Extending OmpSs for OpenCL kernel co-execution in heterogeneous systems

© 2017 IEEE. Personal use of this material is permitted. Permission from IEEE must be obtained for all other uses, in any current or future media, including reprinting/republishing this material for advertising or promotional purposes,creating new collective works, for resale or redistribution to servers or lists, or reuse of any copyrighted component of this work in other works.Heterogeneous systems have a very high potential performance but present difficulties in their programming. OmpSs is a well known framework for task based parallel applications, which is an interesting tool to simplify the programming of these systems. However, it does not support the co-execution of a single OpenCL kernel instance on several compute devices. To overcome this limitation, this paper presents an extension of the OmpSs framework that solves two main objectives: the automatic division of datasets among several devices and the management of their memory address spaces. To adapt to different kinds of applications, the data division can be performed by the novel HGuided load balancing algorithm or by the well known Static and Dynamic. All this is accomplished with negligible impact on the programming. Experimental results reveal that there is always one load balancing algorithm that improves the performance and energy consumption of the system.This work has been supported by the University of Cantabria with grant CVE-2014-18166, the Generalitat de Catalunya under grant 2014-SGR-1051, the Spanish Ministry of Economy, Industry and Competitiveness under contracts TIN2016- 76635-C2-2-R (AEI/FEDER, UE) and TIN2015-65316-P. The Spanish Government through the Programa Severo Ochoa (SEV-2015-0493). The European Research Council under grant agreement No 321253 European Community’s Seventh Framework Programme [FP7/2007-2013] and Horizon 2020 under the Mont-Blanc Projects, grant agreement n 288777, 610402 and 671697 and the European HiPEAC Network.Peer ReviewedPostprint (published version

Architectural support for task dependence management with flexible software scheduling

The growing complexity of multi-core architectures has motivated a wide range of software mechanisms to improve the orchestration of parallel executions. Task parallelism has become a very attractive approach thanks to its programmability, portability and potential for optimizations. However, with the expected increase in core counts, finer-grained tasking will be required to exploit the available parallelism, which will increase the overheads introduced by the runtime system. This work presents Task Dependence Manager (TDM), a hardware/software co-designed mechanism to mitigate runtime system overheads. TDM introduces a hardware unit, denoted Dependence Management Unit (DMU), and minimal ISA extensions that allow the runtime system to offload costly dependence tracking operations to the DMU and to still perform task scheduling in software. With lower hardware cost, TDM outperforms hardware-based solutions and enhances the flexibility, adaptability and composability of the system. Results show that TDM improves performance by 12.3% and reduces EDP by 20.4% on average with respect to a software runtime system. Compared to a runtime system fully implemented in hardware, TDM achieves an average speedup of 4.2% with 7.3x less area requirements and significant EDP reductions. In addition, five different software schedulers are evaluated with TDM, illustrating its flexibility and performance gains.This work has been supported by the RoMoL ERC Advanced Grant (GA 321253), by the European HiPEAC Network of Excellence, by the Spanish Ministry of Science and Innovation (contracts TIN2015-65316-P, TIN2016-76635-C2-2-R and TIN2016-81840-REDT), by the Generalitat de Catalunya (contracts 2014-SGR-1051 and 2014-SGR-1272), and by the European Union’s Horizon 2020 research and innovation programme under grant agreement No 671697 and No. 671610. M. Moretó has been partially supported by the Ministry of Economy and Competitiveness under Juan de la Cierva postdoctoral fellowship number JCI-2012-15047.Peer ReviewedPostprint (author's final draft

To distribute or not to distribute: The question of load balancing for performance or energy

Heterogeneous systems are nowadays a common choice in the path to Exascale. Through the use of accelerators they offer outstanding energy efficiency. The programming of these devices employs the host-device model, which is suboptimal as CPU remains idle during kernel executions, but still consumes energy. Making the CPU contribute computin effort might improve the performance and energy consumption of the system. This paper analyses the advantages of this approach and sets the limits of when its beneficial. The claims are supported by a set of models that determine how to share a single data-parallel task between the CPU and the accelerator for optimum performance, energy consumption or efficiency. Interestingly, the models show that optimising performance does not always mean optimum energy or efficiency as well. The paper experimentally validates the models, which represent an invaluable tool for programmers when faced with the dilemma of whether to distribute their workload in these systems.This work has been supported by the University of Cantabria (CVE-2014-18166), the Spanish Science and Technology Commission (TIN2016-76635-C2-2-R), the European Research Council (G.A. No 321253) and the European HiPEAC Network of Excellence. The Mont-Blanc project has received funding from the European Unions Horizon 2020 research and innovation programme under grant agreement No 671697.Peer ReviewedPostprint (author's final draft

