CHPC Presentations - Archive

CHPC has developed a series of courses to help users make the most of the use of CHPC resources. We continue to add to and improve this series and present it every Fall-Winter. During Spring we present an abbreviated series of our most popular talks. We welcome suggestions for additional presentations.

Unless otherwise specified, all talks are held at 1:00 p.m. in the INSCC Auditorium (rm 110).

View Upcoming Presentations

Using Python for Scientific Computing

No upcoming schedule for this presentation.
Presented: March 4th, 2014 1:00pm
By:  Wim Cardoen
   

LOCATION: INSCC Auditorium (Room 110)
TIME: 1:00 - 2:00 p.m.

In this talk we will discuss several features which make Python a viable tool for scientific computing:

  • 1. strength and flexibility of the Python language
  • 2. mathematical libraries (numpy,scipy,..)
  • 3. graphical libraries (matplotlib,..)
  • 4. extending Python using C/C++ and Fortran

Download recording (October 3, 2013)


Introduction to GPU Programming

No upcoming schedule for this presentation.
Presented: February 27th, 2014 1:00pm
By:  Wim Cardoen
   

LOCATION: INSCC Auditorium (Room 110)
TIME: 1:00 - 2:00 p.m.

In this talk we will first of all explain why GPUs can form an alternative to traditional CPUs in the field of high-performance computing. Subsequently, we will spend some time on discussing the hardware especially the GPU cards as they are installed on several Ember nodes.

In the main part of the talk we will show a few examples where the basic concepts such as thread, block, and grid will be elucidated as well as the concept of shared memory.

The last part of the presentation covers topics such as compilation, mathematical libraries,..

Experience with C/C++ is strongly advised.

Download recording (October 22, 2013)


Using Gaussian09 and Gaussview

No upcoming schedule for this presentation.
Presented: February 25th, 2014 1:00pm
By:  Anita Orendt
   

LOCATION: INSCC Auditorium (Room 110)
TIME: 1:00 - 2:00 p.m.

This presentation will focus on the use of Gaussian09 and Gaussview on the CHPC clusters. Batch scripts and input file formats will be discussed. Parallel scaling and timings with the different scratch options will also be presented, along with a discussion of scratch needs of Gaussian09. Finally several demonstrations on the use of GaussView to build molecules, input structures, set up input files and to analyze output files will be presented.

Download recording (October 10, 2013)


Protected Environment, AI and NLP Services at CHPC, HSEB, 1:00-2:00 p.m.

No upcoming schedule for this presentation.
Presented: February 20th, 2014 2:00pm
By:  Sean Igo
   

LOCATION: HSEB 2908
TIME: 1:30 - 2:30 p.m.

This presentation is an overview of the equipment and software presently available at CHPC for Natural Language Processing (NLP) and includes an overview of the HIPAA-compliant protected environment for storage and processing of PHI data at CHPC. It will also cover related resources for general Artificial Intelligence use such as machine learning and data mining, and will include a brief description of CHPC's general resources and how to access them.


Introduction to Parallel Computing

No upcoming schedule for this presentation.
Presented: February 18th, 2014 1:00pm
By:  Martin Cuma
   

LOCATION: INSCC Auditorium (Room 110)
TIME: 1:00 - 2:00 p.m.

In this talk, we first discuss various parallel architectures and note which ones are represented at the CHPC, in particular, shared and distributed memory parallel computers. A very short introduction into two programming solutions for these machines, MPI and OpenMP, will then be given followed by instructions on how to compile, run, debug and profile parallel applications on the CHPC parallel computers. Although this talk is more directed towards those starting to explore parallel programming, more experienced users can gain from the second half of the talk, that will provide details on software development tools available at the CHPC.

Download recording (September 12, 2013)


Introductory Linux for HPC Part 2

No upcoming schedule for this presentation.
Presented: February 13th, 2014 1:00pm
By:  Martin Cuma
   

LOCATION: INSCC Auditorium (Room 110)
TIME: 1:00 - 3:00 p.m.

In the second of this two-part class we will learn how to write simple shell scripts and how to compile and run programs. Each class is two hours.

You will need to bring a laptop with a functional connection to the campus WiFi. If you do not have an account with CHPC, please register for the class by sending an email indicating that you want to participate in this class and need an account to: issues@chpc.utah.edu. Please include your name, department, e-mail, phone number and your University of Utah uNID. CHPC accounts will be provisioned for you for the duration of this class.


Introductory Linux for HPC Part 1

No upcoming schedule for this presentation.
Presented: February 11th, 2014 1:00pm
By:  Martin Cuma
   

LOCATION: INSCC Auditorium (Room 110)
TIME: 1:00 - 3:00 p.m.

In the first of this two-part class we will talk about ways to connect to CHPC Linux systems. Then we will go over the most important Linux commands and learn how to edit files with the VI editor. Each class is two hours.

You will need to bring a laptop with a functional connection to the campus WiFi. If you do not have an account with CHPC, please register for the class by sending an email indicating that you want to participate in this class and need an account to: issues@chpc.utah.edu. Please include your name, department, e-mail, phone number and your University of Utah uNID. CHPC accounts will be provisioned for you for the duration of this class.

Download recording (September 17, 2013)


Overview of CHPC

No upcoming schedule for this presentation.
Presented: February 6th, 2014 1:00pm
Supplemental Materials:  OverviewCHPC-Spring2014.pptx
By:  Wim Cardoen
   

LOCATION: INSCC Auditorium (Room 110)
TIME: 1:00 - 2:00 p.m.

This presentation gives users new to CHPC, or interested in High Performance Computing an overview of the resources available at CHPC, and the policies and procedures to access these resources.

Topic covered will include:

  • The platforms available
  • Filesystems
  • Access
  • An overview of the batch system and policies
  • Service Unit Allocations

Download recording (September 5, 2013)


Introduction to BRISC Services

No upcoming schedule for this presentation.
Presented: November 26th, 2013 1:00pm
By:  Bernard LaSalle
   

LOCATION: INSCC Auditorium (Room 110)
TIME: 1:00 - 2:00 p.m.

The Biomedical Research Informatics Service Core (BRISC) provides "point of service" response by combining administration, technical staff and collaborations with key HSC and main campus information technology resources. BRISC has two service locations: the Health Science Center Information Technology office (615 Arapeen) and the Center for Clinical and Translational Science (4B475 SOM). In addition to custom programming BRISC supports the Research Electronic Data Capture (REDCAp) application and the Federated Utah Research Translational Health e-Repository (FURTHeR) informatics platform.


Fast Parallel I/O at the CHPC

No upcoming schedule for this presentation.
Presented: November 19th, 2013 1:00pm
Supplemental Materials:  MPI-IO13.pdf
By:  Martin Cuma
   

LOCATION: INSCC Auditorium (Room 110)
TIME: 1:00 - 2:00 p.m.

In this talk we explain how to perform fast parallel I/O operations on the CHPC computers. It should be beneficial for all users who are interested in speeding up their parallel applications via faster file operations. First, we describe in detail PVFS (Parallel Virtual File System), installed on arches. Then we go over several examples on how to perform parallel I/O on this file system, in particular, MPI-I/O extension to the MPI standard and native PVFS function calls. Subsequently we detail ways how to compile and run MPI-I/O applications on PVFS. We conclude the talk with an insight into some more advanced aspects of MPI-I/O.

Download recording (November 19, 2013)


Hybrid MPI-OpenMP Programming

No upcoming schedule for this presentation.
Presented: November 14th, 2013 1:00pm
Supplemental Materials:  MPI-OMP13.pdf
By:  Martin Cuma
   

LOCATION: INSCC Auditorium (Room 110)
TIME: 1:00 - 2:00 p.m.

In this talk we will introduce hybrid MPI-OpenMP programming model designed for distributed shared memory parallel (DSMP) computers. The CHPC clusters are representative of this family having two or more shared memory processors per node. OpenMP generally provides better performing alternative for parallelization inside a node and MPI is used for communication between the distributed processors. We will discuss cases when hybrid programming model is beneficial and provide examples of simple MPI-OpenMP codes.

Download recording (November 14, 2013)


Introduction to Programming with OpenMP

No upcoming schedule for this presentation.
Presented: November 12th, 2013 1:00pm
Supplemental Materials:  IntroOpenMP13.pdf
By:  Martin Cuma
   

LOCATION: INSCC Auditorium (Room 110)
TIME: 1:00 - 2:00 p.m.

This talk introduces OpenMP, an increasingly popular and relatively simple shared memory parallel programming model. Two parallelizing schemes, parallel do loops and parallel sections, were detailed using examples. Various clauses that allow user to modify the parallel execution were also presented, including sharing and privatizing of the variables, scheduling, synchronization and mutual exclusion of the parallel tasks. Finally, few hints were given on removing loop dependencies in order to obtain effective parallelization.


Introduction To Programming With MPI

No upcoming schedule for this presentation.
Presented: November 7th, 2013 1:00pm
Supplemental Materials:  IntroMPI13.pdf
By:  Martin Cuma
   

LOCATION: INSCC Auditorium (Room 110)
TIME: 1:00 - 2:00 p.m.

