Generating Efficient Data Movement Code for Heterogeneous Architectures with Distributed-Memory

Programming for parallel architectures that do not have a shared address space is extremely difficult due to the need for explicit communication between memories of different compute devices. A heterogeneous system with CPUs and multiple GPUs, or a distributed-memory cluster are examples of such systems. Past works that try to automate data movement for distributed-memory architectures can lead to excessive redundant communication. In this paper, we propose an automatic data movement scheme that minimizes the volume of communication between compute devices in heterogeneous and distributed-memory systems. We show that by partitioning data dependences in a particular non-trivial way, one can generate data movement code that results in the minimum volume for a vast majority of cases. The techniques are applicable to any sequence of affine loop nests and works on top of any choice of loop transformations, parallelization, and computation placement. The data movement code generated minimizes the volume of communication for a particular configuration of these. We use a combination of powerful static analyses relying on the polyhedral compiler framework and lightweight runtime routines they generate, to build a source-to-source transformation tool that automatically generates communication code. We demonstrate that the tool is scalable and leads to substantial gains in efficiency. On a heterogeneous system, the communication volume is reduced by a factor of 11X to 83X over state-of-the-art, translating into a mean execution time speedup of 1.53X. On a distributed-memory cluster, our scheme reduces the communication volume by a factor of 1.4X to 63.5X over state-of-the-art, resulting in a mean speedup of 1.55X. In addition, our scheme yields a mean speedup of 2.19X over hand-optimized UPC codes.

Anticancer Effects of Brominated Indole Alkaloid Eudistomin H from Marine Ascidian Eudistoma viride Against Cervical Cancer Cells (HeLa)

Marine invertebrates called ascidians are prolific producers of bioactive substances. The ascidian Eudistoma viride, distributed along the Southeast coast of India, was investigated for its in vitro cytotoxic activity against human cervical carcinoma (HeLa) cells by the MTT assay. The crude methanolic extract of E. viride, with an IC50 of 53 mu g/ml, was dose-dependently cytotoxic. It was more potent at 100 mu g/ml than cyclohexamide (1 mu g/ml), reducing cell viability to 9.2%. Among nine fractions separated by chromatography, ECF-8 exhibited prominent cytoxic activity at 10 mu g/ml. The HPLC fraction EHF-21 of ECF-8 was remarkably dose- and time-dependently cytotoxic, with 39.8% viable cells at 1 mu g/ml compared to 51% in cyclohexamide-treated cells at the same concentration; the IC50 was 0.49,mu g/ml. Hoechst staining of HeLa cells treated with EHF-2I at 0.5 mu g/ml revealed apoptotic events such an cell shrinkage, membrane blebbing, chromatin condensation and formation of apoptotic bodies. Cell size and granularity study showed changes in light scatter, indicating the characteristic feature of cells dying by apoptosis. The cell-cycle analysis of HeLa cells treated with fraction EHF-21 at 1 mu g/ml showed the marked arrest of cells in G(0)/G(1), S and G(2)/M phases and an increase in the sub G(0)/G(1) population indicated an increase in the apoptotic cell population. The statistical analysis of the sub-G(1) region showed a dose-dependent induction of apoptosis. DNA fragmentation was also observed in HeLa cells treated with EHF-21. The active EHF-2I fraction, a brominated indole alkaloid Eudistomin H, led to apoptotic death of HeLa cells.

Improving the Rigor and Consistency of the Thermodynamic Theory for Clathrate Hydrates through Incorporation of Movement of Water Molecules of Hydrate Lattice

Current applications of statistical thermodynamic theories for clathrate hydrates do not incorporate the translational and rotational movement of water molecules of the hydrate lattice,in a rigorous manner. Previous studies have shown that the movement of water molecules has a significant effect on the properties of clathrate hydrates. In this Article, a method is presented to incorporate the effect of water movement with as much rigor as possible. This method is then used to calculate the Langmuir constant of the guest species in a clathrate hydrate. Unlike previous studies on modeling of clathrate hydrate thermodynamics, the method presented in this paper does not regress either the intermolecular potentials or the properties of the empty hydrate from clathrate phase equilibria data. Also the properties of empty hydrate used in the theory do not depend on the nature and composition of the guest molecules. The predicted phase equilibria from the resulting theory are shown to be highly accurate and thermodynamically consistent by comparing them with the phase equilibria computed directly from molecular simulations.