Experimental and Theoretical Studies of the Factors Affecting the Cycloplatination of the Chiral Ferrocenylaldimine (SC)-[(η5-C5H5)Fe{(η5-C5H4) C(H)=N CH(Me)(C6H5)}]

The study of the reactivity of the enantiopure ferrocenyl Schiff base (SC)-[FcCH=N CH(Me)(C6H5)] (1) (Fc = (η5-C5H5)Fe(η5-C5H4)) with cis-[PtCl2(dmso)2] under different experimental conditions is reported. Four different types of chiral Pt(II) have been isolated and characterized. One of them is the enantiomerically pure trans-(SC)-[Pt{κ1-N[FcCH=N CH(Me)(C6H5)]}Cl2(dmso)] (2a) in which the imine acts as a neutral N-donor ligand; while the other three are the cycloplatinated complexes: [Pt{κ2-C,N [(C6H4) N=CHFc]}Cl(dmso)] (7a) and the two diastereomers {(Sp,SC) and (Rp,SC)} of [Pt{κ2-C,N[(η5-C5H3) CH=N {CH(Me)(C6H5)}]Fe(η5-C5H5)}Cl(dmso)] (8a and 9a, respectively). Isomers 7a-9a, differ in the nature of the metallated carbon atom [CPh (in 7a) or CFc (in 8a and 9a)] or the planar chirality of the 1,2-disubstituted ferrocenyl unit (8a and 9a). Reactions of 7a 9a with PPh3 gave [Pt{κ2-C,N[(C6H4) N=CHFc]}Cl(PPh3)] (in 7b) and the diastereomers (Sp,SC) and (Rp,SC) of [Pt{κ2-C,N[(η5-C5H3) CH=N {CH(Me)(C6H5)}] Fe(η5-C5H5)}Cl(PPh3)] (8b and 9b, respectively). Comparative studies of the electrochemical properties and cytotoxic activities on MCF7 and MDA-MB231 breast cancer cell lines of 2a and cycloplatinated complexes 7b-9b are also reported. Theoretical studies based on DFT calculations have also been carried out in order to rationalize the results obtained from the cycloplatination of 1, the stability of the Pt(II) complexes and their electrochemical properties

A study of the properties, reactivity and anticancer activity of novel N- methylated-3-thiazolyl or 3-thienyl carbazoles and their Pd(II) and Pt(II) complexes

The synthesis and characterization of two hybrid N-methylated carbazole derivatives containing a thiazolyl or a thienyl ring is reported. The thiazolyl derivative has been also characterised by X-ray diffraction analysis. The study of its reactivity in front of [MCl2(dmso)(2)] (M = Pd or Pt) or Na-2[PdCl4] in methanol has allowed us to isolate and characterize its complexes. However, for the thienyl analogue, the formation of any Pd(II) or Pt(II) complex was not detected, indicating that it is less prone to bind to the M(II) ions than its thiazolyl analogue. Density Functional Theory (DFT) and Time-Dependent Density Functional Theory (TD-DFT) calculations have also been carried out in order to rationalize the influence of the nature of the thiazolyl or thienyl group on the electronic delocalization. Molecular mechanics calculations show that the free rotation of the thiazolyl in relation to the carbazole requires a greater energy income than for its thienyl analogue. Studies of the cytotoxic activity of the new compounds on colon (HCT116) and breast (MDA-MB231 and MCF7) cancer cell lines show that the thiazolyl carbazole ligand and its Pt(II) complex are the most active agents of the series and in the MCF7 line their potency is higher than that of cisplatin. In the non-tumoral human skin fibroblast BJ cell line, all the compounds were less toxic than cisplatin. Their potential ability to modify the electrophoretic mobility of pBluescript SK+ plasmid DNA and to act as inhibitors of Topoisomerases I and II alpha or cathepsin B has also been investigated

