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At least 253 records · Page 14

Evaluating Performance and Power Efficiency of Scientific Applications on Multi-threaded Systems

The power and energy walls are changing the way users utilize supercomputers: Time-to-completion is not the only important goal but other metrics, such as the energy required to solve a problem or the power efficiency, are becoming as important as performance. In this paper we analyze the performance, power efficiency and energy consumption of scientific applications programmed in MPI, OpenMP and MPI+OpenMP on two different architectures that have take different approach to limit power consumption, IBM POWER7+ and AMD Interlagos.

Gioiosa, Roberto↗

Elastic-plastic analysis using a triangular ring element in NASTRAN

An elastic plastic triangular ring element is implemented in NASTRAN computer program. The plane strain problem of partially plastic thick walled cylinder under internal pressure is solved and compared with the earlier finite difference solution. A very good agreement has been reached. In order to demonstrate its application to more general problems, an overloaded thread problem for the British Standard Buttress is examined. The maximum axial and principal stresses are located and their values are determined as functions of loadings.

Chen, P. C. T.↗

Efficient Parallelization of a Dynamic Unstructured Application on the Tera MTA

The success of parallel computing in solving real-life computationally-intensive problems relies on their efficient mapping and execution on large-scale multiprocessor architectures. Many important applications are both unstructured and dynamic in nature, making their efficient parallel implementation a daunting task. This paper presents the parallelization of a dynamic unstructured mesh adaptation algorithm using three popular programming paradigms on three leading supercomputers. We examine an MPI message-passing implementation on the Cray T3E and the SGI Origin2OOO, a shared-memory implementation using cache coherent nonuniform memory access (CC-NUMA) of the Origin2OOO, and a multi-threaded version on the newly-released Tera Multi-threaded Architecture (MTA). We compare several critical factors of this parallel code development, including runtime, scalability, programmability, and memory overhead. Our overall results demonstrate that multi-threaded systems offer tremendous potential for quickly and efficiently solving some of the most challenging real-life problems on parallel computers.

Oliker, Leonid↗

Cooperative Data Sharing: Simple Support for Clusters of SMP Nodes

Libraries like PVM and MPI send typed messages to allow for heterogeneous cluster computing. Lower-level libraries, such as GAM, provide more efficient access to communication by removing the need to copy messages between the interface and user space in some cases. still lower-level interfaces, such as UNET, get right down to the hardware level to provide maximum performance. However, these are all still interfaces for passing messages from one process to another, and have limited utility in a shared-memory environment, due primarily to the fact that message passing is just another term for copying. This drawback is made more pertinent by today's hybrid architectures (e.g. clusters of SMPs), where it is difficult to know beforehand whether two communicating processes will share memory. As a result, even portable language tools (like HPF compilers) must either map all interprocess communication, into message passing with the accompanying performance degradation in shared memory environments, or they must check each communication at run-time and implement the shared-memory case separately for efficiency. Cooperative Data Sharing (CDS) is a single user-level API which abstracts all communication between processes into the sharing and access coordination of memory regions, in a model which might be described as "distributed shared messages" or "large-grain distributed shared memory". As a result, the user programs to a simple latency-tolerant abstract communication specification which can be mapped efficiently to either a shared-memory or message-passing based run-time system, depending upon the available architecture. Unlike some distributed shared memory interfaces, the user still has complete control over the assignment of data to processors, the forwarding of data to its next likely destination, and the queuing of data until it is needed, so even the relatively high latency present in clusters can be accomodated. CDS does not require special use of an MMU, which can add overhead to some DSM systems, and does not require an SPMD programming model. unlike some message-passing interfaces, CDS allows the user to implement efficient demand-driven applications where processes must "fight" over data, and does not perform copying if processes share memory and do not attempt concurrent writes. CDS also supports heterogeneous computing, dynamic process creation, handlers, and a very simple thread-arbitration mechanism. Additional support for array subsections is currently being considered. The CDS1 API, which forms the kernel of CDS, is built primarily upon only 2 communication primitives, one process initiation primitive, and some data translation (and marshalling) routines, memory allocation routines, and priority control routines. The entire current collection of 28 routines provides enough functionality to implement most (or all) of MPI 1 and 2, which has a much larger interface consisting of hundreds of routines. still, the API is small enough to consider integrating into standard os interfaces for handling inter-process communication in a network-independent way. This approach would also help to solve many of the problems plaguing other higher-level standards such as MPI and PVM which must, in some cases, "play OS" to adequately address progress and process control issues. The CDS2 API, a higher level of interface roughly equivalent in functionality to MPI and to be built entirely upon CDS1, is still being designed. It is intended to add support for the equivalent of communicators, reduction and other collective operations, process topologies, additional support for process creation, and some automatic memory management. CDS2 will not exactly match MPI, because the copy-free semantics of communication from CDS1 will be supported. CDS2 application programs will be free to carefully also use CDS1. CDS1 has been implemented on networks of workstations running unmodified Unix-based operating systems, using UDP/IP and vendor-supplied high- performance locks. Although its inter-node performance is currently unimpressive due to rudimentary implementation technique, it even now outperforms highly-optimized MPI implementation on intra-node communication due to its support for non-copy communication. The similarity of the CDS1 architecture to that of other projects such as UNET and TRAP suggests that the inter-node performance can be increased significantly to surpass MPI or PVM, and it may be possible to migrate some of its functionality to communication controllers.

