Leveraging OpenStack and Ceph for a Controlled-Access Data Cloud

While traditional HPC has and continues to satisfy most workflows, a new generation of researchers has emerged looking for sophisticated, scalable, on-demand, and self-service control of compute infrastructure in a cloud-like environment. Many also seek safe harbors to operate on or store sensitive and/or controlled-access data in a high capacity environment. To cater to these modern users, the Minnesota Supercomputing Institute designed and deployed Stratus, a locally-hosted cloud environment powered by the OpenStack platform, and backed by Ceph storage. The subscription-based service complements existing HPC systems by satisfying the following unmet needs of our users: a) on-demand availability of compute resources, b) long-running jobs (i.e., $> 30$ days), c) container-based computing with Docker, and d) adequate security controls to comply with controlled-access data requirements. This document provides an in-depth look at the design of Stratus with respect to security and compliance with the NIH's controlled-access data policy. Emphasis is placed on lessons learned while integrating OpenStack and Ceph features into a so-called "walled garden", and how those technologies influenced the security design. Many features of Stratus, including tiered secure storage with the introduction of a controlled-access data "cache", fault-tolerant live-migrations, and fully integrated two-factor authentication, depend on recent OpenStack and Ceph features.Comment: 7 pages, 5 figures, PEARC '18: Practice and Experience in Advanced Research Computing, July 22--26, 2018, Pittsburgh, PA, US

Contrasting local and long-range-transported warm ice-nucleating particles during an atmospheric river in coastal California, USA

Ice-nucleating particles (INPs) have been found to influence the amount, phase and efficiency of precipitation from winter storms, including atmospheric rivers.Warm INPs, those that initiate freezing at temperatures warmer than -10°C, are thought to be particularly impactful because they can create primary ice in mixed-phase clouds, enhancing precipitation efficiency. The dominant sources of warm INPs during atmospheric rivers, the role of meteorology in modulating transport and injection of warm INPs into atmospheric river clouds, and the impact of warm INPs on mixed-phase cloud properties are not well-understood. In this case study, time-resolved precipitation samples were collected during an atmospheric river in northern California, USA, during winter 2016. Precipitation samples were collected at two sites, one coastal and one inland, which are separated by about 35 km. The sites are sufficiently close that air mass sources during this storm were almost identical, but the inland site was exposed to terrestrial sources of warm INPs while the coastal site was not. Warm INPs were more numerous in precipitation at the inland site by an order of magnitude. Using FLEXPART (FLEXible PARTicle dispersion model) dispersion modeling and radar-derived cloud vertical structure, we detected influence from terrestrial INP sources at the inland site but did not find clear evidence of marine warm INPs at either site.We episodically detected warm INPs from long-range-transported sources at both sites. By extending the FLEXPART modeling using a meteorological reanalysis, we demonstrate that long-range-transported warm INPs were observed only when the upper tropospheric jet provided transport to cloud tops. Using radar-derived hydrometeor classifications, we demonstrate that hydrometeors over the terrestrially influenced inland site were more likely to be in the ice phase for cloud temperatures between 0 and -10°C. We thus conclude that terrestrial and long-rangetransported aerosol were important sources of warm INPs during this atmospheric river. Meteorological details such as transport mechanism and cloud structure were important in determining (i) warm INP source and injection temperature and (ii) ultimately the impact of warm INPs on mixed-phase cloud properties

Descriptive Complexity of Deterministic Polylogarithmic Time and Space

We propose logical characterizations of problems solvable in deterministic polylogarithmic time (PolylogTime) and polylogarithmic space (PolylogSpace). We introduce a novel two-sorted logic that separates the elements of the input domain from the bit positions needed to address these elements. We prove that the inflationary and partial fixed point vartiants of this logic capture PolylogTime and PolylogSpace, respectively. In the course of proving that our logic indeed captures PolylogTime on finite ordered structures, we introduce a variant of random-access Turing machines that can access the relations and functions of a structure directly. We investigate whether an explicit predicate for the ordering of the domain is needed in our PolylogTime logic. Finally, we present the open problem of finding an exact characterization of order-invariant queries in PolylogTime.Comment: Submitted to the Journal of Computer and System Science

