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At least 55 records · Page 3

Nonparallel transcriptional divergence during parallel adaptation

Abstract How underlying mechanisms bias evolution toward predictable outcomes remains an area of active debate. In this study, we leveraged phenotypic plasticity and parallel adaptation across independent lineages of Trinidadian guppies ( Poecilia reticulata ) to assess the predictability of gene expression evolution during parallel adaptation. Trinidadian guppies have repeatedly and independently adapted to high‐ and low‐predation environments in the wild. We combined this natural experiment with a laboratory breeding design to attribute transcriptional variation to the genetic influences of population of origin and developmental plasticity in response to rearing with or without predators. We observed substantial gene expression plasticity, as well as the evolution of expression plasticity itself, across populations. Genes exhibiting expression plasticity within populations were more likely to also differ in expression between populations, with the direction of population differences more likely to be opposite those of plasticity. While we found more overlap than expected by chance in genes differentially expressed between high‐ and low‐predation populations from distinct evolutionary lineages, the majority of differentially expressed genes were not shared between lineages. Our data suggest alternative transcriptional configurations associated with shared phenotypes, highlighting a role for transcriptional flexibility in the parallel phenotypic evolution of a species known for rapid adaptation.

Fischer, Eva K.↗

Parallel Architectures and Parallel Algorithms for Integrated Vision Systems

Computer vision is regarded as one of the most complex and computationally intensive problems. An integrated vision system (IVS) is a system that uses vision algorithms from all levels of processing to perform for a high level application (e.g., object recognition). An IVS normally involves algorithms from low level, intermediate level, and high level vision. Designing parallel architectures for vision systems is of tremendous interest to researchers. Several issues are addressed in parallel architectures and parallel algorithms for integrated vision systems.

Choudhary, Alok Nidhi↗

Low Mach number parallel and quasi-parallel shocks

The properties of low-Mach-number parallel and quasi-parallel shocks are studied using the results of one-dimensional hybrid simulations. It is shown that both the structure and ion dissipation at the shocks differ considerably. In the parallel limit, the shock remains coupled to the piston and consists of large-amplitude magnetosonic-whistler waves in the upstream, through the shock and into the downstream region, where the waves eventually damp out. These waves are generated by an ion beam instability due to the interaction between the incident and piston-reflected ions. The excited waves decelerate the plasma sufficiently that it becomes stable far into the downstream. The increase in ion temperature along the shock normal in the downstream region is due to superposition of incident and piston-rflected ions. These two populations of ions remain distinct through the downstream region. While they are both gyrophase-bunched, their counterstreaming nature results in a 180-deg phase shift in their perpendicular velocities.

Omidi, N.↗

Bit-parallel arithmetic in a massively-parallel associative processor

A simple but powerful new architecture based on a classical associative processor model is presented. Algorithms for performing the four basic arithmetic operations both for integer and floating point operands are described. For m-bit operands, the proposed architecture makes it possible to execute complex operations in O(m) cycles as opposed to O(m exp 2) for bit-serial machines. A word-parallel, bit-parallel, massively-parallel computing system can be constructed using this architecture with VLSI technology. The operation of this system is demonstrated for the fast Fourier transform and matrix multiplication.

Scherson, Isaac D.↗

MLP: A Parallel Programming Alternative to MPI for New Shared Memory Parallel Systems

Recent developments at the NASA AMES Research Center's NAS Division have demonstrated that the new generation of NUMA based Symmetric Multi-Processing systems (SMPs), such as the Silicon Graphics Origin 2000, can successfully execute legacy vector oriented CFD production codes at sustained rates far exceeding processing rates possible on dedicated 16 CPU Cray C90 systems. This high level of performance is achieved via shared memory based Multi-Level Parallelism (MLP). This programming approach, developed at NAS and outlined below, is distinct from the message passing paradigm of MPI. It offers parallelism at both the fine and coarse grained level, with communication latencies that are approximately 50-100 times lower than typical MPI implementations on the same platform. Such latency reductions offer the promise of performance scaling to very large CPU counts. The method draws on, but is also distinct from, the newly defined OpenMP specification, which uses compiler directives to support a limited subset of multi-level parallel operations. The NAS MLP method is general, and applicable to a large class of NASA CFD codes.

