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Efficient Execution of Microscopy Image Analysis on CPU, GPU, and MIC Equipped Cluster Systems

G. Andrade, R. Ferreira, George Teodoro, Leonardo Rocha, Joel H. Saltz, Tahsin Kurc
2014 2014 IEEE 26th International Symposium on Computer Architecture and High Performance Computing  
outperforms other efficient scheduling techniques, such as Heterogeneous Earliest Finish Time - HEFT, in cooperative executions using CPUs, GPUs, and MICs.  ...  These processors have made available a tremendous computing power at low cost, and are transforming machines into hybrid systems equipped with CPUs and accelerators.  ...  from the NLM, and part by CNPq, CAPES, FINEP, Fapemig, and INWEB.  ... 
doi:10.1109/sbac-pad.2014.15 pmid:26640423 pmcid:PMC4670037 fatcat:u3puegccpzfzncwpxjzr5ye4su

Application performance analysis and efficient execution on systems with multi-core CPUs, GPUs and MICs: a case study with microscopy image analysis

George Teodoro, Tahsin Kurc, Guilherme Andrade, Jun Kong, Renato Ferreira, Joel Saltz
2016 The international journal of high performance computing applications  
We carry out a comparative performance study of multi-core CPUs, GPUs and Intel Xeon Phi (Many Integrated Core-MIC) with a microscopy image analysis application.  ...  GPUs are more efficient than MICs for operations that access data irregularly, because of the lower bandwidth of the MIC for random data accesses.  ...  , National Institutes of Health (NIH) K25CA181503 and by CNPq, CAPES, FINEP, Fapemig, and INWEB.  ... 
doi:10.1177/1094342015594519 pmid:28239253 pmcid:PMC5319667 fatcat:tchtmfozwfc57hosfna43behoy

Performance Analysis and Efficient Execution on Systems with multi-core CPUs, GPUs and MICs [article]

George Teodoro, Tahsin Kurc, Guilherme Andrade, Jun Kong, Renato Ferreira, Joel Saltz
2015 arXiv   pre-print
We carry out a comparative performance study of multi-core CPUs, GPUs and Intel Xeon Phi (Many Integrated Core - MIC) with a microscopy image analysis application.  ...  GPUs are more efficient than MICs for operations that access data irregularly, because of the lower bandwidth of the MIC for random data accesses.  ...  of Health (NIH) K25CA181503 and by CNPq, CAPES, FINEP, Fapemig, and INWEB.  ... 
arXiv:1505.03819v1 fatcat:g5x5gwaubrc5bbfl7pmlbepzb4

Comparative Performance Analysis of Intel (R) Xeon Phi (TM), GPU, and CPU: A Case Study from Microscopy Image Analysis

George Teodoro, Tahsin Kurc, Jun Kong, Lee Cooper, Joel Saltz
2014 2014 IEEE 28th International Parallel and Distributed Processing Symposium  
We systematically implement and evaluate the performance of these operations on modern CPUs, GPUs, and MIC systems for a microscopy image analysis application.  ...  This allows applications to obtain high performance efficiency on CPU-MIC systems - the example application attained an efficiency of 84% on 192 nodes (3072 CPU cores and 192 MICs).  ...  NHLBI, by R01LM011119-01 and R01LM009239 from the NLM, and RC4MD005964 from the NIH, and CNPq (including projects 151346/2013-5 and 313931/2013-5).  ... 
doi:10.1109/ipdps.2014.111 pmid:25419088 pmcid:PMC4240026 fatcat:nyqwqlx5mjdjdhq365w6uig3ti

ATIP/A*CRC Workshop on Accelerator Technologies for High-Performance Computing: Does Asia Lead the Way? Programme Handbook [article]

Michalewicz Marek, Kahaner David
2012 Zenodo  
Three of these five systems boast GPU accelerators.  ...  , as well as the advantages and limitations of accelerated HPC systems.  ...  I/O capabilities will become increasingly crucial as new generation of high-performance CPUs and GPUs become available.  ... 
doi:10.5281/zenodo.3977457 fatcat:v2aftckqinasxk5ugdw27vinpa

