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At least 847 records · Page 47

Modular performance prediction for scientific workflows using Machine Learning

Scientific workflows provide an opportunity for declarative computational experiment design in an intuitive and efficient way. A distributed workflow is typically executed on a variety of resources, and it uses a variety of computational algorithms or tools to achieve the desired outcomes. Such a variety imposes additional complexity in scheduling these workflows on large scale computers. As computation becomes more distributed, insights into expected workload that a workflow presents become critical for effective resource allocation. In this paper, we present a modular framework that leverages Machine Learning for creating precise performance predictions of a workflow. The central idea is to partition a workflow in such a way that makes the task of forecasting each atomic unit manageable and gives us a way to combine the individual predictions efficiently. We recognize a combination of an executable and a specific physical resource as a single module. This gives us a handle to characterize workload and machine power as a single unit of prediction. Overall, our modular technique of creating atomic modules and deployment of longest-path approach to estimate workflow performance, allows the framework to adapt to highly complex nested directed acyclic workflows and scale to new scenarios, since it does not make assumptions of underlying workflow structure. We present performance estimation results of independent workflow modules executed on the XSEDE SDSC Comet cluster using various Machine Learning algorithms. The results provide insights into the behavior and effectiveness of different algorithms in the context of scientific workflow performance prediction.

97 MATHEMATICS AND COMPUTING↗

An X-ray magnetic circular dichroism (XMCD) study of Fe ordering in a synthetic MgAl2O4 – Fe3O4 (spinel – magnetite) solid solution series; implications for magnetic properties and cation site ordering

Fe L2,3-edge XAS and XMCD studies have been used to unravel structural trends in the MgAl2O4–Fe3O4, solid solution where thermodynamic modelling has represented a challenge due to the complex ordering arrangements of the end-members. Partitioning of Fe3+ and Fe2+ between tetrahedral (Td) and octahedral (Oh) sites has been established. In the most Fe-rich samples, despite rapid quenching from a disordered state, Fe2+Td is not present which matches the ordered, inverse spinel nature of end-member magnetite (Mgt) at room-T. However, in intermediate compositions Al and Mg substantially replace Fe and small amounts of Fe2+Td are found, stabilized or trapped by decreasing occurrence of the continuous nearest neighbour Fe – Fe interactions which facilitate charge redistribution by electron transfer. Furthermore, in the composition range ~Mgt0.4-0.9, XAS and XMCD bonding and site occupancy data suggest that nano-scale, magnetite-like Fe clusters are present. By contrast, at the spinel-rich end of the series, Mgt0.17 and Mgt0.23 have a homogeneous long-range distribution of Fe, Mg and Al. These relationships are consistent with the intermediate and Fe-rich samples falling within a wide solvus in this system such that the Fe-clusters occur as proto-nuclei for phases which would exsolve following development of long-range crystalline order during slow cooling. Calculated saturation magnetic moments (Ms) for the Fe-rich samples show excellent agreement with measured values but for the most Mg-rich samples are displaced to slightly higher values; this displacement is due to the presence of abundant Mg and Al disrupting the anti-parallel alignment of electron spins for Fe atoms.

Henderson, C. Michael B.↗

Ordering Traces Logically to Identify Lateness in Parallel Programs

Event traces are a valuable tool for understanding the behavior of parallel programs. Automatically analyzing a large trace, however, especially without a specific objective, is difficult. We aid this process by extracting a trace’s logical structure, an ordering of events derived from their happened before relationships. From this perspective, we can calculate delays relative to peers rather than duration and determine where they begin and how they propagate. The logical structure also acts as a platform for comparing and clustering processes as well as showing communication patterns in a trace visualization. We present an algorithm for determining this idealized logical structure from a trace and develop metrics to quantify delays and differences among processes. We implement this in our novel trace visualizer, Ravel, and apply our approach to several applications, demonstrating the accuracy of our extracted structure and its utility in analyzing these codes.

97 MATHEMATICS AND COMPUTING↗

Density Irregularities Inside the Plasmasphere: Cluster Observations

The electron density profiles derived from the EFW and WHISPER instruments onboard the four Cluster spacecraft reveal small-scale density irregularities inside the plasmasphere and at its outer boundary, the plasmapause. We review statistics of the plasmapause position and thickness, as well as statistics of these density structures. We focus on a particular plasmasphere crossing on 11 April 2002, with several density irregularities, as well as two plasma tails, observed by Cluster on the legs of the inbound and outbound passes. We derive the density gradient vectors from simultaneous density measurements by the four spacecraft. We determine also the normal velocity of the surface of these irregularities, assuming they are planar boundaries, from the time delays between density structures in the four individual density profiles. These new observations yield novel insights about (1) the dimensions of plasma irregularities across and parallel to magnetic field lines, (2) the dynamics of these small-scale structures, (3) their bulk velocities, and (4) their position and distribution as a function of the magnetic local time (MLT) and the geomagnetic conditions (as determined by Kp).

