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OSG All Hands Meeting

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UCSD/SDSC

UCSD/SDSC
Description
This year’s All Hands Meeting of the Open Science Grid will be hosted by the San Diego Supercomputer Center, March 6-10, 2017, La Jolla, California.
Link to Details and Registration
As has been the custom, the 2017 OSG AHM will be co-located with the U.S. Large Hadron Collider (LHC at CERN) computing facility meetings.
  • Agenda for the US ATLAS Facilities Meeting here

  • Monday, March 6
    • Registration and Continental Breakfast
    • Welcome
    • US ATLAS SDSC Synthesis Center

      SDSC Synthesis Center

      UCSD/SDSC

      See agenda in CERN Indico Page

      Convener: Robert Gardner (University of Chicago)
    • US CMS SDSC Autorium

      SDSC Autorium

      UCSD/SDSC

      U.S. CMS University Facilities session agenda can be found at: https://indico.cern.ch/event/608392/

      Conveners: Dr JAMES LETTS (UCSD), Prof. Kevin Lannon (University of Notre Dame)
    • Coffee break
    • Intensity & Cosmic Frontiers: (Remote:https://IU.zoom.us/j/680888506)
      Convener: Dr Kenneth Herner (Fermilab)
      • 1
        Introduction
        Speaker: Dr Kenneth Herner (Fermilab)
        Slides
      • 2
        DES
        Speaker: Dr Kenneth Herner (Fermilab)
        Slides
      • 3
        IPAC
        Speaker: Steve Groom (IPAC)
        Slides
      • 4
        LIGO/LIGO India
        Speaker: Jayanti Prasad
        Slides
    • US Atlas SDSC Synthesis Center

      SDSC Synthesis Center

      UCSD/SDSC
      Convener: Robert Gardner (University of Chicago)
    • US CMS SDSC Auditorium

      SDSC Auditorium

      UCSD/SDSC

      U.S. CMS University Facilities session agenda can be found at: https://indico.cern.ch/event/608392/

      Conveners: Dr JAMES LETTS (UCSD), Prof. Kevin Lannon (University of Notre Dame)
    • Lunch
    • Intensity & Cosmic Frontiers: (Remote:https://IU.zoom.us/j/680888506)
      Convener: Dr Kenneth Herner (Fermilab)
      • 5
        SPT
        Speaker: Dr Benedikt Riedel (University of Chicago)
        Slides
      • 6
        AMS
        Speaker: Baosong Shan (MIT)
      • 7
        JPL
        Speaker: Bryan Bales (JPL)
        Slides
      • 8
        FIFE (includes DUNE)
        Speaker: Mrs Tanya Levshina (Fermilab)
        Slides
      • 9
        Distributed Computing in IceCube
        Speaker: David Schultz
        Slides
    • US Atlas SDSC Synthesis Center

      SDSC Synthesis Center

      UCSD/SDSC
      Convener: Robert Gardner (University of Chicago)
    • US CMS SDSC Auditorium

      SDSC Auditorium

      UCSD/SDSC

      U.S. CMS University Facilities session agenda can be found at: https://indico.cern.ch/event/608392/

      Conveners: Dr JAMES LETTS (UCSD), Prof. Kevin Lannon (University of Notre Dame)
    • Coffee break
    • Joint ATLAS, CMS Session SDSC Auditorium

      SDSC Auditorium

      UCSD/SDSC
      Conveners: Dr JAMES LETTS (UCSD), Prof. Kevin Lannon (University of Notre Dame), Robert Gardner (University of Chicago)
      • 10
        Singularity in CMS
        Speaker: Dr Brian Bockelman (University of Nebraska-Lincoln)
        Slides
      • 11
        ATLAS use of large scale DOE HPC resources
        Speaker: Kaushik De (Univ. of Texas at Arlington)
        Slides
      • 12
        CMS use of HPC resources
        Speaker: Dirk Hufnagel (Fermilab)
        Slides
      • 13
        HEPCloud
        Speakers: Dr Burt Holzman (FNAL), Mr John Hover (Brookhaven National Laboratory)
        Slides
  • Tuesday, March 7
    • Registration and Continental Breakfast SDSC Auditorium