Efficient Methods and Parallel Execution for Algorithm Sensitivity Analysis with Parameter Tuning on Microscopy Imaging Datasets [article]

George Teodoro, Tahsin Kurc, Luis F. R. Taveira, Alba C. M. A. Melo, Jun Kong, Joel Saltz
2016 arXiv   pre-print
Results: We carried out an empirical evaluation of the proposed method on high performance computing clusters with multi-core CPUs and co-processors (GPUs and Intel Xeon Phis).  ...  Our results show that (1) the framework achieves excellent scalability and efficiency on a high performance computing cluster -- execution efficiency remained above 85% in all experiments; (2) the parameter  ...  This research used resources of the XSEDE Science Gateways program under grant TG-ASC130023.  ... 
arXiv:1612.03413v1 fatcat:iny3igenvncgxoe7paike7f36e

Accelerating the Pace of Protein Functional Annotation With Intel Xeon Phi Coprocessors

Wei P. Feinstein, Juana Moreno, Mark Jarrell, Michal Brylinski
2015 IEEE Transactions on Nanobioscience  
Compared to a serial version, the parallel code runs 11.8 and 10.1 times faster on the CPU and the coprocessor, respectively; when both resources are utilized simultaneously, the speedup is 17.6.  ...  For example, ligand-binding predictions for 501 benchmarking proteins are completed in 2.1 hours on a single Stampede node equipped with the Intel Xeon Phi card compared to 3.1 hours without the accelerator  ...  ACKNOWLEDGMENT The authors are grateful for discussions and comments from the members of the Heterogeneous Computing group formed within the Louisiana Alliance for Simulation-Guided Materials Applications  ... 
doi:10.1109/tnb.2015.2403776 pmid:25769169 fatcat:v2gcceuczjc5tebepjg34qc5bq

Efficient Execution of Irregular Wavefront Propagation Pattern on Many Integrated Core Architecture [article]

Jeremias Gomes, George Teodoro
2016 arXiv   pre-print
The efficient execution of image processing algorithms is an active area of Bioinformatics.  ...  The objective of this study is to redesign the Irregular Wavefront Propagation Pattern algorithm in order to enable the efficient execution on processors with Many Integrated Core architecture using SIMD  ...  Saltz, and T. Kurc. Efficient Execution of Microscopy Image Analysis on CPU, GPU, and MIC Equipped Cluster Systems.  ... 
arXiv:1605.00930v1 fatcat:qoi5bpnap5dztgmpppjgmj7sgy

D6.3: Analysis of New Services

Janez Povh, Andrej Kastrin, Miroslaw Kupczyk, Luigi Calori, Marcin Krotkiewski, Felip Moll, Andreas Panteli, Zoltan Kiss, Nevena Ilieva-Litova
2015 Zenodo  
At the end Task 6.2 will assess the functionality of these services and promote their adoption in the future if the analysis is a success.  ...  In Deliverable D6.3 we consider all 4 services and describe the state-of-the-art in the corresponding area, the standards that the new services will rely on, the potential users of the new services and  ...  As of today, for data processing and analysis NSC uses the Tier-1 system available at UiO -the Abel cluster.  ... 
doi:10.5281/zenodo.6801709 fatcat:spsbse5x4fdfxhumy6jmem5oca

Feuille de route IFB 2021-2028: MUDIS4LS [article]

Jacques Van Helden, Julien Seiler, Gildas Le Corguillé, Claudine Médigue, IFB Teams
2021 Zenodo  
the intermediate phases of analysis and exploitation.  ...  The main goal of MuDiS4LS (Mutualized Digital Space for FAIR data in Life and Health Sciences) is to develop a framework that will rely on the national and regional data centers to enable scientists controlling  ...  (GPU cluster on Jean Zay computer e.g.).  ... 
doi:10.5281/zenodo.5229330 fatcat:speqf7rjcjc5hiaqeemlmvjg7m

Deliverable 1.3 Mid-Term Report [article]

