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All sources NASA NTRS DOE OSTI

DOE OSTI2012

Award ER25844: Minimizing System Noise Effects for Extreme-Scale Scientific Simulation Through Function Delegation

In software running on distributed computing clusters, time spent on communication between nodes in the cluster can be a significant portion of the overall computation time; background operating system tasks and other computational noise on the nodes of the system can have a significant impact on the amount of time this communication takes, especially on large systems. The research completed in this period has improved understanding of when such noise will have a significant impact. Specifically, it was demonstrated that not just noise on the nodes, but also noise on the network between nodes can have a significant impact on computation time. It was also demonstrated that noise patterns matter more than noise intensity: very regular noise can cause less disruption than lighter (on average) but less regular noise. It was also demonstrated that the effect of noise is more prominent as the speed of the network between nodes is increased. Furthermore, a tracing tool, Netgauge, was improved via our work, and a system simulator, LogGOPSim, was developed; they can be used by application developers to improve performance of their program and by system designers to mitigate the effects of noise by adjusting the noise characteristics of the operating system. Both have been made freely available as open source programs. In the course of developing these tools, we demonstrated weaknesses in existing methodologies for modeling communication, and we introduced a more detailed model, LogGOPS, for simulating systems. Not only were the deleterious effects of noise explored but we have also offered solutions. Our studies of simulations of system noise have led to specific recommendations on tuning systems to mitigate noise. We have also improved existing approaches to mitigating noise. Non-blocking collective communication avoids the effects of noise by letting communication continue simultaneously with computation (thus being non-blocking), so that the delays in communication introduced by noise have a smaller impact on overall computation time. Potentially, noise can be reduced much further by offloading communication tasks to a separate processing element than the operating system is using. We have improved our library LibNBC, which provides an implementation of non-blocking collectives, via this work. During this research, our proposal to include non-blocking collectives (which used LibNBC as a reference implementation) in the upcoming MPI-3 standard was accepted. As MPI is a ubiquitous and important standard for communication in parallel computing, this demonstrates a certain acceptance of the practicality and desirability of non-blocking collectives. Now that non-blocking collectives are a part of the standard we can expect to see optimized platform-specific implementations of non-blocking collectives. Also as part of this work we have also developed a language GOAL (Global Operation Assembly Language) that can be used as a starting point for defining languages to express optimized communication algorithms.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2013

Elementary Particle Physics (Final Report)

vATLAS and the LHC are delivering on the promise of discovery physics at the high energy frontier. Using 4.8 fb -1 of 2011 $\sqrt{s}$=7 TeV data and the first 5.8 fb -1 of 2012 $\sqrt{s}$=8 TeV data, ATLAS published the observation of a new particle with a mass of 126 GeV with a significance of 5.9σ that is compatible with a Standard Model (SM) Higgs. The LHC is outperforming initial projections for the 2012 run, and ATLAS is on track to integrate ~20 fb -1 of proton-proton collisions in 2012 before Long Shutdown 1 (LS1) begins in Spring 2013. University of Texas at Dallas (UTD) physicists will complete work on two ATLAS analyses this fall. The first is the search for the gauge bosons of a hypothesized dark sector. For 2011 data, UTD is responsible for the dark photon search in the electron-jet channel, and we are looking forward to an expanded leadership role in the dark photon search using the full 2012 data set. Our second analysis interest is the study of X/Y/Z exotic states having cc content, which builds on our experience in this field from the BABAR experiment After completing a measurement of the Xc(3872) production cross section this fall, we will search for evidence of the Z(4430)+ which is reported by Belle but not confirmed by BABAR. The UTD group has played a strong role in ATLAS operations, with group members serving as Pixel Run Coordinator, ATLAS Shift Leader, and Pixel/Inner Detector Shifter. For most of the current 3-year funding cycle, a group member coordinated the development of the Pixel DAQ code, and another continues to build and maintain the data quality monitoring (DQM) application that is used by the Inner Detector control room shifter. Additionally, members of our group take Pixel on-call expert shifts for DQM and DAQ. We led an optoboard lifetime study to assess concerns of premature on-detector VCSEL failure using the Pixel working prototype detector at CERN. Physicists based at UTD participated through Pixel Offline DQM and ATLAS Distributed Computing Operations Shifts (ADCoS) During Summer 2012, UTD joined upgrade activities in preparation for LS1. We took a major role in the testing of Electro-Readout (ER) Bundle testing for new Service Quarter Panels (nSQPs), and we developed two utilities to measure the timing jitter and bit error rate of the Pixel readout chain for use commissioning Pixel detector upgrades. During BABAR's heyday, the UTD group pioneered the use of e + e - annihilation events with hard Initial State Radiation (ISR) to study the charm threshold region, and we carried out the first BABAR double-cc analysis. Our most recent ISR paper, written in collaboration with A. Palano (Bari) is Exclusive Production of Ds + Ds - , D S *+ Ds - , and Ds *+ Ds *- via e+ e- Annihilation with Initial-State-Radiation was published in Physical Review D 82, 052004 (2010). Work continues on a study of ISR Λc + Λc - production, and a new search to establish and study double-ss production is starting.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2015

