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At least 1,765 records · Page 98

SMC 2021 : Analyzing Resource Utilization and User Behavior on Titan Supercomputer

Resource utilization statistics of submitted jobs on a supercomputer can help us understand how users from various scientific domains use HPC platforms and better design a job scheduler. We explore to generate insight regarding workload distribution and usage pattern domains from job scheduler trace, GPU failure information, and project-specific information collected from Titan supercomputer. Furthermore, we want to know how the scheduler performance varies over time and how the users' scheduling behavior changes following a system failure. These observations have the potential to provide valuable insight, which is helpful to prepare for system failures. These practices will help us develop and apply novel machine learning algorithms in understanding system behavior, requirement, and better scheduling of HPC systems. There are two datasets, RUR and GPU. RUR: This dataset is the job scheduler traces collected from the Titan supercomputerfrom 01/01/2015 to 07/31/2019 (2015.csv - 2019.csv). These were collected usingResource Utilization Report (RUR), a Cray-developed resource-usage data collectionand reporting system. It contains the usage information of its critical resources (CPU,Memory, GPU, and I/O) of each running job on Titan during that period [2]. ProjectAreas: Every job is associated with a project ID. TheProjectAreas.csvdatasetprovides a mapping of the project ID to its domain science. GPU: There have been some hardware-related issues in the GPUs in Titan that caused some GPUs to fail, sometimes irrecoverably during some job runs. This dataset provides information regarding these failures during the execution of the submitted jobs. GPUs on Titan are uniquely identified by a serial number (SN), and they are installed in a location. A GPU can be installed in a location, then removed from that location following a failure, and then re-installed in a different location after fixing the problem. If the failure can't be recovered, the GPU might be removed entirely from Titan. There are two prominent types of failures that resulted in the removal of GPUs from Titan: Double Bit Error (DBE) and Out of the Bus (OTB). The dataset (gc_full.csv) has the following fields: 1. SN : Serial number of a GPU 2. location : The location where it is installed 3. insert : The time when it was inserted into that location 4. remove : The time when it was removed from that location 5. duration : Amount of time the GPU spent in this location 6. out : If the device was taken out entirely w/o a re-installment into a new location. 7. event : If the GPU was taken out entirely, the reason for its removal. To learn more about this dataset, please refer to the git repositoryhttps://github.com/olcf/TitanGPULifeand the related publication [1]. References [1] George Ostrouchov, Don Maxwell, Rizwan A Ashraf, Christian Engelmann, MallikarjunShankar, and James H Rogers. Gpu lifetimes on titan supercomputer: Survival analysisand reliability. InSC20: International Conference for High Performance Computing,Networking, Storage and Analysis, pages 1-14. IEEE, 2020. [2] Feiyi Wang, Sarp Oral, Satyabrata Sen, and Neena Imam. Learning from five-yearresource-utilization data of titan system. In2019 IEEE International Conference onCluster Computing (CLUSTER), pages 1-6. IEEE, 2019.

42 ENGINEERING↗

Pellet cladding mechanical interaction as a potential failure mechanism during a control rod drop accident in a boiling water reactor

Boiling water reactors (BWRs) represent approximately one-third of the operating fleet in the United States, contributing significantly towards the global effort in reducing carbon emissions. Even though most of the operating fleet has been in operation for quite some time, continued advancements in new nuclear fuel (such as accident tolerant fuel) or operating regimes (such as power up-rates and higher burnup operation) necessitates similar advancements in modeling and simulation capabilities. Bison, a component of the Virtual Environment for Reactor Applications (VERA), is a high-fidelity fuel performance code able to explore the fuel performance of a wide variety of fuel types in one-, two-, and three-dimensions. Until recently, the code had not been used for analyses of BWRs. Modeling capabilities have been added for Gd-bearing UO{sub 2} and pure zirconium liners. New models have been added based upon the U.S. Nuclear Regulatory Commission (NRC) guide-lines for hydrogen pickup in Zircaloy-2 claddings and pellet-clad mechanical interaction (PCMI) failure during a reactivity insertion accident (RIA), known as a rod drop accident (CRDA) in BWRs. Implementing and/or improving Bison modeling capabilities extended its analytical reach to areas beyond its original intended purpose. This paper demonstrates one of these capabilities as a proof of concept. Recently developed models enable Bison to provide an alternate approach for cladding integrity determination in CRDA evaluations, which currently use bounding conservative estimates. As part of this demonstration, NRC guidance on hydrogen-pickup and PCMI failure models were utilized in this research. Even though more research is needed in establishing right inputs and process in this area, this paper demonstrates Bison's ability to determine cladding integrity in a CRDA evaluation. This first of a kind demonstration is a proof of concept in this area, which could potentially be extended to a number of other areas where a more accurate cladding integrity determination would be needed. (authors)

