Framework for Adaptable Operating and Runtime Systems: Final Project Report

In this grant, we examined a wide range of techniques for constructing high-performance con#12;gurable system software for HPC systems and its application to DOE-relevant problems. Overall, research and development on this project focused in three specifc areas: (1) software frameworks for constructing and deploying con#12;gurable system software, (2) applcation of these frameworks to HPC-oriented adaptable networking software, (3) performance analysis of HPC system software to understand opportunities for performance optimization

Measuring Thread Timing to Assess the Feasibility of Early-bird Message Delivery

Early-bird communication is a communication/computation overlap technique that combines fine-grained communication with partitioned communication to improve application run-time. Communication is divided among the compute threads such that each individual thread can initiate transmission of its portion of the data as soon as it is complete rather than waiting for all of the threads. However, the benefit of early-bird communication depends on the completion timing of the individual threads. In this paper, we measure and evaluate the potential overlap, the idle time each thread experiences between finishing their computation and the final thread finishing. These measurements help us understand whether a given application could benefit from early-bird communication. We present our technique for gathering this data and evaluate data collected from three proxy applications: MiniFE, MiniMD, and MiniQMC. To characterize the behavior of these workloads, we study the thread timings at both a macro level, i.e., across all threads across all runs of an application, and a micro level, i.e., within a single process of a single run. We observe that these applications exhibit significantly different behavior. While MiniFE and MiniQMC appear to be well-suited for early-bird communication because of their wider thread distribution and more frequent laggard threads, the behavior of MiniMD may limit its ability to leverage early-bird communication

The adenovirus E4-ORF3 protein stimulates SUMOylation of general transcription factor TFII-I to direct proteasomal degradation

Modulation of host cell transcription, translation, and posttranslational modification processes is critical for the ability of many viruses to replicate efficiently within host cells. The human adenovirus (Ad) early region 4 open reading frame 3 (E4-ORF3) protein forms unique inclusions throughout the nuclei of infected cells and inhibits the antiviral Mre11-Rad50-Nbs1 DNA repair complex through relocalization. E4-ORF3 also induces SUMOylation of Mre11 and Nbs1. We recently identified additional cellular targets of E4-ORF3 and found that E4-ORF3 stimulates ubiquitin-like modification of 41 cellular proteins involved in a wide variety of processes. Among the proteins most abundantly modified in an E4-ORF3-dependent manner was the general transcription factor II–I (TFII-I). Analysis of Ad-infected cells revealed that E4-ORF3 induces TFII-I relocalization and SUMOylation early during infection. In the present study, we explored the relationship between E4-ORF3 and TFII-I. We found that Ad infection or ectopic E4-ORF3 expression leads to SUMOylation of TFII-I that precedes a rapid decline in TFII-I protein levels. We also show that E4-ORF3 is required for ubiquitination of TFII-I and subsequent proteasomal degradation. This is the first evidence that E4-ORF3 regulates ubiquitination. Interestingly, we found that E4-ORF3 modulation of TFII-I occurs in diverse cell types but only E4-ORF3 of Ad species C regulates TFII-I, providing critical insight into the mechanism by which E4-ORF3 targets TFII-I. Finally, we show that E4-ORF3 stimulates the activity of a TFII-I-repressed viral promoter during infection. Our results characterize a novel mechanism of TFII-I regulation by Ad and highlight how a viral protein can modulate a critical cellular transcription factor during infection

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 appli- cation 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 rea

An examination of content similarity within the memory of HPC applications.

Memory content similarity has been e ectively exploited for more than a decade to reduce memory consumption. By consolidating duplicate and similar pages in the address space of an application, we can reduce the amount of memory it consumes without negatively a ecting the application's perception of the memory resources available to it. In addition to memory de-duplication, there may be many other ways that we can exploit memory content similarity to improve system characteristics. In this paper, we examine the memory content similarity of several HPC applications. By characterizing the memory contents of these applications, we hope to provide a basis for ef- forts to e ectively exploit memory content similarity to improve system performance beyond memory deduplication. We show that several applications exhibit signi cant similarity and consider the source of the similarity

Discovery of a Probable CH Star in the Globular Cluster M14 and Implications for the Evolution of Binaries in Clusters

