XARK: an extensible framework for automatic recognition of computational kernels

This is a post-peer-review, pre-copyedit version of an article published in ACM Transactions on Programming Languages and Systems. The final authenticated version is available online at: http://dx.doi.org/10.1145/1391956.1391959[Abstract] The recognition of program constructs that are frequently used by software developers is a powerful mechanism for optimizing and parallelizing compilers to improve the performance of the object code. The development of techniques for automatic recognition of computational kernels such as inductions, reductions and array recurrences has been an intensive research area in the scope of compiler technology during the 90's. This article presents a new compiler framework that, unlike previous techniques that focus on specific and isolated kernels, recognizes a comprehensive collection of computational kernels that appear frequently in full-scale real applications. The XARK compiler operates on top of the Gated Single Assignment (GSA) form of a high-level intermediate representation (IR) of the source code. Recognition is carried out through a demand-driven analysis of this high-level IR at two different levels. First, the dependences between the statements that compose the strongly connected components (SCCs) of the data-dependence graph of the GSA form are analyzed. As a result of this intra-SCC analysis, the computational kernels corresponding to the execution of the statements of the SCCs are recognized. Second, the dependences between statements of different SCCs are examined in order to recognize more complex kernels that result from combining simpler kernels in the same code. Overall, the XARK compiler builds a hierarchical representation of the source code as kernels and dependence relationships between those kernels. This article describes in detail the collection of computational kernels recognized by the XARK compiler. Besides, the internals of the recognition algorithms are presented. The design of the algorithms enables to extend the recognition capabilities of XARK to cope with new kernels, and provides an advanced symbolic analysis framework to run other compiler techniques on demand. Finally, extensive experiments showing the effectiveness of XARK for a collection of benchmarks from different application domains are presented. In particular, the SparsKit-II library for the manipulation of sparse matrices, the Perfect benchmarks, the SPEC CPU2000 collection and the PLTMG package for solving elliptic partial differential equations are analyzed in detail.Ministeiro de Educación y Ciencia; TIN2004-07797-C02Ministeiro de Educación y Ciencia; TIN2007-67537-C03Xunta de Galicia; PGIDIT05PXIC10504PNXunta de Galicia; PGIDIT06PXIB105228P

Compiler support for parallel code generation through kernel recognition

[Abstract] Summary form only given. The automatic parallelization of loops that contain complex computations is still a challenge for current parallelizing compilers. The main limitations are related to the analysis of expressions that contain subscripted subscripts, and the analysis of conditional statements that introduce complex control flows at run-time. We use the term complex loop to designate loops with such characteristics. We describe the parallelization of sequential complex loop nests using a generic compiler framework (proposed in an earlier paper [Arenaz et al., ICS'2003] ) that accomplishes kernel recognition through the analysis of the gated single assignment program representation. Specifically, we focus on an extension of this framework that enables its use as a powerful tool for gathering source code information that is relevant for the parallelization of each computational kernel. A set of example codes are analyzed in detail to illustrate the potential of our approach. Experimental results using a benchmark suite of complex loop nests are also presented

Soft Actuated Hybrid Hydrogel with Bioinspired Complexity to Control Mechanical Flexure Behavior for Tissue Engineering

Hydrogels exhibit excellent properties that enable them as nanostructured scaffolds for soft tissue engineering. However, single-component hydrogels have significant limitations due to the low versatility of the single component. To achieve this goal, we have designed and characterized different multi-component hydrogels composed of gelatin, alginate, hydroxyapatite, and a protein (BSA and fibrinogen). First, we describe the surface morphology of the samples and the main characteristics of the physiological interplay by using fourier transform infrared (FT-IR), and confocal Raman microscopy. Then, their degradation and swelling were studied and mechanical properties were determined by rheology measurements. Experimental data were carefully collected and quantitatively analyzed by developing specific approaches and different theoretical models to determining the most important parameters. Finally, we determine how the nanoscale of the system influences its macroscopic properties and characterize the extent to which degree each component maintains its own functionality, demonstrating that with the optimal components, in the right proportion, multifunctional hydrogels can be developedThe authors acknowledge Ministerio de Ciencia e Innovación (PID2019-111327GB-100) and Xunta de Galicia (ED41E2018/08)S

Useful Life of Prescribed Fires in a Southern Mediterranean Basin: An Application to Pinus pinaster Stands in the Sierra Morena Range

