ECSS staff share technical solutions to scientific computing challenges monthly in this open forum.
The ECSS Symposium allows the over 70 ECSS staff members to exchange on a monthly basis information about successful techniques used to address challenging science problems. Tutorials on new technologies may be featured. Two 30-minute, technically-focused talks are presented each month and include a brief question and answer period. This series is open to everyone.
Day and Time: Third Tuesdays @ 1 pm Eastern / 12 pm Central / 10 am Pacific
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Meeting ID: 114 343 187
Upcoming events are also posted to the Training category of XSEDE News.
Due to the large number of attendees, only the presenters and host broadcast audio. Attendees may submit chat questions to the presenters through a moderator.
September 19, 2017
COSMIC2 - A Science Gateway for Cryo-Electron Microscopy with Globus for Terabyte-sized Dataset
Presenter(s): Mona Wong-Barnum (SDSC)
Principal Investigator(s): Andres Leschziner (UCSD) Michael Cianfrocco (University of Michigan)
Structural biology is in the midst of a revolution. Instrumentation and software improvements have allowed for the full realization of cryo-electron microscopy (cryo-EM) as a tool capable of determining atomic structures of protein and macromolecular samples. These advances open the door to solving new structures that were previously unattainable, which will soon make cryo-EM a ubiquitous tool for structural biology worldwide, serving both academic and commercial purposes. However, despite its power, new users to cryo-EM face significant obstacles. One major barrier consists of the handling of large datasets (10+ terabytes), where new cryo-EM users must learn how to interface with the Linux command line while also dealing with managing and submitting jobs to high performance computing resources. To address this barrier, we are developing the COSMIC2 Science Gateway as an easy, web-based, science gateway to simplify cryo-EM data analysis using a standardized workflow. Specifically, we have adapted the successful and mature Cyberinfrastructure for Phylogenetic Research (CIPRES) Workbench  and integrated Globus Auth  and Globus Transfer  to enable federated user identity management and large dataset transfers to Extreme Science and Engineering Discovery Environment's (XSEDE)  high performance computing (HPC) systems. With the support of XSEDE's Extended Collaborative Support Services (ECSS)  and the Science Gateway Community Institute's (SGCI) Extended Developer Support (EDS), this gateway will lower the barrier to high performance computing tools and facilitate the growth of cryo-EM to become a routine tool for structural biology. Talk previously given at PEARC'17
First steps in optimising Cosmos++: A C++ MPI code for simulating black holes
Presenter(s): Damon McDougall (ICES)
Principal Investigator(s): Patrick C. Fragile (College of Charleston)
This ECSS project is to have Cosmos++ run on Stampede2 effectively. Stampede2, at present, is made up entirely of Intel Xeon Phi nodes. These are low clock-frequency but high core-count nodes, and there are some challenges associated with running on this hardware efficiently. Although the project's end goal is to hybridise a pure MPI code, this talk will focus on some of the initial steps we have taken to improve serial performance and how these steps relate to C++ software design. Prior knowledge of compiled languages and custom types would be beneficial but isn't required.
August 15, 2017
HTC with a Sprinkle of HPC: Finding Gravitational Waves with LIGO
Presenter(s): Lars Koesterke (TACC)
Principal Investigator(s): Duncan Brown (Syracuse University) Josh Willis (Abilene Christian University)
XSEDE is supporting the LIGO project to detect signatures of gravitational waves in a stream of data generated by (currently) two observatories in the U.S., located in Washington State and Louisiana. I will report on an ECSS project tasked to improve the performance of one of the largest (most resource demanding) pipelines called pycbc (python compact binary collision). The software evolved from a slow and performance-unaware state to a high-performing pipeline capable of utilizing Xeon, Xeon Phi, and Nvidia GPU architectures alike. Achieving high performance required only a few sprinkles of HPC (High Performance Computing) on top of a HTC (High Throughput Computing) pipeline. While the HPC pieces relevant for this particular project are all well known to ECSS staff it may be surprising what was missing in the considerations of the software developers. Hence this is more a story of how to educate users than a story of new and groundbreaking HPC concepts. Nevertheless I am confident that my fellow ECSS staffers will find this project interesting and enlightening.