This course discusses introductory and selected intermediate topics in MPI programming. We base this presentation on two simple examples and explain the MPI parallel development of them. The first example encompasses MPI initialization and simple point to point communication (which takes place between two processes). The second example includes introduction to collective communication calls (where all active processes are involved) and options for effective data communication strategies, such as derived data types and packing the data. Some ideas on more advanced MPI programming options are discussed in the end of the talk.

Download recording (November 7, 2013)


Introduction to I/O in the HPC Environment

No upcoming schedule for this presentation.
Presented: October 24th, 2013 1:00pm
By:  Brian Haymore
   

LOCATION: INSCC Auditorium (Room 110)
TIME: 1:00 - 2:00 p.m.

This presentation will introduce users to the I/O performance characteristics of the various types of storage available to users of CHPC systems. Our goal for the presentation is to increase user understanding of various I/O patterns and how they relate to the shared computing environments at CHPC.

Topics will include general overview of I/O, best practices, file operations, application I/O, as well as troubleshooting techniques. We will present examples to illustrate the impact and performance characteristics of common usage cases. We will conclude with an open discussion driven by users' questions.

Download recording (October 24, 2013)


Introduction to GPU Programming

No upcoming schedule for this presentation.
Presented: October 22nd, 2013 1:00pm
By:  Wim Cardoen
   

LOCATION: INSCC Auditorium (Room 110)
TIME: 1:00 - 2:00 p.m.

In this talk we will first of all explain why GPUs can form an alternative to traditional CPUs in the field of high-performance computing. Subsequently, we will spend some time on discussing the hardware especially the GPU cards as they are installed on several Ember nodes.

In the main part of the talk we will show a few examples where the basic concepts such as thread, block, and grid will be elucidated as well as the concept of shared memory.

The last part of the presentation covers topics such as compilation, mathematical libraries,..

Experience with C/C++ is strongly advised.

Download recording (October 22, 2013)


Using Gaussian09 and Gaussview

No upcoming schedule for this presentation.
Presented: October 10th, 2013 1:00pm
By:  Anita Orendt
   

LOCATION: INSCC Auditorium (Room 110)
TIME: 1:00 - 2:00 p.m.

This presentation will focus on the use of Gaussian09 and Gaussview on the CHPC clusters. Batch scripts and input file formats will be discussed. Parallel scaling and timings with the different scratch options will also be presented, along with a discussion of scratch needs of Gaussian09. Finally several demonstrations on the use of GaussView to build molecules, input structures, set up input files and to analyze output files will be presented.

Download recording (October 10, 2013)


Chemistry Packages at CHPC

No upcoming schedule for this presentation.
Presented: October 8th, 2013 1:00pm
By:  Anita Orendt
   

LOCATION: INSCC Auditorium (Room 110)
TIME: 1:00 - 2:00 p.m.

This presentation will focus on the computational chemistry related applications that are available on CHPC computer systems. An overview of the packages and their capabilities, focusing on details of how users can access the installations at CHPC, will be given. This talk is the precursor for a second talk scheduled for next week that will focus on the use of Gaussian 09 and GaussView.

Download recording (October 8, 2013)


Using Python for Scientific Computing

No upcoming schedule for this presentation.
Presented: October 3rd, 2013 1:00pm
By:  Wim Cardoen
   

LOCATION: INSCC Auditorium (Room 110)
TIME: 1:00 - 2:00 p.m.

In this talk we will discuss several features which make Python a viable tool for scientific computing:

  • 1. strength and flexibility of the Python language
  • 2. mathematical libraries (numpy,scipy,..)
  • 3. graphical libraries (matplotlib,..)
  • 4. extending Python using C/C++ and Fortran

Download recording (October 3, 2013)


Protected Environment, AI and NLP Services at CHPC, HSEB, 1:00-2:00 p.m.

No upcoming schedule for this presentation.
Presented: September 26th, 2013 1:30pm
By:  Sean Igo
   

LOCATION: HSEB 2908
TIME: 1:30 - 2:30 p.m.

This presentation is an overview of the equipment and software presently available at CHPC for Natural Language Processing (NLP) and includes an overview of the HIPAA-compliant protected environment for storage and processing of PHI data at CHPC. It will also cover related resources for general Artificial Intelligence use such as machine learning and data mining, and will include a brief description of CHPC's general resources and how to access them.


Debugging with Totalview

No upcoming schedule for this presentation.
Presented: September 26th, 2013 1:00pm
Supplemental Materials:  Totalview13.pdf
By:  Martin Cuma
   

LOCATION: INSCC Auditorium (Room 110)
TIME: 1:00 - 2:00 p.m.

This talk introduces Totalview, a debugger that has become a standard in the Unix code development comunity. After short introduction to its major features, we will present three examples, serial, parallel OpenMP and parallel MPI codes. Using these examples, we will show common and specific features for debugging these codes. We will also spend short time introducing Intel Thread Checker, which is an useful tool for OpenMP code checking. Finally, those interested can stay for an extra half hour, between 2pm and 2.30pm, for informal practical presentation of various useful Totalview features.

Download recording (September 26, 2013)


Mathematical Libraries at CHPC

No upcoming schedule for this presentation.
Presented: September 24th, 2013 1:00pm
By:  Martin Cuma
   

LOCATION: INSCC Auditorium (Room 110)
TIME: 1:00 - 2:00 p.m.

In this talk we introduce the users to the mathematical libraries that are installed on the CHPC systems, which are designed to ease the programming and speed-up scientific applications. First, we will talk about BLAS, which is a standardized library of Basic Linear Algebra Subroutines, and present few examples. Then we briefly focus on other libraries that are in use, including freeware LAPACK, ScaLAPACK, PETSc and FFTW.

Download recording (September 24, 2013)


Introductory Linux for HPC Part 2

No upcoming schedule for this presentation.
Presented: September 19th, 2013 1:00pm
By:  Martin Cuma
   

LOCATION: INSCC Auditorium (Room 110)
TIME: 1:00 - 3:00 p.m.

In the second of this two-part class we will learn how to write simple shell scripts and how to compile and run programs. Each class is two hours.

You will need to bring a laptop with a functional connection to the campus WiFi. If you do not have an account with CHPC, please register for the class by sending an email indicating that you want to participate in this class and need an account to: issues@chpc.utah.edu. Please include your name, department, e-mail, phone number and your University of Utah uNID. CHPC accounts will be provisioned for you for the duration of this class.


Introductory Linux for HPC Part 1

No upcoming schedule for this presentation.
Presented: September 17th, 2013 1:00pm
By:  Martin Cuma
   

LOCATION: INSCC Auditorium (Room 110)
TIME: 1:00 - 3:00 p.m.

In the first of this two-part class we will talk about ways to connect to CHPC Linux systems. Then we will go over the most important Linux commands and learn how to edit files with the VI editor. Each class is two hours.

You will need to bring a laptop with a functional connection to the campus WiFi. If you do not have an account with CHPC, please register for the class by sending an email indicating that you want to participate in this class and need an account to: issues@chpc.utah.edu. Please include your name, department, e-mail, phone number and your University of Utah uNID. CHPC accounts will be provisioned for you for the duration of this class.

Download recording (September 17, 2013)


Introduction to Parallel Computing

No upcoming schedule for this presentation.
Presented: September 12th, 2013 1:00pm
Supplemental Materials:  IntroPar13.pdf
By:  Martin Cuma
   

LOCATION: INSCC Auditorium (Room 110)
TIME: 1:00 - 2:00 p.m.

In this talk, we first discuss various parallel architectures and note which ones are represented at the CHPC, in particular, shared and distributed memory parallel computers. A very short introduction into two programming solutions for these machines, MPI and OpenMP, will then be given followed by instructions on how to compile, run, debug and profile parallel applications on the CHPC parallel computers. Although this talk is more directed towards those starting to explore parallel programming, more experienced users can gain from the second half of the talk, that will provide details on software development tools available at the CHPC.

Download recording (September 12, 2013)


XSEDE Resource Support at CHPC

No upcoming schedule for this presentation.
Presented: September 10th, 2013 1:00pm
Supplemental Materials:  XSEDE_ResourceSupportatCHPC.pdf
By:  Julia Harrison
   

LOCATION: INSCC Auditorium (Room 110)
TIME: 1:00 - 2:00 p.m.

In this short course we will introduce you to the resources available through XSEDE (Extreme Science and Engineering Discovery Environment) and initial steps required to access these resources. The University of Utah Campus Champion (Julia D. Harrison) has a small allocation on a few of these resources, and can help you with questions and support.

This course will go through:

  1. Current XSEDE Resources
  2. Signing up for an XSEDE User Portal (XUP) account
  3. Short review of User Responsibility and Security
  4. Requesting an allocation on XSEDE Resources
  5. Accessing allocated XSEDE resources
  6. Transfer of your files to XSEDE resources
  7. Short review of the XSEDE Computing Environment
  8. Signing up for XSEDE Training
  9. Where to Get Help on XSEDE

Download recording (September 10, 2013)


Overview of CHPC

No upcoming schedule for this presentation.
Presented: September 5th, 2013 1:00pm
By:  Wim Cardoen
   

LOCATION: INSCC Auditorium (Room 110)
TIME: 1:00 - 2:00 p.m.