Isomeric and hybrid ferrocenyl/cyrhetrenylaldimines: a new family of multifunctional compounds

The synthesis and characterization of two novel and isomeric hybrid ferrocenyl/cyrhetrenyl aldimines [(η5-C5H5)Fe{(η5-C5H4)-CHvN-(η5-C5H4)}Re(CO)3] (1) and [(η5-C5H5)Fe{(η5-C5H4)-NvCH-(η5-C5H4)}Re (CO)3] (2) are reported. Their X-ray crystal structures reveal that both adopt the E form. However, molecules of 1 and 2 differ in the relative arrangement of the 'Fe(η5-C5H5)' and 'Re(CO)3' units (anti in 1 and syn in 2). This affects the type of intermolecular interactions, the assembly of the molecules and therefore their crystal architecture. Comparative studies of their electrochemical, spectroscopic and photo-physical properties have allowed us to clarify the effect produced by the location of the organometallic arrays (ferrocenyl or cyrhetrenyl) on electronic delocalization, the proclivity of the metals to undergo oxidation and their emissive properties. Theoretical studies based on Density Functional Theory (DFT) calculations on the two compounds have also been carried out in order to rationalize the experimental results and to assign the bands detected in their electronic spectra. The cytotoxic activities of compounds 1 and 2 against human adenocarcinoma cell lines [breast (MCF7 and MDA-MB-231) and colon (HCT-116)] reveal that imine 2 has a greater inhibitory growth effect than 1 and it is ca. 1.8 times more potent than cisplatin in the triple negative MDA-MB 231 and in the cisplatin resistant HCT-116 cell lines. A comparative study of their effect on the normal and non-tumour human skin fibroblast BJ cell lines is also reported

A novel type of organometallic 2-R-2,4-dihydro- 1H-3,1-benzoxazine with R = [M(η5-C5H4)(CO)3] (M = Re or Mn) units. Experimental and computational studies of the effect of substituent R on ring-chain tautomerism

The syntheses, characterization, X-ray crystal structures, electrochemical properties and anticancer and 35 antichagasic activities of the first examples of 2-substituted 2,4-dihydro-1H-3,1-benzoxazines with 36 halfsandwich organometallic arrays, [M(η5-C5H4)(CO)3] (M = Re or Mn), at position-2 are described. 37 Experimental and computational studies based on DFT calculations on the open forms [Schiff bases of 38 general formulae R-CHvN-C6H4-2-CH2OH] (5), with R = ferrocenyl (a), phenyl (b), cyrhetrenyl (c) or 39 cymantrenyl (d), and their tautomeric forms (2-substituted 2,4-dihydro-1H-3,1 benzoxazines) 40 haveallowed us to establish the influence of substituents a-d and solvents on: (a) the extent of 41 tautomeric equilibria (5a-5d) ↔ (6a-6d) and (b) their electrochemical properties and the electronic 42 distribution on the open and closed forms. Despite the formal similarity between 6c and 6d, their 43 anticancer and antiparasitic activities are markedly different. Compound 6d is inactive in the HCT116, 44 MDA-MB231 and MCF7 cancer cell lines, but 6c shows moderate activity in the latter cell line, while 45 the Mn(I) complex (6d) is a more potent anti-Trypanosoma cruzi agent than its Re(I) analogue (6c)

A New Family of Doubly Cyclopalladated Diimines. A Remarkable Effect of the Linker between the Metalated Units on Their Cytotoxicity

The cyclopalladation of a series of symmetric diimines with the formula (RC6H4CHNZ)2, where Z = CH2 or (CH2)2OCH2 and R = p-Cl, p-OMe, p-NO2, and o-Cl, is described. Optimal conditions to obtain the dimetalated compounds were found to be palladium(II) acetate, in toluene, at 60 °C and with a reaction time of 2−4 h. The reactivity of the dimetalated compounds with monodentate, bidentate, and bis(monodentate) Lewis bases was also studied. The cytotoxic activity of some selected compounds was evaluated against a panel of adenocarcinoma cell lines (colon HCT116 and breast MCF7 and MDA-MB231). Compounds containing the fragment NCH2CH2OCH2CH2OCH2CH2N exhibited a remarkable cytotoxic activity in the three cancer cells assayed, but complexes containing the NCH2CH2N fragment showed no activity. It seems that the length and flexibility of the central saturated chain in the imine molecule, as well as its lipophilicity and hydrophilicity, explain the different cytotoxicity of the two series of coordination compounds here reported

