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Two-photon absorption cross sections within equation-of-motion coupled-cluster formalism using resolution-of-the-identity and Cholesky decomposition representations: Theory, implementation, and benchmarks

The equation-of-motion coupled-cluster (EOM-CC) methods provide a robust description of electronically excited states and their properties. Here, we present a formalism for two-photon absorption (2PA) cross sections for the equation-of-motion for excitation energies CC with single and double substitutions (EOM-CC for electronically excited states with single and double substitutions) wave functions. Rather than the response theory formulation, we employ the expectation-value approach which is commonly used within EOM-CC, configuration interaction, and algebraic diagrammatic construction frameworks. In addition to canonical implementation, we also exploit resolution-of-the-identity (RI) and Cholesky decomposition (CD) for the electron-repulsion integrals to reduce memory requirements and to increase parallel efficiency. The new methods are benchmarked against the CCSD and CC3 response theories for several small molecules. We found that the expectation-value 2PA cross sections are within 5% from the quadratic response CCSD values. The RI and CD approximations lead to small errors relative to the canonical implementation (less than 4%) while affording computational savings. RI/CD successfully address the well-known issue of large basis set requirements for 2PA cross sections calculations. The capabilities of the new code are illustrated by calculations of the 2PA cross sections for model chromophores of the photoactive yellow and green fluorescent proteins.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

ABWR start-up test analysis using BWR core simulator with three-dimensional direct response matrix method

The ABWR start-up test analysis has been done with the BWR core simulator using the three--dimensional direct response matrix (3D-DRM) method. The Monte Carlo code VMONT made the sub-response matrices for the 3D-DRM method. Each boundary surface was subdivided by 4 x 4 for transverse segments, by 4 for angular segments and by 4 for axial zones in a node. For the calculation speedup, the 3D-DRM code used the divided sub-response matrices data set. The code used the MPI and OpenMP for the parallelized method. The median value is set as the average critical eigenvalues. The changes from the maximum value to the minimum value are 0.34 %{Delta}k with the spectral history method and 0.40 %{Delta}k without it, and the respective standard deviations were 0.12 % and 0.14 %. Using the spectral history method decreased the variation by 0.06 %{Delta}k. The root mean square differences of the axial power distribution were about 6 % between the analysis results and the plant data. Using the currents which converged in the previous exposure step reduced the number of iterations when the CR pattern changed only slightly. The averaged calculation time for each exposure step was about 5 hours on 12 PC Linux cluster servers with Core 2 Quad 3 GHz. (authors)

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

FitCache: A Transparent Drop-In Framework for Multi-Tier Caching to Accelerate Distributed Deep Learning Workloads

Training in Deep learning (DL) remains highly compute- and data-intensive, with I/O becoming a critical bottleneck as models and datasets scale. Recent studies report that data loading can dominate training time, especially on large-scale HPC systems with shared parallel file systems (PFS). Existing caching approaches either rely on single-tier designs or require intrusive modifications to training pipelines, limiting their portability and effectiveness. In this work, we present FitCache, a transparent drop-in framework for multi-tier caching to accelerate distributed DL training by coordinating fast local memory (e.g., DRAM, Persistent Memory (PMem)) and NVMe as hierarchical caches atop PFS. Our design adapts to hardware diversity, i.e., if NVMe is missing, memory transparently acts as a caching tier, ensuring stable performance. FitCache transparently intercepts I/O requests and issues concurrent fetches across all tiers, returning data from the fastest responder without centralized metadata or static redirection paths. FitCache adapts to dynamic workloads and heterogeneous clusters while maintaining POSIX compatibility. Experiments on Frontier (2048 GPUs) and smaller research clusters show that FitCache reduces training time by up to 40% and per-batch I/O latency by up to 71.6% compared to Lustre Orion PFS, offering a drop-in solution for scalable DL training.

