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Investigating Operating System Noise in Extreme-Scale High-Performance Computing Systems using Simulation

Hardware/software co-design for future-generation high-performance computing (HPC) systems aims at closing the gap between the peak capabilities of the hardware and the performance realized by applications (application-architecture performance gap). Performance profiling of architectures and applications is a crucial part of this iterative process. The work in this paper focuses on operating system (OS) noise as an additional factor to be considered for co-design. It represents the first step in including OS noise in HPC hardware/software co-design by adding a noise injection feature to an existing simulation-based co-design toolkit. It reuses an existing abstraction for OS noise with frequency (periodic recurrence) and period (duration of each occurrence) to enhance the processor model of the Extreme-scale Simulator (xSim) with synchronized and random OS noise simulation. The results demonstrate this capability by evaluating the impact of OS noise on MPI_Bcast() and MPI_Reduce() in a simulated future-generation HPC system with 2,097,152 compute nodes.

Engelmann, Christian↗

On noise and the performance benefit of nonblocking collectives

Relaxed synchronization offers the potential of maintaining application scalability by allowing many processes to make independent progress when some processes suffer delays. Yet, the benefits of this approach in important parallel workloads have not been investigated in detail. In this paper, we use a validated simulation approach to explore the noise mitigation effects of idealized nonblocking collectives in workloads where these collectives are a major contributor to total execution time. In conclusion, although nonblocking collectives are unlikely to provide significant noise mitigation to applications in the low-OS-noise environments expected in next-generation HPC systems, we show that they can potentially improve application runtime with respect to other noise types.

97 MATHEMATICS AND COMPUTING↗

A Case for Application Oblivious Energy-Efficient MPI Runtime

Power has become the major impediment in designing large scale high-end systems. Message Passing Interface (MPI) is the {\em de facto} communication interface used as the back-end for designing applications, programming models and runtime for these systems. Slack --- the time spent by an MPI process in a single MPI call --- provides a potential for energy and power savings, if an appropriate power reduction technique such as core-idling/Dynamic Voltage and Frequency Scaling (DVFS) can be applied without perturbing application's execution time. Existing techniques that exploit slack for power savings assume that application behavior repeats across iterations/executions. However, an increasing use of adaptive, data-dependent workloads combined with system factors (OS noise, congestion) makes this assumption invalid. This paper proposes and implements Energy Aware MPI (EAM) --- an application-oblivious energy-efficient MPI runtime. EAM uses a combination of communication models of common MPI primitives (point-to-point, collective, progress, blocking/non-blocking) and an online observation of slack for maximizing energy efficiency. Each power lever incurs time overhead, which must be amortized over slack to minimize degradation. When predicted communication time exceeds a lever overhead, the lever is used {\em as soon as possible} --- to maximize energy efficiency. When mis-prediction occurs, the lever(s) are used automatically at specific intervals for amortization. We implement EAM using MVAPICH2 and evaluate it on ten applications using up to 4096 processes. Our performance evaluation on an InfiniBand cluster indicates that EAM can reduce energy consumption by 5--41\% in comparison to the default approach, with negligible (less than 4\% in all cases) performance loss.

Venkatesh, Akshay↗

A simulation infrastructure for examining the performance of resilience strategies at scale

Fault-tolerance is a major challenge for many current and future extreme-scale systems, with many studies showing it to be the key limiter to application scalability. While there are a number of studies investigating the performance of various resilience mechanisms, these are typically limited to scales orders of magnitude smaller than expected for next-generation systems and simple benchmark problems. In this paper we show how, with very minor changes, a previously published and validated simulation framework for investigating application performance of OS noise can be used to simulate the overheads of various resilience mechanisms at scale. Using this framework, we compare the failure-free performance of this simulator against an analytic model to validate its performance and demonstrate its ability to simulate the performance of two popular rollback recovery methods on traces from real.

