OSG All Hands Meeting

6 Mar 2017, 08:00 → 9 Mar 2017, 18:00 US/Pacific

UCSD/SDSC

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, 6 March

Registration and Continental Breakfast

Welcome

US ATLAS

See agenda in CERN Indico Page

Convener: Robert Gardner (University of Chicago)

US CMS

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 OSG_AHM_2017_IF_CF_Intro.pdf

2 DES

Speaker: Dr Kenneth Herner (Fermilab)

Slides DES_OSG_AHM_2017.pdf

3 IPAC

Speaker: Steve Groom (IPAC)

Slides OSG_Groom_20170306.pdf

4 LIGO/LIGO India

Speaker: Jayanti Prasad

Slides jayanti-osg-march-2017.pdf

US Atlas

Convener: Robert Gardner (University of Chicago)

US CMS

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 2017.03.05_SPT_and_OSG_All_Hands_Meeting_.pdf

6 AMS

Speaker: Baosong Shan (MIT)

7 JPL

Speaker: Bryan Bales (JPL)

Slides Open_Science_Grid_AHM_-_JPL_intro.pptx

8 FIFE (includes DUNE)

Speaker: Mrs Tanya Levshina (Fermilab)

Slides FIFE_OSGAHM_2017.pdf

9 Distributed Computing in IceCube

Speaker: David Schultz

Slides Distributed_Computing_In_IceCube_-_OSG_AHM_2017.pdf

US Atlas

Convener: Robert Gardner (University of Chicago)

US CMS

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

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 Singularity-in-CMS.pdf

11 ATLAS use of large scale DOE HPC resources

Speaker: Kaushik De (Univ. of Texas at Arlington)

Slides hpc-osg-mar17.ppt

12 CMS use of HPC resources

Speaker: Dirk Hufnagel (Fermilab)

Slides cms_hpc.pdf

13 HEPCloud

Speakers: Dr Burt Holzman (FNAL), Mr John Hover (Brookhaven National Laboratory)

Slides OSG_AHM_HEPCloud.pptx

Tuesday, 7 March

Registration and Continental Breakfast

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 OSGforCampusITMarch2017.pdf

15 Connecting Resources to Science via HTCondor-CE

Speaker: Brian Lin (University of Wisconsin-Madison)

Slides Connecting_Resources_with_Science.pdf Connecting_Resources_with_Science.pptx

16 OSG Managed Services and CE-Bosco

Speakers: Dr Derek Weitzel (University of Nebraska - Lincoln), Mr Suchandra Thapa (Computation Institute / University of Chicago)

Slides https://docs.google.com/presentation/d/1WKER_MltH-3v5IjfPlgusYsfQUGq8gAFiuQm3kGea2M/edit?usp=sharing

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 CaRC-at-OSG-mar17.pdf

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 osc_cc_20170307.pptx

20 Integrating NSF HPC Resources and the Grid: Stampede and Blue Waters

Speaker: Mark Neubauer (University of Illinois at Urbana-Champaign)

Slides OSG_AHM_BlueWaters_Stampede_Jetstream.pdf

21 The (Not-so) Virtual Reality of OSG on Blue Waters, Comet, and Jetstream

Speaker: Mr Edgar Fajardo Hernandez (UCSD)

Slides Comet-BlueWaters-JetStream.pdf

22 OSG on Titan via PanDA

Speaker: Kaushik De (Univ. of Texas at Arlington)

Slides PanDA-Titan-osg-mar17.ppt

Group Photo

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 OSG2017SanDiego.pdf

24 STAR Data Reconstruction at NERSC/Cori

Speaker: Mustafa Mustafa (LBL)

Slides 2017-03-06.pdf

25 GlueX

Speaker: Dr Richard Jones (University of Connecticut)

Slides https://docs.google.com/presentation/d/11GtMLmWbeF0294q10JlB-W5aiNuNZiV81HL5e3WvsuQ/view

26 XENON1T

Speaker: Dr Benedikt Riedel (University of Chicago)

Slides 2017.03.07__X1T_and_OSG_All_Hands_Meeting_.pdf

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 Fernando_OSG_UCSD_030717.pdf

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 Ahmad_OSG_AHM17.pdf

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 Intoy_OSG_All_Hands_2017.pdf

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 Scott-AHM17-Fabric-Python-Brains-Final.pdf

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 2017_OSGMeeting_jshu_v2.pdf

32 Pegasus - Enhancing User Experience on OSG

Speaker: Mats Rynge (USC / Information Sciences Institute)

Slides Pegasus-OSG-AHM-2017.pdf

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 CancerComputerAtOSG_AH20170307.pptx

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 FreeSurfer_analysis_services_on_OSG.pdf https://docs.google.com/presentation/d/13w8AbakKIarni711ObboKqzgr-VN4z2Rt5to6-qWNmo/edit?usp=sharing

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 OanaCarja_OSGAllHangsMarch2017SD.pdf

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 Poehlman_Ficklin_Feltus_OSG_AHM_3_7_17.pptx

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 GRACC-OSG_AHM_2017.pdf

38 Singularity on OSG

Speaker: Dr Derek Weitzel (University of Nebraska - Lincoln)

Slides weitzel-SingularityOnOSG.pdf

39 Single Sign-On in the OSG

Speaker: Marina Krenz (Indiana University)