      SDSC Auditorium

      UCSD/SDSC
    • Services for OSG Resource Providers: (Remote:https://IU.zoom.us/j/376841850)
      Convener: Prof. Frank Wuerthwein (UCSD)
      • 14
        Options for Integrating your cluster with the national HTC fabric supported by OSG
        Speaker: Prof. Frank Wuerthwein (UCSD)
        Slides
      • 15
        Connecting Resources to Science via HTCondor-CE
        Speaker: Brian Lin (University of Wisconsin-Madison)
        Slides
      • 16
        OSG Managed Services and CE-Bosco
        Speakers: Dr Derek Weitzel (University of Nebraska - Lincoln), Mr Suchandra Thapa (Computation Institute / University of Chicago)
        Slides
      • 17
        Integrating OSG Into a Broader Research Computing Strategy
        Speaker: Eric Sedore (Syracuse University)
      • 18
        Campus Research Computing (CaRC) consortium
        Speaker: Prof. Tom Cheatham (University of Utah)
        Slides
    • Coffee break
    • National Cyberinfrastructure Projects: (Remote:https://IU.zoom.us/j/376841850)
      Convener: Prof. Robert Gardner (University of Chicago)
      • 19
        XSEDE Campus Champions
        Speaker: Prof. Dana Brunson (Oklahoma State University)
        Slides
      • 20
        Integrating NSF HPC Resources and the Grid: Stampede and Blue Waters
        Speaker: Mark Neubauer (University of Illinois at Urbana-Champaign)
        Slides
      • 21
        The (Not-so) Virtual Reality of OSG on Blue Waters, Comet, and Jetstream
        Speaker: Mr Edgar Fajardo Hernandez (UCSD)
        Slides
      • 22
        OSG on Titan via PanDA
        Speaker: Kaushik De (Univ. of Texas at Arlington)
        Slides
    • Group Photo SDSC Entry Stairs

