Connected component identification and cluster update on GPU

Cluster identification tasks occur in a multitude of contexts in physics and engineering such as, for instance, cluster algorithms for simulating spin models, percolation simulations, segmentation problems in image processing, or network analysis. While it has been shown that graphics processing units (GPUs) can result in speedups of two to three orders of magnitude as compared to serial codes on CPUs for the case of local and thus naturally parallelized problems such as single-spin flip update simulations of spin models, the situation is considerably more complicated for the non-local problem of cluster or connected component identification. I discuss the suitability of different approaches of parallelization of cluster labeling and cluster update algorithms for calculations on GPU and compare to the performance of serial implementations.Comment: 15 pages, 14 figures, one table, submitted to PR

Cal Poly State University Robert E. Kennedy Library Fire Protection Analysis Report

This report determines whether or not the fire protection and life safety features of Robert E. Kennedy Library are consistent with the fire protection objectives established in nationally recognized fire protection codes and standards. This analysis is performed to establish a technical baseline for identification of fire protection deficiencies. Kennedy Library is the campus student library at California Polytechnic State University. The facility provides resources and services in a variety of media to meet the needs of university students and faculty. This analysis consists of a prescriptive analysis and a performance-based analysis. The prescriptive analysis is an analysis of the building and its compliance with the building code and other industrial codes and standards. The performance-based analysis is based on guidance from NFPA 101 and evaluates the fire protection features of the building against specific performance criteria. The prescriptive analysis consists of a review of Kennedy Library’s fire protection features against code requirements. The features reviewed include structural fire resistance, automatic alarm and detection, suppression, and life safety. The results of the prescriptive analysis include the identification of two deficiencies, one potential deficiency that should be analyzed further and one recommendation for improving the safety posture of the facility. The deficiencies are (1) inadequate visual notification coverage of the fire alarm system and (2) incorrect door swing direction of two doorways in the means of egress from the building’s interior courtyard. The potential deficiency is the coverage provided by the fire alarm system for audible notification. The recommendation is for the installation of an automatic fire sprinkler system. Whereas adherence to prescriptive codes and standards provides an implicit assurance of safety, a performance-based analysis is performed with explicit safety objectives as the criteria for measuring success. The performance-based analysis evaluates whether the fire protection features in the building will protect the building occupants in the event of a fire. The criteria for acceptability are based on industry accepted tenability thresholds for building occupants. There are many criteria that can be used; the criteria used in this analysis are visibility reduction (13 m and 4 m) and temperature exposure (80ºC for 15 min). During this analysis a fire was modeled inside the library’s main entrance. The fire resulted in the main entrance being blocked prior to completion of egress (16 min), which has been determined through the use of hydraulic calculations. The results of the performance-based design indicate that, with the main entrance to Kennedy Library blocked by a large fire, the fire protection features of the building provide sufficient protection for all occupants to be able to escape prior to being exposed to untenable conditions. The analysis concludes that the intent of nationally recognized fire protection codes and standards is met for Kennedy Library and the fire protection objectives of NFPA 101(8) will be met when the deficiencies identified in this report are resolved

Characterization of Synthetic DNA Bar Codes in Saccharomyces Cerevisiae Gene-Deletion Strains

Incorporation of strain-specific synthetic DNA tags into yeast Saccharomyces cerevisiae gene-deletion strains has enabled identification of gene functions by massively parallel growth rate analysis. However, it is important to confirm the sequences of these tags, because mutations introduced during construction could lead to significant errors in hybridization performance. To validate this experimental system, we . sequenced 11,812 synthetic 20-mer molecular bar codes and adjacent sequences (\u3e1.8 megabases synthetic DNA) by pyrosequencing and Sanger methods. At least 31% ofthe genome-integrated 20-mer tags contain differences from those originally synthesized. However, these mutations result in anomalous hybridization in only a small subset of strains, and the sequence information enables redesign of hybridization probes for arrays. The robust performance of the yeast gene-deletion dual oligonucleotide bar-code design in array hybridization validates the use of molecular bar codes in living cells for tracking their growth phenotype