DiNucci, David C.↗

Fiscal Year 2024 Software Quality Assurance Activities for the ARC Software

The continued goal of the ARC SQA project in the Advanced Reactor Technologies program of DOE is to resolve the QA gaps for the ARC software that limit, or prevent, commercialization of the software for industry users. This project started in earnest in fiscal year 2023 which saw the entire code system moved from a SVN repository to a GitLab repository and an associated software quality assurance plan (SQAP) developed and ratified. Most of the QA gaps in the ARC software were identified in collaboration with industry partners and work begin in fiscal year 2023 and continued in 2024. The primary documentation that is missing includes user manuals, user guides, software verification reports, and code coverage assessments. The SUMMAR manual was completed this fiscal year and work was started on creating manuals for SE2ANL, SE2RCT, and DASSH. Software verification work was carried out for DIF3D and REBUS in a previous program and the current fiscal year saw the completion of software verification reports for GAMSOR, GAMSRC, VARPOW, EvaluateFlux, and SUMMAR. The goal for the next fiscal year is to complete the PERSENT software verification work and begin planning the software verification work for DASSH, SE2ANL, and SE2RCT. The code coverage reports for DIF3D and MC2-3 were completed in the previous fiscal year and the goal is to generate code coverage reports for REBUS, GAMSOR, PERSENT, and DASSH in the coming fiscal year. A considerable amount of effort was spent in the current fiscal year working on the continuous integration capability for automated regression testing in GitLab. The first version of the testing was created in the previous fiscal year and applied to DIF3D and its utility programs. That testing was extended this year to cover GAMSOR, REBUS, and PERSENT. To accomplish this, the first version of the new testing methodology had to be updated to make a single output checking methodology viable for all of the ARC software. This will result in a single document to detail the automated regression testing methodology and minor documents to detail the tolerance settings that have been applied to the output for each ARC code. The previous methodology put into place with SVN would have required a separate document for each ARC code to detail the output checking methodology and the tolerance settings for the output from each code. Because some of our industry partners are providing funds to add new capabilities to the ARC software to meet their needs, all of which must be reviewed and approved by the SQA program funded by this project, a summary of that development work is detailed in this report. Overall progress on resolving the QA gaps has been good this year with the most impactful improvement for our industry partners in capability being the creation of a threaded version of DIF3D-VARIANT that allows the DIF3D, REBUS, and GAMSOR run times to be reduced by a factor of 4-6. The most impactful QA gap that was resolved was the software verification of GAMSRC and VARPOW.

97 MATHEMATICS AND COMPUTING↗

Lessons Learned in Architecting Human Spaceflight Programs

This paper discusses the fundamentals of architecting a major human spaceflight program and the lessons that can be learned from Constellation. Constellation is/was NASA's program to implement a new generation of human exploration missions to the moon and beyond. It is/was a tightly-coupled program where a unique set of architectural challenges can be seen and evaluated to better understand how architecting of such systems can be improved upon in the future. While the specific issues discussed in this paper derive from the current Constellation architecture they share threads with previously-crewed systems including Apollo and Shuttle and are likely to be common to any human exploration system or system of significant technical and programmatic complexity.

