arXiv subjects

Christian Plessl

Publications and source records attributed to Christian Plessl.

26 records · Page 2Linked to original sources

arXiv2020

Efficient Ab-Initio Molecular Dynamic Simulations by Offloading Fast Fourier Transformations to FPGAs

A large share of today's HPC workloads is used for Ab-Initio Molecular Dynamics (AIMD) simulations, where the interatomic forces are computed on-the-fly by means of accurate electronic structure calculations. They are computationally intensive and thus constitute an interesting application class for energy-efficient hardware accelerators such as FPGAs. In this paper, we investigate the potential of offloading 3D Fast Fourier Transformations (FFTs) as a critical routine of plane-wave-based electronic structure calculations to FPGA and in conjunction demonstrate the tolerance of these simulations to lower precision computations.

cs.DC↗

arXiv2020

Evaluating FPGA Accelerator Performance with a Parameterized OpenCL Adaptation of the HPCChallenge Benchmark Suite

FPGAs have found increasing adoption in data center applications since a new generation of high-level tools have become available which noticeably reduce development time for FPGA accelerators and still provide high quality of results. There is however no high-level benchmark suite available which specifically enables a comparison of FPGA architectures, programming tools and libraries for HPC applications. To fill this gap, we have developed an OpenCL-based open source implementation of the HPCC benchmark suite for Xilinx and Intel FPGAs. This benchmark can serve to analyze the current capabilities of FPGA devices, cards and development tool flows, track progress over time and point out specific difficulties for FPGA acceleration in the HPC domain. Additionally, the benchmark documents proven performance optimization patterns. We will continue optimizing and porting the benchmark for new generations of FPGAs and design tools and encourage active participation to create a valuable tool for the community.

cs.DC↗

arXiv2020

Accurate Sampling with Noisy Forces from Approximate Computing

In scientific computing, the acceleration of atomistic computer simulations by means of custom hardware is finding ever growing application. A major limitation, however, is that the high efficiency in terms of performance and low power consumption entails the massive usage of low-precision computing units. Here, based on the approximate computing paradigm, we present an algorithmic method to rigorously compensate for numerical inaccuracies due to low-accuracy arithmetic operations, yet still obtaining exact expectation values using a properly modified Langevin-type equation.

physics.comp-ph↗

arXiv2020

CP2K: An Electronic Structure and Molecular Dynamics Software Package -- Quickstep: Efficient and Accurate Electronic Structure Calculations

CP2K is an open source electronic structure and molecular dynamics software package to perform atomistic simulations of solid-state, liquid, molecular and biological systems. It is especially aimed at massively-parallel and linear-scaling electronic structure methods and state-of-the-art ab-initio molecular dynamics simulations. Excellent performance for electronic structure calculations is achieved using novel algorithms implemented for modern high-performance computing systems. This review revisits the main capabilities of CP2k to perform efficient and accurate electronic structure simulations. The emphasis is put on density functional theory and multiple post-Hartree-Fock methods using the Gaussian and plane wave approach and its augmented all-electron extension.

physics.chem-ph↗

arXiv2018

A Massively Parallel Algorithm for the Approximate Calculation of Inverse p-th Roots of Large Sparse Matrices

We present the submatrix method, a highly parallelizable method for the approximate calculation of inverse p-th roots of large sparse symmetric matrices which are required in different scientific applications. We follow the idea of Approximate Computing, allowing imprecision in the final result in order to be able to utilize the sparsity of the input matrix and to allow massively parallel execution. For an n x n matrix, the proposed algorithm allows to distribute the calculations over n nodes with only little communication overhead. The approximate result matrix exhibits the same sparsity pattern as the input matrix, allowing for efficient reuse of allocated data structures. We evaluate the algorithm with respect to the error that it introduces into calculated results, as well as its performance and scalability. We demonstrate that the error is relatively limited for well-conditioned matrices and that results are still valuable for error-resilient applications like preconditioning even for ill-conditioned matrices. We discuss the execution time and scaling of the algorithm on a theoretical level and present a distributed implementation of the algorithm using MPI and OpenMP. We demonstrate the scalability of this implementation by running it on a high-performance compute cluster comprised of 1024 CPU cores, showing a speedup of 665x compared to single-threaded execution.

cs.DC↗

arXiv2018

A General Algorithm to Calculate the Inverse Principal $p$-th Root of Symmetric Positive Definite Matrices

We address the general mathematical problem of computing the inverse $p$-th root of a given matrix in an efficient way. A new method to construct iteration functions that allow calculating arbitrary $p$-th roots and their inverses of symmetric positive definite matrices is presented. We show that the order of convergence is at least quadratic and that adaptively adjusting a parameter $q$ always leads to an even faster convergence. In this way, a better performance than with previously known iteration schemes is achieved. The efficiency of the iterative functions is demonstrated for various matrices with different densities, condition numbers and spectral radii.

math.RA↗

arXiv2017

Using Approximate Computing for the Calculation of Inverse Matrix p-th Roots

Approximate computing has shown to provide new ways to improve performance and power consumption of error-resilient applications. While many of these applications can be found in image processing, data classification or machine learning, we demonstrate its suitability to a problem from scientific computing. Utilizing the self-correcting behavior of iterative algorithms, we show that approximate computing can be applied to the calculation of inverse matrix p-th roots which are required in many applications in scientific computing. Results show great opportunities to reduce the computational effort and bandwidth required for the execution of the discussed algorithm, especially when targeting special accelerator hardware.

math.NA↗

arXiv2014

Easy-to-Use On-the-Fly Binary Program Acceleration on Many-Cores

This paper introduces Binary Acceleration At Runtime (BAAR), an easy-to-use on-the-fly binary acceleration mechanism which aims to tackle the problem of enabling existent software to automatically utilize accelerators at runtime. BAAR is based on the LLVM Compiler Infrastructure and has a client-server architecture. The client runs the program to be accelerated in an environment which allows program analysis and profiling. Program parts which are identified as suitable for the available accelerator are exported and sent to the server. The server optimizes these program parts for the accelerator and provides RPC execution for the client. The client transforms its program to utilize accelerated execution on the server for offloaded program parts. We evaluate our work with a proof-of-concept implementation of BAAR that uses an Intel Xeon Phi 5110P as the acceleration target and performs automatic offloading, parallelization and vectorization of suitable program parts. The practicality of BAAR for real-world examples is shown based on a study of stencil codes. Our results show a speedup of up to 4x without any developer-provided hints and 5.77x with hints over the same code compiled with the Intel Compiler at optimization level O2 and running on an Intel Xeon E5-2670 machine. Based on our insights gained during implementation and evaluation we outline future directions of research, e.g., offloading more fine-granular program parts than functions, a more sophisticated communication mechanism or introducing on-stack-replacement.

cs.DC↗