scholarly journals Menhir: An Environment for High Performance Matlab

1999 ◽  
Vol 7 (3-4) ◽  
pp. 303-312 ◽  
Author(s):  
Stéphane Chauveau ◽  
François Bodin
Keyword(s):  
High Performance ◽  
Specification Language ◽  
Target System ◽  
System Description ◽  
Fortran Code ◽  
Compilation Process ◽  
Parallel Code

In this paper we present Menhir a compiler for generating sequential or parallel code from the Matlab language. The compiler has been designed in the context of using Matlab as a specification language. One of the major features of Menhir is its retargetability to generate parallel and sequential C or Fortran code. We present the compilation process and the target system description for Menhir. Preliminary performances are given and compared with MCC, the MathWorks Matlab compiler.

Electromigration Simulation for Metal Lines

2010 ◽  
Vol 132 (1) ◽  
Author(s):  
JianPing Jing ◽  
Lihua Liang ◽  
Guang Meng
Keyword(s):  
Concentration Gradient ◽  
High Performance ◽  
Simulation Method ◽  
Flux Divergence ◽  
Atomic Concentration ◽  
Atomic Flux ◽  
Fortran Code ◽  
Current Densities ◽  
Void Propagation ◽  
Electron Wind

As the electronics industry continues to push for high performance and miniaturization, the demand for higher current densities, which may cause electromigration failures in an IC, interconnects. Electromigration is a phenomenon that metallic atoms constructing the line are transported by electron wind. The damage induced by electromigration appears as the formation of voids and hillocks. A numerical simulation method for electromigration void incubation, and afterwards, void propagation, based on commercial software ANSYS Multiphysics and FORTRAN code, is presented in this paper. The electronic migration formulation considering the effects of the electron wind force, stress gradients, temperature gradients, and the atomic concentration gradient has been developed for the electromigration failure mechanisms. Due to introducing the atomic concentration gradient driving force in atomic flux formulations, the conventional atomic flux divergence method is no longer valid in electromigration (EM) simulation. Therefore, the corresponding EM atomic concentration redistribution algorithm is proposed using FORTRAN code. Finally, the comparison of voids generation through the numerical example of a standard wafer electromigration accelerated test (SWEAT) structure with the measurement result is discussed.

scholarly journals Kemari: A Portable High Performance Fortran System for Distributed Memory Parallel Processors

1997 ◽  
Vol 6 (1) ◽  
pp. 41-58 ◽  
Author(s):  
T. Kamachi ◽  
A. MÜller ◽  
R. RÜhl ◽  
Y. Seo ◽  
K. Suehiro ◽  
...  
Keyword(s):  
Message Passing ◽  
High Performance ◽  
Message Passing Interface ◽  
Data Distribution ◽  
Programming Environment ◽  
Performance Measurements ◽  
High Performance Fortran ◽  
Additional Control ◽  
Compilation Process ◽  
Structured Problems

We have developed a compilation system which extends High Performance Fortran (HPF) in various aspects. We support the parallelization of well-structured problems with loop distribution and alignment directives similar to HPF's data distribution directives. Such directives give both additional control to the user and simplify the compilation process. For the support of unstructured problems, we provide directives for dynamic data distribution through user-defined mappings. The compiler also allows integration of message-passing interface (MPI) primitives. The system is part of a complete programming environment which also comprises a parallel debugger and a performance monitor and analyzer. After an overview of the compiler, we describe the language extensions and related compilation mechanisms in detail. Performance measurements demonstrate the compiler's applicability to a variety of application classes.

scholarly journals A Linear Algebra Framework for Static High Performance Fortran Code Distribution

1997 ◽  
Vol 6 (1) ◽  
pp. 3-27 ◽  
Author(s):  
Corinne Ancourt ◽  
Fabien Coelho ◽  
FranÇois Irigoin ◽  
Ronan Keryell
Keyword(s):  
Linear Algebra ◽  
High Performance ◽  
Address Space ◽  
Data Parallel ◽  
High Performance Fortran ◽  
Multiple Data ◽  
Fortran Code ◽  
Code Distribution ◽  
Overlap Analysis ◽  
Data Parallel Programming

High Performance Fortran (HPF) was developed to support data parallel programming for single-instruction multiple-data (SIMD) and multiple-instruction multiple-data (MIMD) machines with distributed memory. The programmer is provided a familiar uniform logical address space and specifies the data distribution by directives. The compiler then exploits these directives to allocate arrays in the local memories, to assign computations to elementary processors, and to migrate data between processors when required. We show here that linear algebra is a powerful framework to encode HPF directives and to synthesize distributed code with space-efficient array allocation, tight loop bounds, and vectorized communications forINDEPENDENTloops. The generated code includes traditional optimizations such as guard elimination, message vectorization and aggregation, and overlap analysis. The systematic use of an affine framework makes it possible to prove the compilation scheme correct.

