Performance analysis of massively parallel embedded hardware architectures for retinal image processing

This paper examines the implementation of a retinal vessel tree extraction technique on different hardware platforms and architectures. Retinal vessel tree extraction is a representative application of those found in the domain of medical image processing. The low signal-to-noise ratio of the images leads to a large amount of low-level tasks in order to meet the accuracy requirements. In some applications, this might compromise computing speed. This paper is focused on the assessment of the performance of a retinal vessel tree extraction method on different hardware platforms. In particular, the retinal vessel tree extraction method is mapped onto a massively parallel SIMD (MP-SIMD) chip, a massively parallel processor array (MPPA) and onto an field-programmable gate arrays (FPGA)This work is funded by Xunta de Galicia under the projects 10PXIB206168PR and 10PXIB206037PR and the program Maria BarbeitoS

An Efficient Ant Colony Optimization Framework for HPC Environments

Financiado para publicación en acceso aberto: Universidade da Coruña/CISUG[Abstract] Combinatorial optimization problems arise in many disciplines, both in the basic sciences and in applied fields such as engineering and economics. One of the most popular combinatorial optimization methods is the Ant Colony Optimization (ACO) metaheuristic. Its parallel nature makes it especially attractive for implementation and execution in High Performance Computing (HPC) environments. Here we present a novel parallel ACO strategy making use of efficient asynchronous decentralized cooperative mechanisms. This strategy seeks to fulfill two objectives: (i) acceleration of the computations by performing the ants’ solution construction in parallel; (ii) convergence improvement through the stimulation of the diversification in the search and the cooperation between different colonies. The two main features of the proposal, decentralization and desynchronization, enable a more effective and efficient response in environments where resources are highly coupled. Examples of such infrastructures include both traditional HPC clusters, and also new distributed environments, such as cloud infrastructures, or even local computer networks. The proposal has been evaluated using the popular Traveling Salesman Problem (TSP), as a well-known NP-hard problem widely used in the literature to test combinatorial optimization methods. An exhaustive evaluation has been carried out using three medium and large size instances from the TSPLIB library, and the experiments show encouraging results with superlinear speedups compared to the sequential algorithm (e.g. speedups of 18 with 16 cores), and a very good scalability (experiments were performed with up to 384 cores improving execution time even at that scale).This work was supported by the Ministry of Science and Innovation of Spain (PID2019-104184RB-I00 / AEI / 10.13039/501100011033), and by Xunta de Galicia and FEDER funds of the EU (Centro de Investigación de Galicia accreditation 2019–2022, ref. ED431G 2019/01; Consolidation Program of Competitive Reference Groups, ref. ED431C 2021/30). JRB acknowledges funding from the Ministry of Science and Innovation of Spain MCIN / AEI / 10.13039/501100011033 through grant PID2020-117271RB-C22 (BIODYNAMICS), and from MCIN / AEI / 10.13039/501100011033 and “ERDF A way of making Europe” through grant DPI2017-82896-C2-2-R (SYNBIOCONTROL). Authors also acknowledge the Galician Supercomputing Center (CESGA) for the access to its facilities. Funding for open access charge: Universidade da Coruña/CISUGXunta de Galicia; ED431G 2019/01Xunta de Galicia; ED431C 2021/3

Shaping the edge radial electric field to create shearless transport barriers in tokamaks

In tokamak-confined plasmas, particle transport can be reduced by modifying the radial electric field. In this paper, we investigate the influence of both a well-like and a hill-like shaped radial electric field profile on the creation of shearless transport barriers (STBs) at the plasma edge, which are a type of barrier that can prevent chaotic transport and are related to the presence of extreme values in the rotation number profile. For that, we apply an ExB drift model to describe test particle orbits in large aspect-ratio tokamaks. We show how these barriers depend on the electrostatic fluctuation amplitudes and on the width and depth (height) of the radial electric field well-like (hill-like) profile. We find that, as the depth (height) increases, the STB at the plasma edge becomes more resistant to fluctuations, enabling access to an improved confinement regime that prevents chaotic transport. We also present parameter spaces with the radial electric field parameters, indicating the STB existence for several electric field configurations at the plasma edge, for which we obtain a fractal structure at the barrier/non-barrier frontier, typical of quasi-integrable Hamiltonian systems.Comment: 12 pages and 8 figure

