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Research Computing on the Great Lakes cluster

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This workshop will provide a brief overview of the the new HPC environment and is intended for current Flux and Armis users.  We will use the temporary Beta HPC cluster to demonstrate how jobs will be submitted and managed under the new Great Lakes, Armis2, and Lighthouse clusters available later this year.

There are many differences between the familiar Flux environment and that of the new HPC clusters, including a new batch scheduling system, a new interactive batch job environment, a new HPC web portal, a new module environment, and a new on-demand-only job accounting system.

We will cover these differences in the workshop, and provide hands-on training in creating and running job submission scripts in the new HPC environment.  Students are expected to be conversant with the Linux command line and have experience in creating, submitting, and troubleshooting PBS batch scripts.

Introduction to the Linux Command Line

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This course will familiarize the student with the basics of accessing and interacting with Linux computers using the GNU/Linux operating system’s Bash shell, also generically referred to as “the command line”. Topics include: a brief overview of Linux, the Bash shell, navigating the file system, basic commands, shell redirection, permissions, processes, and the command environment. The workshop will also provide a quick introduction to nano a simple text editor that will be used in subsequent workshops to edit files.

 

Instructor

Kenneth Weiss
IT Project Senior Manager
Medical School Information Services (MSIS)

Ken is a High Performance Computing Consultant in the Computational Research Consulting Division of MSIS at the University of Michigan. He works with a team of IT specialists to provide high performance computing support and training for the Medical School. Prior to this, he spent 21 years managing research computing, including an HPC cluster, for Dr. Charles Sing in the Human Genetics Department.

Materials

Course Preparation

You must register at least three full days prior to the event so that we have time to insure you have proper UM credentials for the workshop. This allows enough time for you to get your account adjusted by ITS in case you do not have access to the Linux systems.

Introduction to the Linux Command Line

By |

This course will familiarize the student with the basics of accessing and interacting with Linux computers using the GNU/Linux operating system’s Bash shell, also generically referred to as “the command line”. Topics include: a brief overview of Linux, the Bash shell, navigating the file system, basic commands, shell redirection, permissions, processes, and the command environment. The workshop will also provide a quick introduction to nano a simple text editor that will be used in subsequent workshops to edit files.

INSTRUCTOR

Kenneth Weiss
IT Project Senior Manager
Medical School Information Services (MSIS)

Ken is a High Performance Computing Consultant in the Computational Research Consulting Division of MSIS at the University of Michigan. He works with a team of IT specialists to provide high performance computing support and training for the Medical School. Prior to this, he spent 21 years managing research computing, including an HPC cluster, for Dr. Charles Sing in the Human Genetics Department.

MATERIALS

COURSE PREPARATION

You must register at least three full days prior to the event so that we have time to insure you have proper UM credentials for the workshop. This allows enough time for you to get your account adjusted by ITS in case you do not have access to the Linux systems.

If you have questions about this workshop, please send an email to the instructor at kgweiss@umich.edu

Research Computing on the Great Lakes cluster

By |

This workshop will provide a brief overview of the the new HPC environment and is intended for current Flux and Armis users.  We will use the temporary Beta HPC cluster to demonstrate how jobs will be submitted and managed under the new Great Lakes, Armis2, and Lighthouse clusters available later this year.

There are many differences between the familiar Flux environment and that of the new HPC clusters, including a new batch scheduling system, a new interactive batch job environment, a new HPC web portal, a new module environment, and a new on-demand-only job accounting system.

We will cover these differences in the workshop, and provide hands-on training in creating and running job submission scripts in the new HPC environment.  Students are expected to be conversant with the Linux command line and have experience in creating, submitting, and troubleshooting PBS batch scripts.

Introduction to the Linux Command Line

By |

This course will familiarize the student with the basics of accessing and interacting with Linux computers using the GNU/Linux operating system’s Bash shell, also generically referred to as “the command line”. Topics include: a brief overview of Linux, the Bash shell, navigating the file system, basic commands, shell redirection, permissions, processes, and the command environment. The workshop will also provide a quick introduction to nano a simple text editor that will be used in subsequent workshops to edit files.