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

Racetrack resonator as a loss measurement platform for photonic components

This work represents the first complete analysis of the use of a racetrack resonator to measure the insertion loss of efficient, compact photonic components. Beginning with an in-depth analysis of potential error sources and a discussion of the calibration procedure, the technique is used to estimate the insertion loss of waveguide width tapers of varying geometry with a resulting 95% confidence interval of 0.007 dB. Furthermore, the work concludes with a performance comparison of the analyzed tapers with results presented for four taper profiles and three taper lengths.

47 OTHER INSTRUMENTATION↗

A nanosecond-scale shift-and-dump Mach-Zehnder switch

We present a Mach-Zehnder-based optical switch with novel electro-optic shift-and-dump phase shifters that have no residual amplitude modulation. As a result, the switch can have a very high extinction ratio with no overhead in power dissipation and insertion loss compared to standard electro-optic Mach-Zehnder switches. We fabricate the switch in an all-digital silicon photonic platform that monolithically integrates the actuation and control electronics together with the photonics. The switch demonstrates an extinction ratio > 33 dB, insertion loss < 1.2 dB, and nanosecond-scale transients.

42 ENGINEERING↗

Visible-telecom tunable dual-band optical isolator based on dynamic modulation in thin-film lithium niobate

Optical isolators are an essential component of photonic systems. Current integrated optical isolators have limited bandwidths due to stringent phase-matching conditions, resonant structures, or material absorption. Here, we demonstrate a wideband integrated optical isolator in thin-film lithium niobate photonics. We use dynamic standing-wave modulation in a tandem configuration to break Lorentz reciprocity and achieve isolation. We measure an isolation ratio of 15 dB and insertion loss below 0.5 dB for a continuous wave laser input at 1550 nm. In addition, we experimentally show that this isolator can simultaneously operate at visible and telecom wavelengths with comparable performance. Isolation bandwidths up to ∼100 nm can be achieved simultaneously at both visible and telecom wavelengths, limited only by the modulation bandwidth. Our device’s dual-band isolation, high flexibility, and real-time tunability can enable novel non-reciprocal functionality on integrated photonic platforms.

Shah, Manav↗

Study of impacts of two types of cellular aging on the yeast bud morphogenesis

Understanding the mechanisms of the cellular aging processes is crucial for attempting to extend organismal lifespan and for studying age-related degenerative diseases. Yeast cells divide through budding, providing a classical biological model for studying cellular aging. With their powerful genetics, relatively short cell cycle, and well-established signaling pathways also found in animals, yeast cells offer valuable insights into the aging process. Recent experiments suggested the existence of two aging modes in yeast characterized by nucleolar and mitochondrial declines, respectively. By analyzing experimental data, this study shows that cells evolving into those two aging modes behave differently when they are young. While buds grow linearly in both modes, cells that consistently generate spherical buds throughout their lifespan demonstrate greater efficacy in controlling bud size and growth rate at young ages. A three-dimensional multiscale chemical-mechanical model was developed and used to suggest and test hypothesized impacts of aging on bud morphogenesis. Experimentally calibrated model simulations showed that during the early stage of budding, tubular bud shape in one aging mode could be generated by locally inserting new materials at the bud tip, a process guided by the polarized Cdc42 signal. Furthermore, the aspect ratio of the tubular bud could be stabilized during the late stage as observed in experiments in this work. The model simulation results suggest that the localization of new cell surface material insertion, regulated by chemical signal polarization, could be weakened due to cellular aging in yeast and other cell types, leading to the change and stabilization of the bud aspect ratio.