Enabling multi-events 3D simulations for earthquake hazard assessment
Presenter(s): Yifeng Cui (SDSC)
Principal Investigator(s): Morgan Moschetti (USGS)
Researchers from USGS use Stampede to perform a series of computationally intensive simulations for improved understanding of earthquake hazards. Hercules, a finite element solver developed at CMU, is used to make the calculations which combines meshing, partitioning and solving functions in a single, self-contained code. Meshing employs a highly efficient octree-based algorithm that scales well. The simulation results are used to investigate the effects of complex geologic structure and topography on seismic wave propagation and ground-shaking hazards, and to evaluate model uncertainties in U.S. seismic hazard models. This talk will provide an overview of current status of the seismic hazard analysis research, and introduce the code performance, the optimizations involved in supporting multi-event simulations for this study through the ECSS project.
June 20, 2017
Visualization of simulated white dwarf collisions as a primary channel for type Ia supernovae
Presenter(s): David Bock (NCSA)
Principal Investigator(s): Doron Kushnir (Princeton)
Type Ia supernovae are an important and significant class of supernovae. While it is known that these events result from thermonuclear explosions of white dwarfs, there is currently no satisfactory scenario to achieve such explosions. Direct collisions of white dwarfs are simulated to study the possibility that the resulting explosions are the main source of type Ia supernovae. An adaptive mesh refinement grid simulates the varying levels of detail and a custom volume renderer is used to visualize density, temperature, and the resulting nickel production during the collision.
Humanities Computing With XSEDE: The Role of ECSS in Past, Present, and Future (upcoming) Projects
Presenter(s): Alan Craig (NCSA)
This symposium will address the role of ECSS in humanities related projects carried out in XSEDE. Humanities related disciplines are typically underrepresented in the XSEDE ecosystem. I will address my experiences and attempt to answer questions such as: "Where do these projects come from?", "What kinds of things are humanities scholars doing with XSEDE?", "What are some hurdles that need to be overcome for successful projects?", "How do the ECSS collaborations work?", and "How do we know if a project is successful?" in the context of several example projects.
May 16, 2017
Presenter(s): Kwai Wong (UTK)
Principal Investigator(s): Matthew DeAngelis (Georgia State University)
Motivated by the increasing tendency for computing power to assist, or even replace, human effort in the acquisition and analysis of financial information and in the execution of trading strategies, this project examines the "scriptability" of firm disclosures, or the relative ease with which a computer program can transform the large amounts of unstructured data contained in various firm disclosures into usable information. The objective of this ECSS project is to provide support to manage and run a set of computer codes examining the scriptability of a large volume of documents. The performance and the workflow procedure of the computations on will be presented.
Visual exploration and analysis of time series earthquake data
Presenter(s): Amit Chourasia (SDSC)
Principal Investigator(s): Keith Richards-Dinger (UC Riverside) James Dieterich (UC Riverside) Yifeng Cui (SDSC)
Earthquake hazard estimation requires systematic investigation of past records as well as fundamental processes that cause the quake. Robust risk estimation requires detailed long-term records of earthquakes at all scales (magnitude, space, time), which are not available. Hence a synthetic method based on first principals could generate such records that could bridge this critical gap of missing data. RSQSim is such a simulator that generates seismic event catalogs for several thousand years at various scales. This synthetic catalog contains rich detail about the events and corresponding properties.
Exploring this data is of vital importance to validate the simulator as well as to identify features of interest such as quake time histories, conduct analysis such as mean recurrence interval of events on each fault section, etc. This work describes and demonstrates a prototype web based visual tool that enables scientists and students explore this rich dataset. It also discusses the refinement and streamlining data management and analysis that is less error prone and scalable.