Darrouzet, F.↗

The P-Mesh: A Commodity-based Scalable Network Architecture for Clusters

We designed a new network architecture, the P-Mesh which combines the scalability and fault resilience of a torus with the performance of a switch. We compare the scalability, performance, and cost of the hub, switch, torus, tree, and P-Mesh architectures. The latter three are capable of scaling to thousands of nodes, however, the torus has severe performance limitations with that many processors. The tree and P-Mesh have similar latency, bandwidth, and bisection bandwidth, but the P-Mesh outperforms the switch architecture (a lower bound for tree performance) on 16-node NAB Parallel Benchmark tests by up to 23%, and costs 40% less. Further, the P-Mesh has better fault resilience characteristics. The P-Mesh architecture trades increased management overhead for lower cost, and is a good bridging technology while the price of tree uplinks is expensive.

Nitzberg, Bill↗

SUPPRESSION OF ELECTRON THERMAL CONDUCTION IN THE HIGH β INTRACLUSTER MEDIUM OF GALAXY CLUSTERS

Understanding the thermodynamic state of the hot intracluster medium (ICM) in a galaxy cluster requires knowledge of the plasma transport processes, especially thermal conduction. The basic physics of thermal conduction in plasmas with ICM-like conditions has yet to be elucidated, however. We use particle-in-cell simulations and analytic models to explore the dynamics of an ICM-like plasma (with small gyroradius, large mean free path, and strongly sub-dominant magnetic pressure) driven by the diffusive heat flux associated with thermal conduction. Linear theory reveals that whistler waves are driven unstable by electron heat flux, even when the heat flux is weak. The resonant interaction of electrons with these waves then plays a critical role in scattering electrons and suppressing the heat flux. In a 1D model where only whistler modes that are parallel to the magnetic field are captured, the only resonant electrons are moving in the opposite direction to the heat flux, and the electron heat flux suppression is small. In 2D or more, oblique whistler modes also resonate with electrons moving in the direction of the heat flux. The overlap of resonances leads to effective symmetrization of the electron distribution function and a strong suppression of heat flux. The results suggest that thermal conduction in the ICM might be strongly suppressed, possibly to negligible levels.

79 ASTRONOMY AND ASTROPHYSICS↗

Enhanced critical current in superconducting FeSe 0.5 Te 0.5 films at all magnetic field orientations by scalable gold ion irradiation

The loss-less electrical current-carrying capability of type II superconductors, measured by the critical current density J c , can be increased by engineering desirable defects in superconductors to pin the magnetic vortices. Here, we demonstrate that such desirable defects can be created in superconducting FeSe 0.5 Te 0.5 films by 6 MeV Au-ions irradiations that produce cluster-like defects with sizes of 10–15 nm over the entire film. The pristine FeSe 0.5 Te 0.5 film exhibits a low anisotropy in the angular dependence of J c . A clear improvement in the J c is observed upon Au-ion irradiation for all field orientations at 4.2 K. Furthermore, a nearly 70% increase in J c is observed at a magnetic field of 9 T applied parallel to the crystallographic c-axis at 10 K with little reduction of the superconducting transition temperature T c . Our studies show that a dose of 1×10 12 Au cm –2 irradiation at a few MeV is sufficient in order to provide a strong isotropic pinning defect landscape in iron-based superconducting films.

36 MATERIALS SCIENCE↗

Deep Generative Models that Solve PDEs: Distributed Computing for Training Large Data-Free Models

Recent progress in scientific machine learning (SciML) has opened up the possibility of training novel neural network architectures that solve complex partial differential equations (PDEs). Several (nearly data free) approaches have been recently reported that successfully solve PDEs, with examples including deep feed forward networks, generative networks, and deep encoder-decoder networks. However, practical adoption of these approaches is limited by the difficulty in training these models, especially to make predictions at large output resolutions (≥1024×1024). Here we report on a software framework for data parallel distributed deep learning that resolves the twin challenges of training these large SciML models - training in reasonable time as well as distributing the storage requirements. Our framework provides several out of the box functionality including (a) loss integrity independent of number of processes, (b) synchronized batch normalization, and (c) distributed higher-order optimization methods. We show excellent scalability of this framework on both cloud as well as HPC clusters, and report on the interplay between bandwidth, network topology and bare metal vs cloud. We deploy this approach to train generative models of sizes hitherto not possible, showing that neural PDE solvers can be viably trained for practical applications. We also demonstrate that distributed higher-order optimization methods are 2-3× faster than stochastic gradient-based methods and provide minimal convergence drift with higher batch-size.

