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

4.45 Pflops Astrophysical N-Body Simulation on K computer -- The Gravitational Trillion-Body Problem

As an entry for the 2012 Gordon-Bell performance prize, we report performance results of astrophysical N-body simulations of one trillion particles performed on the full system of K computer. This is the first gravitational trillion-body simulation in the world. We describe the scientific motivation, the numerical algorithm, the parallelization strategy, and the performance analysis. Unlike many previous Gordon-Bell prize winners that used the tree algorithm for astrophysical N-body simulations, we used the hybrid TreePM method, for similar level of accuracy in which the short-range force is calculated by the tree algorithm, and the long-range force is solved by the particle-mesh algorithm. We developed a highly-tuned gravity kernel for short-range forces, and a novel communication algorithm for long-range forces. The average performance on 24576 and 82944 nodes of K computer are 1.53 and 4.45 Pflops, which correspond to 49% and 42% of the peak speed.Comment: 10 pages, 6 figures, Proceedings of Supercomputing 2012 (http://sc12.supercomputing.org/), Gordon Bell Prize Winner. Additional information is http://www.ccs.tsukuba.ac.jp/CCS/eng/gbp201

2HOT: An Improved Parallel Hashed Oct-Tree N-Body Algorithm for Cosmological Simulation

We report on improvements made over the past two decades to our adaptive treecode N-body method (HOT). A mathematical and computational approach to the cosmological N-body problem is described, with performance and scalability measured up to 256k ($2^{18}$) processors. We present error analysis and scientific application results from a series of more than ten 69 billion ($4096^3$) particle cosmological simulations, accounting for $4 \times 10^{20}$ floating point operations. These results include the first simulations using the new constraints on the standard model of cosmology from the Planck satellite. Our simulations set a new standard for accuracy and scientific throughput, while meeting or exceeding the computational efficiency of the latest generation of hybrid TreePM N-body methods.Comment: 12 pages, 8 figures, 77 references; To appear in Proceedings of SC '1

Enhancing speed and scalability of the ParFlow simulation code

Regional hydrology studies are often supported by high resolution simulations of subsurface flow that require expensive and extensive computations. Efficient usage of the latest high performance parallel computing systems becomes a necessity. The simulation software ParFlow has been demonstrated to meet this requirement and shown to have excellent solver scalability for up to 16,384 processes. In the present work we show that the code requires further enhancements in order to fully take advantage of current petascale machines. We identify ParFlow's way of parallelization of the computational mesh as a central bottleneck. We propose to reorganize this subsystem using fast mesh partition algorithms provided by the parallel adaptive mesh refinement library p4est. We realize this in a minimally invasive manner by modifying selected parts of the code to reinterpret the existing mesh data structures. We evaluate the scaling performance of the modified version of ParFlow, demonstrating good weak and strong scaling up to 458k cores of the Juqueen supercomputer, and test an example application at large scale.Comment: The final publication is available at link.springer.co

Meson-meson scattering lengths at maximum isospin from lattice QCD

We summarize our lattice QCD determinations of the pion-pion, pion-kaon and kaon-kaon s-wave scattering lengths at maximal isospin with a particular focus on the extrapolation to the physical point and the usage of next-to-leading order chiral perturbation theory to do so. We employ data at three values of the lattice spacing and pion masses ranging from around 230 MeV to around 450 MeV, applying Luescher's finite volume method to compute the scattering lengths. We find that leading order chiral perturbation theory is surprisingly close to our data even in the kaon-kaon case for our entire range of pion masses.Comment: 10 pages, 8 figures, Presented at the 9th International Workshop on Chiral Dynamics, Sept. 17-21, 2018, Duke University, Durham, NC, USA , submitted to PoS, (C18-09-17.6). Funding acknowledgements added in v2 replacement, comma added in abstract. In v3 replacement, corrected typo in equation 6.2 which was referring to the pion-kaon reduced mass instead of the pion mas

Analyzing and Modeling the Performance of the HemeLB Lattice-Boltzmann Simulation Environment

We investigate the performance of the HemeLB lattice-Boltzmann simulator for cerebrovascular blood flow, aimed at providing timely and clinically relevant assistance to neurosurgeons. HemeLB is optimised for sparse geometries, supports interactive use, and scales well to 32,768 cores for problems with ~81 million lattice sites. We obtain a maximum performance of 29.5 billion site updates per second, with only an 11% slowdown for highly sparse problems (5% fluid fraction). We present steering and visualisation performance measurements and provide a model which allows users to predict the performance, thereby determining how to run simulations with maximum accuracy within time constraints.Comment: Accepted by the Journal of Computational Science. 33 pages, 16 figures, 7 table

Performance and Power Analysis of HPC Workloads on Heterogenous Multi-Node Clusters

Performance analysis tools allow application developers to identify and characterize the inefficiencies that cause performance degradation in their codes, allowing for application optimizations. Due to the increasing interest in the High Performance Computing (HPC) community towards energy-efficiency issues, it is of paramount importance to be able to correlate performance and power figures within the same profiling and analysis tools. For this reason, we present a performance and energy-efficiency study aimed at demonstrating how a single tool can be used to collect most of the relevant metrics. In particular, we show how the same analysis techniques can be applicable on different architectures, analyzing the same HPC application on a high-end and a low-power cluster. The former cluster embeds Intel Haswell CPUs and NVIDIA K80 GPUs, while the latter is made up of NVIDIA Jetson TX1 boards, each hosting an Arm Cortex-A57 CPU and an NVIDIA Tegra X1 Maxwell GPU.The research leading to these results has received funding from the European Community’s Seventh Framework Programme [FP7/2007-2013] and Horizon 2020 under the Mont-Blanc projects [17], grant agreements n. 288777, 610402 and 671697. E.C. was partially founded by “Contributo 5 per mille assegnato all’Università degli Studi di Ferrara-dichiarazione dei redditi dell’anno 2014”. We thank the University of Ferrara and INFN Ferrara for the access to the COKA Cluster. We warmly thank the BSC tools group, supporting us for the smooth integration and test of our setup within Extrae and Paraver.Peer ReviewedPostprint (published version

Atmospheric dispersion of airborne pollen evidenced by near-surface and columnar measurements in Barcelona, Spain

Hourly measurements of pollen near-surface concentration and lidar-derived profiles of particle backscatter coefficients and of volume and particle depolarization ratios during a 5-day pollination event observed in Barcelona, Spain, between 27 – 31 March, 2015, are presented. Maximum hourly pollen concentrations of 4700 and 1200 m-3 h-1 were found for Platanus and Pinus, respectively, which represented together more than 80 % of the total pollen. Everyday a clear diurnal cycle caused by the vertical transport of the airborne pollen was visible on the lidar-derived profiles of the backscatter coefficient with maxima usually reached between 12 and 15 UT. A method based on the lidar polarization capabilities was used to retrieve the contribution of the pollen to the total signal. On average the diurnal (9 – 17 UT) pollen aerosol optical depth (AOD) was 0.05 which represented 29 % of the total AOD, the volume and particle depolarization ratios in the pollen plume were 0.08 and 0.14, respectively, and the diurnal mean of the height of the pollen plume was found at 1.24 km. The dispersion of the Platanus and Pinus in the atmosphere was simulated with the Nonhydrostatic Multiscale Meteorological Model on the B grid at the Barcelona Supercomputing Center with a newly developed Chemical Transport Model (NMMB/BSC-CTM). Model near-surface daily concentrations were compared to our observations at two sites: in Barcelona and Bellaterra (12 km NE of Barcelona). Model hourly concentrations were compared to our observations in Barcelona.Peer ReviewedPostprint (author's final draft