphic processing unit (GPU) and the Xeon Phi co-processor both obtain substantial speedups over the sequential implementation on general-purpose microprocessor (GPP). The implementation enables real-time service to concurrent data streams with diversified contexts, and can be applied to large problems with multiple local patterns. Experimental results demonstrate high computing performance and memory efficiency. For vehicle abnormal behavior detection, the framework is able to monitor up to 16000 vehicles and their interactions in real-time with a single commodity co-processor, and uses less than 0.2ms for each testing subject. While adapting our streaming anomaly detection model to mobile devices or unmanned systems, the key challenge is to deliver required performance under the stringent power constraint. To address the paradox between performance and power consumption, brain-inspired hardware, such as the IBM Neurosynaptic System, has been developed to enable low power implementation of neural models. As a follow-up to the AnRAD framework, we proposed to port the detection network to the TrueNorth architecture. Implementing inference based anomaly detection on a neurosynaptic processor is not straightforward due to hardware limitations. A design flow and the supporting component library are developed to flexibly map the learned detection networks to the neurosynaptic cores. Instead of the popular rate code, burst code is adopted in the design, which represents numerical value using the phase of a burst of spike trains. This does not only reduce the hardware complexity, but also increases the result\u27s accuracy. A Corelet library, NeoInfer-TN, is implemented for basic operations in burst code and two-phase pipelines are constructed based on the library components. The design can be configured for different tradeoffs between detection accuracy, hardware resource consumptions, throughput and energy. We evaluate the system using network intrusion detection data streams. The results show higher detection rate than some conventional approaches and real-time performance, with only 50mW power consumption. Overall, it achieves 10^8 operations per Joule. In addition to the modeling and implementation of unsupervised anomaly detection, we also investigate a supervised learning model based on neural networks and deep fragment embedding and apply it to text-image retrieval. The study aims at bridging the gap between image and natural language. It continues to improve the bidirectional retrieval performance across the modalities. Unlike existing works that target at single sentence densely describing the image objects, we elevate the topic to associating deep image representations with noisy texts that are only loosely correlated. Based on text-image fragment embedding, our model employs a sequential configuration, connects two embedding stages together. The first stage learns the relevancy of the text fragments, and the second stage uses the filtered output from the first one to improve the matching results. The model also integrates multiple convolutional neural networks (CNN) to construct the image fragments, in which rich context information such as human faces can be extracted to increase the alignment accuracy. The proposed method is evaluated with both synthetic dataset and real-world dataset collected from picture news website. The results show up to 50% ranking performance improvement over the comparison models

Knowledge is power: Quantum chemistry on novel computer architectures

In the first chapter of this thesis, a background of fundamental quantum chemistry concepts is provided. Chapter two contains an analysis of the performance and energy efficiency of various modern computer processor architectures while performing computational chemistry calculations. In chapter three, the processor architectural study is expanded to include parallel computational chemistry algorithms executed across multiple-node computer clusters. Chapter four describes a novel computational implementation of the fundamental Hartree-Fock method which significantly reduces computer memory requirements. In chapter five, a case study of quantum chemistry two-electron integral code interoperability is described. The final chapters of this work discuss applications of quantum chemistry. In chapter six, an investigation of the esterification of acetic acid on acid-functionalized silica is presented. In chapter seven, the application of ab initio molecular dynamics to study the photoisomerization and photocyclization of stilbene is discussed. Final concluding remarks are noted in chapter eight

Knowledge is power: Quantum chemistry on novel computer architectures

In the first chapter of this thesis, a background of fundamental quantum chemistry concepts is provided. Chapter two contains an analysis of the performance and energy efficiency of various modern computer processor architectures while performing computational chemistry calculations. In chapter three, the processor architectural study is expanded to include parallel computational chemistry algorithms executed across multiple-node computer clusters. Chapter four describes a novel computational implementation of the fundamental Hartree-Fock method which significantly reduces computer memory requirements. In chapter five, a case study of quantum chemistry two-electron integral code interoperability is described. The final chapters of this work discuss applications of quantum chemistry. In chapter six, an investigation of the esterification of acetic acid on acid-functionalized silica is presented. In chapter seven, the application of ab initio molecular dynamics to study the photoisomerization and photocyclization of stilbene is discussed. Final concluding remarks are noted in chapter eight