Ferreira, Kurt Brian↗

A Framework for Adaptable Operating and Runtime Systems

The emergence of new classes of HPC systems where performance improvement is enabled by Moore’s Law for technology is manifest through multi-core-based architectures including specialized GPU structures. Operating systems were originally designed for control of uniprocessor systems. By the 1980s multiprogramming, virtual memory, and network interconnection were integral services incorporated as part of most modern computers. HPC operating systems were primarily derivatives of the Unix model with Linux dominating the Top-500 list. The use of Linux for commodity clusters was first pioneered by the NASA Beowulf Project. However, the rapid increase in number of cores to achieve performance gain through technology advances has exposed the limitations of POSIX general-purpose operating systems in scaling and efficiency. This project was undertaken through the leadership of Sandia National Laboratories and in partnership of the University of New Mexico to investigate the alternative of composable lightweight kernels on scalable HPC architectures to achieve superior performance for a wide range of applications. The use of composable operating systems is intended to provide a minimalist set of services specifically required by a given application to preclude overheads and operational uncertainties (“OS noise”) that have been demonstrated to degrade efficiency and operational consistency. This project was undertaken as an exploration to investigate possible strategies and methods for composable lightweight kernel operating systems towards support for extreme scale systems.

97 MATHEMATICS AND COMPUTING↗

Providing Runtime Clock Synchronization With Minimal Node-to-Node Time Deviation on XT4s and XT5s

We present a new high precision clock synchronization algorithm designed for large XT4 and XT5 leadership-class machines. The algorithm, which is designed to support OS noise reduction through co-scheduling, is suitable for usage cases requiring low overhead and minimal time deviation between nodes. Unlike most high-precision algorithms which reach their precision in a post-mortem analysis after the application has completed, the new ORNL developed algorithm rapidly provides precise results during runtime. Previous to our work, the leading high-precision clock synchronization algorithms that made results available during runtime relied on probabilistic schemes that are not guaranteed to result in an answer.

99 GENERAL AND MISCELLANEOUS↗

Linux Kernel Co-Scheduling For Bulk Synchronous Parallel Applications

This paper describes a kernel scheduling algorithm that is based on co-scheduling principles and that is intended for parallel applications running on 1000 cores or more where inter-node scalability is key. Experimental results for a Linux implementation on a Cray XT5 machine are presented.1 The results indicate that Linux is a suitable operating system for this new scheduling scheme, and that this design provides a dramatic improvement in scaling performance for synchronizing collective operations at scale.

99 GENERAL AND MISCELLANEOUS↗

Fast widefield imaging of neuronal structure and function with optical sectioning in vivo

Optical microscopy, owing to its noninvasiveness and subcellular resolution, enables in vivo visualization of neuronal structure and function in the physiological context. Optical-sectioning structured illumination microscopy (OS-SIM) is a widefield fluorescence imaging technique that uses structured illumination patterns to encode in-focus structures and optically sections 3D samples. However, its application to in vivo imaging has been limited. In this study, we optimized OS-SIM for in vivo neural imaging. We modified OS-SIM reconstruction algorithms to improve signal-to-noise ratio and correct motion-induced artifacts in live samples. Incorporating an adaptive optics (AO) module to OS-SIM, we found that correcting sample-induced optical aberrations was essential for achieving accurate structural and functional characterizations in vivo. With AO OS-SIM, we demonstrated fast, high-resolution in vivo imaging with optical sectioning for structural imaging of mouse cortical neurons and zebrafish larval motor neurons, and functional imaging of quantal synaptic transmission at Drosophila larval neuromuscular junctions.