This presentation gives users new to CHPC, or interested in High Performance Computing an overview of the resources available at CHPC, and the policies and procedures to access these resources.

Topic covered will include:

  • The platforms available
  • Filesystems
  • Access
  • An overview of the batch system and policies
  • Service Unit Allocations

Download recording (September 5, 2013)


Introduction to I/O in the HPC Environment

No upcoming schedule for this presentation.
Presented: March 28th, 2013 1:00pm
By:  Brian Haymore
   

LOCATION: INSCC Auditorium (Room 110)
TIME: 1:00 - 2:00 p.m.

This presentation will introduce users to the I/O performance characteristics of the various types of storage available to users of CHPC systems. Our goal for the presentation is to increase user understanding of various I/O patterns and how they relate to the shared computing environments at CHPC.

Topics will include general overview of I/O, best practices, file operations, application I/O, as well as troubleshooting techniques. We will present examples to illustrate the impact and performance characteristics of common usage cases. We will conclude with an open discussion driven by users' questions.

Download recording (October 24, 2013)


Hybrid MPI-OpenMP Programming

No upcoming schedule for this presentation.
Presented: March 26th, 2013 1:00pm
By:  Martin Cuma
   

LOCATION: INSCC Auditorium (Room 110)
TIME: 1:00 - 2:00 p.m.

In this talk we will introduce hybrid MPI-OpenMP programming model designed for distributed shared memory parallel (DSMP) computers. The CHPC clusters are representative of this family having two or more shared memory processors per node. OpenMP generally provides better performing alternative for parallelization inside a node and MPI is used for communication between the distributed processors. We will discuss cases when hybrid programming model is beneficial and provide examples of simple MPI-OpenMP codes.

Download recording (November 14, 2013)


Introduction to Programming with OpenMP

No upcoming schedule for this presentation.
Presented: March 21st, 2013 1:00pm
By:  Martin Cuma
   

LOCATION: INSCC Auditorium (Room 110)
TIME: 1:00 - 2:00 p.m.

This talk introduces OpenMP, an increasingly popular and relatively simple shared memory parallel programming model. Two parallelizing schemes, parallel do loops and parallel sections, were detailed using examples. Various clauses that allow user to modify the parallel execution were also presented, including sharing and privatizing of the variables, scheduling, synchronization and mutual exclusion of the parallel tasks. Finally, few hints were given on removing loop dependencies in order to obtain effective parallelization.


Using Python for Scientific Computing

No upcoming schedule for this presentation.
Presented: March 7th, 2013 1:00pm
By:  Wim Cardoen
   

LOCATION: INSCC Auditorium (Room 110)
TIME: 1:00 - 2:00 p.m.

In this talk we will discuss several features which make Python a viable tool for scientific computing:

  • 1. strength and flexibility of the Python language
  • 2. mathematical libraries (numpy,scipy,..)
  • 3. graphical libraries (matplotlib,..)
  • 4. extending Python using C/C++ and Fortran

Download recording (October 3, 2013)


Introduction to GPU Programming

No upcoming schedule for this presentation.
Presented: February 28th, 2013 1:00pm
By:  Wim Cardoen
   

LOCATION: INSCC Auditorium (Room 110)
TIME: 1:00 - 2:00 p.m.

In this talk we will first of all explain why GPUs can form an alternative to traditional CPUs in the field of high-performance computing. Subsequently, we will spend some time on discussing the hardware especially the GPU cards as they are installed on several Ember nodes.

In the main part of the talk we will show a few examples where the basic concepts such as thread, block, and grid will be elucidated as well as the concept of shared memory.

The last part of the presentation covers topics such as compilation, mathematical libraries,..

Experience with C/C++ is strongly advised.

Download recording (October 22, 2013)


Introduction To Programming With MPI

No upcoming schedule for this presentation.
Presented: February 26th, 2013 1:00pm
By:  Martin Cuma
   

LOCATION: INSCC Auditorium (Room 110)
TIME: 1:00 - 2:00 p.m.

This course discusses introductory and selected intermediate topics in MPI programming. We base this presentation on two simple examples and explain the MPI parallel development of them. The first example encompasses MPI initialization and simple point to point communication (which takes place between two processes). The second example includes introduction to collective communication calls (where all active processes are involved) and options for effective data communication strategies, such as derived data types and packing the data. Some ideas on more advanced MPI programming options are discussed in the end of the talk.

Download recording (November 7, 2013)


Using Gaussian09 and Gaussview

No upcoming schedule for this presentation.
Presented: February 21st, 2013 1:00pm
By:  Anita Orendt
   

LOCATION: INSCC Auditorium (Room 110)
TIME: 1:00 - 2:00 p.m.

This presentation will focus on the use of Gaussian09 and Gaussview on the CHPC clusters. Batch scripts and input file formats will be discussed. Parallel scaling and timings with the different scratch options will also be presented, along with a discussion of scratch needs of Gaussian09. Finally several demonstrations on the use of GaussView to build molecules, input structures, set up input files and to analyze output files will be presented.

Download recording (October 10, 2013)


Introduction to Parallel Computing

No upcoming schedule for this presentation.
Presented: February 19th, 2013 1:00pm
By:  Martin Cuma
   

LOCATION: INSCC Auditorium (Room 110)
TIME: 1:00 - 2:00 p.m.

In this talk, we first discuss various parallel architectures and note which ones are represented at the CHPC, in particular, shared and distributed memory parallel computers. A very short introduction into two programming solutions for these machines, MPI and OpenMP, will then be given followed by instructions on how to compile, run, debug and profile parallel applications on the CHPC parallel computers. Although this talk is more directed towards those starting to explore parallel programming, more experienced users can gain from the second half of the talk, that will provide details on software development tools available at the CHPC.

Download recording (September 12, 2013)


Protected Environment, AI and NLP Services at CHPC, HSEB, 1:00-2:00 p.m.

No upcoming schedule for this presentation.
Presented: February 19th, 2013 1:00pm
By:  Sean Igo
   

LOCATION: HSEB 2908
TIME: 1:30 - 2:30 p.m.

This presentation is an overview of the equipment and software presently available at CHPC for Natural Language Processing (NLP) and includes an overview of the HIPAA-compliant protected environment for storage and processing of PHI data at CHPC. It will also cover related resources for general Artificial Intelligence use such as machine learning and data mining, and will include a brief description of CHPC's general resources and how to access them.


Introductory Linux for HPC Part 2

No upcoming schedule for this presentation.
Presented: February 14th, 2013 1:00pm
By:  Martin Cuma
   

LOCATION: INSCC Auditorium (Room 110)
TIME: 1:00 - 3:00 p.m.

In the second of this two-part class we will learn how to write simple shell scripts and how to compile and run programs. Each class is two hours.

You will need to bring a laptop with a functional connection to the campus WiFi. If you do not have an account with CHPC, please register for the class by sending an email indicating that you want to participate in this class and need an account to: issues@chpc.utah.edu. Please include your name, department, e-mail, phone number and your University of Utah uNID. CHPC accounts will be provisioned for you for the duration of this class.


Introductory Linux for HPC Part 1

No upcoming schedule for this presentation.
Presented: February 12th, 2013 1:00pm
By:  Martin Cuma
   

LOCATION: INSCC Auditorium (Room 110)
TIME: 1:00 - 3:00 p.m.

In the first of this two-part class we will talk about ways to connect to CHPC Linux systems. Then we will go over the most important Linux commands and learn how to edit files with the VI editor. Each class is two hours.

You will need to bring a laptop with a functional connection to the campus WiFi. If you do not have an account with CHPC, please register for the class by sending an email indicating that you want to participate in this class and need an account to: issues@chpc.utah.edu. Please include your name, department, e-mail, phone number and your University of Utah uNID. CHPC accounts will be provisioned for you for the duration of this class.

Download recording (September 17, 2013)


Introduction to BRISC Services

No upcoming schedule for this presentation.
Presented: February 7th, 2013 1:00pm
By:  Bernard LaSalle
   

LOCATION: INSCC Auditorium (Room 110)
TIME: 1:00 - 2:00 p.m.

The Biomedical Research Informatics Service Core (BRISC) provides "point of service" response by combining administration, technical staff and collaborations with key HSC and main campus information technology resources. BRISC has two service locations: the Health Science Center Information Technology office (615 Arapeen) and the Center for Clinical and Translational Science (4B475 SOM). In addition to custom programming BRISC supports the Research Electronic Data Capture (REDCAp) application and the Federated Utah Research Translational Health e-Repository (FURTHeR) informatics platform.


Overview of CHPC

No upcoming schedule for this presentation.
Presented: February 5th, 2013 1:00pm
By:  Wim Cardoen
   

LOCATION: INSCC Auditorium (Room 110)
TIME: 1:00 - 2:00 p.m.

