All Tutorials

  • Fri Feb 28, 1:00 pm - 3:00 pm
    Walter Library

    Matlab currently is one of the most practical software used for numerical calculations. This tutorial will introduce the basic components of general purpose GPU (GPGPU) computing that can dramatically accelerate some Matlab applications. In addition to accessing the hardware resources (Cascade cluster, Koronis and GPUT nodes), we will discuss what type of applications can be run, how to execute the calculations on GPU device, and what kind of performance gains it can provide.

    A hands-on practice session will follow the lecture. Provided examples will enable the attendees to get direct experience of porting a matlab code and executing it on GPU and CPU, so that one can compare the performance and evaluate its enhancement by GPU.

  • Tue Feb 25, 10:00 am - 3:00 pm
    Walter Library

    The tutorial will consist of lectures and hands-on exercises covering the following topics: MSI’s GPGPU resources, basics of GPU Computing with CUDA and better use of memory hierarchy for performance enhancement.

  • Wed Feb 19, 1:00 pm - 4:00 pm
    Walter Library

    Instructor: Rob Mervis, CLC Bio

    This hands on tutorial accompanies the morning lecture. The tutorial is limited to 18 registrants but if you are interested and can't register, still stop by and we will try to fit you in. Bringing your own laptop is encouraged.

  • Wed Feb 19, 9:00 am - 1:00 pm
    Walter Library

    Instructor: Rob Mervis, CLC Bio

    An Introduction to Analysis of Next Generation Sequencing Data using the CLC Genomics Workbench and Genomics Server. MSI has purchased licenses to a new commercial comprehensive bioinformatics framework, to co-exist along with the open-source Galaxy. CLC Genomics Workbench offers well-integrated easy-to-use analysis pipelines for many Next-Generation Sequencing (NGS) applications. This one-day course will be a demonstration of the types of applications and work-flows that can be performed on deep sequencing data generated by the latest instruments from Illumina, Life Technologies (SOLiD and Ion Torrent), Roche/454 and others.

    Applications include the following (Please enter in the comment field up to 3 items from the itemized list below of most importance to you):

    · Data import – Raw sequence reads (FASTQ, .sff etc.) and aligned reads (SAM/BAM)

    · Curating reference sequences with annotations of interest

    · Working with Annotation Tracks

    · Read mapping to reference sequence(s) and Local Re-alignment

    · Variant detection, filtering and annotation

    · De novo assembly

    · Transcriptome assembly

    · Digital gene expression analysis by RNA Sequencing

    · ChIP Seq Analysis

    · Small RNA analysis

    · BLAST - Find and compare genes, protein products and place contigs

    · Workflows- Visually Creating and Editing Analysis Pipelines

    An overview of the CLC Genomics Server including basic user-side configuration and best practice use can also be discussed, time permitting.

    9 AM – noon: lecture style overview in Walter Library 402 on the above topics, highlighting the topics most requested in the comment field at registration

    Noon – 1 PM: lunch, pizza will be served

    1 PM – 4 PM:SEPARATE REGISTRATION Hands-on exercises in Walter Library 575. For this part, please register for tutorial titled:CLC Genomics Workbench Hands On Tutorial

  • Tue Feb 18, 1:00 pm - 4:00 pm
    Walter Library

    This half-day tutorial provides an introduction on how to write a parallel program using OpenMP and will help researchers write better and portable parallel codes for shared-memory Linux nodes. The tutorial will focus on basic OpenMP directives for loop parallelization, and OpenMP routines

  • Thu Feb 13, 1:00 pm - 3:00 pm
    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. Attendees should have a basic knowledge of Linux and rudimentary knowledge of a programming language.

  • Thu Jan 30, 1:00 pm - 3:00 pm
    Walter Library

    Instructors: Sean Geronimo Anderson, Nancy Rowe

    This tutorial is geared to new MSI users and will provide an introduction to the facilities and computational resources at MSI. The quick start portion of the tutorial will provide instructions for accessing these resources such as setting up accounts, accessing the various machines, etc. We will conclude with a brief introduction of the MSI Unix environment, including hands-on examples. The UNIX operating system is a fundamental part of the MSI experience for people using the MSI 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 an introduction to using the UNIX operating environment to navigate around and use MSI resources.

  • Thu Dec 19, 1:00 pm - 4:00 pm
    Walter Library

    The Intel Xeon PHI accelerator was recently released, and MSI now has PHI nodes available to users in the phi queue on cascade. This tutorial will provide the basic information needed to:

    1. Explain the hardware of the Intel PHI.

    2. Determine whether the PHI coprocessor could be beneficial for their application's performance.

    3. Port their codes to use the Intel PHI, using native or offload mode.

    4. Explain how to optimize the performance of a code for the PHI coprocessor.

    5. Use the PHI in offload mode for relevant MKL routines.

    6. Give an example of a code that uses the PHI to achieve performance gains.

  • Wed Nov 20, 1:00 pm - Thu Nov 21, 4:00 pm
    Walter Library

    This two day tutorial (held from 1:00pm to 4:00pm on both days, Nov 20 & 21) covers topics typical of sequencing experiments in eukaryotic species with high-quality genomes and genome annotation available. Participants are expected to be familiar with next-generation sequence data and basic theory of variant detection.

    Participants will perform analyses from start to finish with the goal of identifying SNP variants using data from a de-identified human DNA sample. This will include (1) sample QA/QC, (2) mapping via BWA, (3) post-processing of alignment files to remove PCR duplicates, re-calibrate basecalls and cleanup regions near indels, (4) genotype calling, (5) SNP annotation, and (6) SNP filtering and quality re-calibration.

  • Thu Nov 7, 2:30 pm - 4:00 pm
    Walter Library

    In this tutorial/webinar by nVidia, Application codes that will be covered include,

    • NAMD


    • Amber

    • LAMMPS

    • Desmond

    • HOOMD-Blue

    • GAMESS

    • Gaussian

    • NWChem

    • Octopus

    • Quantum Espresso

    • ParaChem

    • VASP

    Tutorial Attendees:

    If you plan on attending the tutorial then please register for it.

    Webinar Information:

    If you plan on attending the webinar ONLY, here is meeting information,

    Meeting information
    Topic: GPU-accelerated MD & QC
    Date: Thursday, November 7, 2013
    Time: 12:30 pm, Pacific Standard Time (San Francisco, GMT-08:00)
    Meeting Number: 621 179 241
    Meeting Password: Gpumdqc1
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    Go to
    Audio conference information
    Toll-free dial-in number (U.S. and Canada): (800) 214-4489, x7690906#
    International dial-in number: (404) 410-4582, x7690906#
    Conference code: 7690906#
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