High Fidelity Simulations of Large-Scale Wireless Networks

The worldwide proliferation of wireless connected devices continues to accelerate. There are 10s of billions of wireless links across the planet with an additional explosion of new wireless usage anticipated as the Internet of Things develops. Wireless technologies do not only provide convenience for mobile applications, but are also extremely cost-effective to deploy. Thus, this trend towards wireless connectivity will only continue and Sandia must develop the necessary simulation technology to proactively analyze the associated emerging vulnerabilities. Wireless networks are marked by mobility and proximity-based connectivity. The de facto standard for exploratory studies of wireless networks is discrete event simulations (DES). However, the simulation of large-scale wireless networks is extremely difficult due to prohibitively large turnaround time. A path forward is to expedite simulations with parallel discrete event simulation (PDES) techniques. The mobility and distance-based connectivity associated with wireless simulations, however, typically doom PDES and fail to scale (e.g., OPNET and ns-3 simulators). We propose a PDES-based tool aimed at reducing the communication overhead between processors. The proposed solution will use light-weight processes to dynamically distribute computation workload while mitigating communication overhead associated with synchronizations. This work is vital to the analytics and validation capabilities of simulation and emulation at Sandia. We have years of experience in Sandia’s simulation and emulation projects (e.g., MINIMEGA and FIREWHEEL). Sandia’s current highly-regarded capabilities in large-scale emulations have focused on wired networks, where two assumptions prevent scalable wireless studies: (a) the connections between objects are mostly static and (b) the nodes have fixed locations.

Onunkwo, Uzoma↗

DOE OSTI2018

dV/dt - Accelerating the Rate of Progress towards Extreme Scale Collaborative Science

This report introduces publications that report the results of a project that aimed to design a computational framework that enables computational experimentation at scale while supporting the model of “submit locally, compute globally”. The project focuses on estimating application resource needs, finding the appropriate computing resources, acquiring those resources,deploying the applications and data on the resources, managing applications and resources during run.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2018

Embedded 100 Gbps Photonic Components

This innovation to fiber optic component technology increases the performance, reduces the size and reduces the power consumption of optical communications within dense network systems, such as advanced distributed computing systems and data centers. VCSEL technology is enabling short-reach (< 100 m) and >100 Gbps optical interconnections over multi-mode fiber in commercial applications.

42 ENGINEERING↗

DOE OSTI2021

Exploring OpenSNAPI Use Cases and Evolving Requirements [Slides]

Emerging system architectures are rapidly transforming in order to meet shifting requirements. Motivated by expanding data volumes, energy efficiency concerns, and the omnipresent need to improve performance, architectures are increasingly adopting a data-centric approach. At the core of this concept is the goal of minimizing data motion and instead processing data in-situ to the greatest degree possible. Therefore, data-centric designs, in contrast to conventional CPU-centric models, typically distribute compute capabilities throughout the architecture. As part of this paradigm shift, a novel class of devices known as data processing units (DPUs), alongside CPUs and GPUs, are quickly forming a third pillar of data-centric systems. These devices, which include smart network adapters and switches, seek to offload computation on data at the network edge as well as in-flight within the network fabric. The Open Smart Network API (OpenSNAPI) project seeks to develop a unified API for DPU devices. In our previous talks, we introduced the OpenSNAPI project and detailed our investigations regarding the viability of offloading compute intensive kernels to BlueField DPUs. In contrast, in this talk we detail our efforts to offload application-level file I/O to the DPU. We also discuss plans and early efforts to explore in-network compute capabilities. Finally, we describe our observations with respect to the evolving design of OpenSNAPI.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2023

User Manual - HydraGNN: Distributed PyTorch Implementation of Multi-Headed Graph Convolutional Neural Networks

This document serves as user manual for HydraGNN, a scalable graph neural network (GNN) architecture that allows for a simultaneous prediction of multiple target properties using multi-task learning (MTL). The HydraGNN architecture is constructed by successive superposition of three different sets of layers. The first set is made of message-passing layers to exchange information across nodes in the graph and use this to update the nodal features. The second set is made of global pooling layers that aggregate information from all the nodes in the graph and map it into a scalar, and is needed only for global target properties that are related to the entire graph. The third set of layers is dedicated to the implementation of MTL, which is enabled by forking of the architecture into separate heads, each one of them dedicated to the predictive task of one specific target property. Through an object-oriented programming paradigm, HydraGNN is templated over different message-passing policies, which allows for a user-friendly hyperparameter study to assess the sensitivity of the predictive performance of the HydraGNN architecture on a specific dataset with respect to the choice of the message-passing policy. The object-oriented paradigm used by HydraGNN also allows for a user-friendly inclusion of newly developed message passing policies within the existing framework. HydraGNN supports distributed computing capabilities for scalable data reading and scalable training on leadership-class supercomputers.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2024

