Subscribe to the gold package and get unlimited access to Shamra Academy
Register a new userSoftware Abstractions and Methodologies for HPC Simulation Codes on Future Architectures
149
0
0.0
(
0
)
Added by
Anshu Dubey
Publication date
2013
fields
Informatics Engineering
and research's language is
English
Ask ChatGPT about the research
No Arabic abstract
Large, complex, multi-scale, multi-physics simulation codes, running on high performance com-puting (HPC) platforms, have become essential to advancing science and engineering. These codes simulate multi-scale, multi-physics phenomena with unprecedented fidelity on petascale platforms, and are used by large communities. Continued ability of these codes to run on future platforms is as crucial to their communities as continued improvements in instruments and facilities are to experimental scientists. However, the ability of code developers to do these things faces a serious challenge with the paradigm shift underway in platform architecture. The complexity and uncertainty of the future platforms makes it essential to approach this challenge cooperatively as a community. We need to develop common abstractions, frameworks, programming models and software development methodologies that can be applied across a broad range of complex simulation codes, and common software infrastructure to support them. In this position paper we express and discuss our belief that such an infrastructure is critical to the deployment of existing and new large, multi-scale, multi-physics codes on future HPC platforms.
rate research
Read More
The Landau collision integral is an accurate model for the small-angle dominated Coulomb collisions in fusion plasmas. We investigate a high order accurate, fully conservative, finite element discretization of the nonlinear multi-species Landau integral with adaptive mesh refinement using the PETSc library (www.mcs.anl.gov/petsc). We develop algorithms and techniques to efficiently utilize emerging architectures with an approach that minimizes memory usage and movement and is suitable for vector processing. The Landau collision integral is vectorized with Intel AVX-512 intrinsics and the solver sustains as much as 22% of the theoretical peak flop rate of the Second Generation Intel Xeon Phi, Knights Landing, processor.
This deliverable reports the results of white-box methodologies and early results of the first prototype of libraries and programming abstractions as available by project month 18 by Work Package 2 (WP2). It reports i) the latest results of Task 2.2 on white-box methodologies, programming abstractions and libraries for developing energy-efficient data structures and algorithms and ii) the improved results of Task 2.1 on investigating and modeling the trade-off between energy and performance of concurrent data structures and algorithms. The work has been conducted on two main EXCESS platforms: Intel platforms with recent Intel multicore CPUs and Movidius Myriad1 platform. Regarding white-box methodologies, we have devised new relaxed cache-oblivious models and proposed a new power model for Myriad1 platform and an energy model for lock-free queues on CPU platforms. For Myriad1 platform, the im- proved model now considers both computation and data movement cost as well as architecture and application properties. The model has been evaluated with a set of micro-benchmarks and application benchmarks. For Intel platforms, we have generalized the model for concurrent queues on CPU platforms to offer more flexibility according to the workers calling the data structure (parallel section sizes of enqueuers and dequeuers are decoupled). Regarding programming abstractions and libraries, we have continued investigat- ing the trade-offs between energy consumption and performance of data structures such as concurrent queues and concurrent search trees based on the early results of Task 2.1.The preliminary results show that our concurrent trees are faster and more energy efficient than the state-of-the-art on commodity HPC and embedded platforms.
Many applications from geosciences require simulations of seismic waves in porous media. Biots theory of poroelasticity describes the coupling between solid and fluid phases and introduces a stiff source term, thereby increasing computational cost and motivating efficient methods utilising High-Performance Computing. We present a novel realisation of the discontinuous Galerkin scheme with Arbitrary DERivative time stepping (ADER-DG) that copes with stiff source terms. To integrate this source term with a reasonable time step size, we use an element-local space-time predictor, which needs to solve medium-sized linear systems - with 1000 to 10000 unknowns - in each element update (i.e., billions of times). We present a novel block-wise back-substitution algorithm for solving these systems efficiently. In comparison to LU decomposition, we reduce the number of floating-point operations by a factor of up to 25. The block-wise back-substitution is mapped to a sequence of small matrix-matrix multiplications, for which code generators are available to generate highly optimised code. We verify the new solver thoroughly in problems of increasing complexity. We demonstrate high-order convergence for 3D problems. We verify the correct treatment of point sources, material interfaces and traction-free boundary conditions. In addition, we compare against a finite difference code for a newly defined layer over half-space problem. We find that extremely high accuracy is required to resolve the slow P-wave at a free surface, while solid particle velocities are not affected by coarser resolutions. By using a clustered local time stepping scheme, we reduce time to solution by a factor of 6 to 10 compared to global time stepping. We conclude our study with a scaling and performance analysis, demonstrating our implementations efficiency and its potential for extreme-scale simulations.
In this work we present a robust interface coupling algorithm called Compact Interface quasi-Newton (CIQN). It is designed for computationally intensive applications using an MPI multi-code partitioned scheme. The algorithm allows to reuse information from previous time steps, feature that has been previously proposed to accelerate convergence. Through algebraic manipulation, an efficient usage of the computational resources is achieved by: avoiding construction of dense matrices and reduce every multiplication to a matrix-vector product and reusing the computationally expensive loops. This leads to a compact version of the original quasi-Newton algorithm. Altogether with an efficient communication, in this paper we show an efficient scalability up to 4800 cores. Three examples with qualitatively different dynamics are shown to prove that the algorithm can efficiently deal with added mass instability and two-field coupled problems. We also show how reusing histories and filtering does not necessarily makes a more robust scheme and, finally, we prove the necessity of this HPC version of the algorithm. The novelty of this article lies in the HPC focused implementation of the algorithm, detailing how to fuse and combine the composing blocks to obtain an scalable MPI implementation. Such an implementation is mandatory in large scale cases, for which the contact surface cannot be stored in a single computational node, or the number of contact nodes is not negligible compared with the size of the domain. c{opyright} <2020> Elsevier. This manuscript version is made available under the CC-BY-NC-ND 4.0 license http://creativecommons.org/licenses/by-nc-nd/4.0/
To facilitate flexible and efficient structural bioinformatics analyses, new functionality for three-dimensional structure processing and analysis has been introduced into PyCogent -- a popular feature-rich framework for sequence-based bioinformatics, but one which has lacked equally powerful tools for handling stuctural/coordinate-based data. Extensible Python modules have been developed, which provide object-oriented abstractions (based on a hierarchical representation of macromolecules), efficient data structures (e.g. kD-trees), fast implementations of common algorithms (e.g. surface-area calculations), read/write support for Protein Data Bank-related file formats and wrappers for external command-line applications (e.g. Stride). Integration of this code into PyCogent is symbiotic, allowing sequence-based work to benefit from structure-derived data and, reciprocally, enabling structural studies to leverage PyCogents versatile tools for phylogenetic and evolutionary analyses.
Log in to be able to interact and post comments
comments
Fetching comments
Sign in to be able to follow your search criteria