This work was performed in collaboration with Keith Richards-Dinger, James Dieterich and Yilfeng Cui and supported by ECSS.
April 18, 2017
Securing Access to Science Gateways with CILogon and Role-based Access Control
Presenter(s): Marcus Christie (IU)
CILogon is a service that allows users to securely access cyberinfrastructure resources by authenticating with their home institutions. Users benefit by not needing to learn a new username and password, and science gateway administrators benefit by not needing to securely manage user passwords.
Apache Airavata is a software framework for building science gateways. Apache Airavata provides abstractions for describing compute and storage resources and the applications that can run on them. Through a web interface, users can launch and monitor applications running on a local cluster, the commercial cloud, or national cyberinfrastructure.
The Apache Airavata project recently integrated support for CILogon into it's web portal. In this talk this integration will be discussed along with the role-based access control authorization system developed for Airavata. Together, CILogon and role-based access control significantly ease the burden on users and administrators of securing access to science gateways.
Statistical Analysis for Partially-Observed Markov Processes with Marked Point Process Observation
Presenter(s): Mitchel Horton (NICS) Junqi Yin (NICS)
Principal Investigator(s): Professor Yong Zeng (University of Missouri at Kansas City)
Volatility is influential in investment, monetary policy making, risk management and security valuation, and is regarded as one of the most important financial market indicators. Recently, a general partially-observed framework of Markov processes with Marked Point Process (MPP) observations has been proposed for streaming financial ultra-high frequency (UHF) data.
For this project, particle Markov Chain Monte Carlo (PMCMC), is applied to the parameter estimation for two models: Geometric Brownian Motion (GBM), and Heston Stocastic Volatility (HSV). Both models operate under 1/8 and 1/100 tick mark rules.
This method combines particle filtering with Markov Chain Monte Carlo (MCMC) to achieve sequential parameter learning in a Bayesian way. MCMC is used to propose new values for model parameters; particle filtering is used to detect values of marginal likelihood in the state-space model based on the proposed parameters.
The CUDA codes to compute the Bayes factors for model comparison and selection between GBM and HSV are donei, and in the simulation testing stage. With the time remaining for this project, new features will be added to HSV (another, even more highly-parallelizable particle filtering (namely, sequential Monte Carlo) method, will be used to solve the same filtering equations which are stochastic PDEs).
March 21, 2017
The Paleoscape Project for Studies of Modern Human Origins
Presenter(s): David O'Neal (PSC)
Principal Investigator(s): Curtis Marean. (Arizona State)
There is widespread consensus in human origins research (paleoanthropology) that the modern human lineage evolved in Africa and all modern humans are descended from that population. The archaeological record for the behavior of this crucial phase is richest in the southern African sub-region and particularly rich in the Cape. It has been hypothesized that the Cape, due to its uniquely rich coastal and terrestrial food resources, may have been the refuge region for the progenitor lineage of all modern humans during harsh global glacial phases.
During this phase of human origins, the economy was based entirely on hunting and gathering, and hunter-gatherer adaptations are tied to the way that climate and environment shape the food and technological resource base. For this reason human origins research recognizes the evolutionary significance of paleoclimate and paleoenvironment, and has a long tradition of engaging with climate and environmental scientists in an effort to understand if and how bio-behavioral evolution in the hominin line responded to climate change.
This XSEDE ECSS project implements the following workflow:
1) run a South African regional climate model to hindcast the climate parameters needed to project vegetation and other resources into the past, 2) run vegetation projections from these climate projections, and 3) run multiple agent-based simulations of the foragers on the these ancient paleoscapes. This unique endeavor is made possible by an unprecedented collaboration of scientists from several countries and many disciplines.
