Neophytos Neophytou

MPI-FT: PORTABLE FAULT TOLERANCE SCHEME FOR MPI

In this paper, we propose the design and development of a fault tolerant and recovery scheme for the Message Passing Interface (MPI). The proposed scheme consists of a detection mechanism for detec...

Space-time points: 4D splatting on efficient grids

4D datasets, such as time-varying datasets, usually come on 4D Cartesian Cubic (CC) grids. In this paper, we explore the use of 4D Body Centered Cubic (BCC) grids to provide a more efficient sampling lattice. We use this lattice in conjunction with a point-based renderer that further reduces the data into an RLE-encoded list of relevant points. We achieve compression ranging from 50 to 80% in our experiments. Our 4D visualization approach follows the hyperslice paradigm: the user first specifies a 4D slice to extract a 3D volume, which is then viewed using a regular point-based full volume renderer. The slicing of a 4D BCC volume yields a 3D BCC volume, which theoretically has 70% of the datapoints of an equivalent CC volume. We reach compressions close to this in practice. The visual quality of the rendered BCC volume is virtually identical with that obtained from the equivalent CC volume, at 70-80% of the CC grid rendering time. Finally, we also describe a 3.5D visualization approach that uses motion blur to indicate the transition of objects along the dimension orthogonal to the extracted hyperslice in one still image. Our approach uses interleaved rendering of a motion volume and the current iso-surface volume to acid the motion blurring effect with proper occlusion and depth relationships.

GPU-accelerated volume splatting with elliptical RBFs

Radial Basis Functions (RBFs) have become a popular rendering primitive, both in surface and in volume rendering. This paper focuses on volume visualization, giving rise to 3D kernels. RBFs are especially convenient for the representation of scattered and irregularly distributed point samples, where the RBF kernel is used as a blending function for the space in between samples. Common representations employ radially symmetric RBFs, and various techniques have been introduced to render these, also with efficient implementations on programmable graphics hardware (GPUs). In this paper, we extend the existing work to more generalized, ellipsoidal RBF kernels, for the rendering of scattered volume data. We devise a post-shaded kernel-centric rendering approach, specifically designed to run efficiently on GPUs, and we demonstrate our renderer using datasets from subdivision volumes and computational science.

Net-dbx: a web-based debugger of MPI programs over low-bandwidth lines

This paper describes Net-dbx, a tool that utilizes Java and other World Wide Web tools for the debugging of MPI programs from anywhere in the Internet. Net-dbx is a source-level interactive debugger with the full power of gdb (the GNU Debugger) augmented with the debug functionality of the public-domain MPI implementation environments. The main effort was on a low overhead, yet powerful, graphical interface supported by low-bandwidth connections. The portability of the tool is of great importance as well because it enables the tool to be used on heterogeneous nodes that participate in an MPI multicomputer. Both needs are satisfied a great deal by the use of WWW browsing tools and the Java programming language. The user of our system simply points his/her browser to the Net-dbx page, logs in to the destination system, and starts debugging by interacting with the tool, just as with any GUI environment. The user can dynamically select which MPI processes to view/debug. A special WWW-based environment has been designed and implemented to host the system prototype.

Color-Space CAD: Direct Gamut Editing in 3D

Color-space CAD is an interactive image-processing framework that lets users manipulate colors directly in 3D perceptual color space. Unlike traditional 2D color- manipulation tools, which often require multiple iterations, color-space CAD allows direct 3D navigation of the solution space. The framework uses graphics hardware to accelerate the computation-intensive mapping operations.

