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  • Trainings offered on Beagle

Introduction to Python:

  • Trainer: Ana Marija Sokovic
  • Outline: This introductory class is mainly intended for people who have just started using Python or consider using it on Beagle (Cray XE6) and maybe have a previous experience in programming languages like Matlab or R.
  • Topics will include:
    • Python on Beagle
    • Datatypes, functions
    • Modules, plotting, iteration
    • Object orientation, debugging
    • NumPy arrays
    • SciPy
    • Importing and cleaning data in Python

If you would like to get slides from previous training or have requests related to what you would like to learn about in future Python related trainings please write to: anamarija@uchicago.edu

Introduction to Beagle2:

  • Trainer: Lorenzo Pesce
  • Outline: This introductory class is mainly intended for people who have just started working on the Cray XE6 Beagle2 or are considering using it. It aims at familiarizing new users with the hardware and software architecture (e.g., compilation, submission). Cray’s performance analysis tools will briefly be introduced as well. We plan to include small practical exercises about compilation, data transfer and submission of jobs. Users are strongly invited to ask specific questions about how to port their specific calculations to Beagle and how to submit jobs.
  • Topics will include (depending upon users desires and abilities):
    • General overview of Beagle2’s team and the computational institute
    • overview of Beagle2’s Cray XE6 system architecture
    • basic access and navigation operations
    • using compilers and applications
    • appropriate use of local and network filesystems
    • submitting jobs and monitoring jobs
    • data transfer
    • Specific topics requested by users (e.g., using R or Matlab on Beagle2)
  • Requirements: Open to every Beagle user and people interested into becoming users; users need to have access to Beagle and should bring their laptop to do the exercises and to read the slides that will be distributed electronically to the users that RSVP.

Presentation material can be found here: Beagle2 Intro

HPC Python

  • Trainer: Ana Marija Sokovic
  • Topics will include:
    • Get a better grasp of Numpy, Cython, MPI for Python, and profilers
    • Learn how Python abstracts the underlying computer architecture
    • Use profiling to find bottlenecks in CPU time and memory usage
    • Write efficient programs by choosing appropriate data structures
    • Speed up matrix and vector computations
    • Use tools to compile Python down to machine code
    • Manage multiple I/O and computational operations concurrently
    • Convert multiprocessing code to run on a local or remote cluster
    • Solve large problems while using less RAM
  • If you would like to get slides from previous training or have requests related to what you would like to learn about in future Python related trainings please write to: anamarija@uchicago.edu

Parallel scripting lectures

  • Topics will include:
    • Why we need to pack jobs on Beagle: data location hierarchies and types of parallel problems
    • How to write pbs/bash scripts that run many applications sequentially: Megaseq
    • How to write swift scripts that run many applications sequentially and in parallel : SwiftSeq
    • Quick introduction to Hadoop (do we have it?)
    • Hands on user problem solution (if there are any)

HPC on Beagle: CPUs and GPUs

  • Beagle hardware in more detail
  • HPC and parallel processing: data location hierarchies and movement
  • HPC problems on Beagle:
  • °Embarrassing parallel tasks (see parallel scripting lecture): bash or Swift

    °Threaded applications: OpenMP

    °GPU applications: options

    °Large scale distributed applications: MPI

    °Mixed applications

  • Compilers, how to use them basic options
  • Parallel debugger
  • Parallel profiler
  • Hands on user problem solution (if there are any)

Getting started on the Cray XE6 Beagle and parallel scripting with Swift

  • Trainers: The catalysts and administrators of Beagle team at the Computational Institute of the University of Chicago and Argonne National Laboratory.
  • Outline: This introductory class is mainly intended for people who have just started working on the Cray XE6 Beagle. It aims at familiarizing new users with the hardware and software architecture (e.g., compilation, submission). Cray’s performance analysis tools will briefly be introduced as well. We will have a lecture which involves small practical exercises about compilation, data transfer and submission of jobs. Users are strongly invited to ask specific questions about how to port their specific calculations to Beagle and how to submit jobs.
  • Topics will include (depending upon users desires and abilities):
    • overview of Beagle’s Cray XE6 system architecture
    • basic access and navigation operations
    • using compilers and applications
    • appropriate use of local and network filesystems
    • Introduction to Parallel scripting with Swift (see also the paper “Swift: A language for distributed parallel scripting” for examples of using this parallel scripting language)
    • submitting jobs and scheduler operations
  • Requirements: Open to every Beagle user, users need to have access to beagle and bring their laptop for the exercises and to read the slides that will be distributed electronically to the users that RSVP.

Day of the Beagle Symposium

“Scientific Discovery on the Computation Institute/BSD Cray ‘Beagle’ Supercomputer”

April 23, 2013
8:30 AM – 5:00 PM
Searle 240, University of Chicago

RVSP by April 17, 2013
ninfa@ci.uchicago.edu

Description:
For Charles Darwin, the HMS Beagle was the ship for the historic voyage in 1831 that inspired his later work on the origin of species. For the University of Chicago, “Beagle” is an 18,000-core Cray XE6 supercomputer that is one of the most powerful supercomputers dedicated to biomedical research. Since its launch in early 2011, Beagle has supported over 80 research projects, more than 300 users and has resulted in over 30 publications. On April 23rd, a “Day of the Beagle” symposium will discuss the innovative research made possible to date by Beagle, with speakers representing the fields of genomics, neurobiology, molecular biology and medicine.

Day of the Beagle Symposium Poster

Day of the Beagle Symposium schedule:

8:30 – 9:00 Continental breakfast

9:00 – 9:30 Ian Foster & Conrad Gilliam
Overview of the Cray Beagle and Diversity of Science on Beagle

9:30 – 10:15 Kazutaka Takahashi & Nicholas Hatsopoulos (PI)
Computation and analysis of time varying large-scale networks of spiking neurons in primary motor cortex using massively-parallel supercomputers

10:15 – 10:30 Coffee Break

10:30 – 11:15 Yves Lussier (PI) & Haiquan Li
Intergenic DNA’s role in complex disease unveiled by supercomputer-obligated analyses of BIG data

11:15 – 12:00 Greg Tietjen & Ka Yee Lee (PI)
Elucidating the molecular details of phosphatidylserine membrane recognition in immune response

12:00 – 13:00 Lunch

12:45 – 13:00 Esmael Jafari Haddadian
Using Beagle in an actual undergraduate biology course

13:00 – 13:45 Benoit Roux (PI)
Theoretical studies of biomolecular systems on Beagle: highly-scalable computational strategies

13:45 – 14:30 Edwin Munro (PI), TaeYoon Kim
Using agent-based models and supercomputing to probe self-organized contractility and stress dissipation in active cytoskeletal networks

14:30 – 14:45 Coffee Break

14:45 – 15:30 Jason J. Pitt, Chai Bandlamudi & Kevin White (PI)
Genome sequence analysis workflows

15:30 – 16:15 Elizabeth McNally (PI), Megan Puckelwartz & Lorenzo Pesce
Supercomputing for the parallelization of whole genome sequence analysis

16:15 – 16:45 Carlos Sosa (Cray)
Cray Supercomputers – Life Sciences

16:45 – 17:00 Ian Foster – Closing Remarks & Future Directions