All Tutorials

  • Tue Feb 21, 10:00 am - 4:00 pm
    575
    Walter Library

    OpenMP is a parallel programming interface for shared-memory architectures and is available on all the core clusters. This one-day workshop will help users to use OpenMP programming more productively for high-performance computing by addressing the different aspects of OpenMP, such as parallel and worksharing constructs, data scope attribute clauses, and synchronization constructs. In addition, the new features in the OpenMP II standard will be covered.


    A hands-on practice will follow the lecture. Examples we provide will enable you to insert OpenMP directives for different parallel tasks and data scope attribute clauses. You are also encouraged to bring in your serial application codes. The instructors will help you parallelize the code with OpenMP.


  • Thu Feb 2, 1:00 pm - 3:00 pm
    575
    Walter Library

    MATLAB is a general computational platform for rapid development of programs. It also has several toolboxes that allow specialized computation on images. One such toolbox, the Image Processing Toolbox, has hundreds of functions that can be used to perform operations on images.


    The various image processing operations can be classified into reading, processing and writing images. We will begin the tutorial by performing simple image reading operations on jpeg, gif, etc. We will also discuss reading complex image formats like DICOM. We will then perform various image processing operations like filtering, visualization and analysis. We will output these images to different formats to be read by other applications.


    Finally, we will conclude with hands-on practice using various example images. You are also welcome to bring specific questions and problems that you would like to discuss.


  • Thu Jan 26, 9:30 am - 4:00 pm
    575
    Walter Library

    This one-day work shop on general purpose GPU computing (GPGPU) is hosted jointly by the Supercomputing Institute and the Department of Electrical and Computer Engineering. The workshop will consist of a lecture and hands-on exercises covering the following topics: MSI’s GPGPU resources, basic CUDA programing, use of acceleration tools, and memory hierarchy for performance enhancement.


  • Tue Jan 24, 1:00 pm - 3:00 pm
    575
    Walter Library

    The UNIX operating system is a fundamental part of the MSI experience for people using the labs’ Linux workstations and core systems. Many of MSI’s scientific codes require that the user understand basic UNIX operating commands and functionality. This tutorial will give the novice user a hands-on guide to using the UNIX operating environment to navigate around and use MSI resources.


  • Wed Dec 14, 1:00 pm - 3:30 pm
    419
    University Square

    Galaxy (http://usegalaxy.org; http://galaxy.msi.umn.edu) is a bioinformatics workflow framework designed to provide a web interface to bioinformatics tools that are routinely used though generally accessed by command line. The ease with which users can share data and results, review analytical logs and create analytical pipelines contributes to the user-friendliness of the Galaxy tool. Within this framework, biologists can carry out a variety of computational analyses including meta-genomics, gene expression profiling (RNA-seq), selective re-sequencing (ChIP-seq), and Next Generation Sequencing (NGS) sequence data manipulations, without needing any programming skills. Statistical tools are also available through Galaxy. Initially developed at Pennsylvania State University, this international open source platform was adopted by the University of Minnesota as the informatics component of the Minnesota partnership HAITI (High throughput sequence Analysis Infrastructure Technology Investigation) project and implemented at MSI. Galaxy has become a key informatics resource for University of Minnesota researchers. In this tutorial, participants will become familiar with the layout of Galaxy, the scope of the tools provided, getting data into and out of Galaxy, the execution of selected tasks, the creation and manipulation of workflows, the modification of histories and their attributes, the sharing of data, workflows and histories with other users, and visualizing genomic tracks of information. For more information about Galaxy, visit http://galaxy.msi.umn.edu/home or view a Galaxy video tour at http://www.openhelix.com/galaxy.


    Access to galaxy.msi.umn.edu requires an active MSI account.


  • Thu Dec 8, 1:00 pm - 3:15 pm
    402
    Walter Library

    OpenFOAM is an open source software package which is designed to scale well on large distributed memory systems. While originally written for CFD, with its open source strategy and a large user base OpenFOAM has grown to be a general purpose finite element toolbox. This tutorial will cover the basics of using OpenFOAM to set up, solve, and view results for a variety of physical models. Techniques for running OpenFOAM on thousands of cores will be discussed. A hands-on session in 575 Walter will immediately follow this one-hour presentation.


    Presentation: 1:00-2:00 in 402 Walter


    Optional hands-on session: 2:15-3:15 in 575 Walter


  • Wed Dec 7, 1:00 pm - 3:00 pm
    575
    Walter Library

    ProTIP is a package of services that integrates analysis tools into the TROPIX framework. As part of the ProTIP project, standard analysis tools such as Sequest, X!Tandem, and Scaffold are executable from within the TINT graphical interface.


    The tutorial will include a walk-through on using ProTIP and new features included in ProTIP.


  • Tue Dec 6, 1:00 pm - 2:00 pm

    The technology behind data acquisition and especially image acquisition have grown enormously over the years. Data sets of size greater than 1GB are common. Such datasets present a unique problem during the visualization process. They need large memory, powerful CPUs and good graphic capabilities in the form of graphics cards. Such technologies are expensive for individual researchers to buy and maintain, so MSI has been working on creating such an infrastructure.


    In this tutorial, we will introduce the remote visualization capabilities of MSI. We will discuss the details of the various visualization systems users can access. We will also discuss the software, VirtualGL, for connecting to these systems.


    This tutorial utilizes UMConnect and takes place entirely online. Please register as usual. Registered users will receive meeting information by email within 24 hours of the workshop 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.


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

    MSI has a new high-performance computing system named Koronis. It features an SGI Altix UV 1000, one of the largest global shared memory (GSM) systems available. Koronis offers unprecedented opportunities for NIH researchers to conduct memory-intensive calculations. At the same time, it poses great computational challenges from the system-memory complexity that - combined with the flexibility in the selection of the number of computing cores - can severely degrade the performance. This tutorial will help Koronis users improve application performance. We will show examples of programs that can take advantage of this computer. We will also describe tactics that can be used in the calculations within the CPUset regime to achieve optimal performance.


  • Tue Nov 29, 1:00 pm - 3:00 pm
    575
    Walter Library

    Image manipulation includes such functions as cropping, rotating, resizing, adding text, photo retouching, color conversion, and much more. Image manipulation can be used when preparing photos for print or the web or when creating animation. MSI has several programs that can be used for image manipulation; this tutorial will introduce you to three of those programs.


    Adobe Photoshop is the most popular commercial package for image manipulation. ImageMagick is a free collection of programs to display, manipulate and convert images from one format to another. ImageMagick can be used from a GUI or from the command line. GNU Image Manipulation Program (Gimp) is a free, general image processing program for editing images.


    This tutorial serves varying interest groups ranging from medicine, biology, chemistry, physics, material sciences, geophysics, astronomy, and engineering.


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