Tsai, Kevin↗

Structural and Histone Binding Ability Characterizations of Human PWWP Domains

The PWWP domain was first identified as a structural motif of 100-130 amino acids in the WHSC1 protein and predicted to be a protein-protein interaction domain. It belongs to the Tudor domain 'Royal Family', which consists of Tudor, chromodomain, MBT and PWWP domains. While Tudor, chromodomain and MBT domains have long been known to bind methylated histones, PWWP was shown to exhibit histone binding ability only until recently. The PWWP domain has been shown to be a DNA binding domain, but sequence analysis and previous structural studies show that the PWWP domain exhibits significant similarity to other 'Royal Family' members, implying that the PWWP domain has the potential to bind histones. In order to further explore the function of the PWWP domain, we used the protein family approach to determine the crystal structures of the PWWP domains from seven different human proteins. Our fluorescence polarization binding studies show that PWWP domains have weak histone binding ability, which is also confirmed by our NMR titration experiments. Furthermore, we determined the crystal structures of the BRPF1 PWWP domain in complex with H3K36me3, and HDGF2 PWWP domain in complex with H3K79me3 and H4K20me3. PWWP proteins constitute a new family of methyl lysine histone binders. The PWWP domain consists of three motifs: a canonical {beta}-barrel core, an insertion motif between the second and third {beta}-strands and a C-terminal {alpha}-helix bundle. Both the canonical {beta}-barrel core and the insertion motif are directly involved in histone binding. The PWWP domain has been previously shown to be a DNA binding domain. Therefore, the PWWP domain exhibits dual functions: binding both DNA and methyllysine histones.

59 BASIC BIOLOGICAL SCIENCES↗

Targeting of Herpes Simplex Virus 1 Thymidine Kinase Gene Sequences into the OCT4 Locus of Human Induced Pluripotent Stem Cells

The in vitro differentiation of human induced pluripotent stem cells (hiPSC) to generate specific types of cells is inefficient, and the remaining undifferentiated cells may form teratomas. This raises safety concerns for clinical applications of hiPSC-derived cellular products. To improve the safety of hiPSC, we attempted to site-specifically insert a herpes simplex virus 1 thymidine kinase (HSV1-TK) suicide gene at the endogenous OCT4 (POU5F1) locus of hiPSC. Since the endogenous OCT4 promoter is active in undifferentiated cells only, we speculated that the HSV1-TK suicide gene will be transcribed in undifferentiated cells only and that the remaining undifferentiated cells can be depleted by treating them with the prodrug ganciclovir (GCV) prior to transplantation. To insert the HSV1-TK gene at the OCT4 locus, we cotransfected hiPSC with a pair of plasmids encoding an OCT4-specific zinc finger nuclease (ZFN) and a donor plasmid harboring a promoter-less transgene cassette consisting of HSV1-TK and puromycin resistance gene sequences, flanked by OCT4 gene sequences. Puromycin resistant clones were established and characterized regarding their sensitivity to GCV and the site of integration of the HSV1-TK/puromycin resistance gene cassette. Of the nine puromycin-resistant iPSC clones analyzed, three contained the HSV1-TK transgene at the OCT4 locus, but they were not sensitive to GCV. The other six clones were GCV-sensitive, but the TK gene was located at off-target sites. These TK-expressing hiPSC clones remained GCV sensitive for up to 90 days, indicating that TK transgene expression was stable. Possible reasons for our failed attempt to selectively target the OCT4 locus are discussed.