Muirhead, Brian↗

Kokkos: Enabling manycore performance portability through polymorphic memory access patterns

The manycore revolution can be characterized by increasing thread counts, decreasing memory per thread, and diversity of continually evolving manycore architectures. High performance computing (HPC) applications and libraries must exploit increasingly finer levels of parallelism within their codes to sustain scalability on these devices. We found that a major obstacle to performance portability is the diverse and conflicting set of constraints on memory access patterns across devices. Contemporary portable programming models address manycore parallelism (e.g., OpenMP, OpenACC, OpenCL) but fail to address memory access patterns. The Kokkos C++ library enables applications and domain libraries to achieve performance portability on diverse manycore architectures by unifying abstractions for both fine-grain data parallelism and memory access patterns. In this paper we describe Kokkos’ abstractions, summarize its application programmer interface (API), present performance results for unit-test kernels and mini-applications, and outline an incremental strategy for migrating legacy C++ codes to Kokkos. Furthermore, the Kokkos library is under active research and development to incorporate capabilities from new generations of manycore architectures, and to address a growing list of applications and domain libraries.

97 MATHEMATICS AND COMPUTING↗

Report on Progress of correlation of in-situ and ex-situ data and the use of artificial intelligence to predict defects

The Transformational Challenge Reactor (TCR) program is leveraging additive manufacturing (AM) technologies to fabricate nuclear components which will be assembled into a fully functional microreactor core. Compared with traditional manufacturing technologies, AM technologies allow (1) real-time observation of the manufacturing process at a much higher resolution using in-situ monitoring technologies to capture the sensor signatures that scientifically describe each event occurring over time and space and (2) validation of the manufacturing process quality using domain-informed data analytics techniques as a potential qualification and certification methodology for the final component. This report provides an update on the program work on in-situ and ex-situ data correlation and associated data analytics results. Examples are provided to illustrate progress with respect to laser powder bed fusion (L-PBF), binder jetting, computed tomography (CT) reconstruction, and mechanical testing. Elements of the Digital Thread and data management infrastructure are discussed in the main document, and an extensive supplemental appendix is provided detailing the Digital Platform, as well as its implementation and subcomponents. In conclusion, the path forward for the next fiscal year is also discussed.

42 ENGINEERING↗

Effects of Ordering Strategies and Programming Paradigms on Sparse Matrix Computations

The Conjugate Gradient (CG) algorithm is perhaps the best-known iterative technique to solve sparse linear systems that are symmetric and positive definite. For systems that are ill-conditioned, it is often necessary to use a preconditioning technique. In this paper, we investigate the effects of various ordering and partitioning strategies on the performance of parallel CG and ILU(O) preconditioned CG (PCG) using different programming paradigms and architectures. Results show that for this class of applications: ordering significantly improves overall performance on both distributed and distributed shared-memory systems, that cache reuse may be more important than reducing communication, that it is possible to achieve message-passing performance using shared-memory constructs through careful data ordering and distribution, and that a hybrid MPI+OpenMP paradigm increases programming complexity with little performance gains. A implementation of CG on the Cray MTA does not require special ordering or partitioning to obtain high efficiency and scalability, giving it a distinct advantage for adaptive applications; however, it shows limited scalability for PCG due to a lack of thread level parallelism.

Oliker, Leonid↗

NSTX-U Advances in Real-Time C++11 on Linux

Programming languages like C and Ada combined with proprietary embedded operating systems have dominated the real-time application space for decades. The new C++11standard includes native, language-level support for concurrency, a required feature for any nontrivial event-oriented real-time software. Threads, Locks, and Atomics now exist to provide the necessary tools to build the structures that make up the foundation of a complex real-time system. The National Spherical Torus Experiment Upgrade (NSTX-U) at the Princeton Plasma Physics Laboratory (PPPL) is breaking new ground with the language as applied to the needs of fusion devices. A new Digital Coil Protection System (DCPS) will serve as the main protection mechanism for the magnetic coils, and it is written entirely in C++11 running on Concurrent Computer Corporation's real-time operating system, RedHawk Linux. It runs over 600 algorithms in a 5 kHz control loop that determine whether or not to shut down operations before physical damage occurs. To accomplish this, NSTX-U engineers developed software tools that do not currently exist elsewhere, including real-time atomic synchronization, real-time containers, and a real-time logging framework. Together with a recent (and carefully configured) version of the GCC compiler, these tools enable data acquisition, processing, and output using a conventional operating system to meet a hard real-time deadline (that is, missing one periodic is a failure) of 200 microseconds.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

The Kokkos Ecosystem [Brief]