This presentation gives users new to CHPC, or interested in High Performance Computing an overview of the resources available at CHPC, and the policies and procedures to access these resources.

Topic covered will include:

  • The platforms available
  • Filesystems
  • Access
  • An overview of the batch system and policies
  • Service Unit Allocations

Download recording (September 5, 2013)


Introduction to I/O in the HPC Environment

No upcoming schedule for this presentation.
Presented: November 6th, 2012 1:00pm
By:  Brian Haymore
   

LOCATION: INSCC Auditorium (Room 110)
TIME: 1:00 - 2:00 p.m.

This presentation will introduce users to the I/O performance characteristics of the various types of storage available to users of CHPC systems. Our goal for the presentation is to increase user understanding of various I/O patterns and how they relate to the shared computing environments at CHPC.

Topics will include general overview of I/O, best practices, file operations, application I/O, as well as troubleshooting techniques. We will present examples to illustrate the impact and performance characteristics of common usage cases. We will conclude with an open discussion driven by users' questions.

Download recording (October 24, 2013)


Fast Parallel I/O at the CHPC

No upcoming schedule for this presentation.
Presented: November 1st, 2012 1:00pm
By:  Martin Cuma
   

LOCATION: INSCC Auditorium (Room 110)
TIME: 1:00 - 2:00 p.m.

In this talk we explain how to perform fast parallel I/O operations on the CHPC computers. It should be beneficial for all users who are interested in speeding up their parallel applications via faster file operations. First, we describe in detail PVFS (Parallel Virtual File System), installed on arches. Then we go over several examples on how to perform parallel I/O on this file system, in particular, MPI-I/O extension to the MPI standard and native PVFS function calls. Subsequently we detail ways how to compile and run MPI-I/O applications on PVFS. We conclude the talk with an insight into some more advanced aspects of MPI-I/O.

Download recording (November 19, 2013)


Debugging with Totalview

No upcoming schedule for this presentation.
Presented: October 30th, 2012 1:00pm
By:  Martin Cuma
   

LOCATION: INSCC Auditorium (Room 110)
TIME: 1:00 - 2:00 p.m.

This talk introduces Totalview, a debugger that has become a standard in the Unix code development comunity. After short introduction to its major features, we will present three examples, serial, parallel OpenMP and parallel MPI codes. Using these examples, we will show common and specific features for debugging these codes. We will also spend short time introducing Intel Thread Checker, which is an useful tool for OpenMP code checking. Finally, those interested can stay for an extra half hour, between 2pm and 2.30pm, for informal practical presentation of various useful Totalview features.

Download recording (September 26, 2013)


Using Gaussian09 and Gaussview

No upcoming schedule for this presentation.
Presented: October 18th, 2012 1:00pm
Supplemental Materials:  Gaussian-fall2012.pptx
By:  Anita Orendt
   

LOCATION: INSCC Auditorium (Room 110)
TIME: 1:00 - 2:00 p.m.

This presentation will focus on the use of Gaussian09 and Gaussview on the CHPC clusters. Batch scripts and input file formats will be discussed. Parallel scaling and timings with the different scratch options will also be presented, along with a discussion of scratch needs of Gaussian09. Finally several demonstrations on the use of GaussView to build molecules, input structures, set up input files and to analyze output files will be presented.

Download recording (October 10, 2013)


Chemistry Packages at CHPC

No upcoming schedule for this presentation.
Presented: October 16th, 2012 1:00pm
Supplemental Materials:  CHPC-ChemPkg-fall2012.pptx
By:  Anita Orendt
   

LOCATION: INSCC Auditorium (Room 110)
TIME: 1:00 - 2:00 p.m.

This presentation will focus on the computational chemistry related applications that are available on CHPC computer systems. An overview of the packages and their capabilities, focusing on details of how users can access the installations at CHPC, will be given. This talk is the precursor for a second talk scheduled for next week that will focus on the use of Gaussian 09 and GaussView.

Download recording (October 8, 2013)


Hybrid MPI-OpenMP Programming

No upcoming schedule for this presentation.
Presented: October 2nd, 2012 12:00am
By:  Martin Cuma
   

LOCATION: INSCC Auditorium (Room 110)
TIME: 1:00 - 2:00 p.m.

In this talk we will introduce hybrid MPI-OpenMP programming model designed for distributed shared memory parallel (DSMP) computers. The CHPC clusters are representative of this family having two or more shared memory processors per node. OpenMP generally provides better performing alternative for parallelization inside a node and MPI is used for communication between the distributed processors. We will discuss cases when hybrid programming model is beneficial and provide examples of simple MPI-OpenMP codes.

Download recording (November 14, 2013)


Using Python for Scientific Computing

No upcoming schedule for this presentation.
Presented: September 27th, 2012 1:00pm
By:  Wim Cardoen
   

LOCATION: INSCC Auditorium (Room 110)
TIME: 1:00 - 2:00 p.m.

In this talk we will discuss several features which make Python a viable tool for scientific computing:

  • 1. strength and flexibility of the Python language
  • 2. mathematical libraries (numpy,scipy,..)
  • 3. graphical libraries (matplotlib,..)
  • 4. extending Python using C/C++ and Fortran

Download recording (October 3, 2013)


Mathematical Libraries at CHPC

No upcoming schedule for this presentation.
Presented: September 25th, 2012 1:00pm
By:  Martin Cuma
   

LOCATION: INSCC Auditorium (Room 110)
TIME: 1:00 - 2:00 p.m.

In this talk we introduce the users to the mathematical libraries that are installed on the CHPC systems, which are designed to ease the programming and speed-up scientific applications. First, we will talk about BLAS, which is a standardized library of Basic Linear Algebra Subroutines, and present few examples. Then we briefly focus on other libraries that are in use, including freeware LAPACK, ScaLAPACK, PETSc and FFTW.

Download recording (September 24, 2013)


Introduction to GPU Programming

No upcoming schedule for this presentation.
Presented: September 20th, 2012 1:00pm
By:  Wim Cardoen
   

LOCATION: INSCC Auditorium (Room 110)
TIME: 1:00 - 2:00 p.m.

In this talk we will first of all explain why GPUs can form an alternative to traditional CPUs in the field of high-performance computing. Subsequently, we will spend some time on discussing the hardware especially the GPU cards as they are installed on several Ember nodes.

In the main part of the talk we will show a few examples where the basic concepts such as thread, block, and grid will be elucidated as well as the concept of shared memory.

The last part of the presentation covers topics such as compilation, mathematical libraries,..

Experience with C/C++ is strongly advised.

Download recording (October 22, 2013)


Introduction to Programming with OpenMP

No upcoming schedule for this presentation.
Presented: September 18th, 2012 1:00pm
By:  Martin Cuma
   

LOCATION: INSCC Auditorium (Room 110)
TIME: 1:00 - 2:00 p.m.

This talk introduces OpenMP, an increasingly popular and relatively simple shared memory parallel programming model. Two parallelizing schemes, parallel do loops and parallel sections, were detailed using examples. Various clauses that allow user to modify the parallel execution were also presented, including sharing and privatizing of the variables, scheduling, synchronization and mutual exclusion of the parallel tasks. Finally, few hints were given on removing loop dependencies in order to obtain effective parallelization.


Introduction To Programming With MPI

No upcoming schedule for this presentation.
Presented: September 13th, 2012 1:00pm
By:  Martin Cuma
   

LOCATION: INSCC Auditorium (Room 110)
TIME: 1:00 - 2:00 p.m.

This course discusses introductory and selected intermediate topics in MPI programming. We base this presentation on two simple examples and explain the MPI parallel development of them. The first example encompasses MPI initialization and simple point to point communication (which takes place between two processes). The second example includes introduction to collective communication calls (where all active processes are involved) and options for effective data communication strategies, such as derived data types and packing the data. Some ideas on more advanced MPI programming options are discussed in the end of the talk.

Download recording (November 7, 2013)


Protected Environment, AI and NLP Services at CHPC, HSEB, 1:00-2:00 p.m.

No upcoming schedule for this presentation.
Presented: September 11th, 2012 2:30pm
By:  Sean Igo
   

LOCATION: HSEB 2908
TIME: 1:30 - 2:30 p.m.

This presentation is an overview of the equipment and software presently available at CHPC for Natural Language Processing (NLP) and includes an overview of the HIPAA-compliant protected environment for storage and processing of PHI data at CHPC. It will also cover related resources for general Artificial Intelligence use such as machine learning and data mining, and will include a brief description of CHPC's general resources and how to access them.


Introduction to Parallel Computing

No upcoming schedule for this presentation.
Presented: September 11th, 2012 1:00pm
By:  Martin Cuma
   

LOCATION: INSCC Auditorium (Room 110)
TIME: 1:00 - 2:00 p.m.

