1,681 research outputs found
Tackling Exascale Software Challenges in Molecular Dynamics Simulations with GROMACS
GROMACS is a widely used package for biomolecular simulation, and over the
last two decades it has evolved from small-scale efficiency to advanced
heterogeneous acceleration and multi-level parallelism targeting some of the
largest supercomputers in the world. Here, we describe some of the ways we have
been able to realize this through the use of parallelization on all levels,
combined with a constant focus on absolute performance. Release 4.6 of GROMACS
uses SIMD acceleration on a wide range of architectures, GPU offloading
acceleration, and both OpenMP and MPI parallelism within and between nodes,
respectively. The recent work on acceleration made it necessary to revisit the
fundamental algorithms of molecular simulation, including the concept of
neighborsearching, and we discuss the present and future challenges we see for
exascale simulation - in particular a very fine-grained task parallelism. We
also discuss the software management, code peer review and continuous
integration testing required for a project of this complexity.Comment: EASC 2014 conference proceedin
HeTM: Transactional Memory for Heterogeneous Systems
Modern heterogeneous computing architectures, which couple multi-core CPUs
with discrete many-core GPUs (or other specialized hardware accelerators),
enable unprecedented peak performance and energy efficiency levels.
Unfortunately, though, developing applications that can take full advantage of
the potential of heterogeneous systems is a notoriously hard task. This work
takes a step towards reducing the complexity of programming heterogeneous
systems by introducing the abstraction of Heterogeneous Transactional Memory
(HeTM). HeTM provides programmers with the illusion of a single memory region,
shared among the CPUs and the (discrete) GPU(s) of a heterogeneous system, with
support for atomic transactions. Besides introducing the abstract semantics and
programming model of HeTM, we present the design and evaluation of a concrete
implementation of the proposed abstraction, which we named Speculative HeTM
(SHeTM). SHeTM makes use of a novel design that leverages on speculative
techniques and aims at hiding the inherently large communication latency
between CPUs and discrete GPUs and at minimizing inter-device synchronization
overhead. SHeTM is based on a modular and extensible design that allows for
easily integrating alternative TM implementations on the CPU's and GPU's sides,
which allows the flexibility to adopt, on either side, the TM implementation
(e.g., in hardware or software) that best fits the applications' workload and
the architectural characteristics of the processing unit. We demonstrate the
efficiency of the SHeTM via an extensive quantitative study based both on
synthetic benchmarks and on a porting of a popular object caching system.Comment: The current work was accepted in the 28th International Conference on
Parallel Architectures and Compilation Techniques (PACT'19
Proceedings of the First PhD Symposium on Sustainable Ultrascale Computing Systems (NESUS PhD 2016)
Proceedings of the First PhD Symposium on Sustainable Ultrascale Computing Systems (NESUS PhD 2016) Timisoara, Romania. February 8-11, 2016.The PhD Symposium was a very good opportunity for the young researchers to share information and knowledge, to
present their current research, and to discuss topics with other students in order to look for synergies and common research
topics. The idea was very successful and the assessment made by the PhD Student was very good. It also helped to
achieve one of the major goals of the NESUS Action: to establish an open European research network targeting sustainable
solutions for ultrascale computing aiming at cross fertilization among HPC, large scale distributed systems, and big
data management, training, contributing to glue disparate researchers working across different areas and provide a meeting
ground for researchers in these separate areas to exchange ideas, to identify synergies, and to pursue common activities in
research topics such as sustainable software solutions (applications and system software stack), data management, energy
efficiency, and resilience.European Cooperation in Science and Technology. COS
Insights on Memory Controller Scaling for Multicore Embedded Systems
In recent years, the growth of the number of cores as well as the frequency of cores along different processor generations has proportionally increased bandwidth needs simultaneously in both CPU and GPU systems. In order to address the communication latency between CPU and GPU memories in recent implementation of heterogeneous mobile embedded systems with hard or firm real-time requirements, sharing the same address space adds significant levels of contention. In addition, when heterogeneous cores are simultaneously present in a single system, memory parallelism is significantly restricted by a small amount of memory controllers (MCs). As a strategy to approach these significant levels of memory pressure, it is proposed in this paper evaluations of the impact of scaling MCs up to four to eight units - limited by motherboard size for embedded purposes. Our findings show that performance is enhanced by a factor of 4Ă— when employing only CPU cores, 4.6Ă— when only GPU cores and finally, 2Ă— when both CPU and GPU cores are simultaneously considered
GPU devices for safety-critical systems: a survey
Graphics Processing Unit (GPU) devices and their associated software programming languages and frameworks can deliver the computing performance required to facilitate the development of next-generation high-performance safety-critical systems such as autonomous driving systems. However, the integration of complex, parallel, and computationally demanding software functions with different safety-criticality levels on GPU devices with shared hardware resources contributes to several safety certification challenges. This survey categorizes and provides an overview of research contributions that address GPU devices’ random hardware failures, systematic failures, and independence of execution.This work has been partially supported by the European Research Council with Horizon 2020 (grant agreements No. 772773 and 871465), the Spanish Ministry of Science and Innovation under grant PID2019-107255GB, the HiPEAC Network of Excellence and the Basque Government under grant KK-2019-00035. The Spanish Ministry of Economy and Competitiveness has also partially supported Leonidas Kosmidis with a Juan de la Cierva Incorporación postdoctoral fellowship (FJCI-2020- 045931-I).Peer ReviewedPostprint (author's final draft
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