      SDSC Entry Stairs

      UCSD/SDSC
    • Lunch
    • Intensity & Cosmic Frontiers: (Remote:https://IU.zoom.us/j/126578418)
      Convener: Dr Kenneth Herner (Fermilab)
      • 23
        VERITAS
        Speaker: Prof. Nepomuk Otte (Georgia Institute of Technology)
        Slides
      • 24
        STAR Data Reconstruction at NERSC/Cori
        Speaker: Mustafa Mustafa (LBL)
        Slides
      • 25
        GlueX
        Speaker: Dr Richard Jones (University of Connecticut)
        Slides
      • 26
        XENON1T
        Speaker: Dr Benedikt Riedel (University of Chicago)
        Slides
    • OSG Users: (Remote:https://IU.zoom.us/j/376841850)
      Convener: Dr Bala Desinghu (Scientific Computing Consultant)
      • 27
        Counterfactual Analysis in Economics: Using OSG to Solve Dynamic Games
        Speaker: Prof. Fernando Luco (Texas A&M University)
        Slides
      • 28
        Monte Carlo Simulation for Next Generation Source and Channel Coding on OSG Connect
        Lossy source coding is an efficient data compression technique that aims to minimize the distortion in the reconstructed sequence. Our research involves the investigation of the distortion performance of state-of-the art protograph-based SC-LDGM codes. We show that performance close to Shannon's optimal rate-distortion limits can be achieved with an efficient windowed encoding (WE) algorithm that takes advantage of the convolutional structure of the SC-LDGM codes. The idea is numerically verified by running extensive and highly parallelizable Monte Carlo simulation using distributed high throughput computing, OSG connect
        Speaker: Mr Ahmad Golmohammadi (New Mexico State University)
        Slides
      • 29
        Effects of Spatial Diffusion on a Model for Prebiotic Evolution
        In previous work (Physical Review E 89, 022725 (2014)), a Kauffman-like model for prebiotic evolution was used to explore the effects of requiring that the final steady states generated be out of chemical equilibrium. That constraint, consistent with intuitive ideas of the meaning of 'lifelike', had a significant impact on the probability of the appearance of lifelike states in the model. The model assumed that the constituent 'molecules' were in a 'well-mixed' reactor so that effects of spatial diffusion played no role. I will review that earlier work and describe our present studies in which spatial heterogeneity and spatial diffusion are introduced. The competition between chemical reaction and diffusion leads to various kinds of nonequilibrium steady states, some spatially equilibrated but out of chemical equilibrium, some chemically equilibrated but out of spatial equilibrium and still others, perhaps the most lifelike, which are not equilibrated in either way but are in dynamic steady states far from equilibrium. Using data from simulations that were performed on the Open Science Grid, I will present estimated probabilities of the generation of these various kinds of states as a function of the two parameters of the model (Physical Review E 94 (4), 042424 (2016)).
        Speaker: Dr Ben Intoy (University of Minnesota)
        Slides
      • 30
        Using Python and Fabric for analyzing brain signals on OSG Connect
        https://docs.google.com/presentation/d/1s5n-ObLv5In3lVpqUJoUqO7RZDEMf5WjXzYmJJGdraA/edit?usp=sharing As data collection systems are augmented, more individual labs require high-throughput computing in order to process all of their data. In these labs, researchers are continuously developing their own analytics methods in scripting languages. These facts are especially true in the neuroscience community, in which brain recordings often contain several hundred channels, sampled at over 1000Hz, for sometimes weeks at a time. New methodology for extracting information from these signals are being developed in Python due to its wide variety of packages, great documentation, and open-source culture. This presentation will cover an example application of OSG to parallelize analysis of multiple neural signals using both public and private libraries and transferring output. It will also cover the Python package Fabric to automate the process of logging into and running commands on the OSG submit server. This tutorial's release led to an increase in OSG connect users interested in using Python, which will help to improve the support for Python usage on OSG connect.
        Speaker: Mr Scott Cole (University of California San Diego)
        Slides
      • 31
        A large-scale metagenomic analysis using OSG
        t is well known that exosomes play an important role in cell-to-cell communication by transferring all types of molecules from donor cells to recipient cells. The objective of this study was to assess the microbial mRNA cargos in exosomes of one type of body fluids. To identify the possible microbial species in the samples, we conducted a large-scale metagenomic analysis by using the Open Science Grid (OSG) and 4,742 microbial genomes were assessed on each of 6 samples. The result shows that, across all samples, microbial sequences consistently account for a large percentage of the mRNAs in exosomes. Moreover, through the highly efficient system of OSG, the tasks of ~81K CPU hours were completed in 17 days.
        Speaker: Jiang Shu (UNL)
        Slides
      • 32
        Pegasus - Enhancing User Experience on OSG
        Speaker: Mats Rynge (USC / Information Sciences Institute)
        Slides
    • Coffee break
    • Life Sciences: (Remote:https://IU.zoom.us/j/376841850)
      Convener: Rob Quick (Indiana University)
      • 33
        Cancer Computer
        Cancer Computer is a non-profit with a goal to create a computing platform, as a service, for cancer researchers. In just under 2 years since founding, we've received enough donations, to deploy a modest cluster, supporting OSG, the Galaxy Project, researchers in private virtual environments, and scavenging spare CPU and GPU cycles for public projects such as Rosetta and Folding at Home, and the World Community Grid. We've recently hired an ex-fortune 500 VP as our Executive Director, a professional fundraiser has offered to volunteer time to us, and we are about to sign an agreement, with a Federal Canadian Agency, to secure all of their evergreened computing, networking, and storage hardware, for several years.
        Speaker: Roy Chartier
        Slides
      • 34
        fsurf: an OSG FreeSurfer execution service
        FreeSurfer is a software suite for processing and analyzing human MRI images. Freesurfer takes several hours to process a typical MRI scan (~40MB in size) and generates about 300MB of results. This makes it a good fit for computation on OSG. We present FSurf, a computational service that allows users to easily run typical FreeSurfer workflows on OSG.
        Speaker: Mr Suchandra Thapa (Computation Institute / University of Chicago)
        Slides
      • 35
        Evolving strategies for life in an uncertain world
        Molecular processes are fundamentally stochastic. Randomness is the rule in transcription, translation, cell-to-cell variation in protein levels, and heterogeneity in interactions. One common assumption is that such phenotypic variation is simply noise, and scientists often appeal to the statistics of large numbers when developing deterministic theories, ignoring any potentially adaptive role of stochasticity. Yet evidence is accumulating that phenotypic variance constitutes an evolutionary driving force across diverse biological processes, including the adaptive immune system, the development of cancerous neoplasms, and the persistence of pathogens under drug pressure. All these systems are fundamentally characterized by high levels of environmental change and uncertainty: either persistent, global, temporal fluctuations in selection pressure, or local, micro-environmental and spatially-defined selective forces. Can evolution prepare organisms for this environmental stochasticity? I will talk about the genetic signatures of this commonplace yet unpredictable environmental variation. I will particularly focus on exploring the evolutionary advantage of alleles that confer the ability to express a range of phenotypes, a type of evolutionary bet-hedging that need not confer a direct benefit to a single individual, but can increase the chance of long-term survival of a lineage. I will also discuss implications of these results in the context of therapies designed to eradicate populations of pathogens or aberrant cellular lineages.
        Speaker: Dr Oana Carja (University of Pennsylvania)
        Slides
      • 36
        Large-Scale Genomics Experiments Enabled by OSG Connect Resources
        Several petabytes of raw DNA sequencing data have been deposited into public databases in recent years, introducing novel opportunities for mining useful biological information. The Open Science Grid (OSG) provides hardware and software infrastructure that have enabled us to address complex biological questions at a larger scale than previously possible with our local HPC resources at Clemson. With the help of the OSG support staff, we have developed two functional Pegasus workflows for processing and interpreting large genomic datasets. From software compilation to workflow optimization, we have encountered technical challenges that were quickly eased by the dedicated support of the OSG staff. The successes and challenges that we have encountered throughout this process will be discussed.
        Speakers: Prof. Stephen Ficklin (Washington State University), Mr William Poehlman (Clemson University)
        Slides
    • Technology & Software: (Remote:https://IU.zoom.us/j/126578418)
      Convener: Dr Brian Bockelman (University of Nebraska-Lincoln)
      • 37
        Accounting with GRÅCC
        Speaker: Kevin Retzke (FNAL)
        Slides
      • 38
        Singularity on OSG
        Speaker: Dr Derek Weitzel (University of Nebraska - Lincoln)
        Slides
      • 39
        Single Sign-On in the OSG
        Speaker: Marina Krenz (Indiana University)
        Slides
      • 40
        HTCondor Annex
        Speaker: Todd Miller (University of Wisconsin–Madison)
        Slides
    • Conference Dinner: Bus departs from outside auditorium at or about 17:45 Liberty Station, 2816 Historic Decatur Rd #116 (Stone Brewing World Bistro & Gardens - Libeerty Station)