Slides AHM_-SSO.pdf

40 HTCondor Annex

Speaker: Todd Miller (University of Wisconsin–Madison)

Slides HTCondor_Annex_v05.pptx

Conference Dinner: Bus departs from outside auditorium at or about 17:45

Wednesday, 8 March

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 osgAHMMarch8th2017.pdf

43 State of OSG - OSG Council Chair’s Perspective

Speaker: David Swanson (University of Nebraska Lincoln)

Slides OSGchairPerspective.pdf

44 Diversity of Science on the OSG

Speaker: Prof. Robert Gardner (University of Chicago)

Slides 2017.03.08_diversity_of_science.pdf

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 malkusOSG2017.pdf

46 From Hospitals to Molecules: Uncovering Biology Through Observational Clinical Data

Speaker: Rami Vanguri (Columbia University)

Slides Vanguri_03082017.pdf

47 Enabling Cosmic Microwave Background Cosmology with High-Performance Computing

Speaker: Prof. Kam Arnold (University of California San Diego)

Slides OSG_AHM_Arnold.pdf

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 OSG_all-hands-meeting.key OSG_all-hands-meeting.pdf

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 YearinReview-OSGAHM.pdf

50 State of OSG Technology

Speaker: Dr Brian Bockelman (University of Nebraska-Lincoln)

Slides Technology-Status.pdf

51 State of OSG Networking

Speaker: Dr Shawn McKee (Univ. of Michigan)

Slides Networking-OSG-AHM-07Mar2017.pptx

52 State of OSG Security

Speaker: Susan Sons (Indiana University)

Slides osg-sec-2017-03.pdf

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 osgAHMMarch8th2017panel.pdf

Thursday, 9 March

Registration and Continental Breakfast

OSG Council Meeting: Remote https://IU.zoom.us/j/828138311

Convener: Dr David Swanson (University of Nebraska-Lincoln)

Minutes F2F2017AHMnotes.pdf

53 Introductory Remarks

54 RR: CMS (Bloom)

55 Year 6 plans

Speaker: Prof. Frank Wuerthwein (UCSD)

Slides osgAHMMarch8th2017council.pdf

56 RR: FNAL (Liz)

57 RR: ATLAS (Kaushik)

Security Training: Security Office Hours; Ask us Anything!

Convener: Susan Sons (Indiana University)

Site Admin Training: Software Office Hours; Ask us Anything!

Convener: Brian Lin (University of Wisconsin-Madison)

User Training

58 Introduction to OSG Connect

Speaker: Mats Rynge (USC / Information Sciences Institute)

Website https://osgconnect.github.io/osg-ahm-17/

59 Job Scheduling with HTCondor

Speaker: Mr Suchandra Thapa (Computation Institute / University of Chicago)

Website https://osgconnect.github.io/osg-ahm-17

60 Large scale Computation

Speaker: Dr Bala Desinghu (Scientific Computing Consultant)

Website https://osgconnect.github.io/osg-ahm-17

10:30 Morning Break

OSG Council Meeting: Remote https://IU.zoom.us/j/828138311

Convener: Dr David Swanson (University of Nebraska-Lincoln)

Minutes F2F2017AHMnotes.pdf

61 RR: SDSC (Norman)

62 Production update

63 AGIS integration

64 RR: DOSAR (Horst)

65 RR: STAR (Jerome)

Slides https://docs.google.com/presentation/d/1Vo6cdVxseEg0OztAF3lLrbPzwruQ54zCTQp90cgVpfo

66 RR: Condor (Tim)

67 OAC RFI

Security Training: Security Office Hours; Ask us Anything!

Convener: Susan Sons (Indiana University)

Site Admin Training

Convener: Brian Lin (University of Wisconsin-Madison)

68 Site Install Overview

Speaker: Brian Lin (University of Wisconsin-Madison)

Slides OSG_Site_Installation_Overview.pdf OSG_Site_Installation_Overview.pptx

69 Singularity

Speaker: Dr Derek Weitzel (University of Nebraska - Lincoln)

Slides Singularity-Install.pdf

User Training

70 Large scale Computation (continued)

Speaker: Dr Bala Desinghu (Scientific Computing Consultant)

Website https://osgconnect.github.io/osg-ahm-17

71 Data Management

Speaker: Mats Rynge (USC / Information Sciences Institute)

Website https://osgconnect.github.io/osg-ahm-17

72 Adding Resources from Amazon AWS

Speaker: Mats Rynge (USC / Information Sciences Institute)

73 Close / What's next?

12:30 Lunch

OSG Council Meeting: Remote https://IU.zoom.us/j/828138311

Convener: Dr David Swanson (University of Nebraska-Lincoln)

Minutes F2F2017AHMnotes.pdf

74 Campus / User Support update

Speaker: Prof. Robert Gardner (University of Chicago)

Slides https://docs.google.com/presentation/d/1U_wm4HSJ3Oj5o4EJMSFV-qUNYFGAHXJjNbNhL0X-Yx4/edit?usp=sharing

75 Security update

Slides osg-council-sec-update-2017-03.pdf

76 RR: IU (Rob)

77 RR: Rob (Globus)

78 TBD

15:30 Afternoon Break

OSG Council Meeting: Remote https://IU.zoom.us/j/828138311

Convener: Dr David Swanson (University of Nebraska-Lincoln)

Minutes F2F2017AHMnotes.pdf