In this talk, we first discuss various parallel architectures and note which ones are represented at the CHPC, in particular, shared and distributed memory parallel computers. A very short introduction into two programming solutions for these machines, MPI and OpenMP, will then be given followed by instructions on how to compile, run, debug and profile parallel applications on the CHPC parallel computers. Although this talk is more directed towards those starting to explore parallel programming, more experienced users can gain from the second half of the talk, that will provide details on software development tools available at the CHPC.

Download recording (September 12, 2013)


Introductory Linux for HPC Part 2

No upcoming schedule for this presentation.
Presented: September 6th, 2012 1:00pm
By:  Martin Cuma
   

LOCATION: INSCC Auditorium (Room 110)
TIME: 1:00 - 3:00 p.m.

In the second of this two-part class we will learn how to write simple shell scripts and how to compile and run programs. Each class is two hours.

You will need to bring a laptop with a functional connection to the campus WiFi. If you do not have an account with CHPC, please register for the class by sending an email indicating that you want to participate in this class and need an account to: issues@chpc.utah.edu. Please include your name, department, e-mail, phone number and your University of Utah uNID. CHPC accounts will be provisioned for you for the duration of this class.


Introductory Linux for HPC Part 1

No upcoming schedule for this presentation.
Presented: September 4th, 2012 1:00pm
By:  Martin Cuma
   

LOCATION: INSCC Auditorium (Room 110)
TIME: 1:00 - 3:00 p.m.

In the first of this two-part class we will talk about ways to connect to CHPC Linux systems. Then we will go over the most important Linux commands and learn how to edit files with the VI editor. Each class is two hours.

You will need to bring a laptop with a functional connection to the campus WiFi. If you do not have an account with CHPC, please register for the class by sending an email indicating that you want to participate in this class and need an account to: issues@chpc.utah.edu. Please include your name, department, e-mail, phone number and your University of Utah uNID. CHPC accounts will be provisioned for you for the duration of this class.

Download recording (September 17, 2013)


Introduction to BRISC Services

No upcoming schedule for this presentation.
Presented: August 30th, 2012 1:00pm
Supplemental Materials:  chpc_brisc_august_2012.pdf
By:  Bernard LaSalle
   

LOCATION: INSCC Auditorium (Room 110)
TIME: 1:00 - 2:00 p.m.

The Biomedical Research Informatics Service Core (BRISC) provides "point of service" response by combining administration, technical staff and collaborations with key HSC and main campus information technology resources. BRISC has two service locations: the Health Science Center Information Technology office (615 Arapeen) and the Center for Clinical and Translational Science (4B475 SOM). In addition to custom programming BRISC supports the Research Electronic Data Capture (REDCAp) application and the Federated Utah Research Translational Health e-Repository (FURTHeR) informatics platform.


Overview of CHPC

No upcoming schedule for this presentation.
Presented: August 28th, 2012 1:00pm
Supplemental Materials:  OverviewCHPCFall2012_INSCC.pdf
By:  Wim Cardoen
   

LOCATION: INSCC Auditorium (Room 110)
TIME: 1:00 - 2:00 p.m.

This presentation gives users new to CHPC, or interested in High Performance Computing an overview of the resources available at CHPC, and the policies and procedures to access these resources.

Topic covered will include:

  • The platforms available
  • Filesystems
  • Access
  • An overview of the batch system and policies
  • Service Unit Allocations

Download recording (September 5, 2013)


Introduction to BRISC Services

No upcoming schedule for this presentation.
Presented: April 19th, 2012 1:00pm
By:  Bernard LaSalle
   

LOCATION: INSCC Auditorium (Room 110)
TIME: 1:00 - 2:00 p.m.

The Biomedical Research Informatics Service Core (BRISC) provides "point of service" response by combining administration, technical staff and collaborations with key HSC and main campus information technology resources. BRISC has two service locations: the Health Science Center Information Technology office (615 Arapeen) and the Center for Clinical and Translational Science (4B475 SOM). In addition to custom programming BRISC supports the Research Electronic Data Capture (REDCAp) application and the Federated Utah Research Translational Health e-Repository (FURTHeR) informatics platform.


Protected Environment, AI and NLP Services at CHPC, HSEB, 1:00-2:00 p.m.

No upcoming schedule for this presentation.
Presented: April 12th, 2012 2:30pm
By:  Sean Igo
   

LOCATION: HSEB 2908
TIME: 1:30 - 2:30 p.m.

This presentation is an overview of the equipment and software presently available at CHPC for Natural Language Processing (NLP) and includes an overview of the HIPAA-compliant protected environment for storage and processing of PHI data at CHPC. It will also cover related resources for general Artificial Intelligence use such as machine learning and data mining, and will include a brief description of CHPC's general resources and how to access them.


Using Gaussian09 and Gaussview

No upcoming schedule for this presentation.
Presented: April 12th, 2012 1:00pm
By:  Anita Orendt
   

LOCATION: INSCC Auditorium (Room 110)
TIME: 1:00 - 2:00 p.m.

This presentation will focus on the use of Gaussian09 and Gaussview on the CHPC clusters. Batch scripts and input file formats will be discussed. Parallel scaling and timings with the different scratch options will also be presented, along with a discussion of scratch needs of Gaussian09. Finally several demonstrations on the use of GaussView to build molecules, input structures, set up input files and to analyze output files will be presented.

Download recording (October 10, 2013)


Introduction to I/O in the HPC Environment

No upcoming schedule for this presentation.
Presented: April 5th, 2012 1:00pm
By:  Brian Haymore
   

LOCATION: INSCC Auditorium (Room 110)
TIME: 1:00 - 2:00 p.m.

This presentation will introduce users to the I/O performance characteristics of the various types of storage available to users of CHPC systems. Our goal for the presentation is to increase user understanding of various I/O patterns and how they relate to the shared computing environments at CHPC.

Topics will include general overview of I/O, best practices, file operations, application I/O, as well as troubleshooting techniques. We will present examples to illustrate the impact and performance characteristics of common usage cases. We will conclude with an open discussion driven by users' questions.

Download recording (October 24, 2013)


Introductory Linux for HPC Part 2

No upcoming schedule for this presentation.
Presented: March 29th, 2012 1:00pm
Supplemental Materials:  linux_cheat_sheet.pdf  Linux_intro.pdf
By:  Martin Cuma
   

LOCATION: INSCC Auditorium (Room 110)
TIME: 1:00 - 3:00 p.m.

In the second of this two-part class we will learn how to write simple shell scripts and how to compile and run programs. Each class is two hours.

You will need to bring a laptop with a functional connection to the campus WiFi. If you do not have an account with CHPC, please register for the class by sending an email indicating that you want to participate in this class and need an account to: issues@chpc.utah.edu. Please include your name, department, e-mail, phone number and your University of Utah uNID. CHPC accounts will be provisioned for you for the duration of this class.


Introductory Linux for HPC Part 1

No upcoming schedule for this presentation.
Presented: March 22nd, 2012 1:00pm
By:  Martin Cuma
   

LOCATION: INSCC Auditorium (Room 110)
TIME: 1:00 - 3:00 p.m.

In the first of this two-part class we will talk about ways to connect to CHPC Linux systems. Then we will go over the most important Linux commands and learn how to edit files with the VI editor. Each class is two hours.

You will need to bring a laptop with a functional connection to the campus WiFi. If you do not have an account with CHPC, please register for the class by sending an email indicating that you want to participate in this class and need an account to: issues@chpc.utah.edu. Please include your name, department, e-mail, phone number and your University of Utah uNID. CHPC accounts will be provisioned for you for the duration of this class.

Download recording (September 17, 2013)


Introduction to Parallel Computing

No upcoming schedule for this presentation.
Presented: March 8th, 2012 1:00pm
By:  Martin Cuma
   

LOCATION: INSCC Auditorium (Room 110)
TIME: 1:00 - 2:00 p.m.

In this talk, we first discuss various parallel architectures and note which ones are represented at the CHPC, in particular, shared and distributed memory parallel computers. A very short introduction into two programming solutions for these machines, MPI and OpenMP, will then be given followed by instructions on how to compile, run, debug and profile parallel applications on the CHPC parallel computers. Although this talk is more directed towards those starting to explore parallel programming, more experienced users can gain from the second half of the talk, that will provide details on software development tools available at the CHPC.

Download recording (September 12, 2013)


Overview of CHPC

No upcoming schedule for this presentation.
Presented: March 1st, 2012 1:00pm
By:  Wim Cardoen
   

LOCATION: INSCC Auditorium (Room 110)
TIME: 1:00 - 2:00 p.m.

This presentation gives users new to CHPC, or interested in High Performance Computing an overview of the resources available at CHPC, and the policies and procedures to access these resources.

Topic covered will include:

  • The platforms available
  • Filesystems
  • Access
  • An overview of the batch system and policies
  • Service Unit Allocations

Download recording (September 5, 2013)


Introductory Linux for HPC Part 2

No upcoming schedule for this presentation.
Presented: February 14th, 2012 1:00pm
By:  Martin Cuma
   

LOCATION: INSCC Auditorium (Room 110)
TIME: 1:00 - 3:00 p.m.

In the second of this two-part class we will learn how to write simple shell scripts and how to compile and run programs. Each class is two hours.