Terrigenous Fe input and biogenic sedimentation in the glacial and interglacial equatorial Pacific Ocean

Many ocean regions important to the global carbon budget, including the equatorial Pacific Ocean, have low chlorophyll concentrations despite high levels of conventional nutrients. Iron may instead be the limiting nutrient, and elevated input of terrigenous Fe during windy glacial episodes has been hypothesized to stimulate oceanic productivity through time and thus regulate the oceanic and atmospheric CO2 balance. To test whether particulate Fe input is related to the accumulation of biogenic matter in one important low chlorophyll‐high nutrient area, that is, the equatorial Pacific Ocean, we present results from a suite of sediment cores that collectively record biogenic deposition through the last six glacial‐interglacial cycles (∼600,000 years). Our data set includes new chemical data on total Fe, terrigenous, and biogenic components in three cores as well as previously published mineralogic records of eolian input to the region. Chemical, spectral, and stratigraphic analysis indicates that (1) terrigenous input to the region shows no consistent pattern of either glacial or interglacial maxima, (2) the accumulation of particulate Fe is closely related to the accumulation of terrigenous matter (linear r2 = 0.81–0.98), (3) there are no coherent spectral relationships between Fe input and glacial periodicity (i.e., δ18O) in any of the orbital frequency bands, (4) the linear and cross‐spectral correlations between Fe or eolian input and CaCO3 concentration are most commonly the strongest observed relationships between Fe and any biogenic component, yet indicate a largely inverse pattern, with higher Fe being associated with low CaCO3, (5) there is no consistent linear r2 correlation or spectral coherence between the accumulation of Fe and that of CaCO3, Corg, or opal. Thus in total there is no relationship between terrigenous Fe input and sedimentary sequestering of carbon. Additionally, although we cannot specifically address the potential for changes in solubility of the terrigenous fraction that may be driven by a terrigenous compositional change, the Fe/Ti ratio (which monitors first‐order mineralogic changes) records only slight variations that also are linearly and spectrally unrelated to glacial periodicity, the bulk Fe flux, and the accumulation of any biogenic component. Finally, we find that the paleoceanographic flux of Fe is several order‐of‐magnitudes larger than modern observations of eolian Fe input, suggesting that the long‐term importance of Fe input by dust storms (which deliver Fe on the order of the sedimentary burial) may be underestimated. The removal of particulate terrigenous Fe from the recently discovered source within the Equatorial Undercurrent, however, remains unquantified and may also prove significant

PD-0283: 4D dose accumulation for dose painting by numbers for lung cancer

In conventional radiotherapy of locally advanced lung cancer (LALC) doses levels are homogeneously delivered to the entire PTV, whereat dose escalation is restricted by normal tissue toxicity. Several studies have shown the geometrical correlation between high FDG uptake in a PET scan and tumour recurrence. This is the rationale for FDG-based local dose escalation, e.g. by dose prescription on the voxel values of a PET scan – dose painting by numbers (DPBN). The aim of this study is to investigate the robustness of the DPBN plans against tumour motio

Testing the effects of tropical temperature, productivity, and mixed-layer depth on foraminiferal transfer functions

Statistical transfer functions relate living planktonic foraminiferal species of the central equatorial Pacific to measured sea surfce temperature, integrated primary productivity, and mixed-layer depth. The faunal estimates successfully reconstruct latitudinal patterns observed in both warm (El Niño, February-March 1992) and cool (La Niña, August-September 1992) seasonal settings. Predictions of mixed-layer depth appear to be unbiased by temperature or productivity in our data set but tend to underestimate deep mixed layers. Interactions between productivity and temperature, perhaps through their common influence on respiration and growth rates, bias foraminiferal transfer functions for both properties. Paleoceanographic estimates may be improved by accounting for such biological processes that translate the environment into a faunal response preserved in the geologic record