42 ENGINEERING↗

Image-derived and arterial blood sampled input functions for quantitative PET imaging of the angiotensin II subtype 1 receptor in the kidney

Purpose: The radioligand {sup 11}C-KR31173 has been introduced for positron emission tomography (PET) imaging of the angiotensin II subtype 1 receptor in the kidney in vivo. To study the biokinetics of {sup 11}C-KR31173 with a compartmental model, the input function is needed. Collection and analysis of arterial blood samples are the established approach to obtain the input function but they are not feasible in patients with renal diseases. The goal of this study was to develop a quantitative technique that can provide an accurate image-derived input function (ID-IF) to replace the conventional invasive arterial sampling and test the method in pigs with the goal of translation into human studies. Methods: The experimental animals were injected with [{sup 11}C]KR31173 and scanned up to 90 min with dynamic PET. Arterial blood samples were collected for the artery derived input function (AD-IF) and used as a gold standard for ID-IF. Before PET, magnetic resonance angiography of the kidneys was obtained to provide the anatomical information required for derivation of the recovery coefficients in the abdominal aorta, a requirement for partial volume correction of the ID-IF. Different image reconstruction methods, filtered back projection (FBP) and ordered subset expectation maximization (OS-EM), were investigated for the best trade-off between bias and variance of the ID-IF. The effects of kidney uptakes on the quantitative accuracy of ID-IF were also studied. Biological variables such as red blood cell binding and radioligand metabolism were also taken into consideration. A single blood sample was used for calibration in the later phase of the input function. Results: In the first 2 min after injection, the OS-EM based ID-IF was found to be biased, and the bias was found to be induced by the kidney uptake. No such bias was found with the FBP based image reconstruction method. However, the OS-EM based image reconstruction was found to reduce variance in the subsequent phase of the ID-IF. The combined use of FBP and OS-EM resulted in reduced bias and noise. After performing all the necessary corrections, the areas under the curves (AUCs) of the AD-IF were close to that of the AD-IF (average AUC ratio =1 ± 0.08) during the early phase. When applied in a two-tissue-compartmental kinetic model, the average difference between the estimated model parameters from ID-IF and AD-IF was 10% which was within the error of the estimation method. Conclusions: The bias of radioligand concentration in the aorta from the OS-EM image reconstruction is significantly affected by radioligand uptake in the adjacent kidney and cannot be neglected for quantitative evaluation. With careful calibrations and corrections, the ID-IF derived from quantitative dynamic PET images can be used as the input function of the compartmental model to quantify the renal kinetics of {sup 11}C-KR31173 in experimental animals and the authors intend to evaluate this method in future human studies.

60 APPLIED LIFE SCIENCES↗

The Laser Interferometer Space Antenna (LISA): Current plans and prospects for quantum sensing in future space-based gravitational wave observatories

ESA’s third large class mission is a space-based gravitational wave observatory with NASA as a partner. This talk will describe the current plans for this mission, including the expected science, the instrument design, and a schedule for the development and launch. The noise floor of the system will be described and opportunities for improvement, including possible applications os quantum sensing and measurement techniques.

Jeff Livas↗

WE-G-18A-01: JUNIOR INVESTIGATOR WINNER - Low-Dose C-Arm Cone-Beam CT with Model-Based Image Reconstruction for High-Quality Guidance of Neurosurgical Intervention

Purpose: To address the challenges of image quality, radiation dose, and reconstruction speed in intraoperative cone-beam CT (CBCT) for neurosurgery by combining model-based image reconstruction (MBIR) with accelerated algorithmic and computational methods. Methods: Preclinical studies involved a mobile C-arm for CBCT imaging of two anthropomorphic head phantoms that included simulated imaging targets (ventricles, soft-tissue structures/bleeds) and neurosurgical procedures (deep brain stimulation (DBS) electrode insertion) for assessment of image quality. The penalized likelihood (PL) framework was used for MBIR, incorporating a statistical model with image regularization via an edgepreserving penalty. To accelerate PL reconstruction, the ordered-subset, separable quadratic surrogates (OS-SQS) algorithm was modified to incorporate Nesterov's method and implemented on a multi-GPU system. A fair comparison of image quality between PL and conventional filtered backprojection (FBP) was performed by selecting reconstruction parameters that provided matched low-contrast spatial resolution. Results: CBCT images of the head phantoms demonstrated that PL reconstruction improved image quality (∼28% higher CNR) even at half the radiation dose (3.3 mGy) compared to FBP. A combination of Nesterov's method and fast projectors yielded a PL reconstruction run-time of 251 sec (cf., 5729 sec for OS-SQS, 13 sec for FBP). Insertion of a DBS electrode resulted in severe metal artifact streaks in FBP reconstructions, whereas PL was intrinsically robust against metal artifact. The combination of noise and artifact was reduced from 32.2 HU in FBP to 9.5 HU in PL, thereby providing better assessment of device placement and potential complications. Conclusion: The methods can be applied to intraoperative CBCT for guidance and verification of neurosurgical procedures (DBS electrode insertion, biopsy, tumor resection) and detection of complications (intracranial hemorrhage). Significant improvement in image quality, dose reduction, and reconstruction time of ∼4 min will enable practical deployment of low-dose C-arm CBCT within the operating room. AAPM Research Seed Funding (2013-2014); NIH Fellowship F32EB017571; Siemens Healthcare (XP Division)