Taft, James R.↗

Processing data communications events by awakening threads in parallel active messaging interface of a parallel computer

Processing data communications events in a parallel active messaging interface (`PAMI`) of a parallel computer that includes compute nodes that execute a parallel application, with the PAMI including data communications endpoints, and the endpoints are coupled for data communications through the PAMI and through other data communications resources, including determining by an advance function that there are no actionable data communications events pending for its context, placing by the advance function its thread of execution into a wait state, waiting for a subsequent data communications event for the context; responsive to occurrence of a subsequent data communications event for the context, awakening by the thread from the wait state; and processing by the advance function the subsequent data communications event now pending for the context.

97 MATHEMATICS AND COMPUTING↗

Adapting the serial Alpgen parton-interaction generator to simulate LHC collisions on millions of parallel threads

As the LHC moves to higher energies and luminosity, the demand for computing resources increases accordingly and will soon outpace the growth of the World- wide LHC Computing Grid. To meet this greater demand, event generation Monte Carlo was targeted for adaptation to run on Mira, the supercomputer at the Argonne Leadership Computing Facility. Alpgen is a Monte Carlo event generation application that is used by LHC experiments in the simulation of collisions that take place in the Large Hadron Collider. This paper details the process by which Alpgen was adapted from a single-processor serial-application to a large-scale parallel-application and the performance that was achieved.

HEP↗

Parallelized Screening of Characterized and DFT-Modeled Bimetallic Colloidal Cocatalysts for Photocatalytic Hydrogen Evolution

Using a newly designed and developed parallelized photoreactor and colorimetric detection method, a large sampling of bimetallic co-catalysts (Pd/Sn, Pd/Mo, Pd/Ru, Pd/Pb, Pd/Ni, Ni/Sn, Mo/Sn and Pt/Sn) for photocatalytic water reduction have been tested in this work. Of these co-catalysts, the combination of palladium and tin showed the highest synergistic behavior and peak hydrogen gas production at a low relative fraction of palladium. The resulting Pd/Sn bimetallic co-catalysts were characterized using high-angle annular dark-field (HAADF) and scanning transmission electron microscopy energy dispersive X-ray spectroscopy (STEM-EDS), and specifically, investigation of the palladium/tin mixture indicated that palladium and tin elements reside within the same particle. The experimental catalytic activity for the palladium/tin mixture was compared to density functional theory-derived energy values associated with the adsorption of hydrogen onto a surface. This comparison demonstrated that the typical peak found in electrochemical Sabatier volcano plots at ΔG H* = ~0 eV was replicated in the experimental photocatalytic system with a peak activity observed at ΔG H* = -0.036 eV. Computational confirmation of the results expressed here demonstrates the efficacy of colorimetric detection of hydrogen in parallel and presents a model for increasingly rapid catalyst screening.

08 HYDROGEN↗

Parallel magnetic field suppresses dissipation in superconducting nanostrips

The motion of Abrikosov vortices in type-II superconductors results in a finite resistance in the presence of an applied electric current. Elimination or reduction of the resistance via immobilization of vortices is the "holy grail" of superconductivity research. Common wisdom dictates that an increase in the magnetic field escalates the loss of energy since the number of vortices increases. Here we show that this is no longer true if the magnetic field and the current are applied parallel to each other. Our experimental studies on the resistive behavior of a superconducting Mo0.79Ge0.21 nanostrip reveal the emergence of a dissipative state with increasing magnetic field, followed by a pronounced resistance drop, signifying a reentrance to the superconducting state. Large-scale simulations of the 3D time-dependent Ginzburg-Landau model indicate that the intermediate resistive state is due to an unwinding of twisted vortices. When the magnetic field increases, this instability is suppressed due to a better accommodation of the vortex lattice to the pinning configuration. Our findings show that magnetic field and geometrical confinement can suppress the dissipation induced by vortex motion and thus radically improve the performance of superconducting materials.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Exploiting Multiple Levels of Parallelism in Sparse Matrix-Matrix Multiplication