59 BASIC BIOLOGICAL SCIENCES↗

Discovery of an Inhibitor of Z-Alpha1 Antitrypsin Polymerization

Polymerization of the Z variant alpha-1-antitrypsin (Z-α1AT) results in the most common and severe form of α1AT deficiency (α1ATD), a debilitating genetic disorder whose clinical manifestations range from asymptomatic to fatal liver and/or lung disease. As the altered conformation of Z-α1AT and its attendant aggregation are responsible for pathogenesis, the polymerization process per se has become a major target for the development of therapeutics. Based on the ability of Z-alpha 1AT to aggregate by recruiting the reactive center loop (RCL) of another Z-α1AT into its s4A cavity, we developed a high-throughput screening assay that uses a modified 6-mer peptide mimicking the RCL to screen for inhibitors of Z-α1AT polymer growth. We used a subset of compounds from the Library of Pharmacologically Active Compounds (LOPAC) with molecular weights ranging from 300 to 700 Da, to evaluate the assay's capabilities. The inhibitor S-(4-nitrobenzyl)-6-thioguanosine was identified as a lead compound and its ability to prevent Z-α1AT polymerization confirmed by secondary assays. In order to further investigate the binding location of S-(4-nitrobenzyl)-6-thioguanosine, an in silico strategy was pursued and the intermediate alpha 1AT M* state modeled to allow molecular docking simulations and explore various potential binding sites. Docking results predict that S-(4-nitrobenzyl)-6-thioguanosine can bind at the s4A cavity and at the edge of beta-sheet A. The former binding site would directly block RCL insertion whereas the latter site would prevent beta-sheet A from expanding between s3A/s5A, and thus indirectly impede RCL insertion. Our investigations have revealed a novel compound that inhibits the formation of Z-α1AT polymers, as well as in vitro and in silico strategies for identifying and characterizing additional blocking molecules of Z-α1AT polymerization.

59 BASIC BIOLOGICAL SCIENCES↗

Structure of the T. brucei kinetoplastid RNA editing substrate-binding complex core component, RESC5

Kinetoplastid protists such as Trypanosoma brucei undergo an unusual process of mitochondrial uridine (U) insertion and deletion editing termed kinetoplastid RNA editing (kRNA editing). This extensive form of editing, which is mediated by guide RNAs (gRNAs), can involve the insertion of hundreds of Us and deletion of tens of Us to form a functional mitochondrial mRNA transcript. kRNA editing is catalyzed by the 20 S editosome/RECC. However, gRNA directed, processive editing requires the RNA editing substrate binding complex (RESC), which is comprised of 6 core proteins, RESC1-RESC6. To date there are no structures of RESC proteins or complexes and because RESC proteins show no homology to proteins of known structure, their molecular architecture remains unknown. RESC5 is a key core component in forming the foundation of the RESC complex. To gain insight into the RESC5 protein we performed biochemical and structural studies. We show that RESC5 is monomeric and we report the T . brucei RESC5 crystal structure to 1.95 Å. RESC5 harbors a dimethylarginine dimethylaminohydrolase-like (DDAH) fold. DDAH enzymes hydrolyze methylated arginine residues produced during protein degradation. However, RESC5 is missing two key catalytic DDAH residues and does bind DDAH substrate or product. Implications of the fold for RESC5 function are discussed. This structure provides the first structural view of an RESC protein.

59 BASIC BIOLOGICAL SCIENCES↗

Initiation of RNA Polymerization and Polymerase Encapsidation by a Small dsRNA Virus

During the replication cycle of double-stranded (ds) RNA viruses, the viral RNA-dependent RNA polymerase (RdRP) replicates and transcribes the viral genome from within the viral capsid. How the RdRP molecules are packaged within the virion and how they function within the confines of an intact capsid are intriguing questions with answers that most likely vary across the different dsRNA virus families. In this study, we have determined a 2.4 Å resolution structure of an RdRP from the human picobirnavirus (hPBV). In addition to the conserved polymerase fold, the hPBV RdRP possesses a highly flexible 24 amino acid loop structure located near the C-terminus of the protein that is inserted into its active site. In vitro RNA polymerization assays and site-directed mutagenesis showed that: (1) the hPBV RdRP is fully active using both ssRNA and dsRNA templates; (2) the insertion loop likely functions as an assembly platform for the priming nucleotide to allow de novo initiation; (3) RNA transcription by the hPBV RdRP proceeds in a semi-conservative manner; and (4) the preference of virus-specific RNA during transcription is dictated by the lower melting temperature associated with the terminal sequences. Co-expression of the hPBV RdRP and the capsid protein (CP) indicated that, under the conditions used, the RdRP could not be incorporated into the recombinant capsids in the absence of the viral genome. Additionally, the hPBV RdRP exhibited higher affinity towards the conserved 5’-terminal sequence of the viral RNA, suggesting that the RdRP molecules may be encapsidated through their specific binding to the viral RNAs during assembly.

