Petascale turbulence simulation using a highly parallel fast multipole method on GPUs

This paper reports large-scale direct numerical simulations of homogeneous-isotropic fluid turbulence, achieving sustained performance of 1.08 petaflop/s on gpu hardware using single precision. The simulations use a vortex particle method to solve the Navier-Stokes equations, with a highly parallel fast multipole method (FMM) as numerical engine, and match the current record in mesh size for this application, a cube of 4096^3 computational points solved with a spectral method. The standard numerical approach used in this field is the pseudo-spectral method, relying on the FFT algorithm as numerical engine. The particle-based simulations presented in this paper quantitatively match the kinetic energy spectrum obtained with a pseudo-spectral method, using a trusted code. In terms of parallel performance, weak scaling results show the fmm-based vortex method achieving 74% parallel efficiency on 4096 processes (one gpu per mpi process, 3 gpus per node of the TSUBAME-2.0 system). The FFT-based spectral method is able to achieve just 14% parallel efficiency on the same number of mpi processes (using only cpu cores), due to the all-to-all communication pattern of the FFT algorithm. The calculation time for one time step was 108 seconds for the vortex method and 154 seconds for the spectral method, under these conditions. Computing with 69 billion particles, this work exceeds by an order of magnitude the largest vortex method calculations to date

Cyclic Strength of Undisturbed Mine Tailings

In order to update existing regulations for the seismic design of tailings retention dikes, extensive investigations were undertaken for 15 existing tailings dams throughout Japan. Undisturbed samples procured from the tailings disposal ponds were tested ln the laboratory to determine the cyclic strength of the in-situ tailings deposits. The results of cyclic triaxial tests on these materials are summarized by means of empirical formulae which are recommended for incorporation in the new seismic design code for the tailings dams

Quantum Circuit Simulation by SGEMM Emulation on Tensor Cores and Automatic Precision Selection

Quantum circuit simulation provides the foundation for the development of quantum algorithms and the verification of quantum supremacy. Among the various methods for quantum circuit simulation, tensor network contraction has been increasing in popularity due to its ability to simulate a larger number of qubits. During tensor contraction, the input tensors are reshaped to matrices and computed by a GEMM operation, where these GEMM operations could reach up to 90\% of the total calculation time. GEMM throughput can be improved by utilizing mixed-precision hardware such as Tensor Cores, but straightforward implementation results in insufficient fidelity for deep and large quantum circuits. Prior work has demonstrated that compensated summation with special care of the rounding mode can fully recover the FP32 precision of SGEMM even when using TF32 or FP16 Tensor Cores. The exponent range is a critical issue when applying such techniques to quantum circuit simulation. While TF32 supports almost the same exponent range as FP32, FP16 supports a much smaller exponent range. In this work, we use the exponent range statistics of input tensor elements to select which Tensor Cores we use for the GEMM. We evaluate our method on Random Circuit Sampling (RCS), including Sycamore's quantum circuit, and show that the throughput is 1.86 times higher at maximum while maintaining accuracy.Comment: This paper has been accepted to ISC'2

Teaching remedial grammar through data-driven learning using AntPConc

In most Asian countries, students receive between six and eight years of compulsory English education before they enter university. Despite this massive investment in English education, many students, especially in Japan, continue to show a poor understanding of rudimentary grammar rules. In this paper we report on a unique English course designed specifically to address grammar issues at low (remedial) levels using a Data-Driven Learning (DDL) approach. Applications of DDL are becoming more widely reported, but they are generally at the intermediate or advanced level. One of the challenges of using DDL at the remedial level is the lack of suitably leveled corpora. Another challenge is that most corpus tools used in DDL are designed for researchers or advanced learners and thus can appear overly complex. To address these issues, we have developed a simple English corpus built from standard school texts. We have also created a freeware, parallel corpus tool, AntPConc, that is specially designed to be simple, easy, and intuitive to use by beginner learners. Results from the course show significant gains between pre- and post-tests of grammar understanding for beginner-level EFL university students. We also obtained positive student feedback on the AntPConc software

Clostridium botulinum Type E Toxins Bind to Caco-2 Cells by a Different Mechanism from That of Type A Toxins