Sparse matrix-matrix multiplication (or SpGEMM) is a key primitive for many high-performance graph algorithms as well as for some linear solvers, such as algebraic multigrid. The scaling of existing parallel implementations of SpGEMM is heavily bound by communication. Even though 3D (or 2.5D) algorithms have been proposed and theoretically analyzed in the flat MPI model on Erdös-Rényi matrices, those algorithms had not been implemented in practice and their complexities had not been analyzed for the general case. In this work, we present the first implementation of the 3D SpGEMM formulation that exploits multiple (intranode and internode) levels of parallelism, achieving significant speedups over the state-of-the-art publicly available codes at all levels of concurrencies. We extensively evaluate our implementation and identify bottlenecks that should be subject to further research.

2.5D algorithms↗

Parallel beamlet dose calculation via beamlet contexts in a distributed multi‐GPU framework

Purpose Dose calculation is one of the most computationally intensive, yet essential tasks in the treatment planning process. With the recent interest in automatic beam orientation and arc trajectory optimization techniques, there is a great need for more efficient model‐based dose calculation algorithms that can accommodate hundreds to thousands of beam candidates at once. Foundational work has shown the translation of dose calculation algorithms to graphical processing units ( GPU s), lending to remarkable gains in processing efficiency. But these methods provide parallelization of dose for only a single beamlet, serializing the calculation of multiple beamlets and under‐utilizing the potential of modern GPU s. In this paper, the authors propose a framework enabling parallel computation of many beamlet doses using a novel beamlet context transformation and further embed this approach in a scalable network of multi‐ GPU computational nodes. Methods The proposed context‐based transformation separates beamlet‐local density and TERMA into distinct beamlet contexts that independently provide sufficient data for beamlet dose calculation. Beamlet contexts are arranged in a composite context array with dosimetric isolation, and the context array is subjected to a GPU collapsed‐cone convolution superposition procedure, producing the set of beamlet‐specific dose distributions in a single pass. Dose from each context is converted to a sparse representation for efficient storage and retrieval during treatment plan optimization. The context radius is a new parameter permitting flexibility between the speed and fidelity of the dose calculation process. A distributed manager‐worker architecture is constructed around the context‐based GPU dose calculation approach supporting an arbitrary number of worker nodes and resident GPU s. Phantom experiments were executed to verify the accuracy of the context‐based approach compared to Monte Carlo and a reference CPU ‐ CCCS implementation for single beamlets and broad beams composed by addition of beamlets. Dose for representative 4 π beam sets was calculated in lung and prostate cases to compare its efficiency with that of an existing beamlet‐sequential GPU ‐ CCCS implementation. Code profiling was also performed to evaluate the scalability of the framework across many networked GPU s. Results The dosimetric accuracy of the context‐based method displays <1.35% and 2.35% average error from the existing serialized CPU ‐ CCCS algorithm and Monte Carlo simulation for beamlet‐specific PDD s in water and slab phantoms, respectively. The context‐based method demonstrates substantial speedup of up to two orders of magnitude over the beamlet‐sequential GPU ‐ CCCS method in the tested configurations. The context‐based framework demonstrates near linear scaling in the number of distributed compute nodes and GPU s employed, indicating that it is flexible enough to meet the performance requirements of most users by simply increasing the hardware utilization. Conclusions The context‐based approach demonstrates a new expectation of performance for beamlet‐based dose calculation methods. This approach has been successful in accelerating the dose calculation process for very large‐scale treatment planning problems ‐ such as automatic 4 π IMRT beam orientation and VMAT arc trajectory selection, with hundreds of thousands of beamlets ‐ in clinically feasible timeframes. The flexibility of this framework makes it as a strong candidate for use in a variety of other very large‐scale treatment planning tasks and clinical workflows.