scholarly journals An in vitro affinity-based method for studying herb–drug interactions for direct identification of cytochrome P450 1A2, 3A4, and 2C9 specific ligands from herbal extracts using ultrafiltration-high performance liquid chromatography

RSC Advances ◽  
2018 ◽  
Vol 8 (16) ◽  
pp. 8944-8949 ◽  
Author(s):  
Zhiqiang Wang ◽  
Seung Hwan Hwang ◽  
Guanglei Zuo ◽  
Set Byeol Kim ◽  
Soon Sung Lim
Keyword(s):  
High Performance Liquid Chromatography ◽  
Cytochrome P450 ◽  
Liquid Chromatography ◽  
Natural Product ◽  
High Performance ◽  
Target System ◽  
Herbal Extracts ◽  
Cytochrome P450 1A2 ◽  
Direct Identification

The specific ligands in natural product extracts could be identified from a multi-target system by ultrafiltration-high performance liquid chromatography using competitive probes.

A Systematic Review of Health Dialog Systems

2019 ◽  
Vol 58 (06) ◽  
pp. 179-193
Author(s):  
William R. Kearns ◽  
Nai-Ching Chi ◽  
Yong K. Choi ◽  
Shih-Yin Lin ◽  
Hilaire Thompson ◽  
...  
Keyword(s):  
Health Care ◽  
Natural Language ◽  
High Performance ◽  
Experimental Studies ◽  
Practical Implementation ◽  
Case Control Studies ◽  
System Description ◽  
Dialog Systems ◽  
Natural Language Interface ◽  
Quasi Experimental

Abstract Background Health dialog systems have seen increased adoption by patients, hospitals, and universities due to the confluence of advancements in machine learning and the ubiquity of high-performance hardware that supports real-time speech recognition, high-fidelity text-to-speech, and semantic understanding of natural language. Objectives This review seeks to enumerate opportunities to apply dialog systems toward the improvement of health outcomes while identifying both gaps in the current literature that may impede their implementation and recommendations that may improve their success in medical practice. Methods A search over PubMed and the ACM Digital Library was conducted on September 12, 2017 to collect all articles related to dialog systems within the domain of health care. These results were screened for eligibility with the main criteria being a peer-reviewed study of a system that includes both a natural language interface and either end-user testing or practical implementation. Results Forty-six studies met the inclusion criteria including 24 quasi-experimental studies, 16 randomized control trials, 2 case–control studies, 2 prospective cohort studies, 1 system description, and 1 human–computer conversation analysis. These studies evaluated dialog systems in five application domains: medical education (n = 20), clinical processes (n = 14), mental health (n = 5), personal health agents (n = 5), and patient education (n = 2). Conclusion We found that dialog systems have been widely applied to health care; however, most studies are not reproducible making direct comparison between systems and independent confirmation of findings difficult. Widespread adoption will also require the adoption of standard evaluation and reporting methods for health dialog systems to demonstrate clinical significance.

scholarly journals Simultaneous Fluorescent Detection of Two mRNA Targets by High Performance Signal Amplification

2000 ◽  
Vol 5 (1) ◽  
pp. 44-44
Author(s):  
Frank R. Gonzales
Keyword(s):  
Gene Expression ◽  
Signal Amplification ◽  
High Performance ◽  
Dna Probe ◽  
Fluorescent Detection ◽  
Quantum Yields ◽  
Target System ◽  
Mrna Targets ◽  
Mrna Induction ◽  
Actin Mrna

Development of drug candidates, which modulate cytokine responses or metabolic pathways by targeting gene expression, requires analytical systems that measure specific messenger RNAs rapidly and accurately and that can be adapted to high throughput screening operations. Chromagen's High Performance Signal Amplification (HPSA), system, a DNA probe hybridization method, has been enhanced to measure two different mRNA targets simultaneously in the same micro-plate well. Multi-target testing using HPSA takes advantage of a family of low molecular weight fluorescent dyes with large quantum yields, which exhibit distinct excitation and emission wavelengths. A two-target model system using cultured human THP-1 cells examined IL-1β mRNA induction in response to bacterial lipopolysaccharide (LPS) exposure and also monitored intrinsic β-actin mRNA as a housekeeping gene transcript. An oligonucleotide DNA probe complementary to IL-1β RNA was labeled with a reporter ligand while a β-actin DNA probe was linked directly to an enzyme. Sample mRNA was captured onto the surface of micro-plate wells and hybridized to both DNA probes. After removing non-hybridized probe, a second enzyme conjugate that specifically recognizes the IL-1β DNA probe reporter ligand was allowed to bind. The two enzyme systems were distinguished by using substrates labeled with different fluorescent tags (one for IL-1β and the other for β-actin). Resolution of the two fluorescent products was carried out with Chromagen's high-sensitivity, photon-counting fluorometer. This system was capable of detecting synthetic RNA targets for IL-1β and β-actin in the attomole range. Authentic β-actin mRNA was measured in 50,000 uninduced cells and this signal could be specifically competed away by addition of excess unlabeled β-actin probe during hybridization. A time course of IL-1β mRNA induction in THP-1 cells by LPS revealed that peak induction occurred after 2–3 hours. The β-actin mRNA level showed an initial decrease, but remained relatively constant throughout the remaining time points. Results obtained with the dual detection format paralleled those generated when each target was measured separately in its single-target gene expression assay. Chromagen's HPSA two-target system not only augments screening information, but also saves testing time and conserves reagents. The potential of this system is being explored with different gene targets of therapeutic value and other housekeeping genes.