PDEs↗

The Structure and Stability of B(n)H(+) Clusters

The geometries of the B(n)H(+) clusters for n=1-13 have been optimized at the B3LYP level of theory. Excluding B2H(+) all clusters are low-spin coupled. The structures appear to be related to the bare B(+)(n) clusters in two ways: 1) an H atom is added to the B(+)(n) cluster or 2) a BH is added to the B(+)(n-1) cluster. The B(+)(n)-H binding energies are computed at the B3LYP level of theory, and calibrated n using the CCSD(T) level of theory. The computed results tend to fall between the experimental best estimates and the experimental lower bounds. The B(+)(n)-H binding energies show an inverse correspondence with the B+(n-1)-B values) while the B(+)(n-1)-B and B(+)(n-1)-BH results tend to parallel each other.

Ricca, Alessandra↗

Theoretical study of the CO 2 –O 2 van der Waals complex: potential energy surface and applications

A four-dimensional-potential energy surface (4D-PES) of the atmospherically relevant carbon dioxide–oxygen molecule (CO 2 –O 2 ) van der Waals complex is mapped using the ab initio explicitly correlated coupled cluster method with single, double, and perturbative triple excitations (UCCSD(T)-F12b), and extrapolation to the complete basis set (CBS) limit using the cc-pVTZ-F12/cc-pVQZ-F12 bases and the l –3 formula. An analytic representation of the 4D-PES was fitted using the method of interpolating moving least squares (IMLS). These calculations predict that the most stable configuration of CO 2 –O 2 complex corresponds to a planar slipped-parallel structure with a binding energy of V ~ –243 cm –1 . Another isomer is found on the PES, corresponding to a non-planar cross-shaped structure, with V ~ –218 cm –1 . The transition structure connecting the two minima is found at V ~ –211 cm –1 . We also performed comparisons with some CO 2 –X van der Waals complexes. Moreover, we provide a SAPT analysis of this molecular system. Then, we discuss the complexation induced shifts of CO 2 and O 2 . Afterwards, this new 4D-PES is employed to compute the second virial coefficient including temperature dependence. A comparison between quantities obtained in our calculations and those from experiments found close agreement attesting to the high quality of the PES and to the importance of considering a full description of the anisotropic potential for the derivation of thermophysical properties of CO 2 –O 2 mixtures.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Aces4: A Platform for Computational Chemistry Calculations with Extremely Large Block-Sparse Arrays

Aces4 is a parallel programming platform comprising a DSL for Computational Chemistry and its runtime system. It offers a convenient way to express parallelism together with extensive support for extremely large, possibly sparse, distributed arrays. It aids scientists in the creation of performant, scalable, massively parallel programs that can effectively take advantage of leadership class computing systems to address important scientific questions. Aces4 has enabled the development and implementation of new methods in electronic structure theory which are breaking new ground in their ability to perform highly accurate calculations on ever larger molecular systems. In this paper the design of Aces4, which is based on the the Super Instruction Architecture approach, is described. Experimental scaling results for Molecular Cluster Perturbation Theory, a new method enabled by Aces4, and CCSD, a widely used computational chemistry method are given.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Comparing the Performance of Julia on CPUs versus GPUs and Julia-MPI versus Fortran-MPI: a case study with MPAS-Ocean (Version 7.1)

Abstract. Some programming languages are easy to develop at the cost of slow execution, while others are fast at runtime but much more difficult to write. Julia is a programming language that aims to be the best of both worlds – a development and production language at the same time. To test Julia's utility in scientific high-performance computing (HPC), we built an unstructured-mesh shallow water model in Julia and compared it against an established Fortran-MPI ocean model, the Model for Prediction Across Scales–Ocean (MPAS-Ocean), as well as a Python shallow water code. Three versions of the Julia shallow water code were created: for single-core CPU, graphics processing unit (GPU), and Message Passing Interface (MPI) CPU clusters. Comparing identical simulations revealed that our first version of the Julia model was 13 times faster than Python using NumPy, where both used an unthreaded single-core CPU. Further Julia optimizations, including static typing and removing implicit memory allocations, provided an additional 10–20× speed-up of the single-core CPU Julia model. The GPU-accelerated Julia code was almost identical in terms of performance to the MPI parallelized code on 64 processes, an unexpected result for such different architectures. Parallelized Julia-MPI performance was identical to Fortran-MPI MPAS-Ocean for low processor counts and ranges from 2× faster to 2× slower for higher processor counts. Our experience is that Julia development is fast and convenient for prototyping but that Julia requires further investment and expertise to be competitive with compiled codes. We provide advice on Julia code optimization for HPC systems.

