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Evaluating GPU Passthrough in Xen for High Performance Cloud Computing

Andrew J. Younge, John Paul Walters, Stephen Crago, Geoffrey C. Fox
2014 2014 IEEE International Parallel & Distributed Processing Symposium Workshops  
We look to bridge the gap between supercomputing and clouds by providing GPU-enabled virtual machines (VMs) and investigating their feasibility for advanced scientific computation.  ...  With the advent of virtualization and Infrastructure-as-a-Service (IaaS), the broader scientific computing community is considering the use of clouds for their technical computing needs.  ...  Test-bed" Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the NSF.  ... 
doi:10.1109/ipdpsw.2014.97 dblp:conf/ipps/YoungeWCF14 fatcat:nwpmtctgbnai7nyjdyh54xqr6m

Expanding the boundaries of ligand–target modeling by exascale calculations

Viacheslav Bolnykh, Giulia Rossetti, Ursula Rothlisberger, Paolo Carloni
2021 Wiley Interdisciplinary Reviews. Computational Molecular Science  
Molecular simulations and molecular docking are widely used tools to investigate ligand/target interactions and in drug design.  ...  computing, molecular dynamics, ligand-target modeling | INTRODUCTION Modeling plays a key role in drug discovery and design. 1,2 Developing a new drug molecule can cost up to $2.6 billion: the use of computational  ...  focusing on technical aspects of high-performance computing (HPC) aspects particularly relevant for MD and molecular docking.  ... 
doi:10.1002/wcms.1535 fatcat:wwu4ixhvhngivkz4olvzm3c6r4

On the Feasibility of FPGA Acceleration of Molecular Dynamics Simulations [article]

Michael Schaffner, Luca Benini
2018 arXiv   pre-print
Classical molecular dynamics (MD) simulations are important tools in life and material sciences since they allow studying chemical and biological processes in detail.  ...  However, we also note that scaled multi-node systems could potentially benefit from a hybrid composition, where GPUs are used for compute intensive parts and FPGAs for latency and communication sensitive  ...  Possible arrangements could be 1 FPGA network card per node and a 2D or 3D torus. To this end, initial studies on 3D FFTs for molecular dynamics on FPGA clouds by Herbordt, et al.  ... 
arXiv:1808.04201v1 fatcat:yzos5gym5ndojoooesfsmw2iwq

D9.2.1: First Report on Multi-Petascale to Exascale Software

Volker Strumpen
2011 Zenodo  
To that end we have surveyed and evaluated the state-of-the-art in high-performance computer systems, parallel programming languages, and system software and tools.  ...  We summarize our findings separately by topic: computer systems, parallel programming languages and system software and tools.  ...  Our discussion focuses on the implications of the hardware trends on the software for exascale supercomputer systems.  ... 
doi:10.5281/zenodo.6552877 fatcat:2bluglv435ew5chaauw2ppdhl4

Eurolab-4-HPC Long-Term Vision on High-Performance Computing [article]

Theo Ungerer, Paul Carpenter
2018 arXiv   pre-print
The objective of the Eurolab-4-HPC vision is to provide a long-term roadmap from 2023 to 2030 for High-Performance Computing (HPC).  ...  The proposal on research topics is derived from the report and discussions within the road mapping expert group.  ...  Accelerators will be "application class" based, e.g. for deep learning (such as Google's TPU and Fujitsu's DLU), molecular dynamics, or other important domains.  ... 
arXiv:1807.04521v1 fatcat:5neetrgubjhnvcajcktpkohrzq

ETP4HPC's Strategic Research Agenda for High-Performance Computing in Europe 4 [article]

Michael Malms, Marcin Ostasz, Maike Gilliot, Pascale Bernier-Bruna, Laurent Cargemel, Estela Suarez, Herbert Cornelius, Marc Duranton, Benny Koren, Pascale Rosse-Laurent, María S. Pérez-Hernández, Manolis Marazakis (+11 others)
2020 Zenodo  
This Strategic Research Agenda (SRA) is the fourth High Performance Computing (HPC) technology roadmap developed and maintained by ETP4HPC, with the support of the EXDCI-2 project.  ...  The main objective of this SRA is to identify the European technology research priorities in the area of HPC and High-Performance Data Analytics (HPDA), which should be used by EuroHPC to build its 2021  ...  commercial clouds and HPC centres5.  ... 
doi:10.5281/zenodo.4605343 fatcat:lcsgbea5dzgdfmj5dkw6pr7vni

Toxicity Analysis and Cry Gene Profiling of Bacillus Thuringiensis Isolated from Western Ghats of Tamil Nadu State, India

A. Ramalakshmi, P. Annakodi, V. Udayasurian, V. Balasubramani
2018 Proceedings of the Indian National Science Academy  
In fact, there were methods of storing like Quipu of Incas and tools for calculating like Chinese counting rods.  ...  Computing as a discipline is a recent one even though the practice of using mechanical aids for calculation can have various dates based on the perspective of the reader like Blaise Pascal in 1600s, George  ...  for 3D parallel basin modelling along with results [Mello et al., 2009] using 1024 nodes on Blue Gene/P.  ... 
doi:10.16943/ptinsa/2018/49413 fatcat:2w6rohpbava5zh6m26tsiz7qky

French SKA White Book - The French Community towards the Square Kilometre Array [article]