Prescribed fire is a globally relevant fuel treatment for surface fuel management and wildfire hazard reduction. However, Mediterranean ecosystems are adapted to low and moderate fires; hence, the useful life of prescribed fires is limited. Useful life is defined as the effective rotation length of prescribed fires to mitigate fire spread based on critical surface intensity for crown combustion. In this sense, the useful life of a prescribed fire focuses on surface fuel dynamics and its potential fire behavior. In Pinus pinaster stands, the useful life can be established between 0 and 4 years. Canopy base height, time elapsed from the burning, postfire precipitation, and fine fuel moisture content during the burning were identified as the most important variables in postburn fuel dynamics. Other stand characteristics and postfire precipitation can improve the fine fuel and live fuel dynamics models. Our findings support prescribed fires as an effective fuel treatment in the medium term for forest fire prevention, according to stand characteristics and burning implementation conditions. In this sense, forest managers can use the proposed decision tree to identify the useful life of each prescribed fire based on fine fuel moisture content during burning implementation

Predicting growing stock volume of Eucalyptus plantations using 3-D point clouds derived from UAV imagery and ALS data

Estimating forest inventory variables is important in monitoring forest resources and mitigating climate change. In this respect, forest managers require flexible, non-destructive methods for estimating volume and biomass. High-resolution and low-cost remote sensing data are increasingly available to measure three-dimensional (3D) canopy structure and to model forest structural attributes. The main objective of this study was to evaluate and compare the individual tree volume estimates derived from high-density point clouds obtained from airborne laser scanning (ALS) and digital aerial photogrammetry (DAP) in Eucalyptus spp. plantations. Object-based image analysis (OBIA) techniques were applied for individual tree crown (ITC) delineation. The ITC algorithm applied correctly detected and delineated 199 trees from ALS-derived data, while 192 trees were correctly identified using DAP-based point clouds acquired fromUnmannedAerialVehicles(UAV), representing accuracy levels of respectively 62% and 60%. Addressing volume modelling, non-linear regression fit based on individual tree height and individual crown area derived from the ITC provided the following results: Model E ciency (Mef) = 0.43 and 0.46, Root Mean Square Error (RMSE) = 0.030 m3 and 0.026 m3, rRMSE = 20.31% and 19.97%, and an approximately unbiased results (0.025 m3 and 0.0004 m3) using DAP and ALS-based estimations, respectively. No significant di erence was found between the observed value (field data) and volume estimation from ALS and DAP (p-value from t-test statistic = 0.99 and 0.98, respectively). The proposed approaches could also be used to estimate basal area or biomass stocks in Eucalyptus spp. plantationsinfo:eu-repo/semantics/publishedVersio

Potential Effects of Climate Change on Fire Behavior, Economic Susceptibility and Suppression Costs in Mediterranean Ecosystems: Córdoba Province, Spain

The potentially large ecological, economic, and societal impacts of climate change makes it a significant problem of the 21st century. These consequences have led to tremendous development in climate change scenarios and new technologies to increase knowledge on the effect and efficiency of mitigation and adaptation measures. Large fires will occur at a higher rate than currently because of lower fuel moisture content resulting in a lower resistance to burning. This is also evidenced by more extreme fire behavior that contributes to higher economic impacts, suppression difficulties and suppression costs. The economic susceptibility concept integrates a set of economic valuation approaches for valuing timber and non-timber resources, considering the fire behavior, and as a consequence, the net value changes for each resource. Flame length increased by 4.6% to 15.69%, according to the different future climate scenarios. Climate change is expected to cause widespread changes to economic susceptibility and suppression costs because of higher flame length and fire intensity. Therefore, our outcomes show an increase in the economic susceptibility of Córdoba Province in the medium and long term (2041–2070) between 6.05% and 25.99%, respectively. In addition, we have found an increase between 65.67% and 86.73% in suppression costs in the last decade. The digital version of the economic susceptibility model using Geographic Information Systems improves its operational capabilities enhancing also its dynamism and simplicity to accept modifications and predictions revisions

Automated and accurate cache behavior analysis for codes with irregular access patterns