You will need to bring a laptop with a functional connection to the campus WiFi. If you do not have an account with CHPC, please register for the class by sending an email indicating that you want to participate in this class and need an account to: issues@chpc.utah.edu. Please include your name, department, e-mail, phone number and your University of Utah uNID. CHPC accounts will be provisioned for you for the duration of this class.


Introduction to GPU Programming

No upcoming schedule for this presentation.
Presented: December 8th, 2011 1:00pm
Supplemental Materials:  GPUDec2011.pdf
By:  Wim Cardoen
   

LOCATION: INSCC Auditorium (Room 110)
TIME: 1:00 - 2:00 p.m.

In this talk we will first of all explain why GPUs can form an alternative to traditional CPUs in the field of high-performance computing. Subsequently, we will spend some time on discussing the hardware especially the GPU cards as they are installed on several Ember nodes.

In the main part of the talk we will show a few examples where the basic concepts such as thread, block, and grid will be elucidated as well as the concept of shared memory.

The last part of the presentation covers topics such as compilation, mathematical libraries,..

Experience with C/C++ is strongly advised.

Download recording (October 22, 2013)


Introduction to I/O in the HPC Environment

No upcoming schedule for this presentation.
Presented: December 1st, 2011 1:00pm
By:  Brian Haymore
   

LOCATION: INSCC Auditorium (Room 110)
TIME: 1:00 - 2:00 p.m.

This presentation will introduce users to the I/O performance characteristics of the various types of storage available to users of CHPC systems. Our goal for the presentation is to increase user understanding of various I/O patterns and how they relate to the shared computing environments at CHPC.

Topics will include general overview of I/O, best practices, file operations, application I/O, as well as troubleshooting techniques. We will present examples to illustrate the impact and performance characteristics of common usage cases. We will conclude with an open discussion driven by users' questions.

Download recording (October 24, 2013)


Using Python for Scientific Computing

No upcoming schedule for this presentation.
Presented: November 29th, 2011 1:00pm
By:  Wim Cardoen
   

LOCATION: INSCC Auditorium (Room 110)
TIME: 1:00 - 2:00 p.m.

In this talk we will discuss several features which make Python a viable tool for scientific computing:

  • 1. strength and flexibility of the Python language
  • 2. mathematical libraries (numpy,scipy,..)
  • 3. graphical libraries (matplotlib,..)
  • 4. extending Python using C/C++ and Fortran

Download recording (October 3, 2013)


Using Gaussian09 and Gaussview

No upcoming schedule for this presentation.
Presented: November 17th, 2011 1:00pm
Supplemental Materials:  Gaussian-fall2011.pdf
By:  Anita Orendt
   

LOCATION: INSCC Auditorium (Room 110)
TIME: 1:00 - 2:00 p.m.

This presentation will focus on the use of Gaussian09 and Gaussview on the CHPC clusters. Batch scripts and input file formats will be discussed. Parallel scaling and timings with the different scratch options will also be presented, along with a discussion of scratch needs of Gaussian09. Finally several demonstrations on the use of GaussView to build molecules, input structures, set up input files and to analyze output files will be presented.

Download recording (October 10, 2013)


Chemistry Packages at CHPC

No upcoming schedule for this presentation.
Presented: November 10th, 2011 1:00pm
Supplemental Materials:  CHPC-ChemPkg-fall2011.pdf
By:  Anita Orendt
   

LOCATION: INSCC Auditorium (Room 110)
TIME: 1:00 - 2:00 p.m.

This presentation will focus on the computational chemistry related applications that are available on CHPC computer systems. An overview of the packages and their capabilities, focusing on details of how users can access the installations at CHPC, will be given. This talk is the precursor for a second talk scheduled for next week that will focus on the use of Gaussian 09 and GaussView.

Download recording (October 8, 2013)


Fast Parallel I/O at the CHPC

No upcoming schedule for this presentation.
Presented: November 6th, 2011 1:00pm
By:  Martin Cuma
   

LOCATION: INSCC Auditorium (Room 110)
TIME: 1:00 - 2:00 p.m.

In this talk we explain how to perform fast parallel I/O operations on the CHPC computers. It should be beneficial for all users who are interested in speeding up their parallel applications via faster file operations. First, we describe in detail PVFS (Parallel Virtual File System), installed on arches. Then we go over several examples on how to perform parallel I/O on this file system, in particular, MPI-I/O extension to the MPI standard and native PVFS function calls. Subsequently we detail ways how to compile and run MPI-I/O applications on PVFS. We conclude the talk with an insight into some more advanced aspects of MPI-I/O.

Download recording (November 19, 2013)


High-Performance Networks and Long-Distance Data Transfers

No upcoming schedule for this presentation.
Presented: November 3rd, 2011 1:00pm
Supplemental Materials:  Video
By:  Tom Ammon
   

LOCATION: INSCC Auditorium (Room 110)
TIME: 1:00 - 2:00 p.m.

This presentation will give an overview of Infiniband, a high-performance network fabric used for interprocess communication on CHPC clusters. Additionally, this presentation will give a brief introduction to high-performance Ethernet networks and the challenges associated with moving data across long geographical distances.


Debugging with Totalview

No upcoming schedule for this presentation.
Presented: November 1st, 2011 1:00pm
By:  Martin Cuma
   

LOCATION: INSCC Auditorium (Room 110)
TIME: 1:00 - 2:00 p.m.

This talk introduces Totalview, a debugger that has become a standard in the Unix code development comunity. After short introduction to its major features, we will present three examples, serial, parallel OpenMP and parallel MPI codes. Using these examples, we will show common and specific features for debugging these codes. We will also spend short time introducing Intel Thread Checker, which is an useful tool for OpenMP code checking. Finally, those interested can stay for an extra half hour, between 2pm and 2.30pm, for informal practical presentation of various useful Totalview features.

Download recording (September 26, 2013)


Hybrid MPI-OpenMP Programming

No upcoming schedule for this presentation.
Presented: October 27th, 2011 1:00pm
By:  Martin Cuma
   

LOCATION: INSCC Auditorium (Room 110)
TIME: 1:00 - 2:00 p.m.

In this talk we will introduce hybrid MPI-OpenMP programming model designed for distributed shared memory parallel (DSMP) computers. The CHPC clusters are representative of this family having two or more shared memory processors per node. OpenMP generally provides better performing alternative for parallelization inside a node and MPI is used for communication between the distributed processors. We will discuss cases when hybrid programming model is beneficial and provide examples of simple MPI-OpenMP codes.

Download recording (November 14, 2013)


Mathematical Libraries at CHPC

No upcoming schedule for this presentation.
Presented: October 18th, 2011 1:00pm
By:  Martin Cuma
   

LOCATION: INSCC Auditorium (Room 110)
TIME: 1:00 - 2:00 p.m.

In this talk we introduce the users to the mathematical libraries that are installed on the CHPC systems, which are designed to ease the programming and speed-up scientific applications. First, we will talk about BLAS, which is a standardized library of Basic Linear Algebra Subroutines, and present few examples. Then we briefly focus on other libraries that are in use, including freeware LAPACK, ScaLAPACK, PETSc and FFTW.

Download recording (September 24, 2013)


Introduction to Programming with OpenMP

No upcoming schedule for this presentation.
Presented: October 6th, 2011 1:00pm
Supplemental Materials:  IntroOpenMP09.pdf
By:  Martin Cuma
   

LOCATION: INSCC Auditorium (Room 110)
TIME: 1:00 - 2:00 p.m.

This talk introduces OpenMP, an increasingly popular and relatively simple shared memory parallel programming model. Two parallelizing schemes, parallel do loops and parallel sections, were detailed using examples. Various clauses that allow user to modify the parallel execution were also presented, including sharing and privatizing of the variables, scheduling, synchronization and mutual exclusion of the parallel tasks. Finally, few hints were given on removing loop dependencies in order to obtain effective parallelization.


Introduction To Programming With MPI

No upcoming schedule for this presentation.
Presented: October 4th, 2011 1:00pm
Supplemental Materials:  IntroMPI11.pdf
By:  Martin Cuma
   

LOCATION: INSCC Auditorium (Room 110)
TIME: 1:00 - 2:00 p.m.

This course discusses introductory and selected intermediate topics in MPI programming. We base this presentation on two simple examples and explain the MPI parallel development of them. The first example encompasses MPI initialization and simple point to point communication (which takes place between two processes). The second example includes introduction to collective communication calls (where all active processes are involved) and options for effective data communication strategies, such as derived data types and packing the data. Some ideas on more advanced MPI programming options are discussed in the end of the talk.

Download recording (November 7, 2013)


Introductory Linux for HPC Part 2

No upcoming schedule for this presentation.
Presented: September 29th, 2011 1:00pm
By:  Martin Cuma
   

LOCATION: INSCC Auditorium (Room 110)
TIME: 1:00 - 3:00 p.m.

In the second of this two-part class we will learn how to write simple shell scripts and how to compile and run programs. Each class is two hours.