Performance-Based Design in Structural Fire Engineering

The performance-based design of structures in fire is gaining growing interest as a rational alternative to the traditionally adopted prescriptive code approach. This interest has led to its introduction in different codes and standards around the world. Although engineers widely use performance-based methods to design structural components in earthquake engineering, the adoption of such methods in fire engineering is still very limited. This Special Issue addresses this shortcoming by providing engineers with the needed knowledge and recent research activities addressing performance-based design in structural fire engineering, including the use of hotspot analysis to estimate the magnitude of risk to people and property in urban areas; simulations of the evacuation of large crowds; and the identification of fire effects on concrete, steel, and special structures

Alignment of vaccine codes using an ontology of vaccine descriptions

BACKGROUND: Vaccine information in European electronic health record (EHR) databases is represented using various clinical and database-specific coding systems and drug vocabularies. The lack of harmonization constitutes a challenge in reusing EHR data in collaborative benefit-risk studies about vaccines. METHODS: We designed an ontology of the properties that are commonly used in vaccine descriptions, called Ontology of Vaccine Descriptions (VaccO), with a dictionary for the analysis of multilingual vaccine descriptions. We implemented five algorithms for the alignment of vaccine coding systems, i.e., the identification of corresponding codes from different coding ystems, based on an analysis of the code descriptors. The algorithms were evaluated by comparing their results with manually created alignments in two reference sets including clinical and database-specific coding systems with multilingual code descriptors. RESULTS: The best-performing algorithm represented code descriptors as logical statements about entities in the VaccO ontology and used an ontology reasoner to infer common properties and identify corresponding vaccine codes. The evaluation demonstrated excellent performance of the approach (F-scores 0.91 and 0.96). CONCLUSION: The VaccO ontology allows the identification, representation, and comparison of heterogeneous descriptions of vaccines. The automatic alignment of vaccine coding systems can accelerate the readiness of EHR databases in collaborative vaccine studies

Domain-Specific Acceleration and Auto-Parallelization of Legacy Scientific Code in FORTRAN 77 using Source-to-Source Compilation

Massively parallel accelerators such as GPGPUs, manycores and FPGAs represent a powerful and affordable tool for scientists who look to speed up simulations of complex systems. However, porting code to such devices requires a detailed understanding of heterogeneous programming tools and effective strategies for parallelization. In this paper we present a source to source compilation approach with whole-program analysis to automatically transform single-threaded FORTRAN 77 legacy code into OpenCL-accelerated programs with parallelized kernels. The main contributions of our work are: (1) whole-source refactoring to allow any subroutine in the code to be offloaded to an accelerator. (2) Minimization of the data transfer between the host and the accelerator by eliminating redundant transfers. (3) Pragmatic auto-parallelization of the code to be offloaded to the accelerator by identification of parallelizable maps and reductions. We have validated the code transformation performance of the compiler on the NIST FORTRAN 78 test suite and several real-world codes: the Large Eddy Simulator for Urban Flows, a high-resolution turbulent flow model; the shallow water component of the ocean model Gmodel; the Linear Baroclinic Model, an atmospheric climate model and Flexpart-WRF, a particle dispersion simulator. The automatic parallelization component has been tested on as 2-D Shallow Water model (2DSW) and on the Large Eddy Simulator for Urban Flows (UFLES) and produces a complete OpenCL-enabled code base. The fully OpenCL-accelerated versions of the 2DSW and the UFLES are resp. 9x and 20x faster on GPU than the original code on CPU, in both cases this is the same performance as manually ported code.Comment: 12 pages, 5 figures, submitted to "Computers and Fluids" as full paper from ParCFD conference entr

Performance analysis & optimization of DLR High-Performance Computing codes

The importance of High Performance Computing (HPC) in the field of aircraft design is significantly growing. However, capabilities of current HPC systems are inadequate for scale-resolving simulations of in-flight aircraft. Consequently, coordinated advances in algorithms, hardware, and software are needed. For instance, with the end of Moore’s law, processors evolve towards an ever-increasing core count which raises requirements on the scalability of scientific software. Therefore, this submission provides an in-depth scalability analysis of the DLR flow solvers CODA and Musubi. Performance profiles guide the identification of critical aspects of both codes. The presented analysis reveals potentially sub-optimal communication patterns, proposes possible solutions, and shows first improvements of the codes