Neph, Ryan↗

GPU-accelerated Tersoff potentials for massively parallel Molecular Dynamics simulations

The Tersoff potential is one of the empirical many-body potentials that has been widely used in simulation studies at atomic scales. Unlike pair-wise potentials, the Tersoff potential involves three-body terms, which require much more arithmetic operations and data dependency. In this contribution, we have implemented the GPU-accelerated version of several variants of the Tersoff potential for LAMMPS, an open-source massively parallel Molecular Dynamics code. Compared to the existing MPI implementation in LAMMPS, the GPU implementation exhibits a better scalability and offers a speedup of 2.2X when run on 1000 compute nodes on the Titan supercomputer. On a single node, the speedup ranges from 2.0 to 8.0 times, depending on the number of atoms per GPU and hardware configurations. The most notable features of our GPU-accelerated version include its design for MPI/accelerator heterogeneous parallelism, its compatibility with other functionalities in LAMMPS, its ability to give deterministic results and to support both NVIDIA CUDA- and OpenCL-enabled accelerators. Our implementation is now part of the GPU package in LAMMPS and accessible for public use.

Computer Science↗

Modelling of parallel dynamics of a pellet-produced plasmoid

The parallel expansion of a dense, pellet-produced plasmoid is modelled with parameters relevant to pellet fuelling experiments in the Wendelstein7-X stellarator. Good agreement is found between the analytical theory and more detailed modelling. In particular, much of the energy deposited in the pellet by the ambient plasma is transferred to the pellet ions by the ambipolar electric field during the expansion. The validity of the hydrodynamic treatment of the plasmoid and the ambient plasma is discussed.

Physics↗

Electron parallel closures for various ion charge numbers

Electron parallel closures for the ion charge number Z = 1 [J.-Y. Ji and E. D. Held, Phys. Plasmas 21, 122116 (2014)] are extended for 1 ≤ Z ≤ 10. Parameters are then computed for various Z with the same form of the Z = 1 kernels adopted. The parameters are smoothly varying in Z and hence can be used to interpolate parameters and closures for noninteger, effective ion charge numbers.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Accelerating ring-polymer molecular dynamics with parallel-replica dynamics

Nuclear quantum effects are important for systems containing light elements, and the effects are more prominent in the low temperature regime where the dynamics also becomes sluggish. We show that parallel replica (ParRep) dynamics, an accelerated molecular dynamics approach for infrequent-event systems, can be effectively combined with ring-polymer molecular dynamics, a semiclassical trajectory approach that gives a good approximation to zero-point and tunneling effects in activated escape processes. The resulting RP-ParRep method is a powerful tool for reaching long time scales in complex infrequent-event systems where quantum dynamics are important. Two illustrative examples, symmetric Eckart barrier crossing and interstitial helium diffusion in Fe and Fe–Cr alloy, are presented to demonstrate the accuracy and long-time scale capability of this approach.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Automatic and Transparent Resource Contention Mitigation for Improving Large-Scale Parallel File System Performance

Proportional to the scale increases in HPC systems, many scientific applications are becoming increasingly data intensive, and parallel I/O has become one of the dominant factors impacting the large-scale HPC application performance. On a typical large-scale HPC system, we have observed that the lack of a global workload coordination coupled with the shared nature of storage systems cause load imbalance and resource contention over the end-to-end I/O paths resulting in severe performance degradation. I/O load imbalance on HPC systems is generally a self-inflicted wound and mostly occurs between the I/O paths and resources consumed by each individual job. In this paper, we introduce TAPP-IO, a dynamic, shared load balancing framework for mitigating resource contention. TAPP-IO extends our previous work and solves two major limitations: First, it transparently intercepts file creation calls during runtime to balance the workload over all available storage targets. The usage of TAPP-IO requires no application source code modifications and is independent from any I/O middleware. The framework can be applied to almost any HPC platform and is suitable for systems that lack a centralized file system resource manager. Second, the framework proposes a new placement strategy to support not only file-per-process I/O, but also single shared file I/O. This opens the door to a new class of scientific applications that can leverage the placement library for improved performance. We demonstrate the effectiveness of our integration on the Titan system at the Oak Ridge National Laboratory. Our experiments with a synthetic benchmark and real-world HPC workload show that, even in a noisy production environment, TAPP-IO can improve large-scale application performance significantly.

Neuwirth, Sarah↗