      Liberty Station, 2816 Historic Decatur Rd #116

      Stone Brewing World Bistro & Gardens - Libeerty Station
  • Wednesday, March 8
    • Registration and Continental Breakfast
    • State of OSG: Remote https://IU.zoom.us/j/815975158
      Convener: Prof. Frank Wuerthwein (UCSD)
      • 41
        Welcome
        Speaker: Dr Michael Norman (San Diego Supercomputer Center)
      • 42
        State of OSG - Executive Director’s Perspective
        Speaker: Prof. Frank Wuerthwein (UCSD)
        Slides
      • 43
        State of OSG - OSG Council Chair’s Perspective
        Speaker: David Swanson (University of Nebraska Lincoln)
        Slides
      • 44
        Diversity of Science on the OSG
        Speaker: Prof. Robert Gardner (University of Chicago)
        Slides
    • Coffee break
    • Science on OSG: Remote https://IU.zoom.us/j/815975158
      • 45
        Exploring Lung Microstructure with Monte Carlo
        Speaker: Annie Malkus (University of Wisconsin–Madison)
        Slides
      • 46
        From Hospitals to Molecules: Uncovering Biology Through Observational Clinical Data
        Speaker: Rami Vanguri (Columbia University)
        Slides
      • 47
        Enabling Cosmic Microwave Background Cosmology with High-Performance Computing
        Speaker: Prof. Kam Arnold (University of California San Diego)
        Slides
      • 48
        A Data-Driven Approach to Quantifying the Shear Viscosity of Nature’s Most Ideal Liquid
        Speakers: Dr Jerome Lauret (Brookhaven National Laboratory), Prof. Steffen Bass (Duke University)
        Slides
    • Lunch
    • State of OSG: Remote https://IU.zoom.us/j/815975158
      Convener: Prof. Frank Wuerthwein (UCSD)
      • 49
        OSG: A Year in Review
        A look back at the successes of the past year of OSG.
        Speaker: Rob Quick (Indiana University)
        Slides
      • 50
        State of OSG Technology
        Speaker: Dr Brian Bockelman (University of Nebraska-Lincoln)
        Slides
      • 51
        State of OSG Networking
        Speaker: Dr Shawn McKee (Univ. of Michigan)
        Slides
      • 52
        State of OSG Security
        Speaker: Susan Sons (Indiana University)
        Slides
    • Coffee break
    • Preview of Training Sessions: Remote https://IU.zoom.us/j/815975158
      Convener: Prof. Frank Wuerthwein (UCSD)
    • Panel Discussion on the S2I2 Conceptualization for HL-LHC: Kaushik De, Peter Elmer, Oli Gutsche, Mark Neubauer (Remote https://IU.zoom.us/j/815975158)
      slides
  • Thursday, March 9
    • Registration and Continental Breakfast
    • OSG Council Meeting: Remote https://IU.zoom.us/j/828138311
      Convener: Dr David Swanson (University of Nebraska-Lincoln)
      Minutes
      • 53
        Introductory Remarks
      • 54
        RR: CMS (Bloom)
      • 55
        Year 6 plans
        Speaker: Prof. Frank Wuerthwein (UCSD)
        Slides
      • 56
        RR: FNAL (Liz)
      • 57
        RR: ATLAS (Kaushik)
    • Security Training: Security Office Hours; Ask us Anything! SDSC Auditorium