Neutral and ionic platinum compounds containing a cyclometalated chiral primary amine: Synthesis, antitumor activity, DNA interaction and topoisomerase I - cathepsin B inhibition

The synthesis and preliminary biological evaluation of neutral and cationic platinum derivatives of chiral 1-(1-naphthyl)ethylamine are reported, namely cycloplatinated neutral complexes [PtCl{(R or S)-NH(2)CH(CH(3))C(10)H(6)}(L)] [L = SOMe(2) ( 1-R or 1-S ), L = PPh(3) (2-R or 2-S), L = P(4-FC(6)H(4))(3) (3-R), L = P(CH(2))(3)N(3)(CH(2))(3) (4-R)], cycloplatinated cationic complexes [Pt{(R)-NH(2)CH(CH(3))C(10)H(6)}{L}]Cl [L = Ph(2)PCH(2)CH(2)PPh(2) (5-R), L = (C(6)F(5))(2)PCH(2)CH(2)P(C(6)F(5))(2) (6-R)] and the Pt(ii) coordination compound trans-[PtCl(2){(R)-NH(2)CH(CH(3))C(10)H(6)}(2)] (7-R). The X-ray molecular structure of 7-R is reported. The cytotoxic activity against a panel of human adenocarcinoma cell lines (A-549 lung, MDA-MB-231 and MCF-7 breast, and HCT-116 colon), cell cycle arrest and apoptosis, DNA interaction, topoisomerase I and cathepsin B inhibition, and Pt cell uptake of the studied compounds are presented. Remarkable cytotoxicity was observed for most of the synthesized Pt(ii) compounds regardless of (i) the absolute configuration R or S, and (ii) the coordinated/cyclometallated (neutral or cationic) nature of the complexes. The most potent compound 2-R (IC(50) = 270 nM) showed a 148-fold increase in potency with regard to cisplatin in HCT-116 colon cancer cells. Preliminary biological results point out to different biomolecular targets for the investigated compounds. Neutral cyclometallated complexes 1-R and 2-R, modify the DNA migration as cisplatin, cationic platinacycle 5-R was able to inhibit topoisomerase I-promoted DNA supercoiling, and Pt(ii) coordination compound 7-R turned out to be the most potent inhibitor of cathepsin B. Induction of G-1 phase ( 2-R and 5-R ), and S and G-2 phases (6-R) arrests are related to the antiproliferative activity of some representative compounds upon A-549 cells. Induction of apoptosis is also observed for 2-R and 6-R

Platinacycles Containing a Primary Amine Platinum(II) Compounds for Treating Cisplatin-Resistant Cancers by Oxidant Therapy

Cisplatin is an efficient anticancer drug, but its effects are often lost after several chemotherapy cycles, showing important secondary effects. For these reasons, new anticancer agents, with different coordination properties and mechanisms of action, are needed. Here we describe the reaction of 2-phenylaniline with cis-[PtCl2(dmso)(2)] and sodium acetate to afford a cycloplatinated compound 2 and the synthesis and some biological studies of 3-6 (two neutral and two ionic compounds): [PtCl(C-N)(L)], C-N cycloplatinated 2-phenylaniline with L = PPh3(3) or P(4-FC6H4)(3) (4) and [Pt(C-N)(L-L)]Cl with L-L = Ph2PCH2CH2Ph2(5) or (C6F5)(2)PCH2-CH2(C6F5)(2) (6). Ionic platinacycles 5 and 6 show a greater antiproliferative activity than that of cisplatin in human lung, breast, and colon cancer cell lines (A-549, MDA-MB-231 and MCF-7, and HCT-116), a remarkable result given the fact that they do not show covalent interaction with DNA. 5 and 6 have also been found able to oxidize NADH by a catalytic process prod- oducing H2O2 as ROS. The activity of these complexes to generate ROS seems to be the key factor to explain their potent anticancer activity; it should be noted that platinum(II) complexes showing biocatalytic activity for hydride transfer from NADH have not been described so far. Ionic complex 6 shows low affinity to some target proteins; the presence of perfluoroaromatic rings seems to hinder its interaction with some biomolecules