All Tutorials

  • Tue Aug 13, 1:00 pm - 3:00 pm
    575
    Walter Library

    This tutorial will help users learn the basics of compiling and debugging their code on MSI systems. Particular attention will be paid to code written in Fortran, C, and C++. Basic methods for debugging will be outlined, with users being able to explore different debugging tools. This tutorial will focus primarily on compiling serial programs, but brief information on compiling and debugging parallel programs will also be given.


    Prerequisites: Basic knowledge of Linux, rudimentary knowledge of a programming language


  • Thu Aug 8, 1:00 pm - 3:00 pm
    575
    Walter Library

    This tutorial will briefly introduce MSI systems, remote access, and job submission systems, before giving a more detailed tour of hardware and software resources of particular utility to students and researchers in the physical sciences.


    Prerequisites: Basic knowledge of Unix-like systems and command line. Attendance at “Introduction to MSI” is helpful but not required, as that material will be covered in summary form only.


  • Tue Jul 30, 1:00 pm - 3:00 pm

    ProteinPilot™ is a proteomics software program used for analysis of peptide tandem mass spectrometry data and for relative quantification of proteins using the iTRAQ® technology and other modes of stable isotope labeling. Raw data acquired on a mass spectrometer such as Orbitrap-Velos is searched against protein sequence databases; the Paragon scoring algorithm provides confidence levels for protein hits, and the ProGroup algorithm tool (PMID: 17533153) groups related and homologous proteins.The tutorial will include an introduction to the software followed by iTRAQ® Data analysis workflow and FDR analysis overviews within Galaxy-P.


    This tutorial is a webcast utilizing UMConnect. Please register as usual. Registered users will receive meeting information by email within 24 hours of the start date. Please visit http://www.oit.umn.edu/umconnect/ to ensure that your system meets the minimum requirements necessary to participate in this webinar.


  • Tue Jul 23, 10:00 am - 4:00 pm
    575
    Walter Library

    This one-day, hands-on workshop provides an introduction on how to write a parallel program using MPI and will help researchers write better and portable parallel codes for distributed-memory Linux clusters. The tutorial will focus on basic point-to-point communication and collective communications, which are the most commonly used MPI routines in high-performance scientific computation. In addition, the advantage of using MPI non-blocking communication will be introduced. Each session of the workshop will combine a lecture with hands-on practice. The lecture will introduce basic principles, and the hands-on portion will focus on the use of MPI principles via examples.


    Session 1: Introduction to basic concepts of MPI, centering on point-to-point communication.


    Session 2: MPI collective communications including broadcast, gather, scatter, and All-to-All.


    Programming will be done in Fortran and C, so any background in these two languages will be helpful.


  • Thu Jul 18, 1:00 pm - 3:00 pm
    575
    Walter Library

    This tutorial will help users learn the basics of parallel computation methods, including strategies for collecting calculations together for parallel execution. A brief description of parallel programming using MPI message passing will be given. This will be a fast crash course on the most basic parallel computation and programming methods. Examples of how to compile and execute simple parallel programs will be given.


  • Thu Jul 11, 1:00 pm - 3:00 pm
    575
    Walter Library

    Matlab is one of the most practical software packages used for numerical calculations and system design. Matlab applications, however, can run much slower compared to FORTRAN and C codes for the same kind of applications. Matlab code debugging is an unavoidable component of the application development. This tutorial will teach users how to use Matlab’s debugging and profiling tools in addition to the basic techniques to write efficient Matlab codes.


    A hands-on practice will follow the lecture. Provided examples will enable the users to use the debug and profiling tools for writing an efficient Matlab code. Attendees are also encouraged to bring in your application codes. MSI staff will help you debug the code and/or improve the code performance.


  • Tue Jul 9, 1:00 pm - 3:00 pm
    575
    Walter Library

    This tutorial will introduce users to MSI systems, outlining the hardware available, and introducing the module and queueing systems, as well as methods for remote access and file transfer. Users will be shown how to construct queue scripts and submit their calculation jobs on MSI’s high-performance systems. The features of different systems will be compared so that users may determine which might best suit their research needs. Software options and availability will be discussed.


  • Mon Jul 1, 9:00 am - 4:00 pm
    575
    Walter Library

    Due to overwhelming demand, this tutorial initially held on June 25, 2013, is being presented a second time. Here is a brief description:


    Python is a general purpose programming language with a rich syntax and structure. You can learn to use Python and see almost immediate gains in productivity relative to programming with other languages. Python has many modules specializing in various topics of interest to the scientific community and is used as an interface for numerous scientific packages.


    The morning section will provide an introduction to Python. Simple and advanced data types, variable assignment, control structures, mathematical and logical operators, program input and output, and functional programming will be discussed.


    The afternoon section will cover advanced features of Python relevant to high performance computing. Topics will include efficient data processing with NumPy, integrating compiled routines into python programs, and techniques for using python to drive parallel supercomputing tasks.


  • Thu Jun 27, 1:00 pm - 3:00 pm
    575
    Walter Library

    Every experienced developer has a preferred method and toolchain for writing code. This tutorial will help users choose the right tools and improve habits for a better experience with custom and third-party source codes. We begin with a look at build systems (e.g., Make, CMake) and version control (e.g., SVN, Git) for project management. Through examples we will demonstrate: a) generating code documentation for the web, b) unit testing, c) debugging, and d) profiling and optimization. This tutorial pulls examples from multiple languages (C/C++, FORTRAN, Java and Python) to demonstrate that best practices are language agnostic.


    Prerequisites: Experience with at least one programming language and the Unix shell environment.


  • Tue Jun 25, 9:00 am - 4:00 pm
    575
    Walter Library

    Python is a general purpose programming language with a rich syntax and structure. You can learn to use Python and see almost immediate gains in productivity relative to programming with other languages. Python has many modules specializing in various topics of interest to the scientific community and is used as an interface for numerous scientific packages.


    The morning section will provide an introduction to Python. Simple and advanced data types, variable assignment, control structures, mathematical and logical operators, program input and output, and functional programming will be discussed.


    The afternoon section will cover advanced features of Python relevant to high performance computing. Topics will include efficient data processing with NumPy, integrating compiled routines into python programs, and techniques for using python to drive parallel supercomputing tasks.


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