F. Acero, J.-T. Acquaviva, R. Adam, N. Aghanim, M. Allen, M. Alves, R. Ammanouil, R. Ansari, A. Araudo, E. Armengaud, B. Ascaso, E. Athanassoula (+157 others)
2018 arXiv   pre-print
From its Phase 1, the SKA will be one of the most formidable scientific machines ever deployed by mankind, and by far the most impressive in terms of data throughput and required computing power.  ...  The "Square Kilometre Array" (SKA) is a large international radio telescope project characterised, as suggested by its name, by a total collecting area of approximately one square kilometre, and consisting  ...  The nature of the H i associated with a molecular cloud (e.g., its temperature distribution, the velocity field of the H i) is needed to inform on how molecular clouds form and on what timescale.  ... 
arXiv:1712.06950v3 fatcat:t22beqb7s5brtomaqqeroetmyu

Portuguese SKA White Book [article]

Domingos Barbosa, Sonia Antón, João Paulo Barraca, Miguel Bergano, Alexandre C. M. Correia, Dalmiro Maia, Valério A. R. M. Ribeiro
2020 arXiv   pre-print
This white book stems from the contributions presented at the Portuguese SKA Days, held on the 6th and 7th February 2018 with the presence of the SKA Deputy Director General Alistair McPherson and the  ...  and Technology Foundation (FCT) with the contribution of Portuguese policy makers and researchers.  ...  support about the international interest on the Azores VLBI cluster.  ... 
arXiv:2005.01140v1 fatcat:gijmylrmvfcj3i7dt3wbsr6vhm

Accelerating Molecular Docking by Parallelized Heterogeneous Computing - A Case Study of Performance, Quality of Results, and Energy-Efficiency using CPUs, GPUs, and FPGAs

Leonardo Solis Vasquez
While a data-parallel approach has proven its effectiveness in accelerating AutoDock on CPUs and GPUs, it was observed that for FPGAs, such approach resulted in slower executions in the range of three-orders  ...  To overcome this drawback, a task-parallel implementation for FPGAs is discussed as well.  ...  Using this strategy on benchmarks from the Rodinia suite and molecular-dynamic codes results in designs achieving speedups around {37x, 4.8x, 3.5x} over {OpenCL designs on FPGAs, GPUs, and Verilog designs  ... 
doi:10.25534/tuprints-00009288 fatcat:xcrjmaerufe7raqszinr4t7ypa

Reconstructing Hardware Transactional Memory for Workload Optimized Systems [chapter]

Kunal Korgaonkar, Prabhat Jain, Deepak Tomar, Kashyap Garimella, Veezhinathan Kamakoti
2011 Lecture Notes in Computer Science  
The two-day technical program of APPT 2011 provided an excellent venue capturing the state of the art and practice in parallel architectures, parallel software and distributed and cloud computing.  ...  This biennial event provides a forum for representing this community's research efforts and exchanging viewpoints.  ...  However, some irregular applications, like 3D-lbm and gafort, are not so suitable for executing on GPUs, showing poor speedups [2] .  ... 
doi:10.1007/978-3-642-24151-2_1 fatcat:32cx745cn5cfdm5sbeah6eyiey

Towards Closing the Programmability-Efficiency Gap using Software-Defined Hardware [article]

Subhankar Pal, University, My
The solution consists of a tiled hardware architecture, co-designed with the outer product algorithm for Sparse Matrix-Matrix multiplication (SpMM), that uses on-chip memory reconfiguration to accelerate  ...  of 12.6x and 17.1x over a high-end CPU, and serves as a stepping stone towards a full SDH system.  ...  [222] introduce a 3D-stacked logic-in-memory system by placing logic layers between Dynamic Random Access Memory (DRAM) dies to accelerate a 3D-DRAM system for sparse data access and build a custom  ... 
doi:10.7302/2904 fatcat:zraktiwmczc7bkmqqxrvuxdiue

The GAP project: GPU applications for High Level Trigger and Medical Imaging

Matteo Bauce, Andrea Messina, Marco Rescigno, Stefano Giagu, Gianluca Lamanna, Massimiliano Fiorini
In this paper we focus on the application of GPUs in asynchronous trigger systems, employed for the high level trigger of LHC experiments.  ...  In this paper we focus on the application of GPUs in asynchronous trigger systems, employed for the high level trigger of LHC experiments.  ...  All procedures for MC simulations are realized in OpenCL and are optimized for execution on GPUs.  ... 
doi:10.3204/desy-proc-2014-05/1 fatcat:itmpu5ru3vex5oamv4ldjuja3y

Proceedings of the GPU Computing in High-Energy Physics 2014 Conference (GPUHEP2014)

Claudio Bonati, Massimo D'Elia, Gianluca Lamanna, Marco Sozzi
for newcomers interested to learn more about the use of GPUs as accelerators for scientific progress on the elementary constituents of matter and energy.  ...  on GPUs • Use of GPUs in high-level trigger systems • GPUs in tracking and vertexing • Challenges for triggers in future HEP experiments • Reconstruction and Monte Carlo software on GPUs • Software frameworks  ...  All procedures for MC simulations are realized in OpenCL and are optimized for execution on GPUs.  ... 
doi:10.3204/desy-proc-2014-05 fatcat:ghvy6mkhfzcnpgj3rag4jaiyje

Unstructured Computations on Emerging Architectures

Mohammed Al Farhan
We therefore employ low- and high-level algorithmic- and architecture-specific code optimizations and tuning in light of thread- and data-level parallelism, with a focus on strong thread scaling at the  ...  This dissertation describes detailed performance engineering and optimization of an unstructured computational aerodynamics software system with irregular memory accesses on various multi- and many-core  ...  For example, seismic [113] , stencil [114, 115] , electromagnetic [116] , molecular dynamics [117, 118] , FMM [119] , tensors [120] , machine learning and deep learning [121, 122, 123, 124, 125,  ... 
doi:10.25781/kaust-7912h fatcat:znemkptd7vcrddkl2trlygwg4u
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