59 BASIC BIOLOGICAL SCIENCES↗

Online multi-objective Bayesian optimization of injection efficiency and beam lifetime with skew quadrupoles at NSLS-II

At NSLS-II, the vertical emittance of electron beam is typically blown up to ~30 pm with a coupling wave to increase beam lifetime during user operation. As more and more insertion devices are added to the storage ring, injection efficiency to the ring drops noticeably in certain machine states, apparently due to degraded dynamic apertures. To help alleviate this issue, we have recently performed online multi-objective Bayesian optimization to increase injection efficiency while maintaining beam lifetime, by adjusting the strengths of 15 skew quadrupoles in non-dispersive sections. We report the results of this optimization effort.

Hidaka, Yoshiteru [Brookhaven]↗

Spatially Resolved Elemental Analysis, Spectroscopy and Diffraction at the GSECARS Sector at the Advanced Photon Source

X‐ray microprobes (XRM) coupled with high‐brightness synchrotron X‐ray facilities are powerful tools for environmental biogeochemistry research. One such instrument, the XRM at the Geo Soil Enviro Center for Advanced Radiation Sources Sector 13 at the Advanced Photon Source (APS; Argonne National Laboratory, Lemont, IL) was recently improved as part of a canted undulator geometry upgrade of the insertion device port, effectively doubling the available undulator beam time and extending the operating energy of the branch supporting the XRM down to the sulfur K edge (2.3 keV). Capabilities include rapid, high‐resolution, elemental imaging including fluorescence microtomography, microscale X‐ray absorption fine structure spectroscopy including sulfur K edge capability, and microscale X‐ray diffraction. These capabilities are advantageous for (i) two‐dimensional elemental mapping of relatively large samples at high resolution, with the dwell times typically limited only by the count times needed to obtain usable counting statistics for low concentration elements, (ii) three‐dimensional imaging of internal elemental distributions in fragile hydrated specimens, such as biological tissues, avoiding the need for physical slicing, (iii) spatially resolved speciation determinations of contaminants in environmental materials, and (iv) identification of contaminant host phases. In this paper, we describe the XRM instrumentation, techniques, applications demonstrating these capabilities, and prospects for further improvements associated with the proposed upgrade of the APS. Core Ideas X‐ray microprobes are powerful tools for environmental biogeochemistry. Upgraded GSECARS XRM operates down to the sulfur K edge. Capabilities: spatially resolved elemental analysis, spectroscopy, and diffraction. Advanced Photon Source upgrade will further advance XRM capabilities.

Sutton, Stephen R.↗

Connected and Disconnected Sea Partons from CT18 Parametrization of PDFs

The separation of the connected and disconnected sea partons, which were uncovered in the Euclidean path-integral formulation of the hadronic tensor, is accommodated with the CT18 parametrization of the global analysis of the parton distribution functions (PDFs). This is achieved with the help of the distinct small x x behaviors of these two sea parton components and the constraint from the lattice calculation of the ratio of the strange momentum fraction to that of the {\bar u} u ‾ or {\bar d} d ‾ in the disconnected insertion. This allows lattice calculations of separate flavors in both the connected and disconnected insertions to be directly compared with the global analysis results term by term.

Hou, Tie-Jiun↗

Characterization of Energy Savings and Thermal Comfort Improvements Derived from Using Interior Storm Windows

This field study of a single historic home in Seattle, WA documents the performance of Indow ® Windows’s interior storm window inserts. Energy use and the temperature profile of the house were monitored before and after the installation of the window inserts and changes in the two recorded metrics were examined. Using the defined analysis approach, it was determined that the interior storm windows produced a 22% reduction of the HVAC energy bill and had an undetermined effect on the thermal comfort in the house. Although there was no measurable changes in the thermal comfort of the house, the occupant noted the house to be “warmer in the winter and cooler in the summer” and that the “temperatures are more even (throughout the house).” The interior storm windows were found to be not cost effective, largely due to the retrofits completed on its heating system. However, if the economic analysis was conducted based on the old heating system, a 72% efficient oil fired furnace, the Indow Windows proved to be economical and had a simple payback period of 9.0 years.