In 2016/2017, the field of High-Performance Computing (HPC) entered a new era driven by fundamental physics challenges to produce ever more energy and cost-efficient processors. Since the convergence on the Message-Passing Interface (MPI) standard in the mid-1990s, application developers enjoyed a seemingly static view of the underlying machine — that of a distributed collection of homogeneous nodes executing in collaboration. However, after almost two decades of dominance, the sole use of MPI to derive parallelism acted as a limiter to improved future performance. While MPI is widely expected to continue to function as the basic mechanism for communication between compute nodes for the immediate future, additional parallelism is required on the computing node itself if high performance and efficiency goals are to be realized. When reviewing the architectures of the top HPC systems today, the change in paradigm is clear: the compute nodes of the leading machines in the world are either powered by many-core chips with a few dozen cores each, or use heterogeneous designs, where traditional CPUs marshal work to massively parallel compute accelerators which has as many as 200,000 processing threads in flight simultaneously. Complicating matters further for application developers, each processor vendor has its own preferred way of writing code for their architecture.The Kokkos EcoSystem was released by Sandia in 2017 to address this new era in HPC system design by providing a vendor independent performance portable programming system for scientific, engineering, and mathematical software applications written in the C++ programming language. Using Kokkos, application developers can be more productive because they will not have to create and maintain separate versions of their software for each architecture, nor will they have to be experts in each architecture's peculiar requirements. Instead, they will have a single method of programming for the diverse set of modern HPC architectures. While Kokkos started in 2011 as a programming model only, it soon became clear that complex applications needed more. It is also critical to have a portable mathematical functions and developers need tools to debug their applications, gain insight into the performance characteristics of their codes and tune algorithm performance parameters through automated processes. The Kokkos EcoSystem addresses those needs through its three main components: the Kokkos Core programming model, the Kokkos Kernels math library, and the Kokkos Tools project.

97 MATHEMATICS AND COMPUTING↗

Optimizing the hit finding algorithm for liquid argon TPC neutrino detectors using parallel architectures

Neutrinos are particles that interact rarely, so identifying them requires large detectors which produce lots of data. Processing this data with the computing power available is becoming even more difficult as the detectors increase in size to reach their physics goals. Liquid argon time projection chamber (LArTPC) neutrino experiments are expected to grow in the next decade to have 100 times more wires than in currently operating experiments, and modernization of LArTPC reconstruction code, including parallelization both at data- and instruction-level, will help to mitigate this challenge. The LArTPC hit finding algorithm is used across multiple experiments through a common software framework. In this paper we discuss a parallel implementation of this algorithm. Using a standalone setup we find speedup factors of two times from vectorization and 30–100 times from multi-threading on Intel architectures. The new version has been incorporated back into the framework so that it can be used by experiments. On a serial execution, the integrated version is about 10 times faster than the previous one and, once parallelization is enabled, more speedups comparable to the standalone program are achieved.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

VTK-m User's Guide (V.1.6)

High-performance computing relies on ever finer threading. Advances in processor technology include ever greater numbers of cores, hyperthreading, accelerators with integrated blocks of cores, and special vectorized instructions, all of which require more software parallelism to achieve peak performance. Traditional visualization solutions cannot support this extreme level of concurrency. Extreme scale systems require a new programming model and a fundamental change in how we design algorithms. To address these issues we created VTK-m: the visualization toolkit for multi-/many-core architectures.

97 MATHEMATICS AND COMPUTING↗

VTK-m User's' Guide (V.1.7)

High-performance computing relies on ever finer threading. Advances in processor technology include ever greater numbers of cores, hyperthreading, accelerators with integrated blocks of cores, and special vectorized instructions, all of which require more software parallelism to achieve peak performance. Traditional visualization solutions cannot support this extreme level of concurrency. Extreme scale systems require a new programming model and a fundamental change in how we design algorithms. To address these issues we created VTK-m: the visualization toolkit for multi-/many-core architectures. VTK-m supports a number of algorithms and the ability to design further algorithms through a top-down design with an emphasis on extreme parallelism. VTK-m also provides support for finding and building links across topologies, making it possible to perform operations that determine manifold surfaces, interpolate generated values, and find adjacencies. Although VTK-m provides a simplified high-level interface for programming, its template-based code removes the overhead of abstraction. VTK-m simplifies the development of parallel scientific visualization algorithms by providing a framework of supporting functionality that allows developers to focus on visualization operations. Consider the listings in Figure 1.1 that compares the size of the implementation for the Marching Cubes algorithm in VTK-m with the equivalent reference implementation in the CUDA software development kit. Because VTK-m internally manages the parallel distribution of work and data, the VTK-m implementation is shorter and easier to maintain. Additionally, VTK-m provides data abstractions not provided by other libraries that make code written in VTK-m more versatile.This book includes contributions from the VTK-m community including the VTK-m development team and the user community.