You will need to bring a laptop with a functional connection to the campus WiFi. If you do not have an account with CHPC, please register for the class by sending an email indicating that you want to participate in this class and need an account to: issues@chpc.utah.edu. Please include your name, department, e-mail, phone number and your University of Utah uNID. CHPC accounts will be provisioned for you for the duration of this class.


Introductory Linux for HPC Part 1

No upcoming schedule for this presentation.
Presented: September 27th, 2011 1:00pm
Supplemental Materials:  Linux_intro.pdf  linux_cheat_sheet.pdf
By:  Martin Cuma
   

LOCATION: INSCC Auditorium (Room 110)
TIME: 1:00 - 3:00 p.m.

In the first of this two-part class we will talk about ways to connect to CHPC Linux systems. Then we will go over the most important Linux commands and learn how to edit files with the VI editor. Each class is two hours.

You will need to bring a laptop with a functional connection to the campus WiFi. If you do not have an account with CHPC, please register for the class by sending an email indicating that you want to participate in this class and need an account to: issues@chpc.utah.edu. Please include your name, department, e-mail, phone number and your University of Utah uNID. CHPC accounts will be provisioned for you for the duration of this class.

Download recording (September 17, 2013)


Protected Environment, AI and NLP Services at CHPC, HSEB, 1:00-2:00 p.m.

No upcoming schedule for this presentation.
Presented: September 22nd, 2011 2:30pm
By:  Sean Igo
   

LOCATION: HSEB 2908
TIME: 1:30 - 2:30 p.m.

This presentation is an overview of the equipment and software presently available at CHPC for Natural Language Processing (NLP) and includes an overview of the HIPAA-compliant protected environment for storage and processing of PHI data at CHPC. It will also cover related resources for general Artificial Intelligence use such as machine learning and data mining, and will include a brief description of CHPC's general resources and how to access them.


Statistical Resources at CHPC

No upcoming schedule for this presentation.
Presented: September 20th, 2011 1:00pm
By: 
   

LOCATION: INSCC Auditorium (Room 110)
TIME: 1:00 - 2:00 p.m.

This presentation by Byron Davis gives users (and potential users) of CHPC's statistical resources an overview of the equipment and software presently available. Additionally a list of specialized statistical software will be presented that we've supported over the past 10 years or so.


Introduction to Parallel Computing

No upcoming schedule for this presentation.
Presented: September 15th, 2011 1:00pm
Supplemental Materials:  IntroPar09b.pdf
By:  Martin Cuma
   

LOCATION: INSCC Auditorium (Room 110)
TIME: 1:00 - 2:00 p.m.

In this talk, we first discuss various parallel architectures and note which ones are represented at the CHPC, in particular, shared and distributed memory parallel computers. A very short introduction into two programming solutions for these machines, MPI and OpenMP, will then be given followed by instructions on how to compile, run, debug and profile parallel applications on the CHPC parallel computers. Although this talk is more directed towards those starting to explore parallel programming, more experienced users can gain from the second half of the talk, that will provide details on software development tools available at the CHPC.

Download recording (September 12, 2013)


Overview of CHPC

No upcoming schedule for this presentation.
Presented: September 8th, 2011 1:00pm
By:  Wim Cardoen
   

LOCATION: INSCC Auditorium (Room 110)
TIME: 1:00 - 2:00 p.m.

This presentation gives users new to CHPC, or interested in High Performance Computing an overview of the resources available at CHPC, and the policies and procedures to access these resources.

Topic covered will include:

  • The platforms available
  • Filesystems
  • Access
  • An overview of the batch system and policies
  • Service Unit Allocations

Download recording (September 5, 2013)


Protected Environment, AI and NLP Services at CHPC, HSEB, 1:00-2:00 p.m.

No upcoming schedule for this presentation.
Presented: April 28th, 2011 2:30pm
By:  Sean Igo
   

LOCATION: HSEB 2908
TIME: 1:30 - 2:30 p.m.

This presentation is an overview of the equipment and software presently available at CHPC for Natural Language Processing (NLP) and includes an overview of the HIPAA-compliant protected environment for storage and processing of PHI data at CHPC. It will also cover related resources for general Artificial Intelligence use such as machine learning and data mining, and will include a brief description of CHPC's general resources and how to access them.


Using Gaussian09 and Gaussview

No upcoming schedule for this presentation.
Presented: April 21st, 2011 1:00pm
By:  Anita Orendt
   

LOCATION: INSCC Auditorium (Room 110)
TIME: 1:00 - 2:00 p.m.

This presentation will focus on the use of Gaussian09 and Gaussview on the CHPC clusters. Batch scripts and input file formats will be discussed. Parallel scaling and timings with the different scratch options will also be presented, along with a discussion of scratch needs of Gaussian09. Finally several demonstrations on the use of GaussView to build molecules, input structures, set up input files and to analyze output files will be presented.

Download recording (October 10, 2013)


Introduction To Programming With MPI

No upcoming schedule for this presentation.
Presented: April 14th, 2011 1:00pm
Supplemental Materials:  Video
By:  Martin Cuma
   

LOCATION: INSCC Auditorium (Room 110)
TIME: 1:00 - 2:00 p.m.

This course discusses introductory and selected intermediate topics in MPI programming. We base this presentation on two simple examples and explain the MPI parallel development of them. The first example encompasses MPI initialization and simple point to point communication (which takes place between two processes). The second example includes introduction to collective communication calls (where all active processes are involved) and options for effective data communication strategies, such as derived data types and packing the data. Some ideas on more advanced MPI programming options are discussed in the end of the talk.

Download recording (November 7, 2013)


Introduction to Parallel Computing

No upcoming schedule for this presentation.
Presented: April 7th, 2011 1:00pm
Supplemental Materials:  Video (m4v)
By:  Martin Cuma
   

LOCATION: INSCC Auditorium (Room 110)
TIME: 1:00 - 2:00 p.m.

In this talk, we first discuss various parallel architectures and note which ones are represented at the CHPC, in particular, shared and distributed memory parallel computers. A very short introduction into two programming solutions for these machines, MPI and OpenMP, will then be given followed by instructions on how to compile, run, debug and profile parallel applications on the CHPC parallel computers. Although this talk is more directed towards those starting to explore parallel programming, more experienced users can gain from the second half of the talk, that will provide details on software development tools available at the CHPC.

Download recording (September 12, 2013)


Introduction to I/O in the HPC Environment

No upcoming schedule for this presentation.
Presented: March 31st, 2011 1:00pm
Supplemental Materials:  Video  Intro_to_IOfall2010.pdf
By:  Brian Haymore
   

LOCATION: INSCC Auditorium (Room 110)
TIME: 1:00 - 2:00 p.m.

This presentation will introduce users to the I/O performance characteristics of the various types of storage available to users of CHPC systems. Our goal for the presentation is to increase user understanding of various I/O patterns and how they relate to the shared computing environments at CHPC.

Topics will include general overview of I/O, best practices, file operations, application I/O, as well as troubleshooting techniques. We will present examples to illustrate the impact and performance characteristics of common usage cases. We will conclude with an open discussion driven by users' questions.

Download recording (October 24, 2013)


Overview of CHPC

No upcoming schedule for this presentation.
Presented: March 17th, 2011 1:00pm
Supplemental Materials:  Video  Python.pptx  OverviewCHPCSpring2011_INSCC.pptx
By:  Wim Cardoen
   

LOCATION: INSCC Auditorium (Room 110)
TIME: 1:00 - 2:00 p.m.

This presentation gives users new to CHPC, or interested in High Performance Computing an overview of the resources available at CHPC, and the policies and procedures to access these resources.

Topic covered will include:

  • The platforms available
  • Filesystems
  • Access
  • An overview of the batch system and policies
  • Service Unit Allocations

Download recording (September 5, 2013)


Hybrid MPI-OpenMP Programming

No upcoming schedule for this presentation.
Presented: December 16th, 2010 12:00am
Supplemental Materials:  Video
By:  Martin Cuma
   

LOCATION: INSCC Auditorium (Room 110)
TIME: 1:00 - 2:00 p.m.

In this talk we will introduce hybrid MPI-OpenMP programming model designed for distributed shared memory parallel (DSMP) computers. The CHPC clusters are representative of this family having two or more shared memory processors per node. OpenMP generally provides better performing alternative for parallelization inside a node and MPI is used for communication between the distributed processors. We will discuss cases when hybrid programming model is beneficial and provide examples of simple MPI-OpenMP codes.

Download recording (November 14, 2013)


Debugging with Totalview

No upcoming schedule for this presentation.
Presented: December 9th, 2010 4:55pm
Supplemental Materials:  Totalview08.pdf  Video
By:  Martin Cuma
   

LOCATION: INSCC Auditorium (Room 110)
TIME: 1:00 - 2:00 p.m.

This talk introduces Totalview, a debugger that has become a standard in the Unix code development comunity. After short introduction to its major features, we will present three examples, serial, parallel OpenMP and parallel MPI codes. Using these examples, we will show common and specific features for debugging these codes. We will also spend short time introducing Intel Thread Checker, which is an useful tool for OpenMP code checking. Finally, those interested can stay for an extra half hour, between 2pm and 2.30pm, for informal practical presentation of various useful Totalview features.