GBNV encoded movement protein (NSm) remodels ER network via C-terminal coiled coil domain

Plant viruses exploit the host machinery for targeting the viral genome-movement protein complex to plasmodesmata (PD). The mechanism by which the non-structural protein m (NSm) of Groundnut bud necrosis virus (GBNV) is targeted to PD was investigated using Agrobacterium mediated transient expression of NSm and its fusion proteins in Nicotiana benthamiana. GFP:NSm formed punctuate structures that colocalized with mCherry:plasmodesmata localized protein la (PDLP la) confirming that GBNV NSm localizes to PD. Unlike in other movement proteins, the C-terminal coiled coil domain of GBNV NSm was shown to be involved in the localization of NSm to PD, as deletion of this domain resulted in the cytoplasmic localization of NSm. Treatment with Brefeldin A demonstrated the role of ER in targeting GFP NSm to PD. Furthermore, mCherry:NSm co-localized with ER-GFP (endoplasmic reticulum targeting peptide (HDEL peptide fused with GFP). Co-expression of NSm with ER-GFP showed that the ER-network was transformed into vesicles indicating that NSm interacts with ER and remodels it. Mutations in the conserved hydrophobic region of NSm (residues 130-138) did not abolish the formation of vesicles. Additionally, the conserved prolines at positions 140 and 142 were found to be essential for targeting the vesicles to the cell membrane. Further, systematic deletion of amino acid residues from N- and C-terminus demonstrated that N-terminal 203 amino acids are dispensable for the vesicle formation. On the other hand, the C-terminal coiled coil domain when expressed alone could also form vesicles. These results suggest that GBNV NSm remodels the ER network by forming vesicles via its interaction through the C-terminal coiled coil domain. Interestingly, NSm interacts with NP in vitro and coexpression of these two proteins in planta resulted in the relocalization of NP to PD and this relocalization was abolished when the N-terminal unfolded region of NSm was deleted. Thus, the NSm interacts with NP via its N-terminal unfolded region and the NSm-NP complex could in turn interact with the ER membrane via the C-terminal coiled coil domain of NSm to form vesicles that are targeted to PD and there by assist the cell to cell movement of the viral genome complex. (C) 2015 Elsevier Inc. All rights reserved.

Experimental Study on Flow and Sediment Movement in Cavity Circulations

This paper reports a flume experiment of flow and sediment movement in a cavity. The flow velocity, sediment concentration and the mechanism of hydraulic sorting in the circulation flow are discussed. The quantity and patterns of sediment deposition in the circulation area are studied as well.

Gust-Induced Movement of Dusts Suspended in Atmosphere

在气固两相流的单向耦合模型框架下,研究大气悬浮沙尘在阵风作用下的运动轨迹及其随大气风速、沙尘粒径的变化,揭示了在Stokes阻力、Saffman力和重力共同作用下,沙尘悬移可能转换为跃移的现象。

Experimental Investigation Of Particle Velocity Distributions In Windblown Sand Movement

With the PDPA (Phase Doppler Particle Analyzer) measurement technology, the probability distributions of particle impact and lift-off velocities on bed surface and the particle velocity distributions at different heights are detected in a wind tunnel. The results show that the probability distribution of impact and lift-off velocities of sand grains can be expressed by a log-normal function, and that of impact and lift-off angles complies with an exponential function. The mean impact angle is between 28 degrees and 39 degrees, and the mean lift-off angle ranges from 30 degrees to 44 degrees. The mean lift-off velocity is 0.81-0.9 times the mean impact velocity. The proportion of backward-impacting particles is 0.05-0.11, and that of backward-entrained particles ranges from 0.04 to 0.13. The probability distribution of particle horizontal velocity at 4 mm height is positive skew, the horizontal velocity of particles at 20 mm height varies widely, and the variation of the particle horizontal velocity at 80 mm height is less than that at 20 mm height. The probability distribution of particle vertical velocity at different heights can be described as a normal function.

A model experiment of the plate movement

Detailed analysis of some difficult aspects has been made from modeling the platemovement. A new method of using differential density of material (instead of differentialtemperature) has been developed in the experiments. The effect of convection of mantleon the plate movement has been studied using a centrifugal technique, and a patternshowing the recurrence of the plate movement has been successfully obtained. In this paper, a criterion De=Dm is presented for the similarity of the model to thecounterpart of the original mantle. According to the criterion, what happens in the modelin a span of ten minutes suggests a process of the "original model" going on in geologi-cal time of three million years.

Changes in Behavior, Movement, and Home Ranges of Largemouth Bass Following Large-scale Hydrilla Removal in Lake Seminole, Georgia

About 1,200 ha of hydrilla ( Hydrilla verticillata L.f. Royle) was eliminated in the Spring Creek embayment of Lake Seminole, Georgia, using a drip-delivery application of fluridone (1- methyl-3-phenyl-5-[3-(trifluoromethl) phenyl]-4(1H)-pyridinone) in 2000 and 2001. Two groups of 15 and 20 largemouth bass (Micropterus salmoides Lacepede) were implanted with 400-day radio tags in February 2000 and 2001 to determine changes in movement and behavior before and after hydrilla reduction.(PDF contains 8 pages.)