Tsuyoshi Hamada

42 TFlops hierarchical N -body simulations on GPUs with applications in both astrophysics and turbulence

As an entry for the 2009 Gordon Bell price/performance prize, we present the results of two different hierarchical N-body simulations on a cluster of 256 graphics processing units (GPUs). Unlike many previous N-body simulations on GPUs that scale as O(N2), the present method calculates the O(N log N) treecode and O(N) fast multipole method (FMM) on the GPUs with unprecedented efficiency. We demonstrate the performance of our method by choosing one standard application -a gravitational N-body simulation- and one non-standard application -simulation of turbulence using vortex particles. The gravitational simulation using the treecode with 1,608,044,129 particles showed a sustained performance of 42.15 TFlops. The vortex particle simulation of homogeneous isotropic turbulence using the periodic FMM with 16,777,216 particles showed a sustained performance of 20.2 TFlops. The overall cost of the hardware was 228,912 dollars. The maximum corrected performance is 28.1TFlops for the gravitational simulation, which results in a cost performance of 124 MFlops/

Preliminary report on a new, fully covered, metal stent designed for the treatment of pancreatic fluid collections

. This correction is performed by counting the Flops based on the most efficient CPU algorithm. Any extra Flops that arise from the GPU implementation and parameter differences are not included in the 124 MFlops/

Pivotal function for cytoplasmic protein FROUNT in CCR2-mediated monocyte chemotaxis

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Biomolecular electrostatics using a fast multipole BEM on up to 512 gpus and a billion unknowns

BACKGROUND Endoscopic transluminal treatment of pancreatic fluid collections (PFC) has been reported as an effective alternative approach to surgical treatment. A wide, short stent with an anti-migration system has been developed. OBJECTIVE To evaluate a newly developed, fully covered, self-expandable metal stent (FCSEMS) customized for cystogastrostomy. DESIGN Retrospective case series. SETTING Tertiary-care academic medical centers and affiliated hospitals. PATIENTS Nine patients who underwent endoscopic treatment of PFCs (5 with pseudocysts and 4 with walled-off pancreatic necrosis). INTERVENTION Stent deployment after endoscopic US-guided puncture. Irrigation and necrosectomy were performed at the discretion of the endoscopist. MAIN OUTCOME MEASUREMENTS Technical and clinical success rate, complications, and removability. RESULTS The FCSEMS was inserted successfully in all cases (9/9, 100%). Clinical success was achieved in 7 of 9 cases (77.8%). No early complications associated with the procedure were observed. Late complications were observed in 2 cases (bleeding and asymptomatic migration). The FCSEMS was removed without any complications in all 6 cases where it was attempted after the procedure had been completed (100%). LIMITATIONS This was a retrospective evaluation of a small number of cases. The FCSEMS was always inserted via the transgastric route. Follow-up duration was short. CONCLUSION The endoscopic approach that uses this new FCSEMS is feasible for the treatment of PFCs. However, further evaluation is required.

190 TFlops Astrophysical N-body Simulation on a Cluster of GPUs

Ligation of the chemokine receptor CCR2 on monocytes and macrophages with its ligand CCL2 results in activation of the cascade consisting of phosphatidylinositol-3-OH kinase (PI(3)K), the small G protein Rac and lamellipodium protrusion. We show here that a unique clathrin heavy-chain repeat homology protein, FROUNT, directly bound activated CCR2 and formed clusters at the cell front during chemotaxis. Overexpression of FROUNT amplified the chemokine-elicited PI(3)K–Rac–lamellipodium protrusion cascade and subsequent chemotaxis. Blocking FROUNT function by using a truncated mutant or antisense strategy substantially diminished signaling via CCR2. In a mouse peritonitis model, suppression of endogenous FROUNT markedly prevented macrophage infiltration. Thus, FROUNT links activated CCR2 to the PI(3)K–Rac–lamellipodium protrusion cascade and could be a therapeutic target in chronic inflammatory immune diseases associated with macrophage infiltration.

TOKYO criteria 2014 for transpapillary biliary stenting

Abstract We present teraflop-scale calculations of biomolecular electrostatics enabled by the combination of algorithmic and hardware acceleration. The algorithmic acceleration is achieved with the fast multipole method ( fmm ) in conjunction with a boundary element method ( bem ) formulation of the continuum electrostatic model, as well as the bibee approximation to bem . The hardware acceleration is achieved through graphics processors, gpu s. We demonstrate the power of our algorithms and software for the calculation of the electrostatic interactions between biological molecules in solution. The applications demonstrated include the electrostatics of protein–drug binding and several multi-million atom systems consisting of hundreds to thousands of copies of lysozyme molecules. The parallel scalability of the software was studied in a cluster at the Nagasaki Advanced Computing Center, using 128 nodes, each with 4 gpu s. Delicate tuning has resulted in strong scaling with parallel efficiency of 0.8 for 256 and 0.5 for 512 gpu s. The largest application run, with over 20 million atoms and one billion unknowns, required only one minute on 512 gpu s. We are currently adapting our bem software to solve the linearized Poisson–Boltzmann equation for dilute ionic solutions, and it is also designed to be flexible enough to be extended for a variety of integral equation problems, ranging from Poisson problems to Helmholtz problems in electromagnetics and acoustics to high Reynolds number flow.

An Open Approach to Autonomous Vehicles

We present the results of a hierarchical N-body simulation on DEGIMA, a cluster of PCs with 576 graphic processing units (GPUs) and using an InfiniBand interconnect. DEGIMA stands for DEstination for GPU Intensive MAchine, and is located at Nagasaki Advanced Computing Center (NACC), Nagasaki University. In this work, we have upgraded DEGIMA_s interconnect using InfiniBand. DEGIMA is composed by 144 nodes with 576 GT200 GPUs. An astrophysical N-body simulation with 3,278,982,596 particles using a treecode algorithm shows a sustained performance of 190.5 Tflops on DEGIMA. The overall cost of the hardware was

Association of Dietary Patterns With Risk of Colorectal Cancer Subtypes Classified by Fusobacterium nucleatum in Tumor Tissue

411,921 dollars. The maximum corrected performance is 104.8 Tflops for the simulation, resulting in a cost performance of 254.4 MFlops/

Duodenal invasion is a risk factor for the early dysfunction of biliary metal stents in unresectable pancreatic cancer.

. This corrections is performed by counting the FLOPS based on the most efficient CPU algorithm. Any extra FLOPS that arise from the GPU implementation and parameter differences are not included in the 254.4 MFLOPS/

Short- and long-term outcomes of endoscopic papillary large balloon dilation with or without sphincterotomy for removal of large bile duct stones.

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