97 MATHEMATICS AND COMPUTING↗

The VTK-m Users' Guide (V.1.9)

High-performance computing relies on ever finer threading. Advances in processor technology include ever greater numbers of cores, hyperthreading, accelerators with integrated blocks of cores, and special vectorized instructions, all of which require more software parallelism to achieve peak performance. Traditional visualization solutions cannot support this extreme level of concurrency. Extreme scale systems require a new programming model and a fundamental change in how we design algorithms. To address these issues we created VTK-m: the visualization toolkit for multi-/many-core architectures. VTK-m supports a number of algorithms and the ability to design further algorithms through a top-down design with an emphasis on extreme parallelism. VTK-m also provides support for finding and building links across topologies, making it possible to perform operations that determine manifold surfaces, interpolate generated values, and find adjacencies. Although VTK-m provides a simplified high-level interface for programming, its template-based code removes the overhead of abstraction. VTK-m simplifies the development of parallel scientific visualization algorithms by providing a framework of supporting functionality that allows developers to focus on visualization operations. Consider the listings in Figure 1.1 that compares the size of the implementation for the Marching Cubes algorithm in VTK-m with the equivalent reference implementation in the CUDA software development kit. Because VTK-m internally manages the parallel distribution of work and data, the VTK-m implementation is shorter and easier to maintain. Additionally, VTK-m provides data abstractions not provided by other libraries that make code written in VTK-m more versatile.

97 MATHEMATICS AND COMPUTING↗

The VTK-m Users' Guide (V.2.0)

High-performance computing relies on ever finer threading. Advances in processor technology include ever greater numbers of cores, hyperthreading, accelerators with integrated blocks of cores, and special vectorized instructions, all of which require more software parallelism to achieve peak performance. Traditional visualization solutions cannot support this extreme level of concurrency. Extreme scale systems require a new programming model and a fundamental change in how we design algorithms. To address these issues we created VTK-m: the visualization toolkit for multi-/many-core architectures. VTK-m supports a number of algorithms and the ability to design further algorithms through a top-down design with an emphasis on extreme parallelism. VTK-m also provides support for finding and building links across topologies, making it possible to perform operations that determine manifold surfaces, interpolate generated values, and find adjacencies. Although VTK-m provides a simplified high-level interface for programming, its template-based code removes the overhead of abstraction. VTK-m simplifies the development of parallel scientific visualization algorithms by providing a framework of supporting functionality that allows developers to focus on visualization operations. Consider the listings in Figure 1.1 that compares the size of the implementation for the Marching Cubes algorithm in VTK-m with the equivalent reference implementation in the CUDA software development kit. Because VTK-m internally manages the parallel distribution of work and data, the VTK-m implementation is shorter and easier to maintain. Additionally, VTK-m provides data abstractions not provided by other libraries that make code written in VTK-m more versatile.

97 MATHEMATICS AND COMPUTING↗

The VTK-m User's Guide (V. 2.2)

High-performance computing relies on ever finer threading. Advances in processor technology include ever greater numbers of cores, hyperthreading, accelerators with integrated blocks of cores, and special vectorized instructions, all of which require more software parallelism to achieve peak performance. Traditional visualization solutions cannot support this extreme level of concurrency. Extreme scale systems require a new programming model and a fundamental change in how we design algorithms. To address these issues we created VTK-m: the visualization toolkit for multi-/many-core architectures. VTK-m supports a number of algorithms and the ability to design further algorithms through a top-down design with an emphasis on extreme parallelism. VTK-m also provides support for finding and building links across topologies, making it possible to perform operations that determine manifold surfaces, interpolate generated values, and find adjacencies. Although VTK-m provides a simplified high-level interface for programming, its template-based code removes the overhead of abstraction.

97 MATHEMATICS AND COMPUTING↗

The Viskores User's Guide (V.1.0)

High-performance computing relies on ever finer threading. Advances in processor technology include ever greater numbers of cores, hyperthreading, accelerators with integrated blocks of cores, and special vectorized instructions, all of which require more software parallelism to achieve peak performance. Traditional visualization solutions cannot support this extreme level of concurrency. Extreme scale systems require a new programming model and a fundamental change in how we design algorithms. To address these issues we created Viskores: the visualization toolkit for multi-/many-core architectures. Viskores supports a number of algorithms and the ability to design further algorithms through a top-down design with an emphasis on extreme parallelism. Viskores also provides support for finding and building links across topologies, making it possible to perform operations that determine manifold surfaces, interpolate generated values, and find adjacencies. Although Viskores provides a simplified high-level interface for programming, its template-based code removes the overhead of abstraction.

97 MATHEMATICS AND COMPUTING↗