Cultured Clostridium botulinum strains produce progenitor toxins designated as 12S, 16S, and 19S toxins. The 12S toxin consists of a neurotoxin (NTX, 7S) and a non-toxic non-hemagglutinin (NTNH). The 16S and 19S toxins are formed by conjugation of the 12S toxin with hemagglutinin (HA), and the 19S toxin is a dimer of the 16S toxin. Type A cultures produce all 3 of these progenitor toxins, while type E produces only the 12S toxin. The 7S toxin is cleaved into heavy (H) and light (L) chains by a protease(s) in some strains, and the H chain has 2 domains, the N-terminus (Hn) and C-terminus (Hc). It has been reported that type A toxins bind to the intestinal cells or cultured cells via either HA or Hc. In this study, we investigated the binding of type A and E toxins to Caco-2 cells using Western blot analysis. Both the type E 7S and 12S toxins bound to the cells, with the 7S toxin binding more strongly, whereas, in the type A strain, only the 16S/19S toxins showed obvious binding. Pre-incubation of the type E 7S toxin with IgG against recombinant type E Hc significantly inhibited the 7S toxin binding, indicating that Hc might be a main binding domain of the type E toxin

Bacterial-contamination Monitoring

Bacterial contamination of dental unit waterlines (DUWLs) was evaluated by using ATP-bioluminescence analysis and conventional culture method. Water samples (n=44) from DUWLs were investigated for heterotrophic bacteria by culture on R2A agar, which ranged from 1.4×103 to 2.7×105 CFU/mL. The ATP-bioluminescence results for DUWL samples were ranged from 6 to 1189 RLU and obtained within one minutes. These results were well correlated with the culture results (r=0.727-0.855). We conclude that differences in the bacterial contamination of each water supply were confirmed by the ATP-bioluminescence assay. This method would be potentially useful for rapid and simple monitoring of DUWL bacterial contamination

Neutrophil and lymphocyte responses to oral Streptococcus in Adamantiades-Behcet's disease

Immune reactions against microorganisms play an important pathogenic role in Adamantiades-Behçet’s disease (ABD). We had previously obtained Streptococcus sanguinis (strain BD113-20) isolated from the oral cavity of patients with ABD. To investigate the pathogenesis of this isolate, we examined neutrophil 5 reactions and level of cytokine production by lymphocytes after stimulation with the strain. The reactions of neutrophils were examined by chemiluminescence assay using whole blood. The amounts of interferon gamma (IFN-g) and interleukin (IL)-4, IL-8, IL-10, and IL-12 produced by peripheral blood mononuclear cells (PBMCs) were measured by ELISA. 10 Strain BD113-20 activated neutrophils from patients with ABD and healthy volunteers, and, in addition it increased IFN-g production by lymphocytes. Lymphocyte from the patients with ABD showed a dominant T helper 1 (Th-1) immune response. Results indicated that both bacterial stimulation and host hypersensitivity might be involved in the symptoms and pathogenesis of ABD

Use of ATP bioluminescence to survey the spread of aerosol and splatter during dental treatment

Aerosol and splatter produced during dental treatment (ultrasonic scaling and professional mechanical tooth cleaning) are potential sources of infection. Contamination patterns on the operators’ masks, goggles, chests and gowned right arms, and on the patients’ goggles, before and after dental treatment were investigated by using ATP bioluminescence analysis. Contamination on every surface tested increased significantly after dental treatment. Maximum contamination was found on patients’ goggles. Aerosol and splatter produced during dental treatment thus have the potential to spread infection to operators and patients. ATP bioluminescence is a useful tool for monitoring surface contamination

Antibody and Cytokine Responses in Helicobacter pylori-Infected Various Mouse Strains

Helicobacter pylori (H. pylori) infection in the stomach is etiologically closely associated with chronic active gastritis, peptic ulcer, gastric cancer and gastric mucosa-associated lymphoid tissue lymphoma. In this study, we examined the antibody responses and cytokine profiles of three strains of mice (BALB/c, C3H/He, and C57BL/6) infected with H. pylori. Following this, correlations between host-immune reactions and intensity of inflammation were analyzed. H. pylori (ATCC43504) was intragastrically administered once a week to the mice from 4 weeks of age, and they were sacrificed at the ages of 4 and 7 months. In these mice, we examined the histology of the stomach, antibody titers against H. pylori, and serum levels of cytokines (IL-4, IL-10, TNF-alpha, IL-2 and Interferon-gamma). In BALB/c mice, inflammation of the stomach was minimal. Inflammation was observed in 63.6% of C57BL/6 mice and 33.3% of C3h/He mice. In C57BL/6 and C3H/He mice, all the cytokines tended to increase. In contrast, BALB/c mice were inactive in cytokine production except for IL-2. Two C3H/He mice developed severe inflammation with lymph follicles; one showed a response largely typical of Th-1, and the other showed a response largely typical of Th-2. Although a definite correlation was not shown between Th-1/Th-2 response evaluated by cytokine production and intensity of inflammation, it appears that in H. pylori-induced inflammation both cell-mediated (Th-1) and humoral (Th-2) immunity play a role in pathogenesis.</p