Hu, Guangxing [ORNL] (ORCID:0009000283203614)↗

Self-sustaining sound in collisionless, high- β plasma

Using analytical theory and hybrid-kinetic numerical simulations, we demonstrate that, in a collisionless plasma, long-wavelength ion-acoustic waves (IAWs) with amplitudes $δn/n_0≳2/β$ (where $β\gg1$ is the ratio of thermal to magnetic pressure) generate sufficient pressure anisotropy to destabilize the plasma to firehose and mirror instabilities. These kinetic instabilities grow rapidly to reduce the pressure anisotropy by pitch-angle scattering and trapping particles, respectively, thereby impeding the maintenance of Landau resonances that enable such waves’ otherwise potent collisionless damping. The result is wave dynamics that evince a weakly collisional plasma: the ion distribution function is near-Maxwellian, the field-parallel flow of heat resembles its Braginskii form (except in regions where large-amplitude magnetic mirrors strongly suppress particle transport), and the relations between various thermodynamic quantities are more ‘fluid-like’ than kinetic. A nonlinear fluctuation–dissipation relation for self-sustaining IAWs is obtained by solving a plasma-kinetic Langevin problem, which demonstrates suppressed damping, enhanced fluctuation levels and weakly collisional thermodynamics when IAWs with $δn/n_0≳2/β$ are stochastically driven. We investigate how our results depend upon the scale separation between the wavelength of the IAW and the Larmor radius of the ions, and discuss briefly their implications for our understanding of turbulence and transport in the solar wind and the intracluster medium of galaxy clusters.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Parallel Heuristics for Scalable Community Detection

Community detection has become a fundamental operation in numerous graph-theoretic applications. It is used to reveal natural divisions that exist within real world networks without imposing prior size or cardinality constraints on the set of communities. Despite its potential for application, there is only limited support for community detection on large-scale parallel computers, largely owing to the irregular and inherently sequential nature of the underlying heuristics. In this paper, we present parallelization heuristics for fast community detection using the Louvain method as the serial template. The Louvain method is an iterative heuristic for modularity optimization. Originally developed by Blondel et al. in 2008, the method has become increasingly popular owing to its ability to detect high modularity community partitions in a fast and memory-efficient manner. However, the method is also inherently sequential, thereby limiting its scalability to problems that can be solved on desktops. Here, we observe certain key properties of this method that present challenges for its parallelization, and consequently propose multiple heuristics that are designed to break the sequential barrier. Our heuristics are agnostic to the underlying parallel architecture. For evaluation purposes, we implemented our heuristics on shared memory (OpenMP) and distributed memory (MapReduce-MPI) machines, and tested them over real world graphs derived from multiple application domains (internet, biological, natural language processing). Experimental results demonstrate the ability of our heuristics to converge to high modularity solutions comparable to those output by the serial algorithm in nearly the same number of iterations, while also drastically reducing time to solution.

clustering, graph algorithms↗

The Omics of Stem Cell Mediated Regeneration: A Pilot Single Cell RNA-Seq Study of Mechanotransduction

