From Bare Metal to Virtual: Lessons Learned when a Supercomputing Institute Deploys its First Cloud

As primary provider for research computing services at the University of Minnesota, the Minnesota Supercomputing Institute (MSI) has long been responsible for serving the needs of a user-base numbering in the thousands. In recent years, MSI---like many other HPC centers---has observed a growing need for self-service, on-demand, data-intensive research, as well as the emergence of many new controlled-access datasets for research purposes. In light of this, MSI constructed a new on-premise cloud service, named Stratus, which is architected from the ground up to easily satisfy data-use agreements and fill four gaps left by traditional HPC. The resulting OpenStack cloud, constructed from HPC-specific compute nodes and backed by Ceph storage, is designed to fully comply with controls set forth by the NIH Genomic Data Sharing Policy. Herein, we present twelve lessons learned during the ambitious sprint to take Stratus from inception and into production in less than 18 months. Important, and often overlooked, components of this timeline included the development of new leadership roles, staff and user training, and user support documentation. Along the way, the lessons learned extended well beyond the technical challenges often associated with acquiring, configuring, and maintaining large-scale systems.Comment: 8 pages, 5 figures, PEARC '18: Practice and Experience in Advanced Research Computing, July 22--26, 2018, Pittsburgh, PA, US

Nimodipine vs. Milrinone – Equal or Complementary Use? A Retrospective Analysis

Background: Cerebral vasospasm (CVS) continues to account for high morbidity and mortality in patients surviving the initial aneurysmal subarachnoid hemorrhage (SAH). Nimodipine is the only drug known to reduce delayed cerebral ischemia (DCI), but it is believed not to affect large vessel CVS. Milrinone has emerged as a promising option. Our retrospective study focused on the effectiveness of the intra-arterial application of both drugs in monotherapy and combined therapy. Methods: We searched for patients with aneurysmal SAH, angiographically confirmed CVS, and at least one intra-arterial pharmacological angioplasty. Ten defined vessel sections on angiograms were assessed before and after vasodilator infusion. The improvement in vessel diameters was compared to the frequency of DCI-related cerebral infarction before hospital discharge and functional outcome reported as the modified Rankin Scale (mRS) score after 6 months. Results: Between 2014 and 2021, 132 intra-arterial interventions (144 vascular territories, 12 bilaterally) in 30 patients were analyzed for this study. The vasodilating effect of nimodipine was superior to milrinone in all intradural segments. There was no significant intergroup difference concerning outcome in mRS (p = 0.217). Only nimodipine or the combined approach could prevent DCI-related infarction (both 57.1%), not milrinone alone (87.5%). Both drugs induced a doubled vasopressor demand due to blood pressure decrease, but milrinone alone induced tachycardia. Conclusions: The monotherapy with intra-arterial nimodipine was superior to milrinone. Nimodipine and milrinone may be used complementary in an escalation scheme with the administration of nimodipine first, complemented by milrinone in cases of severe CVS. Milrinone monotherapy is not recommended

Code Vectors: Understanding Programs Through Embedded Abstracted Symbolic Traces

With the rise of machine learning, there is a great deal of interest in treating programs as data to be fed to learning algorithms. However, programs do not start off in a form that is immediately amenable to most off-the-shelf learning techniques. Instead, it is necessary to transform the program to a suitable representation before a learning technique can be applied. In this paper, we use abstractions of traces obtained from symbolic execution of a program as a representation for learning word embeddings. We trained a variety of word embeddings under hundreds of parameterizations, and evaluated each learned embedding on a suite of different tasks. In our evaluation, we obtain 93% top-1 accuracy on a benchmark consisting of over 19,000 API-usage analogies extracted from the Linux kernel. In addition, we show that embeddings learned from (mainly) semantic abstractions provide nearly triple the accuracy of those learned from (mainly) syntactic abstractions

Electron-Positron Pair Production in Relativistic Heavy Ion Collisions

In recent years, a large number of papers have appeared that dealt with \EPEM pair production in heavy ion collisions at high energies. To a large extent these studies were motivated by the existence of relativistic heavy ion accelerators all over the world. There pair production can be studied in so called ``ultra-peripheral collisions'', where the ions do not come close enough to interact strongly with each other. Various different methods have been used and it is the purpose of this review to present a unified picture of the present status of the field.Comment: 51 pages, 16 figures, submitted to Physics Report

Postglacial species arrival and diversity buildup of northern ecosystems took millennia

What drives ecosystem buildup, diversity, and stability? We assess species arrival and ecosystem changes across 16 millennia by combining regional-scale plant sedimentary ancient DNA from Fennoscandia with near-complete DNA and trait databases. We show that postglacial arrival time varies within and between plant growth forms. Further, arrival times were mainly predicted by adaptation to temperature, disturbance, and light. Major break points in ecological trait diversity were seen between 13.9 and 10.8 calibrated thousand years before the present (cal ka BP), as well as break point in functional diversity at 12.0 cal ka BP, shifting from a state of ecosystem buildup to a state where most habitat types and biotic ecosystem components were in place. Trait and functional diversity stabilized around 8 cal ka BP, after which both remained stable, although changes in climate took place and species inflow continued. Our ecosystem reconstruction indicates a millennial-scale time phase of formation to reach stable and resilient levels of diversity and functioning.publishedVersio

The first determination of Generalized Polarizabilities of the proton by a Virtual Compton Scattering experiment

Absolute differential cross sections for the reaction (e+p -> e+p+gamma) have been measured at a four-momentum transfer with virtuality Q^2=0.33 GeV^2 and polarization \epsilon = 0.62 in the range 33.6 to 111.5 MeV/c for the momentum of the outgoing photon in the photon-proton center of mass frame. The experiment has been performed with the high resolution spectrometers at the Mainz Microtron MAMI. From the photon angular distributions, two structure functions which are a linear combination of the generalized polarizabilities have been determined for the first time.Comment: 4 pages, 3 figure