 

Instructor

Kenneth Weiss
IT Project Senior Manager
Medical School Information Services (MSIS)

Ken is a High Performance Computing Consultant in the Computational Research Consulting Division of MSIS at the University of Michigan. He works with a team of IT specialists to provide high performance computing support and training for the Medical School. Prior to this, he spent 21 years managing research computing, including an HPC cluster, for Dr. Charles Sing in the Human Genetics Department.

Materials

Course Preparation

You must register at least three full days prior to the event so that we have time to insure you have proper UM credentials for the workshop. This allows enough time for you to get your account adjusted by ITS in case you do not have access to the Linux systems.

Research Computing on the Great Lakes cluster

By |

This workshop will provide a brief overview of the the new HPC environment and is intended for current Flux and Armis users.  We will use the temporary Beta HPC cluster to demonstrate how jobs will be submitted and managed under the new Great Lakes, Armis2, and Lighthouse clusters available later this year.

There are many differences between the familiar Flux environment and that of the new HPC clusters, including a new batch scheduling system, a new interactive batch job environment, a new HPC web portal, a new module environment, and a new on-demand-only job accounting system.

We will cover these differences in the workshop, and provide hands-on training in creating and running job submission scripts in the new HPC environment.  Students are expected to be conversant with the Linux command line and have experience in creating, submitting, and troubleshooting PBS batch scripts.

Research Computing on the Great Lakes cluster

By |

This workshop will provide a brief overview of the the new HPC environment and is intended for current Flux and Armis users.  We will use the temporary Beta HPC cluster to demonstrate how jobs will be submitted and managed under the new Great Lakes, Armis2, and Lighthouse clusters available later this year.

There are many differences between the familiar Flux environment and that of the new HPC clusters, including a new batch scheduling system, a new interactive batch job environment, a new HPC web portal, a new module environment, and a new on-demand-only job accounting system.

We will cover these differences in the workshop, and provide hands-on training in creating and running job submission scripts in the new HPC environment.  Students are expected to be conversant with the Linux command line and have experience in creating, submitting, and troubleshooting PBS batch scripts.

Research Computing on the Great Lakes cluster

By |

This workshop will provide a brief overview of the the new HPC environment and is intended for current Flux and Armis users.  We will use the temporary Beta HPC cluster to demonstrate how jobs will be submitted and managed under the new Great Lakes, Armis2, and Lighthouse clusters available later this year.

There are many differences between the familiar Flux environment and that of the new HPC clusters, including a new batch scheduling system, a new interactive batch job environment, a new HPC web portal, a new module environment, and a new on-demand-only job accounting system.

We will cover these differences in the workshop, and provide hands-on training in creating and running job submission scripts in the new HPC environment.  Students are expected to be conversant with the Linux command line and have experience in creating, submitting, and troubleshooting PBS batch scripts.

Advanced batch computing with Slurm on the Great Lakes cluster

By |

This workshop will cover some more advanced topics in cluster computing on the U-M Great Lakes Cluster. Topics to be covered include a review of common parallel programming models and basic use of Great Lakes; dependent and array scheduling; troubleshooting and analysis; a brief introduction to workflow scripting using bash; parallel processing in one or more of Python, R, and MATLAB; and parallel profiling of C and Fortran code using Allinea Performance Reports and Allinea MAP of one or more of MPI and OpenMP programs. We will issue you a temporary Great Lakes account to use for the course, or you can use your existing Great Lakes accounts, if any.

Course Preparation (PLEASE READ)

Obtain a user login on Flux. If you do not have a Flux user login, go to the application page at: https://arc-ts.umich.edu/fluxform/

Register for Duo authentication.

This course assumes familiarity with the Linux command line as might be got from the CSCAR/ARC-TS workshop Introduction to the Linux Command Line. In particular, participants should understand how files and folders work, be able to create text files using the nano editor, be able to create and remove files and folders, and understand what input and output redirection are and how to use them.

If you are unable to attend the presentation in person we will be offering a link into the live course via BlueJeans. Please register as if attending in person.  This will put you on the wait list but we will get your account setup for remote attendance.