Two-Dimensional Cutting Problem

This paper deals with two-dimensional cutting problems. Firstly the complexity of the problem in question is estimated. Then, several known approaches for the regular (rectangular) and irregular (not necessarily rectangular) cutting problems are described. In the second part, a decision support system for cutting a rectangular sheet of material into pieces of arbitrary shapes, is presented. The system uses two earlier described methods which prefer different types of data and the user may decide which one is more suitable for the problem in question. After brief description of system data files and its manual, some experimental results are presented

A Massive Data Parallel Computational Framework for Petascale/Exascale Hybrid Computer Systems

Heterogeneous systems are becoming more common on High Performance Computing (HPC) systems. Even using tools like CUDA and OpenCL it is a non-trivial task to obtain optimal performance on the GPU. Approaches to simplifying this task include Merge (a library based framework for heterogeneous multi-core systems), Zippy (a framework for parallel execution of codes on multiple GPUs), BSGP (a new programming language for general purpose computation on the GPU) and CUDA-lite (an enhancement to CUDA that transforms code based on annotations). In addition, efforts are underway to improve compiler tools for automatic parallelization and optimization of affine loop nests for GPUs and for automatic translation of OpenMP parallelized codes to CUDA. In this paper we present an alternative approach: a new computational framework for the development of massively data parallel scientific codes applications suitable for use on such petascale/exascale hybrid systems built upon the highly scalable Cactus framework. As the first non-trivial demonstration of its usefulness, we successfully developed a new 3D CFD code that achieves improved performance.Comment: Parallel Computing 2011 (ParCo2011), 30 August -- 2 September 2011, Ghent, Belgiu

From Physics Model to Results: An Optimizing Framework for Cross-Architecture Code Generation

Starting from a high-level problem description in terms of partial differential equations using abstract tensor notation, the Chemora framework discretizes, optimizes, and generates complete high performance codes for a wide range of compute architectures. Chemora extends the capabilities of Cactus, facilitating the usage of large-scale CPU/GPU systems in an efficient manner for complex applications, without low-level code tuning. Chemora achieves parallelism through MPI and multi-threading, combining OpenMP and CUDA. Optimizations include high-level code transformations, efficient loop traversal strategies, dynamically selected data and instruction cache usage strategies, and JIT compilation of GPU code tailored to the problem characteristics. The discretization is based on higher-order finite differences on multi-block domains. Chemora's capabilities are demonstrated by simulations of black hole collisions. This problem provides an acid test of the framework, as the Einstein equations contain hundreds of variables and thousands of terms.Comment: 18 pages, 4 figures, accepted for publication in Scientific Programmin

Sequencing by Hybridization of Long Targets

Sequencing by Hybridization (SBH) reconstructs an n-long target DNA sequence from its biochemically determined l-long subsequences. In the standard approach, the length of a uniformly random sequence that can be unambiguously reconstructed is limited to due to repetitive subsequences causing reconstruction degeneracies. We present a modified sequencing method that overcomes this limitation without the need for different types of biochemical assays and is robust to error

Long-term clinical and experimental/surface analytical studies of carbon/carbon maxillofacial implants

BACKGROUND:Over the past 30-40years, various carbon implant materials have become more interesting, because they are well accepted by the biological environment. The traditional carbon-based polymers give rise to many complications. The polymer complication may be eliminated through carbon fibres bound by pyrocarbon (carbon/carbon). The aim of this study is to present the long-term clinical results of carbon/carbon implants, and the results of the scanning electron microscope and energy dispersive spectrometer investigation of an implant retrieved from the human body after 8years.METHODS:Mandibular reconstruction (8-10years ago) was performed with pure (99.99%) carbon implants in 16 patients (10 malignant tumours, 4 large cystic lesions and 2 augmentative processes). The long-term effect of the human body on the carbon/carbon implant was investigated by comparing the structure, the surface morphology and the composition of an implant retrieved after 8years to a sterilized, but not implanted one.RESULTS:Of the 16 patients, the implants had to be removed earlier in 5 patients because of the defect that arose on the oral mucosa above the carbon plates. During the long-term follow-up, plate fracture, loosening of the screws, infection or inflammations around the carbon/carbon implants were not observed. The thickness of the carbon fibres constituting the implants did not change during the 8-year period, the surface of the implant retrieved was covered with a thin surface layer not present on the unimplanted implant. The composition of this layer is identical to the composition of the underlying carbon fibres. Residual soft tissue penetrating the bulk material between the carbon fibre bunches was found on the retrieved implant indicating the importance of the surface morphology in tissue growth and adhering implants.CONCLUSIONS:The surface morphology and the structure were not changed after 8years. The two main components of the implant retrieved from the human body are still carbon and oxygen, but the amount of oxygen is 3-4 times higher than on the surface of the reference implant, which can be attributed to the oxidative effect of the human body, consequently in the integration and biocompatibility of the implant. The clinical conclusion is that if the soft part cover is appropriate, the carbon implants are cosmetically and functionally more suitable than titanium plates

In vitro and in vivo studies on biocompatibility of carbon fibres

In the present study we focused on the in vitro and in vivo evaluation of two types of carbon fibres (CFs): hydroxyapatite modified carbon fibres and porous carbon fibres. Porous CFs used as scaffold for tissues regeneration could simultaneously serve as a support for drug delivery or biologically active agents which would stimulate the tissue growth; while addition of nanohydroxyapatite to CFs precursor can modify their biological properties (such as bioactivity) without subsequent surface modifications, making the process cost and time effective. Presented results indicated that fibre modification with HAp promoted formation of apatite on the fibre surface during incubation in simulated body fluid. The materials biocompatibility was determined by culturing human osteoblast-like cells of the line MG 63 in contact with both types of CFs. Both tested materials gave good support to adhesion and growth of bone-derived cells. Materials were implanted into the skeletal rat muscle and a comparative analysis of tissue reaction to the presence of the two types of CFs was done. Activities of marker metabolic enzymes: cytochrome c oxidase (CCO) and acid phosphatase were examined to estimate the effect of implants on the metabolic state of surrounding tissues. Presented results evidence the biocompatibility of porous CFs and activity that stimulates the growth of connective tissues. In case of CFs modified with hydroxyapatite the time of inflammatory reaction was shorter than in case of traditional CFs

A Massive Data Parallel Computational Framework for Petascale/Exascale Hybrid Computer Systems

large scale scientific applicatio