Download recording (September 26, 2013)


Using Gaussian09 and Gaussview

No upcoming schedule for this presentation.
Presented: November 18th, 2010 12:00am
Supplemental Materials:  PDF Version  Video  Gaussian-fall2008.pdf  Gaussian_chpc_spr08.pdf
By:  Anita Orendt
   

LOCATION: INSCC Auditorium (Room 110)
TIME: 1:00 - 2:00 p.m.

This presentation will focus on the use of Gaussian09 and Gaussview on the CHPC clusters. Batch scripts and input file formats will be discussed. Parallel scaling and timings with the different scratch options will also be presented, along with a discussion of scratch needs of Gaussian09. Finally several demonstrations on the use of GaussView to build molecules, input structures, set up input files and to analyze output files will be presented.

Download recording (October 10, 2013)


Using Python for Scientific Computing

No upcoming schedule for this presentation.
Presented: November 11th, 2010 12:00am
By:  Wim Cardoen
   

LOCATION: INSCC Auditorium (Room 110)
TIME: 1:00 - 2:00 p.m.

In this talk we will discuss several features which make Python a viable tool for scientific computing:

  • 1. strength and flexibility of the Python language
  • 2. mathematical libraries (numpy,scipy,..)
  • 3. graphical libraries (matplotlib,..)
  • 4. extending Python using C/C++ and Fortran

Download recording (October 3, 2013)


Statistical Resources at CHPC

No upcoming schedule for this presentation.
Presented: November 4th, 2010 12:00am
Supplemental Materials:  stats-chpc-fall-09.pdf  Video (m4v)
By: 
   

LOCATION: INSCC Auditorium (Room 110)
TIME: 1:00 - 2:00 p.m.

This presentation by Byron Davis gives users (and potential users) of CHPC's statistical resources an overview of the equipment and software presently available. Additionally a list of specialized statistical software will be presented that we've supported over the past 10 years or so.


Mathematical Libraries at CHPC

No upcoming schedule for this presentation.
Presented: October 28th, 2010 12:00am
Supplemental Materials:  MatLib06.pdf  Video  MatLib05.pdf
By:  Martin Cuma
   

LOCATION: INSCC Auditorium (Room 110)
TIME: 1:00 - 2:00 p.m.

In this talk we introduce the users to the mathematical libraries that are installed on the CHPC systems, which are designed to ease the programming and speed-up scientific applications. First, we will talk about BLAS, which is a standardized library of Basic Linear Algebra Subroutines, and present few examples. Then we briefly focus on other libraries that are in use, including freeware LAPACK, ScaLAPACK, PETSc and FFTW.

Download recording (September 24, 2013)


Protected Environment, AI and NLP Services at CHPC, HSEB, 1:00-2:00 p.m.

No upcoming schedule for this presentation.
Presented: October 23rd, 2010 5:07pm
Supplemental Materials:  hippa.pdf  CHPC-NLPSoftwareSlideshow-100923.pdf
By:  Sean Igo
   

LOCATION: HSEB 2908
TIME: 1:30 - 2:30 p.m.

This presentation is an overview of the equipment and software presently available at CHPC for Natural Language Processing (NLP) and includes an overview of the HIPAA-compliant protected environment for storage and processing of PHI data at CHPC. It will also cover related resources for general Artificial Intelligence use such as machine learning and data mining, and will include a brief description of CHPC's general resources and how to access them.


Chemistry Packages at CHPC

No upcoming schedule for this presentation.
Presented: October 21st, 2010 12:00am
Supplemental Materials:  CHPC-ChemPkg-fall2008.pdf  Video (m4v)  Video  CCpkg_chpc_spr08.pdf
By:  Anita Orendt
   

LOCATION: INSCC Auditorium (Room 110)
TIME: 1:00 - 2:00 p.m.

This presentation will focus on the computational chemistry related applications that are available on CHPC computer systems. An overview of the packages and their capabilities, focusing on details of how users can access the installations at CHPC, will be given. This talk is the precursor for a second talk scheduled for next week that will focus on the use of Gaussian 09 and GaussView.

Download recording (October 8, 2013)


Introduction To Programming With MPI

No upcoming schedule for this presentation.
Presented: October 7th, 2010 5:21pm
Supplemental Materials:  IntroMPI06.pdf  Video (m4v)  IntroMPI05a.pdf
By:  Martin Cuma
   

LOCATION: INSCC Auditorium (Room 110)
TIME: 1:00 - 2:00 p.m.

This course discusses introductory and selected intermediate topics in MPI programming. We base this presentation on two simple examples and explain the MPI parallel development of them. The first example encompasses MPI initialization and simple point to point communication (which takes place between two processes). The second example includes introduction to collective communication calls (where all active processes are involved) and options for effective data communication strategies, such as derived data types and packing the data. Some ideas on more advanced MPI programming options are discussed in the end of the talk.

Download recording (November 7, 2013)


Introduction to Parallel Computing

No upcoming schedule for this presentation.
Presented: September 16th, 2010 4:56pm
Supplemental Materials:  IntroPar09.pdf
By:  Martin Cuma
   

LOCATION: INSCC Auditorium (Room 110)
TIME: 1:00 - 2:00 p.m.

In this talk, we first discuss various parallel architectures and note which ones are represented at the CHPC, in particular, shared and distributed memory parallel computers. A very short introduction into two programming solutions for these machines, MPI and OpenMP, will then be given followed by instructions on how to compile, run, debug and profile parallel applications on the CHPC parallel computers. Although this talk is more directed towards those starting to explore parallel programming, more experienced users can gain from the second half of the talk, that will provide details on software development tools available at the CHPC.

Download recording (September 12, 2013)


Overview of CHPC

No upcoming schedule for this presentation.
Presented: September 11th, 2010 12:00am
Supplemental Materials:  PDF Version  Video (m4v)  OverviewCHPCFall2008.pdf  OverviewCHPCSpring2008.pdf
By:  Wim Cardoen
   

LOCATION: INSCC Auditorium (Room 110)
TIME: 1:00 - 2:00 p.m.

This presentation gives users new to CHPC, or interested in High Performance Computing an overview of the resources available at CHPC, and the policies and procedures to access these resources.

Topic covered will include:

  • The platforms available
  • Filesystems
  • Access
  • An overview of the batch system and policies
  • Service Unit Allocations

Download recording (September 5, 2013)


Topic to be determined (Multi-media)

No upcoming schedule for this presentation.
Presented: October 29th, 2009 12:00am
By:  Jimmy Miklavcic
    TBD

Parallel performance analysis tools

No upcoming schedule for this presentation.
Presented: December 15th, 2007 12:00am
Supplemental Materials:  PDF Version
By:  Martin Cuma
   

LOCATION: INSCC Auditorium (Room 110)
TIME: 1:00 - 2:00 p.m.

TAU (Tuning and Analysis Utilities) is a profiling and tracing toolkit for performance analysis of parallel programs. In this talk, we will introduce TAU as a new and flexible tool for tracing of parallel programs on CHPC Arches clusters. We detail small changes necessary to turn on the tracing and then explain how to visualize the trace files in Vampir trace viewer. We will conclude with some specific examples and glimpse on other features that TAU provides.


Introduction to Programming with OpenMP

No upcoming schedule for this presentation.
Presented: October 10th, 2007 5:26pm
Supplemental Materials:  IntroOpenMP06.pdf  Video (m4v)  Video  IntroOpenMP04.pdf
By:  Martin Cuma
   

LOCATION: INSCC Auditorium (Room 110)
TIME: 1:00 - 2:00 p.m.

This talk introduces OpenMP, an increasingly popular and relatively simple shared memory parallel programming model. Two parallelizing schemes, parallel do loops and parallel sections, were detailed using examples. Various clauses that allow user to modify the parallel execution were also presented, including sharing and privatizing of the variables, scheduling, synchronization and mutual exclusion of the parallel tasks. Finally, few hints were given on removing loop dependencies in order to obtain effective parallelization.


Fast Parallel I/O at the CHPC

No upcoming schedule for this presentation.
Presented: January 1st, 2007 12:00am
Supplemental Materials:  Video (m4v)  MPI-IO05.pdf
By:  Martin Cuma
   

LOCATION: INSCC Auditorium (Room 110)
TIME: 1:00 - 2:00 p.m.

In this talk we explain how to perform fast parallel I/O operations on the CHPC computers. It should be beneficial for all users who are interested in speeding up their parallel applications via faster file operations. First, we describe in detail PVFS (Parallel Virtual File System), installed on arches. Then we go over several examples on how to perform parallel I/O on this file system, in particular, MPI-I/O extension to the MPI standard and native PVFS function calls. Subsequently we detail ways how to compile and run MPI-I/O applications on PVFS. We conclude the talk with an insight into some more advanced aspects of MPI-I/O.

Download recording (November 19, 2013)


Last Modified: March 27, 2012 @ 12:38:34