60 APPLIED LIFE SCIENCES↗

The R-Process Alliance: Hunting for gold in the near-UV spectrum of 2MASS J05383296–5904280

Over the past few years, the R-Process Alliance (RPA) has successfully carried out a search for stars that are highly enhanced in elements produced via the rapid neutron-capture (r-) process. In particular, the RPA has identified a number of relatively bright, highly r-process-enhanced (r-II) stars, suitable for observations with the Hubble Space Telescope (HST), facilitating abundance derivation of elements such as gold (Au) and cadmium (Cd). This paper presents the detailed abundances derived for the metal-poor ([Fe/H] = −2.55) highly r-process-enhanced ([Eu/Fe] = +1.29) r-II star 2MASS J05383296–5904280. One-dimensional local thermodynamic equilibrium (LTE) elemental abundances were derived via equivalent width and spectral synthesis using high-resolution high signal-to-noise near-UV HST/STIS and optical Magellan/MIKE spectra. Abundances were determined for 43 elements, including 26 neutron-capture elements. In particular, abundances of the rarely studied elements Nb, Mo, Cd, Lu, Os, Pt, and Au are derived from the HST spectrum. These results, combined with RPA near-UV observations of two additional r-II stars, increase the number of Cd abundances derived for r-process-enriched stars from seven to ten and Au abundances from four to seven. A large star-to-star scatter is detected for both of these elements, highlighting the need for more detections enabling further investigations, specifically into possible non-LTE effects.

chemically peculiar stars↗

Procurement of 100 kg of Enriched Xenon for the EXO Prototype and for its Installation at WIPP