Transcriptional Profiling Identifies the Signaling Axes of IGF and Transforming Growth Factor-β as Involved in the Pathogenesis of Osteosarcoma

BackgroundOsteosarcoma is the most common primary bone tumor in adolescents associated with skeletal development. The molecular pathogenesis of osteosarcoma has not been completely determined, although many molecular alterations have been found in human osteosarcomas and cell lines.Questions/purposesWe questioned whether (1) we could identify gene expression in osteosarcoma specimens that differs from normal osteoblasts and mesenchymal stem cells and (2) this would provide clues to the molecular pathogenesis of osteosarcoma?MethodsThe whole-genome transcriptional profiles of osteosarcomas, including two primary biopsy specimens, two cell lines, two xenografts derived from patient specimens, and one from normal osteoblasts and from mesenchymal stem cells, respectively, were quantitatively measured using serial analysis of gene expression. A statistical enrichment was performed, which selects the common genes altered in each of the osteosarcomas compared with each of the normal counterparts independently.ResultsSixty (92%) of 65 total genes that were at least twofold downregulated in osteosarcoma compared with osteoblasts and mesenchymal stem cells, could be classified in four categories: (1) seven genes in the insulin–like growth factor (IGF) signaling axis, including three of the IGF-binding proteins (IGFBP) and three of the IGFBP-related proteins (IGFBPrP); (2) eight genes in the transforming growth factor-β (TGF-β)/bone morphogenetic protein (BMP) signaling cascade; (3) 39 genes encoding cytoskeleton and extracellular matrix proteins that are regulated by TGF-β/BMPs; and (4) six genes involved in cell cycle regulation, including tumor suppressors TP63 and p21.ConclusionsBased on these transcriptional profiles, a coordinated theme of clustered gene deregulation in osteosarcoma has emerged. Cell proliferation driven by the IGF axes during bone growth is unrestrained owing to downregulation of IGFBPs and cell cycle regulators. Tumor cells may be maintained in an undifferentiated state secondary to impaired TGF-β/BMP signaling. This well-preserved pattern suggests that the alterations in the signaling axes of IGF-1 and TGF-β, in concert with cell cycle regulators, may be an important pathogenic basis of osteosarcoma.Clinic RelevanceThis study provides a possible molecular basis of pathogenesis of osteosarcoma. This may help to develop new therapeutic targets and strategy for this disease. Preclinical and subsequently clinical testing of inhibitors of the IGF-1 and TGF pathways would be warranted.

SIMD-Aware Ray-Casting

With the addition of loop and branch capabilities into the GPU programming set, a more natural and free-flowing volume rendering pipeline execution mode recently emerged. While the execution of the looped fragment program is still SIMD, the numerical approximation of the volume integral is no longer broken up into multiple passes, as it was in previous approaches. Although this certainly is an improvement, due to the less tight control, the present framework lacks the capabilities to focus program flow on the relevant data. In fact, due to the GPU-native SIMD programming model, the slowest ray will now determine the rendering speed. Our paper seeks to provide solutions to enforce more control over the rendering process, with the special SIMD programming model in mind, while retaining this new and promising single-pass rendering paradigm. Our efforts were rewarded with speedups of up to 8.

Squeeze: numerical-precision-optimized volume rendering

This paper discusses how to squeeze volume rendering into as few bits per operation as possible while still retaining excellent image quality. For each of the typical volume rendering pipeline stages in texture map volume rendering, ray casting and splatting we provide a quantitative analysis of the theoretical and practical limits for the required bit precision for computation and storage. Applying this analysis to any volume rendering implementation can balance the internal precisions based on the desired final output precision and can result in significant speedups and reduced memory footprint.

Debugging MPI Grid applications using Net-dbx

Application-development in Grid environments is a challenging process, thus the need for grid enabled development tools is also one that has to be fulfilled. In our work we describe the development of a Grid Interface for the Net-dbx parallel debugger, that can be used to debug MPI grid applications. Net-dbx is a web-based debugger enabling users to use it for debugging from anywhere in the Internet. The proposed debugging architecture is platform independent, because it uses Java, and it is accessible from anywhere, anytime because it is web based. Our architecture provides an abstraction layer between the debugger and the grid middleware and MPI implementation used. This makes the debugger easily adaptable to different middlewares. The grid-enabled architecture of our debugger carries the portability and usability advantages of Net-dbx on which we have based our design. A prototype has been developed and tested.