A Flexible Patch-Based Lattice Boltzmann Parallelization Approach for Heterogeneous GPU-CPU Clusters

Sustaining a large fraction of single GPU performance in parallel computations is considered to be the major problem of GPU-based clusters. In this article, this topic is addressed in the context of a lattice Boltzmann flow solver that is integrated in the WaLBerla software framework. We propose a multi-GPU implementation using a block-structured MPI parallelization, suitable for load balancing and heterogeneous computations on CPUs and GPUs. The overhead required for multi-GPU simulations is discussed in detail and it is demonstrated that the kernel performance can be sustained to a large extent. With our GPU implementation, we achieve nearly perfect weak scalability on InfiniBand clusters. However, in strong scaling scenarios multi-GPUs make less efficient use of the hardware than IBM BG/P and x86 clusters. Hence, a cost analysis must determine the best course of action for a particular simulation task. Additionally, weak scaling results of heterogeneous simulations conducted on CPUs and GPUs simultaneously are presented using clusters equipped with varying node configurations.Comment: 20 pages, 12 figure

Validation of T-Track® CMV to assess the functionality of cytomegalovirus-reactive cell-mediated immunity in hemodialysis patients

Background: Uncontrolled cytomegalovirus (CMV) replication in immunocompromised solid-organ transplant recipients is a clinically relevant issue and an indication of impaired CMV-specific cell-mediated immunity (CMI). Primary aim of this study was to assess the suitability of the immune monitoring tool T-Track (R) CMV to determine CMV-reactive CMI in a cohort of hemodialysis patients representative of patients eligible for renal transplantation. Positive and negative agreement of T-Track (R) CMV with CMV serology was examined in 124 hemodialysis patients, of whom 67 (54%) revealed a positive CMV serostatus. Secondary aim of the study was to evaluate T-Track (R) CMV performance against two unrelated CMV-specific CMI monitoring assays, QuantiFERON (R)-CMV and a cocktail of six class I iTAg (TM) MHC Tetramers. Results: Positive T-Track (R) CMV results were obtained in 90% (60/67) of CMV-seropositive hemodialysis patients. In comparison, 73% (45/62) and 77% (40/52) positive agreement with CMV serology was achieved using QuantiFERON (R)-CMV and iTAg (TM) MHC Tetramer. Positive T-Track (R) CMV responses in CMV-seropositive patients were dominated by pp65-reactive cells (58/67 [ 87%]), while IE-1-responsive cells contributed to an improved (87% to 90%) positive agreement of T-Track (R) CMV with CMV serology. Interestingly, T-Track (R) CMV, QuantiFERON (R)-CMV and iTAg (TM) MHC Tetramers showed 79% (45/57), 87% (48/55) and 93% (42/45) negative agreement with serology, respectively, and a strong inter-assay variability. Notably, T-Track (R) CMV was able to detect IE-1-reactive cells in blood samples of patients with a negative CMV serology, suggesting either a previous exposure to CMV that yielded a cellular but no humoral immune response, or TCR cross-reactivity with foreign antigens, both suggesting a possible protective immunity against CMV in these patients. Conclusion: T-Track (R) CMV is a highly sensitive assay, enabling the functional assessment of CMV-responsive cells in hemodialysis patients prior to renal transplantation. T-Track (R) CMV thus represents a valuable immune monitoring tool to identify candidate transplant recipients potentially at increased risk for CMV-related clinical complications

Preference SQL - Design, Implementation, Experiences

Current search engines can hardly cope adequately with complex preferences. The biggest problem of search engines directly implemented with standard SQL is that SQL does not directly understand the notion of preferences. Preference SQL extends standard SQL by a preference model based on strict partial orders, where preference queries behave like soft selection constraints. A variety of built-in base preference types and the powerful Pareto accumulation operator to construct complex preferences, combined with the adherence to declarative SQL programming style, guarantees great programming productivity. The current Preference SQL optimizer does an efficient re-writing into standard SQL, including a high-level implementation of the skyline operator for Pareto-optimal sets. This pre-processor approach enables a seamless application integration, making reference SQL available on a broad variety of SQL platforms including IBM DB2, Oracle, Microsoft SQL Server and Sybase. The benefits of Preference SQL technology comprise cooperative query answering and smart customer advice, leading to a higher e-customer satisfaction and shorter development times of personalized search engines for the e-service provider. We report experiences with practical applications ranging from m-commerce and comparison shopping to a large-scale performance test with real data. Several search engines of commercial B2C portals are powered by Preference SQL

Client-server optimization for multimedia document exchange

The success of the World Wide Web is boosting the development of multimedia database systems and their integration into the internet. For the documents stored and exchanged in the Web there is a variety of multimedia data formats differing in aspects such as resolution, sampling rate, and compression. Furthermore there is a large heterogeneity of Web browsers, the data formats they support, and their network access. Thus storage servers have to store and proxy servers have to transfer many different formats. However, the data formats are not independent from each other but interrelated by conversion tools. There is a large number of alternatives for storage and proxy servers to store some formats or to transfer them via the network and to compute the remaining ones by applying conversion tools. To determine an optimal choice is a nontrivial optimization problem and is subject to changes of the parameters such as query profile, available disk storage, and network bandwidth. We examine the outlined optimization problem in the context of object-oriented databases and illustrate our approach by a practical application

Preference SQL -- Design, Implementation, Experiences

Current search engines can hardly cope adequately with fuzzy predicates defined by complex preferences. The biggest problem of search engines implemented with standard SQL is that SQL does not directly understand the notion of preferences. Preference SQL extends SQL by a preference model based on strict partial orders (presented in more detail in the companion paper [Kie02]), where preference queries behave like soft selection constraints. Several built-in base preference types and the powerful Pareto operator, combined with the adherence to declarative SQL programming style, guarantees great programming productivity. The Preference SQL optimizer does an efficient re-writing into standard SQL, including a high-level implementation of the skyline operator for Pareto-optimal sets. This pre-processor approach enables a seamless application integration, making Preference SQL available on all major SQL platforms. Several commercial B2C portals are powered by Preference SQL. Its benefits comprise cooperative query answering and smart customer advice, leading to higher ecustomer satisfaction and shorter development times of personalized search engines. We report practical experiences ranging from m-commerce and comparison shopping to a large-scale performance test for a job portal

Client-Server Optimization for Multimedia Document Exchange

The success of the World Wide Web is boosting the development of multimedia database systems and their integration into the internet. For the documents stored and exchanged in the Web there are many multimedia data formats di#ering in aspects such as resolution, sampling rate, and compression. Furthermore there is a large variety of Web browsers, the data formats they support, and their network access. Thus storage servers have to store and proxy servers have to transfer many di#erent formats. However, the data formats are not independent from each other but interrelated by conversion tools. Thereisalarge number of alternatives for storage and proxy servers to store some formats or to transfer them via the network and to compute the remaining ones by applying conversion tools. To determine an optimal choice is a nontrivial optimization problem and is subject to changes of the parameters such as query pro#le, available disk storage, and network bandwidth. We examine the outlined optim..