Creating Unit Tests for GlideinWMS using AI tools

GlideinWMS is a workload management system that uses distributed computing to complete tasks, also known as jobs. It is particularly useful for high-throughput computing that’s used in research projects. It relies on Glideins, which are pilot jobs that pull jobs from a queue and provide resources for their completion, based on the jobs requirements. These decisions are made based on resource availability and job requirements. We used new AI tools to add unit tests to GlideinWMS.

Baburashvili, Ilya↗

DOE OSTI2025

Enabling Innovative Analysis on Heterogeneous Clusters through HTCdaskgateway

High energy particle (HEP) physics research is going through fundamental changes as we move to collect larger amounts of data from the Large Hadron Collider (LHC). Analysis facilities and distributed computing, through HTCs, have come together to create the next pythonic generation of analysis by utilizing HTCdaskgateway, a Dask gateway extension, allowing users to spawn workers compatible with both their analysis and heterogeneous clusters in line with authentication requirements. This is enabling physicists to engage with scientific python in ways they had not before because of domain specific C++ tools. An example of HTCdaskgateway’s use is Fermilab’s Elastic Analysis Facility.

Chavez, Elise [U. Wisconsin, Madison (main)]↗

DOE OSTI2022

Drugsniffer: An Open Source Workflow for Virtually Screening Billions of Molecules for Binding Affinity to Protein Targets

The SARS-CoV2 pandemic has highlighted the importance of efficient and effective methods for identification of therapeutic drugs, and in particular has laid bare the need for methods that allow exploration of the full diversity of synthesizable small molecules. While classical high-throughput screening methods may consider up to millions of molecules, virtual screening methods hold the promise of enabling appraisal of billions of candidate molecules, thus expanding the search space while concurrently reducing costs and speeding discovery. Here, we describe a new screening pipeline, called drugsniffer, that is capable of rapidly exploring drug candidates from a library of billions of molecules, and is designed to support distributed computation on cluster and cloud resources. As an example of performance, our pipeline required ~40,000 total compute hours to screen for potential drugs targeting three SARS-CoV2 proteins among a library of ~3.7 billion candidate molecules.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2011

Novel QCD Phenomenology

I review a number of topics where conventional wisdom in hadron physics has been challenged. For example, hadrons can be produced at large transverse momentum directly within a hard higher-twist QCD subprocess, rather than from jet fragmentation. Such 'direct' processes can explain the deviations from perturbative QCD predictions in measurements of inclusive hadron cross sections at fixed x{sub T} = 2p{sub T}/{radical}s, as well as the 'baryon anomaly', the anomalously large proton-to-pion ratio seen in high centrality heavy ion collisions. Initial-state and final-state interactions of the struck quark, the soft-gluon rescattering associated with its Wilson line, lead to Bjorken-scaling single-spin asymmetries, diffractive deep inelastic scattering, the breakdown of the Lam-Tung relation in Drell-Yan reactions, as well as nuclear shadowing and antishadowing. The Gribov-Glauber theory predicts that antishadowing of nuclear structure functions is not universal, but instead depends on the flavor quantum numbers of each quark and antiquark, thus explaining the anomalous nuclear dependence measured in deep-inelastic neutrino scattering. Since shadowing and antishadowing arise from the physics of leading-twist diffractive deep inelastic scattering, one cannot attribute such phenomena to the structure of the nucleus itself. It is thus important to distinguish 'static' structure functions, the probability distributions computed from the square of the target light-front wavefunctions, versus 'dynamical' structure functions which include the effects of the final-state rescattering of the struck quark. The importance of the J = 0 photon-quark QCD contact interaction in deeply virtual Compton scattering is also emphasized. The scheme-independent BLM method for setting the renormalization scale is discussed. Eliminating the renormalization scale ambiguity greatly improves the precision of QCD predictions and increases the sensitivity of searches for new physics at the LHC. Other novel features of QCD are discussed, including the consequences of confinement for quark and gluon condensates.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2011