high performance housing↗

Institute for High Heat Flux Removal (IHHFR). Phases I, II, and III

The IHHFR focused on interdisciplinary applications as it relates to high heat flux engineering issues and problems which arise due to engineering systems being miniaturized, optimized, or requiring increased high heat flux performance. The work in the IHHFR focused on water as a coolant and includes: (1) the development, design, and construction of the high heat flux flow loop and facility; (2) test section development, design, and fabrication; and, (3) single-side heat flux experiments to produce 2-D boiling curves and 3-D conjugate heat transfer measurements for single-side heated test sections. This work provides data for comparisons with previously developed and new single-side heated correlations and approaches that address the single-side heated effect on heat transfer. In addition, this work includes the addition of single-side heated circular TS and a monoblock test section with a helical wire insert. Finally, the present work includes: (1) data base expansion for the monoblock with a helical wire insert (only for the latter geometry), (2) prediction and verification using finite element, (3) monoblock model and methodology development analyses, and (4) an alternate model development for a hypervapotron and related conjugate heat transfer controlling parameters.

2-D Boiling Curves↗

HFIR Dissolution Nuclear Criticality Analysis Information

The purpose of this analysis is to demonstrate the safety of High Flux Isotope Reactor (HFIR) dissolution from a criticality safety perspective and to establish any Criticality Safety Limits (CSLs) that may be necessary. HFIR fuel consists of two annular elements that are designed to be nested together with a beryllium reflector in the reactor configuration. HFIR cores are currently stored in L-Area as separate inner elements and outer elements, each on a unique aluminum carrier. HFIR elements will be shipped to H-Canyon in the 70-ton Cask Railcar and loaded into the dissolver with the HFIR insert installed. The HFIR insert consists of a small well for the inner fuel element and a large well for the outer fuel element.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Helical muon beam cooling channel engineering design

The Helical Cooling Channel (HCC) achieves effective ionization cooling of the six-dimensional (6d) phase space of a muon beam by means of a series of 21st century inventions. In the HCC, hydrogen-pressurized RF cavities enable high RF gradients in strong external magnetic fields. The theory of the HCC, which requires a magnetic field with solenoid, helical dipole, and helical quadrupole components, demonstrates that dispersion in the gaseous hydrogen energy absorber provides effective emittance exchange to enable longitudinal ionization cooling. The 10-year development of a practical implementation of a muon-beam cooling device has involved a series of technical innovations and experiments that imply that an HCC of less than 300 m length can cool the 6d emittance of a muon beam by six orders of magnitude. We describe the design and construction plans for a prototype HCC module based on oxygen-doped hydrogen-pressurized RF cavities that are loaded with dielectric, fed by magnetrons, and operate in a superconducting helical solenoid magnet. The first phase of this project saw the development of a conceptual design for the integration of 805 MHz RF cavities into a 10 T Nb 3 Sn-based HS test section. Two very novel ideas are required to realize the design. The first idea is the use of dielectric inserts in the RF cavities to make them smaller for a given frequency so that the cavities and associated plumbing easily fit inside the magnet cryostat. Calculations indicate that heat loads will be tolerable, while RF breakdown of the dielectric inserts will be suppressed by the pressurized hydrogen gas. The second new idea is the use of a multi-layer Nb 3 Sn helical solenoid. The technology demonstrations for the two aforementioned key components of a 10T, 805 MHz HCC were begun in this project. The work load in the Fermilab Technical Division made it difficult to test a multi-layer Nb 3 Sn solenoid as originally planned. Instead, a complementary project was approved by the DOE Technical Topic Manager to develop magnets for the Mu2e experiment that fit well into the Fermilab Technical Division availability. The difference between the MCC helical solenoid and the Mu2e bent solenoid described in Appendix I is that the helical solenoid is made of coils that are in parallel planes with offset centers, while the coils in the bent solenoid follow the central particle trajectory and look much like a “slinky” toy. The muon-beam cooling-channel technologies developed in this project will enable a muon collider, the next step toward the energy frontier, Higgs/neutrino/Z-factories, and rare muon decay experiments. Commercial uses of the beams made possible by the cooling techniques developed in this project include scanning for nuclear contraband, studies of material properties with spin resonance techniques, and muon-catalyzed fusion.

43 PARTICLE ACCELERATORS↗