Implementation of a motion estimation algorithm for Intel FPGAs using OpenCL

Producción CientíficaMotion Estimation is one of the main tasks behind any video encoder. It is a compu- tationally costly task; therefore, it is usually delegated to specific or reconfigurable hardware, such as FPGAs. Over the years, multiple FPGA implementations have been developed, mainly using hardware description languages such as Verilog or VHDL. Since programming using hardware description languages is a complex task, it is desirable to use higher-level languages to develop FPGA applications.The aim of this work is to evaluate OpenCL, in terms of expressiveness, as a tool for devel- oping this kind of FPGA applications. To do so, we present and evaluate a parallel implementation of the Block Matching Motion Estimation process using OpenCL for Intel FPGAs, usable and tested on an Intel Stratix 10 FPGA. The implementa- tion efficiently processes Full HD frames completely inside the FPGA. In this work, we show the resource utilization when synthesizing the code on an Intel Stratix 10 FPGA, as well as a performance comparison with multiple CPU implementations with varying levels of optimization and vectorization capabilities. We also compare the proposed OpenCL implementation, in terms of resource utilization and perfor- mance, with estimations obtained from an equivalent VHDL implementation.Junta de Castilla y León - Consejería de Educación de la Proyecto PROPHET-2 (VA226P20)Ministerio de Economía, Industria y Competitividad: (PID2019- 104834 GB-I00) and European Regional Development Fund (ERDF) program: Project PCAS (TIN2017-88614-R)Ministerio de Ciencia e Innovación (PID2019-104184RB-I00 / AEI / 10.13039/501100011033)Xunta de Galicia y fondos FEDER de la UE (Centro de Investigación de Galicia acreditación 2019-2022, ref. ED431G 2019/01; Consolidation Program of Competitive Reference Groups, ref. ED431C 2021/30Ministerio de Ciencia e Innovación, Agencia Estatal de Investigación y “European Union NextGenerationEU/PRTR” : (MCIN/ AEI/10.13039/501100011033) - grant TED2021-130367B-I00Publicación en abierto financiada por el Consorcio de Bibliotecas Universitarias de Castilla y León (BUCLE), con cargo al Programa Operativo 2014ES16RFOP009 FEDER 2014-2020 DE CASTILLA Y LEÓN, Actuación:20007-CL - Apoyo Consorcio BUCL

ExB drift particle transport in tokamaks

In tokamaks, modification of the plasma profiles can reduce plasma transport, improving particle confinement. However, this improvement is still not completely understood. In this work, we consider a drift wave test particle model to investigate the influence of the electric and magnetic field profiles on plasma transport. Test particle orbits subjected to ExB drift are numerically integrated and their transport coefficient is obtained. We conclude that sheared profiles reduce particle transport, even for high amplitude perturbations. In particular, nonmonotonic electric and magnetic fields produce shearless transport barriers, which are particularly resistant to perturbations and reduce even more the transport coefficient.Comment: 10 pages, 9 figures, 1 table. Published in Brazilian Journal of Physic

Charge density wave in layered La1-xCexSb2

The layered rare-earth diantimonides RSb2 are anisotropic metals with generally low electronic densities whose properties can be modified by substituting the rare earth. LaSb2 is a nonmagnetic metal with a low residual resistivity presenting a low-temperature magnetoresistance that does not saturate with the magnetic field. It has been proposed that the latter can be associated to a charge density wave (CDW), but no CDW has yet been found. Here we find a kink in the resistivity above room temperature in LaSb2 (at 355 K) and show that the kink becomes much more pronounced with substitution of La by Ce along the La1-xCexSb2 series. We find signatures of a CDW in x-ray scattering, specific heat, and scanning tunneling microscopy (STM) experiments in particular for x≈0.5. We observe a distortion of rare-earth-Sb bonds lying in-plane of the tetragonal crystal using x-ray scattering, an anomaly in the specific heat at the same temperature as the kink in resistivity and charge modulations in STM. We conclude that LaSb2 has a CDW which is stabilized in the La1-xCexSb2 series due to substitutional disorder.E.H. acknowledges the support of Departamento Administrativo de Ciencia, Tecnología e Innovación, COL-CIENCIAS (Colombia) Programa Doctorados en el Exterior Convocatoria 568-2012. This work was supported by the Spanish MINECO (FIS2014-54498-R, MAT2011-27470-C02-02, and CSD-2009-00013), by the European Union (Graphene Flagship Contract No. CNECT-ICT-604391 and COST MP1201 action), and by the Comunidad de Madrid through programs Nanofrontmag-CM (S2013/MIT-2850) and MAD2D-CM (S2013/MIT-3007). We acknowledge MINECO and CSIC for financial support and for provision of synchrotron radiation facilities and would like to thank the SpLine BM25 staff for assistance in using the beamline

Characterizing the involvement of FaMADS9 in the regulation of strawberry fruit receptacle development

FaMADS9 is the strawberry (Fragaria x ananassa) gene that exhibits the highest homology to the tomato (Solanum lycopersicum) RIN gene. Transgenic lines were obtained in which FaMADS9 was silenced. The fruits of these lines did not show differences in basic parameters, such as fruit firmness or colour, but exhibited lower Brix values in three of the four independent lines. The gene ontology MapMan category that was most enriched among the differentially expressed genes in the receptacles at the white stage corresponded to the regulation of transcription, including a high percentage of transcription factors and regulatory proteins associated with auxin action. In contrast, the most enriched categories at the red stage were transport, lipid metabolism and cell wall. Metabolomic analysis of the receptacles of the transformed fruits identified significant changes in the content of maltose, galactonic acid-1,4-lactone, proanthocyanidins and flavonols at the green/white stage, while isomaltose, anthocyanins and cuticular wax metabolism were the most affected at the red stage. Among the regulatory genes that were differentially expressed in the transgenic receptacles were several genes previously linked to flavonoid metabolism, such as MYB10, DIV, ZFN1, ZFN2, GT2, and GT5, or associated with the action of hormones, such as abscisic acid, SHP, ASR, GTE7 and SnRK2.7. The inference of a gene regulatory network, based on a dynamic Bayesian approach, among the genes differentially expressed in the transgenic receptacles at the white and red stages, identified the genes KAN1, DIV, ZFN2 and GTE7 as putative targets of FaMADS9. A MADS9-specific CArG box was identified in the promoters of these genes