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A key goal of this effort is to demonstrate and develop heterogeneous and distributed computing technologies that are applicable to DoD and scientific communities, while maintaining and benefiting from industry standards that could be applied to high performance computing. High performance computing systems based on clusters of compute nodes, connected via a high speed interconnect, are becoming popular for large-scale parallel applications, forming a highly scalable infrastructure. Most large-scale scientific applications are highly I/O-centric and have a tremendous need for a similarly scalable file I/O subsystem. DAFS is a well-defined highperformance protocol for file access across a network as well as set of APIs, uDAFS, for user level OS-bypassing application programming, designed to take advantage of RDMA-based transports, such as Virtual Interface Architecture (VIA), InfiniBand Architecture1, and iWARP.

Two of the current and most popular implementations of the Message-Passing Standard, Message Passing Interface (MPI), were contrasted: MPICH by Argonne National Laboratory, and LAM by the Ohio Supercomputer Center at Ohio State University. A parallel skyline matrix solver was adapted to be run in a heterogeneous environment using MPI. The Message-Passing Interface Forum was held in May 1994 which lead to a specification of library functions that implement the message-passing model of parallel communication. LAM, which creates it's own environment, is more robust in a highly heterogeneous network. MPICH uses the environment native to the machine architecture. While neither of these free-ware implementations provides the performance of native message-passing or vendor's implementations, MPICH begins to approach that performance on the SP-2. The machines used in this study were: IBM RS6000, 3 Sun4, SGI, and the IBM SP-2. Each machine is unique and a few machines required specific modifications during the installation. When installed correctly, both implementations worked well with only minor problems.

We introduce Lemon, an MPI parallel I/O library that is intended to allow for efficient parallel I/O of both binary and metadata on massively parallel architectures. Motivated by the demands of the Lattice Quantum Chromodynamics community, the data is stored in the SciDAC Lattice QCD Interchange Message Encapsulation format. This format allows for storing large blocks of binary data and corresponding metadata in the same file. Even if designed for LQCD needs, this format might be useful for any application with this type of data profile. The design, implementation and application of Lemon are described. We conclude with presenting the excellent scaling properties of Lemon on state of the art high performance computers.

We explore the trade-offs of performing linear algebra using Apache Spark, compared to traditional C and MPI implementations on HPC platforms. Spark is designed for data analytics on cluster computing platforms with access to local disks and is optimized for data-parallel tasks. We examine three widely-used and important matrix factorizations: NMF (for physical plausability), PCA (for its ubiquity) and CX (for data interpretability). We apply these methods to TB-sized problems in particle physics, climate modeling and bioimaging. The data matrices are tall-and-skinny which enable the algorithms to map conveniently into Spark's data-parallel model. We perform scaling experiments on up to 1600 Cray XC40 nodes, describe the sources of slowdowns, and provide tuning guidance to obtain high performance.

Multiple matching algorithms are used to locate the occurrences of patterns from a finite pattern set in a large input string. Aho-Corasick and Wu-Manber, two of the most well known algorithms for multiple matching require an increased computing power, particularly in cases where large-size datasets must be processed, as is common in computational biology applications. Over the past years, Graphics Processing Units (GPUs) have evolved to powerful parallel processors outperforming Central Processing Units (CPUs) in scientific calculations. Moreover, multiple GPUs can be used in parallel, forming hybrid computer cluster configurations to achieve an even higher processing throughput. This paper evaluates the speedup of the parallel implementation of the Aho-Corasick and Wu-Manber algorithms on a hybrid GPU cluster, when used to process a snapshot of the Expressed Sequence Tags of the human genome and for different problem parameters.