Mechanical forces are potent modulators of stem cell based tissue regenerative mechanisms, inducing cell fate decisions and tissue specific commitment. A unique platform for investigating mechanotransduction is spaceflight, where microgravity and altered fluid mechanics provide a loading-null experimental condition. Seminal investigations of regenerative capacity in a wholly regenerative species, the newt model, and in a variety of totipotent and adult stem cell populations have demonstrated the detrimental effects of unloading on maintenance of stem cell based regeneration. Of particular interest is the observation that unloading interferes with the transition of stem cell pools from proliferative state to differentiation commitment. In this work we sought to test the hypothesis that gravity mechanotransduction regulates stem cell tissue regenerative processes by modulating stem cell proliferation and differentiation fates at specific cell cycle stages. To do this, clonally-derived ESCs were plated on a collagen matrix and expanded for 36 hours before re-plating on a non-adherent culture dish in the absence of leukemia inhibitory factor (LIF) to form spheroid aggregate EBs. After formation, the EBs were transferred to a collagen matrix coated culture dishes and given 4 days to allow implantation and outgrowth. In parallel, totipotent ESCs were plated 24 hours before mechanical stimulation on collagen matrix culture dishes in the presence of LIF to maintain totipotency and serve as un-differentiation committed controls. The EBs and ESCs were then subjected to either a 60 minute pulse of gravity (static loading) or 60 minutes of cyclic stretch (dynamic loading) mechanotransduction. Six hours post-stimulation, we used a 10X Genomics Single Cell controller to generate bar-coded single cell Illumina libraries and sequenced expressomes for 5,000 static loaded cells, representative of a change in gravity mechanotransduction, 5,000 dynamic loaded cells, representative of tissue loading associate with physiologic function, and 5,000 unstimulated 1g control cells. The comparison of these 3 libraries by cluster assignment based on like gene expression patterns show substantial alteration in cluster geometry due to mechanical loading. Specifically the mechanically loaded EB outgrowth cells to retain potency markers (PAX6, SOX2, CD34) and suppress early commitment markers (Dhh, VCAN, Igf1). Whereas the EBs cultured under the non-stimulated conditions display clear departure from the ESC expressome with lineage commitment markers upregulated and several tissue specific markers being expressed (BMP "early musculoskeletal development, Mesp1" early cardiovascular cell lineage). These markers are not seen in the mechano-stimulated cultures or the totipotent ESC cultures. Comparison of like clusters between our experimental conditions revealed an array of regenerative and stem cell genes are significantly mechano-regulated. Of particular importance CDKN1a/p21, a gene shown by previous investigation of our research team to be significantly upregulated in unloading, was suppressed in the static and dynamic loaded EBS. In addition to CDKN1a/p21 many genes related to cell cycle and transitory differentiation markers had elevated expression in the mechano-stimulated EBs, but surprisingly these trends were not observed in the ESC cultures. This study is the first of its kind investigating for mechano-signaling and mechano-regulated pathways, and has alre

Single cell RNA-sequecing↗

ON THE FORMATION OF THE PECULIAR LOW-MASS X-RAY BINARY IGR J17480-2446 IN TERZAN 5

IGR J17480-2446 is an accreting X-ray pulsar in a low-mass X-ray binary harbored in the Galactic globular cluster Terzan 5. Compared with other accreting millisecond pulsars, IGR J17480-2446 is peculiar for its low spin frequency (11 Hz), which suggests that it might be a mildly recycled neutron star at the very early phase of mass transfer. However, this model seems to be in contrast with the low field strength deduced from the kilo-Hertz quasi-periodic oscillations observed in IGR J17480-2446. Here, we suggest an alternative interpretation, assuming that the current binary system was formed during an exchange encounter either between a binary (which contains a recycled neutron star) and the current donor, or between a binary and an isolated, recycled neutron star. In the resulting binary, the spin axis of the neutron star could be parallel or anti-parallel with the orbital axis. In the latter case, the abnormally low frequency of IGR J17480-2446 may result from the spin-down to spin-up evolution of the neutron star. We also briefly discuss the possible observational implications of the pulsar in this scenario.

79 ASTRONOMY AND ASTROPHYSICS↗

2016 High Performance Computing Annual Report

Sandia National Laboratories’ California site is celebrating its 60th anniversary (1956 to 2016), and high performance computing has been a key enabler for its scientists and engineers throughout much of its history. Since its founding, Sandia California has helped pioneer the use of HPC platforms including hosting Sandia’s first Cray-1 supercomputer in the 1970s and supporting development of scalable cluster computing platforms to create a new paradigm for cost-effective supercomputing in the 1990s. Recent decades of investment in creation of scalable application frameworks for scientific computing have also enabled new generations of modeling and simulation codes. These resources have facilitated computational analysis of complex phenomena in diverse applications spanning national defense, energy, and homeland security. Today, Sandia California researchers work with partners in academia, industry, and national labs to evolve the state-of-the-art in HPC, modeling, and data analysis (including foundational capabilities for exascale computing platforms) and apply them in transformational ways. Research efforts include mitigating the effects of silent hardware failures that can jeopardize the results of large-scale computations, developing exascale-capable asynchronous task-parallel programming models and runtime systems, formulating new techniques to better explore and analyze extreme-scale data sets, and increasing our understanding of materials and chemical sciences which has applications spanning nuclear weapons stockpile stewardship to more efficient automobile engines. The following section highlights some of these research and applications projects and further illustrates the breadth of our HPC capabilities.