Graham Appleby, Deike Pahl, Thomas Tschentscher
2017 Zenodo  
EUCALL Deliverable 1.3 of EUCALL  ...  For both Tasks 5.1 and 5.2 HZDR has written the Open Source library "ALPAKA" (available on Github) for abstracting many-core hardware programming (AMD & NVIDIA GPUs, Intel MIC, CPUs, ARM) and achieving  ...  Two test examples have been selected and detailed -one which exemplarily discusses an FPGA analysis of digitizer data for x-ray pulse characterization at 7.8 MHz, and one GPU analysis using a raw signal  ... 
doi:10.5281/zenodo.1314768 fatcat:5ncxnl2ok5cavph6fj2rkh4bsi

EGI federated platforms supporting accelerated computing

Marco VERLATO, Paolo Andreetto, Jan Astalos, Miroslav Dobrucky, Andrea Giachetti, David Rebatto, Antonio Rosato, Viet TRAN, Lisa Zangrando
2017 Proceedings of International Symposium on Grids and Clouds (ISGC) 2017 — PoS(ISGC2017)   unpublished
its first OpenStack-based site providing GPU-equipped instances at the end of 2015.  ...  On the other hand, HTC and Cloud middleware support for accelerator cards has been extended, where needed, in order to provide a transparent and uniform way to allocate these resources together with CPU  ...  Figure 3 displays an extract of its gres.conf and slurm.conf files showing that two worker nodes among the ones forming the entire cluster are equipped respectively with 8 CPU cores plus one NVIDIA TM  ... 
doi:10.22323/1.293.0020 fatcat:j3zcg2e3pbbgvdxbtue47iptne

Effect of MR contrast agents on quantitative accuracy of PET in combined whole-body PET/MR imaging

Cristina Lois, Ilja Bezrukov, Holger Schmidt, Nina Schwenzer, Matthias K. Werner, Jürgen Kupferschläger, Thomas Beyer
2012 European Journal of Nuclear Medicine and Molecular Imaging  
Sponsoring Institutes and Companies The 2011 Nuclear Science Symposium and Medical Imaging Conference is  ...  Huang, China Medical University, Taiwan MIC21.S-90 A Fast CPU/GPU Ray Projector for Fully 3D List-Mode PET Reconstruction J. Bert, D.  ...  , Germany MIC9.S-196 Fast and Accurate 3D Compton Cone Projections on GPU Using CUDA J.  ... 
doi:10.1007/s00259-012-2190-0 pmid:22890801 fatcat:gaikvxa6hrc2xobeyxp7gyu3ha

Power pulsing of the CALICE tile hadron calorimeter

Mathias Reinecke
2016 2016 IEEE Nuclear Science Symposium, Medical Imaging Conference and Room-Temperature Semiconductor Detector Workshop (NSS/MIC/RTSD)  
This achievement was recognised through the award of the 2015 Nobel prize for physics to the leaders of the SNO and Super-Kamiokande experiments for the conclusive establishment of the phenomenon of neutrino  ...  Much of what we know about neutrinos comes from studying neutrino flavour oscillations, whereby one type of neutrino transforms into a different type as it propagates over a large distance.  ...  The X-ray imaging based on photon counting with these sensors faces several complications distorting their spectral response and degrading their spatial resolution.  ... 
doi:10.1109/nssmic.2016.8069748 fatcat:zjgd7dmfdbhntb4kfwdtrlejhi

Combined local and global image registration and its application to large-scale images in digital pathology

Johannes Lotz, Jan Modersitzki, Heinz Handels
2020 Zenodo  
Combined local and global image registration and its application to large-scale images in digital pathology, University of Lübeck, http://d-nb.info/1217024069, https://doi.org/10.5281/zenodo.4030986 @thesis  ...  {lotz_johannes_combined_2020, title = {Combined local and global image registration and its application to large-scale images in digital pathology}, rights = {Creative Commons Attribution 4.0 International  ...  The available memory and the number of CPUs in those systems can be scaled by adding additional nodes to the cluster.  ... 
doi:10.5281/zenodo.4030986 fatcat:zd2raw3keffwrdtlsgzabklysu
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