This grant supported the enriched xenon procurement, detector construction and initial operation of the EXO-200 double beta decay experiment at the Waste Isolation Pilot Plant (WIPP). The period of performance was Aug 15, 2002 to Dec 31, 2014. The primary goal of the experiment is to search for the very rare (and to date not observed) neutrino-less double beta decay. Such decay, if observed, would shed the light of the quantum-mechanical structure of neutrinos, and the origins of elementary particle masses. Another goal of the detector is to serve as prototype of a larger neutrino-less double beta decay experiment, currently being considered by DOE-OS. EXO-200 has already been extremely successful in both areas and is, in fact, leading the way world-wide in this area of fundamental physics. In the initial part of the grant the EXO-200 collaboration acquired 200kg of xenon enriched to 80% in the isotope 136 that is a candidate for double beta decay. At the time this was the largest isotope separation program carried out for fundamental science. The enrichment was done in Russia, providing a rare and valuable opportunity for US scientists to work alongside Russian colleagues, in some cases from the former closed cities of their military complex. By now the EXO-200 collaboration include institutions from the US, Canada, South Korea, China, Germany, Switzerland and Russia. Many collaborating scientists from these countries have taken shifts at WIPP or at the various remote monitoring sites world-wide. EXO-200 detector construction was completed in early 2010, with the time projection chamber (TPC) installation in the cleanrooms already placed in NeXA. Detector commissioning at WIPP followed, with the last phase, the filling of the TPC with liquid Xenon, occurring in the spring 2011. EXO-200 is described in [1]. Low background data taking started on Jun 1, 2011 and within the first month of data the 2-neutrino double beta decay of 136Xe was discovered, as reported in [2]. More data provided the best half-life measurement of any 2-neutrino double-beta decay modes [3]. Until Feb 2014 the detector ran continuously producing some of the world leading results in the field and, in particular, two of the most sensitive searches for neutrinoless double beta decay [4,5]. These measurements show that the half life of this decay is longer than 1015 times the age of the universe. This is one of the leading results in this field world-wide and succeeded to put the DOE-funded research on the world stage in a very cost-effective way. Other results from EXO-200 include a search for exotic double-beta decay modes [6], a detailed report on the state of the art background levels achieved in the detector [7], the study of rare ion and neutral atom motion and neutralization rates in liquid Xenon [8], a study of the cosmogenic backgrounds in the detector at WIPP’s depth [9], a search for Lorentz and CPT symmetries violation [10] and a search for double-beta decay to excited states [11]. In Feb 2014 the EXO-200 detector was severely disrupted by the accidents in the WIPP underground (unrelated to EXO-200). The EXO-200 operations team was able to recover the unique stockpile of enriched Xenon to high pressure cylinders and warm-up the detector to room temperature without damaging the very delicate equipment. This was a very impressive achievement as no plan had been made to complete these operations entirely from remote. This validates the robustness of well-designed liquid xenon detectors for this and other measurements in particle and nuclear astrophysics. The operations team re-gained almost regular access to the WIPP underground and the EXO-200 detector in Jan 2015 and spent calendar 2015 cleaning up the soot from the WIPP fire, assessing the damage to the EXO-200 infrastructure, correcting such damage and restarting the detector. This process was successfully carried out and culminated in the re-filling of the detector with liquid xenon, in Jan 2016. As of late Jan 2016 EXO-200 is taking data again. The collaboration is in the process of upgrading the readout electronics and restarting a radon abatement system that had been commissioned just before the Feb 2014 events. The upgraded electronics will provide lower readout noise and, in turn, better signal to background discrimination. The radon abatement system will further reduce the radon in a small air-gap between the EXO-200 cryostat and the lead shielding. In a review in Jun 2015 DOE-OS approved EXO-200 for 2.5 more years of running at the end of which we expect to improve the sensitivity to the neutrino-less double-beta decay by a factor two or three. For the last 5 years the EXO-200 detector, located in the WIPP underground, has been at the center of the hunt for new physics beyond the Standard Model of particle physics!

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

BlackjackBench: Portable Hardware Characterization

DARPA's AACE project aimed to develop Architecture Aware Compiler Environments that automatically characterize the hardware and optimize the application codes accordingly. We present the BlackjackBench suite, a collection of portable micro-benchmarks that automate system characterization, plus statistical analysis techniques for interpreting the results. BlackjackBench discovers the effective sizes and speeds of the hardware environment rather than the often unattainable peak values. We aim at hardware features that can be observed by running executables generated by existing compilers from standard C codes. We characterize the memory hierarchy, including cache sharing and NUMA characteristics of the system, properties of the processing cores affecting execution speed, and the length of the OS scheduler time slot. We show how these features of modern multicores can be discovered programmatically. We also show how the features could interfere with each other resulting in incorrect interpretation of the results, and how established classification and statistical analysis techniques reduce experimental noise and aid automatic interpretation of results.

99 GENERAL AND MISCELLANEOUS↗

Frequency stability of GPS NAVSTAR block 1 and block 2 on-orbit clocks

Analysis of the frequency stability of the on-orbit NAVSTAR clocks os performed by the Naval Research Laboratory. The frequency stability is presented for sample times of one day to 30 days. Composite frequency stability profiles are presented for Block 1 and Block 2 NAVSTAR clocks. Several NAVSTAR cesium clocks show frequency stabilities of a few parts in 10^(14) for long sample times. Time-domain noise-process analysis shows the dominant noise type to be white frequency noise for sample times of one to ten days. The non-stationary stochastic behavior of one of the cesium clocks, illustrated by its frequency stability history, shows that the frequency stability is not always time-invariant.