97 MATHEMATICS AND COMPUTING↗

Investigating the Feedback Path in a Jet-Surface Resonant Interaction

A resonant interaction between an 8:1 aspect ratio rectangular jet and flat-plates, placed parallel to the jet, is studied experimentally. For certain locations of the plate relative to the jet, the resonance takes place with a loud accompanying tone. The sound pressure level spectra are often marked by multiple peaks. The frequencies of the spectral peaks are studied as a function of the streamwise length of the plate, its relative location to the jet as well as the jet Mach number. It is demonstrated that the tones are not due to a simple feedback between the plate's trailing edge and the nozzle's exit; the leading edge of the plate also comes into play in the frequency selection. With parametric variation, it is found that there is an order in the most energetic spectral peaks; their frequencies cluster in distinct bands. The 'fundamental', i.e., the lowest frequency band is explained by an acoustic feedback involving diffraction at the plate's leading edge.

Resonance↗

A scalable approach to solving dense linear algebra problems on hybrid CPU-GPU systems

Aiming to fully exploit the computing power of all CPUs and all graphics processing units (GPUs) on hybrid CPU-GPU systems to solve dense linear algebra problems, in this paper we design a class of heterogeneous tile algorithms to maximize the degree of parallelism, to minimize the communication volume, and to accommodate the heterogeneity between CPUs and GPUs. The new heterogeneous tile algorithms are executed upon our decentralized dynamic scheduling runtime system, which schedules a task graph dynamically and transfers data between compute nodes automatically. The runtime system uses a new distributed task assignment protocol to solve data dependencies between tasks without any coordination between processing units. By overlapping computation and communication through dynamic scheduling, we are able to attain scalable performance for the double-precision Cholesky factorization and QR factorization. Finally, our approach demonstrates a performance comparable to Intel MKL on shared-memory multicore systems and better performance than both vendor (e.g., Intel MKL) and open source libraries (e.g., StarPU) in the following three environments: heterogeneous clusters with GPUs, conventional clusters without GPUs, and shared-memory systems with multiple GPUs.

97 MATHEMATICS AND COMPUTING↗

Crater Flux Transfer Events: Highroad to the X Line?

We examine Cluster observations of a so-called magnetosphere crater FTE, employing data from five instruments (FGM, CIS, EDI, EFW, and WHISPER), some at the highest resolution. The aim of doing this is to deepen our understanding of the reconnection nature of these events by applying recent advances in the theory of collisionless reconnection and in detailed observational work. Our data support the hypothesis of a stratified structure with regions which we show to be spatial structures. We support the bulge-like topology of the core region (R3) made up of plasma jetting transverse to reconnected field lines. We document encounters with a magnetic separatrix as a thin layer embedded in the region (R2) just outside the bulge, where the speed of the protons flowing approximately parallel to the field maximizes: (1) short (fraction of a sec) bursts of enhanced electric field strengths (up to approximately 30 mV/m) and (2) electrons flowing against the field toward the X line at approximately the same time as the bursts of intense electric fields. R2 also contains a density decrease concomitant with an enhanced magnetic field strength. At its interface with the core region, R3, electric field activity ceases abruptly. The accelerated plasma flow profile has a catenary shape consisting of beams parallel to the field in R2 close to the R2/R3 boundary and slower jets moving across the magnetic field within the bulge region. We detail commonalities our observations of crater FTEs have with reconnection structures in other scenarios. We suggest that in view of these properties and their frequency of occurrence, crater FTEs are ideal places to study processes at the separatrices, key regions in magnetic reconnection. This is a good preparation for the MMS mission.