February 21, 2017
Julia on HPC Platform
Presenter(s): Dong Ju Choi (UCSD)
Principal Investigator(s): Christopher Rackauckas (University of California, Irvine)
Julia is a high level programming languge providing both MATLAB like easiness and parallel computing performance. We began to learn the language to assist Chris Rackauckas at University of California Irvine for the development of a Julia differential equation package on SDSC Comet system.
This presentation will introduce the basic Julia usage on HPC platform specially with Comet system during the support.
Low Reynolds Number Hydrodynamics for Micro-robotic Applications
Presenter(s): Anirban Jana (PSC)
Principal Investigator(s): Metin Sitti (CMU)
In this talk, I will present my ECSS project with Prof Metin Sitti from CMU, where I helped develop an efficient simulation capability to perform simulations of microrobots in liquid enviroments at low Reynolds numbers (in the Stokes flow regime). The simulations are based on the boundary element method for Stokes flows. The ECSS project activities included selection of a suitable software stack, workflow development from preprocessing to simulation to analysis, and parallelization of an existing open source Stokes flow BEM code . This enabled simulation time to be reduced from days to minutes, opening up the possibility of comprehensive design space explorations, or more highly resolved simulations, or simulations of much more complex systems such as swarms of microrobots, in the future.
January 17, 2017
Toward Flood Inundation Mapping at the Continental Scale: the Cyberinfrastructure Approach
Presenter(s): Yan Liu (CyberGIS Center and NCSA, UIUC)
Principal Investigator(s): David Maidment (UT Austin) David Tarboton (Utah State University)
Project 1: National Flood Interoperability Experiment (NFIE) As high-resolution national terrain and water data become increasingly available, hydrology researchers have the opportunities to conduct hydrological study directly at continental scale for the conterminous U.S. (CONUS). To enable continental hydrology research, integrated cyberinfrastructure power plays a critical role in coupling interdisciplinary data, software, and multiple types of computational platforms and making them available for the research community to perform methodological experiments on big data and complex computations that they could not handle in lab environment. One leading effort in this direction is the NSF National Flood Interoperability Experiment (NFIE). NFIE aims to combine high-resolution terrain (10m and finer) and water (National Hydrography Dataset) data with NOAA National Water Model (NWM) forecast for real-time national inundation mapping and forecast.
Project 2: Terrain analysis using digital elevation models (TauDEM) Two ECSS projects help achieve NFIE goals on XSEDE resources at NCSA (on ROGER supercomputer, one of the 3rd-tier resources) and TACC (on Stampede). The NFIE ECSS project develops computational solutions to data integration and processing, methodology development, workflow construction, and experiment computation. The TauDEM ECSS project accelerates a core software piece in NFIE workflow, i.e., TauDEM, to conduct high-performance and scalable hydrological information analysis on large geospatial raster data. In this talk, I will introduce the data and computational challenges in these two projects and review the solutions developed to achieve major milestones. Results and their impact in the research community will be presented. I will share our computational experience on the highly-coupled HPC and cloud computing platform on ROGER and discuss the advantages of hybrid supercomputing architecture in building end-to-end solutions for research groups and science gateways.
December 20, 2016
Comet Virtual Cluster 'User' Experience
Presenter(s): Trevor Cooper (SDSC) Fugang Wang (IU)
Comet is an XSEDE HPC resource hosted and operated at SDSC and supported by systems staff at SDSC and user support staff at IU.
This demonstration explores the Virtual Cluster (VC) capability of Comet, a unique feature that provides projects with the ability to fully define their own software environment with a set of dynamically allocated virtual machines.
We will begin the demonstration with an overview on the design and architecture of the virtual cluster capability, and how it compares to other virtualized and cloud services. The high performance of the virtualized clusters combining the full AVX2 feature set of the Haswell processors and the InfiniBand HCAs using SR-IOV for MPI will be discussed.
We will then follow with a demonstration on how to build, configure, and manage virtual clusters using the Cloudmesh client, a tool to easily interface with multiple clouds from the command line and a command shell following a guide originally create for the XSEDE hands-on tutorial. Time-permitting we will demonstrate multiple pre-configured virtual clusters and provide examples of possible administrative workflows available in this unique environment.