We report the discovery of a probable CH star in the core of the Galactic globular cluster M14, identified from an integrated-light spectrum of the cluster obtained with the MOS spectrograph on the CFHT. From a high- resolution echelle spectrum of the same star obtained with the Hydra fiber positioner and bench spectrograph on the WIYN telescope, we measure a radial velocity of $-53.0\pm1.2$ km s$^{-1}$. Although this velocity is inconsistent with published estimates of the systemic radial velocity of M14 (eg, ${\bar {v_r}} \approx -123$ km s$^{-1}$), we use high-precision Hydra velocities for 20 stars in the central 2.6 arcminutes of M14 to calculate improved values for the cluster mean velocity and one-dimensional velocity dispersion: $-59.5\pm1.9$ km s$^{-1}$ and $8.2\pm1.4$ km s$^{-1}$, respectively. Both the star's location near the tip of the red giant branch in the cluster color magnitude diagram and its radial velocity therefore argue for membership in M14. Since the intermediate-resolution MOS spectrum shows not only enhanced CH absorption but also strong Swan bands of C$_2$, M14 joins Omega Cen as the only globular clusters known to contain classical CH stars. Although evidence for its duplicity must await additional radial velocity measurements, the CH star in M14 is probably, like all field CH stars, a spectroscopic binary with a degenerate (white dwarf) secondary. The candidate and confirmed CH stars in M14 and Omega Cen, and in a number of Galactic dSph galaxies, may then owe their existence to the long timescales for the shrinking and coalescence of hard binaries in low-concentration environments.Comment: Accepted to the Astrophysical Journal Letters. 13 pages, AAS LaTeX and three postscript figures (numbers 2,3,4). Entire paper (including Figure 1) available at http://www.hia.nrc.ca/DAO/SCIENCE/science.htm

Dynamics of the Globular Cluster System Associated with M87 (NGC 4486). II. Analysis

We present a dynamical analysis of the globular cluster system associated with M87 (= NGC 4486), the cD galaxy near the dynamical center of the Virgo cluster. The analysis utilizes a new spectroscopic and photometric database which is described in a companion paper (Hanes et al. 2001). Using a sample of 278 globular clusters with measured radial velocities and metallicities, and new surface density profiles based on wide-field Washington photometry, we study the dynamics of the M87 globular cluster system both globally --- for the entire cluster sample --- and separately --- for the metal-rich and metal-poor globular cluster samples. This constitutes the largest sample of radial velocities for pure Population II tracers yet assembled for any galaxy. We discuss the implications of our findings for models for the formation of giant elliptical galaxies, globular cluster systems, and the Virgo cluster. (ABRIDGED)Comment: 28 pages, 19 postscript figures, 1 jpeg image. See http://www.physics.rutgers.edu/ast/ast-rap.html to download the manuscript with higher quality figures. Accepted for publication in the Astrophysical Journa

Hubble Space Telescope Observations of cD Galaxies and their Globular Cluster Systems

We have used WFPC2 on the Hubble Space Telescope to obtain F450W and F814W images of four cD galaxies (NGC 541 in Abell 194, NGC 2832 in Abell 779, NGC 4839 in Abell 1656 and NGC 7768 in Abell 2666) in the range 5400 < cz < 8100 km s^{-1}. For NGC 541, the HST data are supplemented by ground-based B and I images obtained with the FORS1 on the VLT. We present surface brightness and color profiles for each of the four galaxies, confirming their classification as cD galaxies. Isophotal analyses reveal the presence of subarcsecond-scale dust disks in the nuclei of NGC 541 and NGC 7768. Despite the extreme nature of these galaxies in terms of spatial extent and luminosity, our analysis of their globular cluster systems reveals no anomalies in terms of specific frequencies, metallicity gradients, average metallicities, or the metallicity offset between the globulars and the host galaxy. We show that the latter offset appears roughly constant at \Delta [Fe/H] ~ 0.8 dex for early-type galaxies spanning a luminosity range of roughly four orders of magnitude. We combine the globular cluster metallicity distributions with an empirical technique described in a series of earlier papers to investigate the form of the protogalactic mass spectrum in these cD galaxies. We find that the observed GC metallicity distributions are consistent with those expected if cD galaxies form through the cannibalism of numerous galaxies and protogalactic fragments which formed their stars and globular clusters before capture and disruption. However, the properties of their GC systems suggest that dynamical friction is not the primary mechanism by which these galaxies are assembled. We argue that cDs instead form rapidly, via hierarchical merging, prior to cluster virialization.Comment: 36 pages, 20 postscript figures, uses emulateapj. Accepted for publication in the Astronomical Journa