54 ENVIRONMENTAL SCIENCES↗

The Evaporation and Survival of Cluster Galaxies’ Coronae. II. The Effectiveness of Anisotropic Thermal Conduction and Survival of Stripped Galactic Tails

We simulate anisotropic thermal conduction between the intracluster medium (ICM) and the hot coronal interstellar medium (ISM) gas in cluster galaxies. In Paper I, we simulated the evaporation of the hot ISM due to isotropic (possibly saturated) conduction between the ISM and ICM. We found that hot coronae evaporate on ∼10{sup 2} Myr timescales, significantly shorter than the ∼10{sup 3} Myr gas loss times due to ram pressure stripping. No tails of stripped gas are formed. This is in tension with the observed ubiquity and implied longevity of compact X-ray coronae and stripped ISM tails, and requires the suppression of evaporation, possibly due to magnetic fields and anisotropic conduction. We perform a series of wind tunnel simulations similar to that in Paper I, now including ISM and ICM magnetic fields. We simulate the effect of anisotropic conduction for a range of extreme magnetic field configurations: parallel and perpendicular to the ICM wind, and continuous and completely disjointed between the ISM and ICM. We find that when conduction is anisotropic, gas loss due to evaporation is severely reduced; the overall gas loss rates with and without anisotropic conduction do not differ by more than 10%–20%. Magnetic fields also prevent stripped tails from evaporating in the ICM by shielding, and providing few pathways for heat transport between the ICM and ISM. The morphology of stripped tails and magnetic fields in the tails and wakes of galaxies are sensitive to the initial magnetic field configuration.

79 ASTRONOMY AND ASTROPHYSICS↗

THE STAR-FORMATION-RATE-DENSITY RELATION AT 0.6 < z < 0.9 AND THE ROLE OF STAR-FORMING GALAXIES

We study the star formation rates (SFRs) of galaxies as a function of local galaxy density at 0.6 < z < 0.9. We used a low-dispersion prism in IMACS on the 6.5 m Baade (Magellan I) telescope to obtain spectra and measured redshifts to a precision of {sigma}{sub z}/(1 + z) {approx} 1% for galaxies with z{sub AB} < 23.3 mag. We utilized a stellar mass-limited sample of 977 galaxies above M > 1.8 x 10{sup 10} M{sub sun} (log M/M{sub sun} >10.25) to conduct our main analysis. With three different SFR indicators, (1) Spitzer MIPS 24 {mu}m imaging, (2) spectral energy distribution (SED) fitting, and (3) [O II]{lambda}3727 emission, we find the median specific SFR (SSFR) and SFR to decline from the low-density field to the cores of groups and a rich cluster. For the SED- and [O II]-based SFRs, the decline in SSFR is roughly an order of magnitude while for the MIPS-based SFRs, the decline is a factor of {approx}4. We find approximately the same magnitude of decline in SSFR even after removing the sample of galaxies near the cluster. Galaxies in groups and a cluster at these redshifts therefore have lower star formation (SF) activity than galaxies in the field, as is the case at z {approx} 0. We investigated whether the decline in SFR with increasing density is caused by a change in the proportion of quiescent and star-forming galaxies (SFGs) or by a decline in the SFRs of SFGs. Using the rest-frame U - V and V - J colors to distinguish quiescent galaxies from SFGs (including both unattenuated blue galaxies and reddened ones), we find that the fraction of quiescent galaxies increases from {approx}32% to 79% from low to high density. In addition, we find the SSFRs of SFGs, selected based on U - V and V - J colors, to decline with increasing density by factors of {approx}5-6 for the SED- and [O II]-based SFRs. The MIPS-based SSFRs for SFGs decline with a shallower slope. The declining SFRs of SFGs with density are paralleled by a decline in the median A{sub V}, providing indirect evidence that the cold gas content that fuels future SF is diminished in higher density environments. The order of magnitude decline in the SSFR-density relation at 0.6 < z < 0.9 is therefore driven by both a combination of declining SFRs of SFGs as well as a changing mix of SFGs and quiescent galaxies.