      SDSC Auditorium

      UCSD/SDSC
      Convener: Susan Sons (Indiana University)
    • Site Admin Training: Software Office Hours; Ask us Anything! SDSC Auditorium

      SDSC Auditorium

      UCSD/SDSC
      Convener: Brian Lin (University of Wisconsin-Madison)
    • User Training SDSC Synthesis Center

      SDSC Synthesis Center

      UCSD/SDSC
      • 58
        Introduction to OSG Connect
        Speaker: Mats Rynge (USC / Information Sciences Institute)
        Website
      • 59
        Job Scheduling with HTCondor
        Speaker: Mr Suchandra Thapa (Computation Institute / University of Chicago)
        Website
      • 60
        Large scale Computation
        Speaker: Dr Bala Desinghu (Scientific Computing Consultant)
        Website
    • 10:30 AM
      Morning Break
    • OSG Council Meeting: Remote https://IU.zoom.us/j/828138311
      Convener: Dr David Swanson (University of Nebraska-Lincoln)
      Minutes
      • 61
        RR: SDSC (Norman)
      • 62
        Production update
      • 63
        AGIS integration
      • 64
        RR: DOSAR (Horst)
      • 65
        RR: STAR (Jerome)
        Slides
      • 66
        RR: Condor (Tim)
      • 67
        OAC RFI
    • Security Training: Security Office Hours; Ask us Anything! SDSC Auditorium

      SDSC Auditorium

      UCSD/SDSC
      Convener: Susan Sons (Indiana University)
    • Site Admin Training SDSC Auditorium

      SDSC Auditorium

      UCSD/SDSC
      Convener: Brian Lin (University of Wisconsin-Madison)
      • 68
        Site Install Overview
        Speaker: Brian Lin (University of Wisconsin-Madison)
        Slides
      • 69
        Singularity
        Speaker: Dr Derek Weitzel (University of Nebraska - Lincoln)
        Slides
    • User Training SDSC Synthesis Center

      SDSC Synthesis Center

      UCSD/SDSC
      • 70
        Large scale Computation (continued)
        Speaker: Dr Bala Desinghu (Scientific Computing Consultant)
        Website
      • 71
        Data Management
        Speaker: Mats Rynge (USC / Information Sciences Institute)
        Website
      • 72
        Adding Resources from Amazon AWS
        Speaker: Mats Rynge (USC / Information Sciences Institute)
      • 73
        Close / What's next?
    • 12:30 PM
      Lunch
    • OSG Council Meeting: Remote https://IU.zoom.us/j/828138311
      Convener: Dr David Swanson (University of Nebraska-Lincoln)
      Minutes
      • 74
        Campus / User Support update
        Speaker: Prof. Robert Gardner (University of Chicago)
        Slides
      • 75
        Security update
        Slides
      • 76
        RR: IU (Rob)
      • 77
        RR: Rob (Globus)
      • 78
        TBD
    • 3:30 PM
      Afternoon Break
    • OSG Council Meeting: Remote https://IU.zoom.us/j/828138311
      Convener: Dr David Swanson (University of Nebraska-Lincoln)
      Minutes
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