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

Model-Based Acceleration of Look-Locker T1 Mapping

Mapping the longitudinal relaxation time $T_1$ has widespread applications in clinical MRI as it promises a quantitative comparison of tissue properties across subjects and scanners. Due to the long scan times of conventional methods, however, the use of quantitative MRI in clinical routine is still very limited. In this work, an acceleration of Inversion-Recovery Look-Locker (IR-LL) $T_1$ mapping is presented. A model-based algorithm is used to iteratively enforce an exponential relaxation model to a highly undersampled radially acquired IR-LL dataset obtained after the application of a single global inversion pulse. Using the proposed technique, a $T_1$ map of a single slice with 1.6mm in-plane resolution and 4mm slice thickness can be reconstructed from data acquired in only 6s. A time-consuming segmented IR experiment was used as gold standard for $T_1$ mapping in this work. In the subsequent validation study, the model-based reconstruction of a single-inversion IR-LL dataset exhibited a $T_1$ difference of less than 2.6% compared to the segmented IR-LL reference in a phantom consisting of vials with $T_1$ values between 200ms and 3000ms. In vivo, the $T_1$ difference was smaller than 5.5% in WM and GM of seven healthy volunteers. Additionally, the $T_1$ values are comparable to standard literature values. Despite the high acceleration, all model-based reconstructions were of a visual quality comparable to fully sampled references. Finally, the reproducibility of the $T_1$ mapping method was demonstrated in repeated acquisitions. In conclusion, the presented approach represents a promising way for fast and accurate $T_1$ mapping using radial IR-LL acquisitions without the need of any segmentation

Data from: Model-based acceleration of Look-Locker T1 mapping

Mapping the longitudinal relaxation time T1 has widespread applications in clinical MRI as it promises a quantitative comparison of tissue properties across subjects and scanners. Due to the long scan times of conventional methods, however, the use of quantitative MRI in clinical routine is still very limited. In this work, an acceleration of Inversion-Recovery Look-Locker (IR-LL) T1 mapping is presented. A model-based algorithm is used to iteratively enforce an exponential relaxation model to a highly undersampled radially acquired IR-LL dataset obtained after the application of a single global inversion pulse. Using the proposed technique, a T1 map of a single slice with 1.6mm in-plane resolution and 4mm slice thickness can be reconstructed from data acquired in only 6s. A time-consuming segmented IR experiment was used as gold standard for T1 mapping in this work. In the subsequent validation study, the model-based reconstruction of a single-inversion IR-LL dataset exhibited a T1 difference of less than 2.6% compared to the segmented IR-LL reference in a phantom consisting of vials with T1 values between 200ms and 3000ms. In vivo, the T1 difference was smaller than 5.5% in WM and GM of seven healthy volunteers. Additionally, the T1 values are comparable to standard literature values. Despite the high acceleration, all model-based reconstructions were of a visual quality comparable to fully sampled references. Finally, the reproducibility of the T1 mapping method was demonstrated in repeated acquisitions. In conclusion, the presented approach represents a promising way for fast and accurate T1 mapping using radial IR-LL acquisitions without the need of any segmentation

Computational Design of Epitope-Enriched HIV-1 Gag Antigens with Preserved Structure and Function for Induction of Broad CD8+ T Cell Responses

The partially protective phenotype observed in HIV-infected long-term-non-progressors is often associated with certain HLA alleles, thus indicating that cytotoxic T lymphocyte (CTL) responses play a crucial role in combating virus replication. However, both the vast variability of HIV and the HLA diversity impose a challenge on elicitation of broad and effective CTL responses. Therefore, we conceived an algorithm for the enrichment of CD8(+) T cell epitopes in HIV's Gag protein, respecting functional preservation to enable cross-presentation. Experimentally identified epitopes were compared to a Gag reference sequence. Amino-acid-substitutions (AAS) were assessed for their impact on Gag's budding-function using a trained classifier that considers structural models and sequence conservation. Experimental assessment of Gag-variants harboring selected AAS demonstrated an apparent classifier-precision of 100%. Compatible epitopes were assigned an immunological score that incorporates features such as conservation or HLA-association in a user-defined weighted manner. Using a genetic algorithm, the epitopes were incorporated in an iterative manner into novel T-cellepitope-enriched Gag sequences (TeeGag). Computational evaluation showed that these antigen candidates harbor a higher fraction of epitopes with higher score as compared to natural Gag isolates and other artificial antigen designs. Thus, these designer sequences qualify as next-generation antigen candidates for induction of broader CTL responses

MAPrecon

This package "MAPrecon.rar" is an addition to the package "MAPbox.rar". In case you don't want to do any reconstructions yourself and only want to perform the data analysis using already reconstructed data, additionally download this file and follow the instructions in "readme2.txt"

In vivo images.

<p>IR-MAP reconstruction and the segmented IR-LL reference of volunteers V3 and V7 at exemplary inversion times.</p

Phantom measurement.

<p>a: T₁ maps of the segmented IR reconstruction (left), the IR-MAP reconstruction of the single-inversion IR-LL acquisition (center) and the segmented IR-LL reference (right) and the differences (bottom). b: Reference IR-LL images and IR-MAP reconstructions for exemplary inversion times.</p

Acquisition scheme of all acquisitions performed in this work.

<p>The regular IR-MAP acquisition consists of one inversion followed by a spoiled gradient-echo data collection (green). The segmented reference is acquired by performing multiple IR-LL acquisitions, each of which is followed by a 15s break for relaxation before the next inversion (orange). Using IR-MAP reconstructions for multiple of the acquired IR-LL datasets, a reproducibility study was carried out (blue).</p