Finally we will provide references for further information on obtaining an allocation for Comet virtual clusters.
The Science Gateways Community Institute
Presenter(s): Nancy Wilkins-Diehr (SDSC)
Science gateways are a fundamental part of today's research landscape. Beginning in 2013, more users accessed XSEDE resources via gateways than they did from the command line. However, despite the presence of gateways for many years, development of these environments is often done with an ad hoc process, limiting success, resource efficiency, and long-term impact. Developers are often unaware that others have solved similar challenges before, and they do not know where to turn for advice or expertise. Without knowledge of what's possible, projects waste money and time implementing the most basic functions rather than the value-added features for their unique audience. Critically also many gateway efforts fail. Some fail early by not understanding how to build communities of users; others fail later by not developing plans for sustainability.
The Science Gateways Community Institute (SGCI, http://www.sciencegateways.org) is one of the first implementation-phase software institutes to be awarded through NSF's Software Infrastructure for Sustained Innovation (SI2) program. SGCI has been designed as a service organization to address challenges by offering services to and building community among the research communities developing gateways. An application to be an XSEDE level two service provider is planned. The Institute's five-component design is the result of several years of studies, including many focus groups and a 5,000-person survey of the research community. This talk will describe SGCI's offerings and how they might benefit your work.
October 18, 2016
Towards Large-scale Genomics, Transcriptomics, and Metagenomics for All
Presenter(s): Philip Blood (PSC)
Principal Investigator(s): Noushin Ghaffari (Texas A&M) Ping Ma (U. Georgia) James Taylor (Johns Hopkins)
Although increasing numbers of researchers in genomics and related disciplines are utilizing advanced cyberinfrastructure for their work, these still represent a relatively small fraction of the biologists who could benefit from access to the latest genomics tools backed by large-scale computing resources. Rapid advances in these fields have caused an explosion of tools and algorithms that present a dizzying array of constantly changing options. Hence, even for scientists who are adept at using advanced computing infrastructure, it is challenging to determine the optimal mix of tools and employ these effectively to analyze large genomic data sets. In this talk I will highlight several XSEDE ECSS projects aimed at tackling aspects of these problems, both through formal ECSS collaborations and the "Novel and Innovative Projects" (NIP) arm of ECSS. These projects include the development of a pipeline for high-quality transcriptome analysis based on well-characterized RNA Sequencing Quality Control (SEQC) datasets, making memory-hungry sequence assembly tools available through the Galaxy XSEDE Gateway (usegalaxy.org), enabling large-scale analysis of human microbiome data, and facilitating the Critical Assessment of Metagenome Interpretation (CAMI: http://www.cami-challenge.org/).
Petascale DNS Using the Fast Poisson Solver PSH3D
Presenter(s): Darren Adams (NCSA)
Principal Investigator(s): Antonio Ferrante (U Wash)
Direct numerical simulation (DNS) of high Reynolds number (Re = O(105)) turbulent flows requires computational meshes of O(1012) grid points. Thus, DNS requires the use of petascale supercomputers. DNS often requires the solution of a Helmholtz (or Poisson) equation for pressure, which constitutes the bottleneck of the solver. We have developed and implemented a parallel solver of the Helmholtz equation in 3D called petascale Helmholtz 3D (PSH3D). The numerical method underlying PSH3D combines a parallel 2D Fast Fourier transform (P2DFFT) and a parallel linear solver (PLS). Our numerical results show that PSH3D scales up to at least 262,144 cores. PSH3D has a peak performance 6× faster than 3D FFT-based methods (e.g., P3DFFT) when used with the partial-global optimization. We have verified that the use of PSH3D with the partial-global optimization in our DNS solver does not reduce the accuracy of the numerical solution when tested for the Taylor-Green vortex flow.