Arpan Jain, Kawthar Shafie Khorassani https://www.pyohio.org/2019/presentations/123 Deep learning models are a subset of machine learning models and algorithms which are designed to induce Artificial Intelligence in computers. The rise of deep learning can be attributed to the presence of large datasets and growing computational power. Deep learning models are used in face recognition, speech recognition, and many other applications. TensorFlow is a popular deep learning framework for python used to implement and train Deep Neural Networks (DNNs). Message Passing Interface (MPI) is a programming paradigm, often used in parallel applications, that allows processes to communicate with each other. Horovod provides an interface in python to couple DNN written using TensorFlow and MPI to train DNNs in less amount of time using the distributed training approach. MPI functions are optimized to provide multiple communication routines including point-to-point and collective communication. Point-to-point communication refers to a communication pattern that involves a sender process and a receiver process while collective communication involves a group of processes exchanging messages. In particular, the reduction is a collective function widely used in deep learning models to perform group operations. In this talk, we intend to demonstrate the challenges and elements to consider for DNN training using MPI in Python. Deep Learning(DL) has attracted a lot of attention in recent years, and python has been the front runner language when it comes to the framework and implementation. Training of DL models remains a challenge as it requires a huge amount of time and computational resources. We will discuss the distributed training of the Deep Neural Network using the MPI across multiple GPUs or CPUs. === https://pyohio.org A FREE annual conference for anyone interested in Python in and around Ohio, the entire Midwest, maybe even the whole world. Produced by NDV: https://youtube.com/channel/UCQ7dFBzZGlBvtU2hCecsBBg?sub_confirmation=1 Sat Jul 27 11:15:00 2019 at Hays Cape

A QR factorization of a tall and skinny matrix with n columns can be represented as a reduction. The operation used along the reduction tree has in input two n-by-n upper triangular matrices and in output an n-by-n upper triangular matrix which is defined as the R factor of the two input matrices stacked the one on top of the other. This operation is binary, associative, and commutative. We can therefore leverage the MPI library capabilities by using user-defined MPI operations and MPI_Reduce to perform this reduction. The resulting code is compact and portable. In this context, the user relies on the MPI library to select a reduction tree appropriate for the underlying architecture.

Multidisciplinary and multi-zonal applications are an important class of applications in the area of Computational Aerosciences. In these codes, two or more distinct parallel programs or copies of a single program are utilized to model a single problem. To support such applications, it is common to use a programming model where a program is divided into several single program multiple data stream (SPMD) applications, each of which solves the equations for a single physical discipline or grid zone. These SPMD applications are then bound together to form a single multidisciplinary or multi-zonal program in which the constituent parts communicate via point-to-point message passing routines. Unfortunately, simple message passing models, like Intel's NX library, only allow point-to-point and global communication within a single system-defined partition. This makes implementation of these applications quite difficult, if not impossible. In this report it is shown that the new Message Passing Interface (MPI) standard is a viable portable library for implementing the message passing portion of multidisciplinary applications. Further, with the extension of a portable loader, fully portable multidisciplinary application programs can be developed. Finally, the performance of MPI is compared to that of some native message passing libraries. This comparison shows that MPI can be implemented to deliver performance commensurate with native message libraries.

To leverage the last two decades' transition in High-Performance Computing (HPC) towards clusters of compute nodes bound together with fast interconnects, a modern scalable CFD code must be able to efficiently distribute work amongst several nodes using the Message Passing Interface (MPI). MPI can enable very large simulations running on very large clusters, but it is necessary that the bulk of the CFD code be written with MPI in mind, an obstacle to parallelizing an existing serial code. In this work we present the results of extending an existing two-phase 3D Navier-Stokes solver, which was completely serial, to a parallel execution model using MPI. The 3D Navier-Stokes equations for two immiscible incompressible fluids are solved by the continuum surface force method, while the location of the interface is determined by the level-set method. We employ the Portable Extensible Toolkit for Scientific Computing (PETSc) for domain decomposition (DD) in a framework where only a fraction of the code needs to be altered. We study the strong and weak scaling of the resulting code. Cases are studied that are relevant to the fundamental understanding of oil/water separation in electrocoalescers.