79 ASTRONOMY AND ASTROPHYSICS↗

Streamlined spatial and environmental expression signatures characterize the minimalist duckweed Wolffia australiana

Single-cell genomics permits a new resolution in the examination of molecular and cellular dynamics, allowing global, parallel assessments of cell types and cellular behaviors through development and in response to environmental circumstances, such as interaction with water and the light–dark cycle of the Earth. Here, we leverage the smallest, and possibly most structurally reduced, plant, the semiaquaticWolffia australiana, to understand dynamics of cell expression in these contexts at the whole-plant level. We examined single-cell-resolution RNA-sequencing data and foundWolffiacells divide into four principal clusters representing the above- and below-water-situated parenchyma and epidermis. Although these tissues share transcriptomic similarity with model plants, they display distinct adaptations thatWolffiahas made for the aquatic environment. Within this broad classification, discrete subspecializations are evident, with select cells showing unique transcriptomic signatures associated with developmental maturation and specialized physiologies. Assessing this simplified biological system temporally at two key time-of-day (TOD) transitions, we identify additional TOD-responsive genes previously overlooked in whole-plant transcriptomic approaches and demonstrate that the core circadian clock machinery and its downstream responses can vary in cell-specific manners, even in this simplified system. Distinctions between cell types and their responses to submergence and/or TOD are driven by expression changes of unexpectedly few genes, characterizingWolffiaas a highly streamlined organism with the majority of genes dedicated to fundamental cellular processes.Wolffiaprovides a unique opportunity to apply reductionist biology to elucidate signaling functions at the organismal level, for which this work provides a powerful resource.

Biochemistry & Molecular Biology↗

Designing Next Generation Massively Multithreaded Architectures for Irregular Applications

Irregular applications, such as data mining or graph-based computations, show unpredictable memory/network access patterns and control structures. Massively multi-threaded architectures with large node count, like the Cray XMT, have been shown to address their requirements better than commodity clusters. In this paper we present the approaches that we are currently pursuing to design future generations of these architectures. First, we introduce the Cray XMT and compare it to other multithreaded architectures. We then propose an evolution of the architecture, integrating multiple cores per node and next generation network interconnect. We advocate the use of hardware support for remote memory reference aggregation to optimize network utilization. For this evaluation we developed a highly parallel, custom simulation infrastructure for multi-threaded systems. Our simulator executes unmodified XMT binaries with very large datasets, capturing effects due to contention and hot-spotting, while predicting execution times with greater than 90% accuracy. We also discuss the FPGA prototyping approach that we are employing to study efficient support for irregular applications in next generation manycore processors.

Tumeo, Antonino↗

Large-Scale Modeling of Epileptic Seizures: Scaling Properties of Two Parallel Neuronal Network Simulation Algorithms

Our limited understanding of the relationship between the behavior of individual neurons and large neuronal networks is an important limitation in current epilepsy research and may be one of the main causes of our inadequate ability to treat it. Addressing this problem directly via experiments is impossibly complex; thus, we have been developing and studying medium-large-scale simulations of detailed neuronal networks to guide us. Flexibility in the connection schemas and a complete description of the cortical tissue seem necessary for this purpose. In this paper we examine some of the basic issues encountered in these multiscale simulations. We have determined the detailed behavior of two such simulators on parallel computer systems. The observed memory and computation-time scaling behavior for a distributed memory implementation were very good over the range studied, both in terms of network sizes (2,000 to 400,000 neurons) and processor pool sizes (1 to 256 processors). Our simulations required between a few megabytes and about 150 gigabytes of RAM and lasted between a few minutes and about a week, well within the capability of most multinode clusters. Therefore, simulations of epileptic seizures on networks with millions of cells should be feasible on current supercomputers.

59 BASIC BIOLOGICAL SCIENCES↗

Hyperspectral Aquatic Radiative Transfer Modeling Using a High-Performance Cluster Computing-Based Approach

Abstract For aquatic studies, radiative transfer (RT) modeling can be used to compute hyperspectral above-surface remote sensing reflectance that can be utilized for inverse model development. Inverse models can provide bathymetry and inherent-and bottom-optical property estimation. Because measured oceanic field/organic datasets are often spatio-temporally sparse, synthetic data generation is useful in yielding sufficiently large datasets for inversion model development; however, these forward-modeled data are computationally expensive and time-consuming to generate. This study establishes the magnitude of wall-clock-time savings achieved for performing large, aquatic RT batch-runs using parallel computing versus a sequential approach. Given 2,600 simulations and identical compute-node characteristics, sequential architecture required ~100 hours until termination, whereas a parallel approach required only ~2.5 hours (42 compute nodes) a 40x speed-up. Tools developed for this parallel execution are discussed.

58 GEOSCIENCES↗