This is the peer reviewed version of the following article: Andrade, D. , Arenaz, M. , Fraguela, B. B., Touriño, J. and Doallo, R. (2007), Automated and accurate cache behavior analysis for codes with irregular access patterns. Concurrency Computat.: Pract. Exper., 19: 2407-2423. doi:10.1002/cpe.1173, which has been published in final form at https://doi.org/10.1002/cpe.1173. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Use of Self-Archived Versions.[Abstract] The memory hierarchy plays an essential role in the performance of current computers, so good analysis tools that help in predicting and understanding its behavior are required. Analytical modeling is the ideal base for such tools if its traditional limitations in accuracy and scope of application can be overcome. While there has been extensive research on the modeling of codes with regular access patterns, less attention has been paid to codes with irregular patterns due to the increased difficulty in analyzing them. Nevertheless, many important applications exhibit this kind of pattern, and their lack of locality make them more cache‐demanding, which makes their study more relevant. The focus of this paper is the automation of the Probabilistic Miss Equations (PME) model, an analytical model of the cache behavior that provides fast and accurate predictions for codes with irregular access patterns. The information requirements of the PME model are defined and its integration in the XARK compiler, a research compiler oriented to automatic kernel recognition in scientific codes, is described. We show how to exploit the powerful information‐gathering capabilities provided by this compiler to allow the automated modeling of loop‐oriented scientific codes. Experimental results that validate the correctness of the automated PME model are also presented.Ministerio de Educación y Ciencia; TIN2004-07797-C02Xunta de Galicia; PGIDIT03TIC10502PRXunta de Galicia; PGIDT05PXIC10504P

Conformational binding mechanism of lysozyme induced by interactions with penicillin antibiotic drugs

In this study we present an in-depth and detailed analysis of the binding process between two antibiotics (cloxacillin and dicloxacillin) and a blood serum protein (lysozyme). Our objectives have been several: to determine, at the atomic level, the structural and conformational changes that take place in both molecular structures once the complex is formed; to investigate the effect that the substitution of a hydrogen atom for a chlorine atom has on the bonding process; and to relate these local modifications with macromolecular parameters. Achieving these goals requires a multi-pronged approach and effective resource management. In our case, we have combined different experimental (isothermal titration calorimetry, UV–vis and fluorescence spectroscopy) and computational techniques (molecular docking and network models), in order to obtain comprehensive and contrasted information of the interaction process. Both approaches have showed an excellent correlation, confirming that there is a single binding site, that both penicillins are moderate binders and hydrogen bond and van der Waals forces are predominant. On the other hand, the small discrepancies between the two techniques highlighted the pressing need to approach the study of these systems from both atomic and macromolecular perspectivesThe authors acknowledge Ministerio de Ciencia e Innovación (PID2019-111327GB-100)S

Afrontamiento, vida personal y familiar de profesores que pertenecen al Sistema Nacional de Investigadores (SNI) de una universidad del sureste de México

This study aimed to know the self-perception of the dimensions of coping, as well as personal and family life of researchers belonging to the National System of Researchers (SNI) of a public university in southeastern, Mexico. It was developed from a quantitative, descriptive-exploratory perspective. The study was made up of 121 (96%) of the researchers assigned to the SNI, of which 72 (59.5%) are men (M age = 43.3, SD = 9.5 years) and 49 (40.5%) women (M age = 44.2, DE = 8.4 years). The information-gathering instrument was a questionnaire that was answered with a Likert scale, as well as three open questions. It was found that the members of the SNI of the University of the study are young, and have mostly recognition at level I. In relation to the dimensions of coping and personal and family life, the subjects are almost always satisfied with the variables associated with these dimensions. In sum, the factors that influence their permanence or admission to the SNI, are the skills they possess, the interest, the family and the preparation they received in the field of research.El presente estudio tuvo como objetivo conocer la autopercepción de las dimensiones de afrontamiento, vida personal y familiar de investigadores que pertenecen al Sistema Nacional de Investigadores (SNI) de una universidad pública del sureste de México. Se desarrolló desde una perspectiva cuantitativa, descriptiva-exploratoria. El estudio estuvo conformado por 121 (96%) de los investigadores adscritos al SNI, de los cuales 72 (59.5%) son hombres (M edad = 43.3, DE = 9.5 años) y 49 (40.5%) mujeres (M edad = 44.2, DE = 8.4 años). El instrumento de recolección de la información fue un cuestionario con escala tipo Likert, así como tres preguntas abiertas. Se encontró que los miembros del SNI de la Universidad en estudio son jóvenes y tienen mayormente reconocimiento en el nivel I. En relación a las dimensiones de afrontamiento, vida personal y familiar, los sujetos se encuentran satisfechos casi siempre con las variables asociadas a estas dimensiones. En suma, los factores que influyen en su permanencia o ingreso al SNI son las habilidades que poseen, el interés, la familia y la preparación que recibieron en el campo de la investigación