Farrugia, C. J.↗

HipBone: A performance-portable graphics processing unit-accelerated C++ version of the NekBone benchmark

We present hipBone, an open-source performance-portable proxy application for the Nek5000 (and NekRS) computational fluid dynamics applications. HipBone is a fully GPU-accelerated C++ implementation of the original NekBone CPU proxy application with several novel algorithmic and implementation improvements which optimize its performance on modern fine-grain parallel GPU accelerators. Our optimizations include a conversion to store the degrees of freedom of the problem in assembled form in order to reduce the amount of data moved during the main iteration and a portable implementation of the main Poisson operator kernel. We demonstrate near-roofline performance of the operator kernel on three different modern GPU accelerators from two different vendors. We present a novel algorithm for splitting the application of the Poisson operator on GPUs which aggressively hides MPI communication required for both halo exchange and assembly. Our implementation of nearest-neighbor MPI communication then leverages several different routing algorithms and GPU-Direct RDMA capabilities, when available, which improves scalability of the benchmark. We demonstrate the performance of hipBone on three different clusters housed at Oak Ridge National Laboratory, namely, the Summit supercomputer and the Frontier early-access clusters, Spock and Crusher. Our tests demonstrate both portability across different clusters and very good scaling efficiency, especially on large problems.

Computer Science↗

Trinity Benchmarks on the Intel Xeon Phi (Knights Corner)

This report documents the early experiences with porting and performance analysis of the Tri-Lab Trinity benchmark applications on Intel Xeon Phi (Knights Corner) (KNC) processor. KNC, the second generation of the Intel Many Integrated Core (MIC) architectures, uses a large number of small P54C-x86 cores with wide vector units and is deployed as PCI bus attached process accelerators. Sandia has experimental test beds of small InifiniBand clusters and workstations to investigate the performance of the MIC architecture. On these experimental test beds the programming models that may be investigated are "offload", "symmetric" and "native". Among these program usage models our primary interest is in the so called "native" mode, because the planned Trinity system to be deployed in 2016 using the next generation MIC processor architecture called Knights Landing would be self-hosted. Trinity / NERSC-8 benchmark programs cover a variety of scientific disciplines and they were used to guide the procurement of these systems. Architectures such as the Intel MIC are well suited to study evolving processor architectures and a usage model commonly referred to as MPI + X that facilitates migration of our applications to use both coarse grain and fine grain parallelism. Our focus with the applications selected is on the efficacy of algorithms in these applications to take advantage of features like: large number of cores, wide vector units, higher-bandwidth and deeper memory sub-system. This is a first step towards understanding applications, algorithms and programming environments for Trinity and future exascale computing systems.

97 MATHEMATICS AND COMPUTING↗

NVMalloc: Exposing an Aggregate SSD Store as a Memory Partition in Extreme-Scale Machines

DRAM is a precious resource in extreme-scale machines and is increasingly becoming scarce, mainly due to the growing number of cores per node. On future multi-petaflop and exaflop machines, the memory pressure is likely to be so severe that we need to rethink our memory usage models. Fortunately, the advent of non-volatile memory (NVM) offers a unique opportunity in this space. Current NVM offerings possess several desirable properties, such as low cost and power efficiency, but suffer from high latency and lifetime issues. We need rich techniques to be able to use them alongside DRAM. In this talk, we present a novel approach for exploiting NVM as a secondary memory partition so that applications can explicitly allocate and manipulate memory regions therein. More specifically, we propose an NVMalloc library with a suite of services that enables applications to access a distributed NVM storage system. We have devised ways within NVMalloc so that the storage system, built from compute node-local NVM devices, can be accessed in a byte-addressable fashion using the memory mapped I/O interface. Our approach has the potential to re-energize out-of-core computations on largescale machines by having applications allocate certain variables through NVMalloc, thereby increasing the overall memory capacity available. Our evaluation on a 128-core cluster shows that NVMalloc enables applications to compute problem sizes larger than the physical memory in a cost-effective manner. It can bring more performance/efficiency gain with increased computation time between NVM memory accesses or increased data access locality. In addition, our results suggest that while NVMalloc enables transparent access to NVM-resident variables, the explicit control it provides is crucial to optimize application performance.