Thomas B. Mccaskill↗

PhyCA-PhyloChip Analysis

PhyCA allows interpretation of a PhyloChip assay. It takes as input, a text file containing the fluorescent intensity from each feature on the microarray surface. PhyCA will determine the background and noise levels, compare probes against controls and determine response scores for each probe pair. It then summarizes a set of probe pair results to determine presence of an operational taxonomic unit as well as its abundance. The PhyCA software is novel from other microarray interpretation software from the following reasons: 1) It leverages spiked-in Quantitative Standards and non-spike-in Negative Controls to build a per-chip model of positive and non-positive responses. 2) It allows a refinement of Presence/Absence calls by evaluating each responding probe against a putative cross-hybridization network. 3) It can be used with phylogenetic microarrays designed for Bacteria, Archaea or Eukaryotes. Hardware req.: PC, MAC; Software req.: OS: Windows, Mac, Linux; Types of files: source code, control information; user guide. The software depends on other software to be installed on the same machine as PhyCA.

Desantis, Todd↗

XPRESS: eXascale PRogramming Environment and System Software

The XPRESS project is the research and development of a complete software architecture for Exascale computing. The four major R&D thrusts include: 1) an Exascale lightweight kernel operating system (LXK), based on the Kitten operating system (OS), to manage billion way hardware parallelism, management of faults and power, management of global virtual name space, and other features of future system architectures; 2) a runtime system (HPX-5), co-designed with LXK, based on the ParalleX execution model that supports dynamic resource management and task scheduling; 3) system interfaces for interoperability between the runtime system and both the OS and the runtime system (RIOS); 4) compilation strategies and systems to translate MPI and OpenMP legacy codes to a form that can be run with performance at least as good as a native code implementation. The software architecture development has been driven by performance evaluation of mini-applications developed at Department of Energy Co-Design Centers as well as ancillary in-house developed applications and benchmarks. Research on the ParalleX execution model has been driven by the development of formal semantics and model checkers for the execution model. The major components of the software architecture are: ParalleX execution model – guiding principles for co-design of components of the system stack with advances in locality management and task prioritization through introspection; HPX runtime system – support of application dynamic adaptive resource management, task scheduling, and introspective control policies; LXK operating system – lightweight kernel operating system for order-constant scalability and low/no noise to manage resources; RIOS – a realm of Exascale system operation unique in the XPRESS project that includes the relationship between the new generation of lightweight kernel operating systems and runtime system software; XPI advanced programming model – intermediate form and low-level (readable) programming interface reflecting the ParalleX model, providing a target for source-to- source high level parallel language translation, and supporting early direct programming experimentation and measurement; Performance models & metrics – providing parameters and their mutual sensitivities to guide co-design and quantify operational behavior; Legacy migration – ensuring seamless transition of legacy codes and programming methods to the future generation of ParalleX-based Exascale systems; . Experiments and evaluation – critical to determining degree of effectiveness and likelihood of ultimate success as well as guiding corrective design changes to achieve DOE objectives; and Applications – collaborations with Co-Design Centers and other mission critical codes. The exemplar implementation of the ParalleX execution model, HPX-5, has been released along with five fully ported applications (LULESH, HPCG, SSSP, WAMR, and DASHMM) and multiple microbenchmarks. Using these applications, the system architecture demonstrated dynamic load balancing through active migration, legacy code migration, and data-driven approaches to for graph-like applications. Crucially for Exascale and billion way parallelism, the needs and patterns of irregular applications in HPX-5 were addressed using local flow control rather than relying on globally synchronized data structures.

97 MATHEMATICS AND COMPUTING↗