Grid Data Access on Widely Distributed Worker Nodes Using Scalla and SRM

Facing the reality of storage economics, NP experiments such as RHIC/STAR have been engaged in a shift of the analysis model, and now heavily rely on using cheap disks attached to processing nodes, as such a model is extremely beneficial over expensive centralized storage. Additionally, exploiting storage aggregates with enhanced distributed computing capabilities such as dynamic space allocation (lifetime of spaces), file management on shared storages (lifetime of files, pinning file), storage policies or a uniform access to heterogeneous storage solutions is not an easy task. The Xrootd/Scalla system allows for storage aggregation. We will present an overview of the largest deployment of Scalla (Structured Cluster Architecture for Low Latency Access) in the world spanning over 1000 CPUs co-sharing the 350 TB Storage Elements and the experience on how to make such a model work in the RHIC/STAR standard analysis framework. We will explain the key features and approach on how to make access to mass storage (HPSS) possible in such a large deployment context. Furthermore, we will give an overview of a fully 'gridified' solution using the plug-and-play features of Scalla architecture, replacing standard storage access with grid middleware SRM (Storage Resource Manager) components designed for space management and will compare the solution with the standard Scalla approach in use in STAR for the past 2 years. Integration details, future plans and status of development will be explained in the area of best transfer strategy between multiple-choice data pools and best placement with respect of load balancing and interoperability with other SRM aware tools or implementations.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2012

The Use of Proxy Caches for File Access in a Multi-Tier Grid Environment

The use of proxy caches has been extensively studied in the HEP environment for efficient access of database data and showed significant performance with only very moderate operational effort at higher grid tiers (T2, T3). In this contribution we propose to apply the same concept to the area of file access and analyze the possible performance gains, operational impact on site services and applicability to different HEP use cases. Base on a proof-of-concept studies with a modified XROOT proxy server we review the cache efficiency and overheads for access patterns of typical ROOT based analysis programs. We conclude with a discussion of the potential role of this new component at the different tiers of a distributed computing grid.

99 GENERAL AND MISCELLANEOUS↗

DOE OSTI2012

Coordinate-Space Hartree-Fock-Bogoliubov Solvers for Superfluid Fermi Systems in Large Boxes

The self-consistent Hartree-Fock-Bogoliubov problem in large boxes can be solved accurately in the coordinate space with the recently developed solvers HFB-AX (2D) and MADNESS-HFB (3D). This is essential for the description of superfluid Fermi systems with complicated topologies and significant spatial extend, such as fissioning nuclei, weakly-bound nuclei, nuclear matter in the neutron star rust, and ultracold Fermi atoms in elongated traps. The HFB-AX solver based on B-spline techniques uses a hybrid MPI and OpenMP programming model for parallel computation for distributed parallel computation, within a node multi-threaded LAPACK and BLAS libraries are used to further enable parallel calculations of large eigensystems. The MADNESS-HFB solver uses a novel multi-resolution analysis based adaptive pseudo-spectral techniques to enable fully parallel 3D calculations of very large systems. In this work we present benchmark results for HFB-AX and MADNESS-HFB on ultracold trapped fermions.

Pei, J. C.↗

DOE OSTI2014

Completion processing for data communications instructions

Completion processing of data communications instructions in a distributed computing environment, including receiving, in an active messaging interface (`AMI`) data communications instructions, at least one instruction specifying a callback function; injecting into an injection FIFO buffer of a data communication adapter, an injection descriptor, each slot in the injection FIFO buffer having a corresponding slot in a pending callback list; listing in the pending callback list any callback function specified by an instruction, incrementing a pending callback counter for each listed callback function; transferring payload data as per each injection descriptor, incrementing a transfer counter upon completion of each transfer; determining from counter values whether the pending callback list presently includes callback functions whose data transfers have been completed; calling by the AMI any such callback functions from the pending callback list, decrementing the pending callback counter for each callback function called.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2014

Completion processing for data communications instructions

Completion processing of data communications instructions in a distributed computing environment with computers coupled for data communications through communications adapters and an active messaging interface (`AMI`), injecting for data communications instructions into slots in an injection FIFO buffer a transfer descriptor, at least some of the instructions specifying callback functions; injecting a completion descriptor for each instruction that specifies a callback function into an injection FIFO buffer slot having a corresponding slot in a pending callback list; listing in the pending callback list callback functions specified by data communications instructions; processing each descriptor in the injection FIFO buffer, setting a bit in a completion bit mask corresponding to the slot in the FIFO where the completion descriptor was injected; and calling by the AMI any callback functions in the pending callback list as indicated by set bits in the completion bit mask.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2014

Completion processing for data communications instructions

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2014

Send-side matching of data communications messages

Send-side matching of data communications messages in a distributed computing system comprising a plurality of compute nodes, including: issuing by a receiving node to source nodes a receive message that specifies receipt of a single message to be sent from any source node, the receive message including message matching information, a specification of a hardware-level mutual exclusion device, and an identification of a receive buffer; matching by two or more of the source nodes the receive message with pending send messages in the two or more source nodes; operating by one of the source nodes having a matching send message the mutual exclusion device, excluding messages from other source nodes with matching send messages and identifying to the receiving node the source node operating the mutual exclusion device; and sending to the receiving node from the source node operating the mutual exclusion device a matched pending message.

97 MATHEMATICS AND COMPUTING↗