99 GENERAL AND MISCELLANEOUS↗

Speeding up equation of motion coupled cluster theory with the chain of spheres approximation

In the present paper, the chain of spheres exchange (COSX) approximation is applied to the highest scaling terms in the equation of motion (EOM) coupled cluster equations with single and double excitations, in particular, the terms involving integrals with four virtual labels. It is found that even the acceleration of this single term yields significant computational gains without compromising the desired accuracy of the method. For an excitation energy calculation on a cluster of five water molecules using 585 basis functions, the four virtual term is 9.4 times faster using COSX with a loose grid than using the canonical implementation, which yields a 2.6 fold acceleration for the whole of the EOM calculation. For electron attachment calculations, the four virtual term is 15 times and the total EOM calculation is 10 times faster than the canonical calculation for the same system. The accuracy of the new method was tested using Thiel’s test set for excited states using the same settings and the maximum absolute deviation over the whole test set was found to be 12.945 cm{sup −1} (59 μHartree) for excitation energies and 6.799 cm{sup −1} (31 μHartree) for electron attachments. Using MP2 amplitudes for the ground state in combination with the parallel evaluation of the full EOM equations in the manner discussed in this paper enabled us to perform calculations for large systems. Electron affinity values for the two lowest states of a Zn protoporphyrine model compound (224 correlated electrons and 1120 basis functions) were obtained in 3 days 19 h using 4 cores of a Xeon E5-2670 processor allocating 10 GB memory per core. Calculating the lowest two excitation energies for trans-retinal (114 correlated electrons and 539 basis functions) took 1 day 21 h using eight cores of the same processor and identical memory allocation per core.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Unveiling the Universe with emerging cosmological probes

The detection of the accelerated expansion of the Universe has been one of the major breakthroughs in modern cosmology. Several cosmological probes (Cosmic Microwave Background, Supernovae Type Ia, Baryon Acoustic Oscillations) have been studied in depth to better understand the nature of the mechanism driving this acceleration, and they are being currently pushed to their limits, obtaining remarkable constraints that allowed us to shape the standard cosmological model. In parallel to that, however, the percent precision achieved has recently revealed apparent tensions between measurements obtained from different methods. These are either indicating some unaccounted systematic effects, or are pointing toward new physics. Following the development of CMB, SNe, and BAO cosmology, it is critical to extend our selection of cosmological probes. Novel probes can be exploited to validate results, control or mitigate systematic effects, and, most importantly, to increase the accuracy and robustness of our results. This review is meant to provide a state-of-art benchmark of the latest advances in emerging “beyond-standard” cosmological probes. We present how several different methods can become a key resource for observational cosmology. In particular, we review cosmic chronometers, quasars, gamma-ray bursts, standard sirens, lensing time-delay with galaxies and clusters, cosmic voids, neutral hydrogen intensity mapping, surface brightness fluctuations, stellar ages of the oldest objects, secular redshift drift, and clustering of standard candles. The review describes the method, systematics, and results of each probe in a homogeneous way, giving the reader a clear picture of the available innovative methods that have been introduced in recent years and how to apply them. The review also discusses the potential synergies and complementarities between the various probes, exploring how they will contribute to the future of modern cosmology.

79 ASTRONOMY AND ASTROPHYSICS↗

Beam test performance studies of CMS Phase-2 Outer Tracker module prototypes

A new tracking detector will be installed as part of thePhase-2 upgrade of the CMS detector for the high-luminosity LHC era.This tracking detector includes the Inner Tracker, equipped withsilicon pixel sensor modules, and the Outer Tracker, consisting ofmodules with two parallel stacked silicon sensors. The Outer Trackerfront-end ASICs will be able to correlate hits from chargedparticles in these two sensors to perform on-module discriminationof transverse momenta (p$_{T}$). The p$_{T}$information is generated at a frequency of 40 MHz and will be usedin the Level-1 trigger decision of CMS. Prototypes of theso-called 2S modules were tested at the Test Beam Facility at DESYHamburg between 2019 and 2020. These modules use the finalfront-end ASIC, the CMS Binary Chip (CBC), and for the firsttime the Concentrator Integrated Circuit (CIC), optical readoutand on-module power conversion. In total, seven modules were tested,one of which was assembled with sensors irradiated with protons. Animportant aspect was to show that it is possible to read out modulessynchronously. A cluster hit efficiency of about 99.75 % wasachieved for all modules. The CBC p$_{T}$ discriminationmechanism has been verified to work together with the CIC andoptical readout. The measured module performance meets therequirements for operation in the upgraded CMS tracking detector.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