scholarly journals Аnalysis of differential cross sections of 12,14ВЕ+2С with energy of 56 mev / nucleon on the basis of parallel implementation of a four–parameter microscopic nucleus–nucleus scattering model

2020 ◽  
pp. 10-19
Author(s):  
M. V. Bashashin ◽  
A. Yermekova ◽  
E. V. Zemlyanaya ◽  
M. B. Kakenov ◽  
K. V. Lukyanov
Keyword(s):  
Experimental Data ◽  
Cross Sections ◽  
Differential Cross ◽  
High Performance ◽  
Parallel Implementation ◽  
Differential Cross Sections ◽  
Fortran Code ◽  
Wide Range ◽  
Computer Codes ◽  
Nucleus Scattering

The MPI/C++ /Fortran package of computer codes has been developed for high-performance numerical analysis of experimental data on elastic nucleus-nucleus scattering within a microscopic model of optical potential. In the package, a modified DWUCK4 Fortran-code for calculating the physical characteristics of elastic scattering based on a numerical solution of the corresponding Schrödingerequation has been incorporated into the C++ framework, which is responsible for the input-output procedure and a comparison of numerical results with experimental data. MPI-based parallelism allows efficient calculations of the observables depending on a wide range of parameters of real and imaginary parts of the microscopic OP. The package has been used to analyze experimental data on differential cross sections of the 12,14Ве+12Сelastic scattering.

Parallel computing

2018 ◽  
Author(s):  
Joseph F. Boudreau ◽  
Eric S. Swanson
Keyword(s):  
Monte Carlo ◽  
Parallel Computing ◽  
High Performance Computing ◽  
Parallel Programming ◽  
High Performance ◽  
Parallel Application ◽  
Client Server ◽  
Parallel Code ◽  
Performance Computing

This chapter describes various approaches to concurrency, or “parallel programming”. An overview of high performance computing is followed with a review of Flynn’s taxonomy of parallel computing. Three methods for implementing parallel code using the frameworks provided by MPI, openMP, and C++ threads are presented. The use of the C++ constructs mutex and future to resolve issues of synchronization are discussed. All methods are illustrated with an embarrassingly parallel application to a Monte Carlo integral and common pitfalls are presented. The chapter closes with a discussion and example of the utility of forking processes and the use of C++ sockets and their application in a client/server environment.

GraphZero

2021 ◽  
Vol 55 (1) ◽  
pp. 21-37
Author(s):  
Daniel Mawhirter ◽  
Sam Reinehr ◽  
Connor Holmes ◽  
Tongping Liu ◽  
Bo Wu
Keyword(s):  
Group Theory ◽  
Symmetry Breaking ◽  
High Performance ◽  
State Of The Art ◽  
Input Graph ◽  
Query Pattern ◽  
Subgraph Matching ◽  
Compilation Process ◽  
Multiple Query ◽  
Query Patterns

Subgraph matching is a fundamental task in many applications which identifies all the embeddings of a query pattern in an input graph. Compilation-based subgraph matching systems generate specialized implementations for the provided patterns and often substantially outperform other systems. However, the generated code causes significant computation redundancy and the compilation process incurs too much overhead to be used online, both due to the inherent symmetry in the structure of the query pattern. In this paper, we propose an optimizing query compiler, named GraphZero, to completely address these limitations through symmetry breaking based on group theory. GraphZero implements three novel techniques. First, its schedule explorer efficiently prunes the schedule space without missing any high-performance schedule. Second, it automatically generates and enforces a set of restrictions to eliminate computation redundancy. Third, it generalizes orientation, a surprisingly effective optimization that was only used for clique patterns, to apply to arbitrary patterns. Evaluation on multiple query patterns shows that GraphZero outperforms two state-of-the-art compilation and non-compilation based systems by up to 40X and 2654X, respectively.

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