In Matrix multiplication we refer to a concept that is used in technology applications such as digital image processing, digital signal processing and graph problem solving. Multiplication of huge matrices requires a lot of computing time as its complexity is O n3 . Because most engineering science applications require higher computational throughput with minimum time, many sequential and analogue algorithms are developed. In this paper, methods of matrix multiplication are elect, implemented, and analyzed. A performance analysis is evaluated, and some recommendations are given when using open MP and MPI methods of parallel of latitude computing. Adamu Abubakar I | Oyku A | Mehmet K | Amina M. Tako ""Comprehensive Performance Evaluation on Multiplication of Matrices using MPI"" Published in International Journal of Trend in Scientific Research and Development (ijtsrd), ISSN: 2456-6470, Volume-4 | Issue-2 , February 2020, URL: https://www.ijtsrd.com/papers/ijtsrd30015.pdf Paper Url : https://www.ijtsrd.com/engineering/electrical-engineering/30015/comprehensive-performance-evaluation-on-multiplication-of-matrices-using-mpi/adamu-abubakar-i

In Matrix multiplication we refer to a concept that is used in technology applications such as digital image processing, digital signal processing and graph problem solving. Multiplication of huge matrices requires a lot of computing time as its complexity is O n3 . Because most engineering science applications require higher computational throughput with minimum time, many sequential and analogue algorithms are developed. In this paper, methods of matrix multiplication are elect, implemented, and analyzed. A performance analysis is evaluated, and some recommendations are given when using open MP and MPI methods of parallel of latitude computing. Adamu Abubakar I | Oyku A | Mehmet K | Amina M. Tako ""Comprehensive Performance Evaluation on Multiplication of Matrices using MPI"" Published in International Journal of Trend in Scientific Research and Development (ijtsrd), ISSN: 2456-6470, Volume-4 | Issue-2 , February 2020, URL: https://www.ijtsrd.com/papers/ijtsrd30015.pdf Paper Url : https://www.ijtsrd.com/engineering/electrical-engineering/30015/comprehensive-performance-evaluation-on-multiplication-of-matrices-using-mpi/adamu-abubakar-i

The increasing number of processing elements and decreas- ing memory to core ratio in modern high-performance platforms makes efficient strong scaling a key requirement for numerical algorithms. In order to achieve efficient scalability on massively parallel systems scientific software must evolve across the entire stack to exploit the multiple levels of parallelism exposed in modern architectures. In this paper we demonstrate the use of hybrid MPI/OpenMP parallelisation to optimise parallel sparse matrix-vector multiplication in PETSc, a widely used scientific library for the scalable solution of partial differential equations. Using large matrices generated by Fluidity, an open source CFD application code which uses PETSc as its linear solver engine, we evaluate the effect of explicit communication overlap using task-based parallelism and show how to further improve performance by explicitly load balancing threads within MPI processes. We demonstrate a significant speedup over the pure-MPI mode and efficient strong scaling of sparse matrix-vector multiplication on Fujitsu PRIMEHPC FX10 and Cray XE6 systems.

The increasing number of processing elements and decreas- ing memory to core ratio in modern high-performance platforms makes efficient strong scaling a key requirement for numerical algorithms. In order to achieve efficient scalability on massively parallel systems scientific software must evolve across the entire stack to exploit the multiple levels of parallelism exposed in modern architectures. In this paper we demonstrate the use of hybrid MPI/OpenMP parallelisation to optimise parallel sparse matrix-vector multiplication in PETSc, a widely used scientific library for the scalable solution of partial differential equations. Using large matrices generated by Fluidity, an open source CFD application code which uses PETSc as its linear solver engine, we evaluate the effect of explicit communication overlap using task-based parallelism and show how to further improve performance by explicitly load balancing threads within MPI processes. We demonstrate a significant speedup over the pure-MPI mode and efficient strong scaling of sparse matrix-vector multiplication on Fujitsu PRIMEHPC FX10 and Cray XE6 systems.

Includes bibliographical references (p. [295]-299) and indexes