Improving HPC IO with IME

By |

OVERVIEW

Supercomputers allow researchers to bring much more computational performance to their projects. One challenge of this additional performance is the increased rate that data may need to be accessed or written while the workloads are running.
This session will train users how to use the IME burst buffer on Great Lakes to reach IO performance potentially 10x greater than scratch or Turbo with their existing applications reaching over 80GBytes/s.
Requirements are basic command line and a Great Lakes user account.

INSTRUCTOR

Brock Palen
Director for Advanced Research Computing – Technology Services (ARC-TS)
Information and Technology Services – Advanced Research Computing – Technology Services

Brock is the director for Advanced Research Computing – Technology Services at the University of Michigan, where he is responsible for implementing the overall strategy of research computing infrastructure, including high-performance computing (HPC), high-throughput computing, research storage, big data (Hadoop, Spark), private/public cloud services, and consulting for researchers at the University of Michigan..

MATERIALS

A Zoom link will be provided to the participants the day before the class. Registration is required.

Please note, this session will be recorded.  

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

 

Session Details


Location:
Your Desktop Remote
, Off Campus (view map) pop up map

 

Session level: All
Sponsor(s): Advanced Research Computing – Technology Services
Presenter(s): Brock Palen

 

 

This session is currently Open.
You are not enrolled.

 

Data Sharing and Archiving

By |

OVERVIEW

For growing data volumes, how we manage data becomes more important. This session will cover the basics of managing data in a research environment such as those at ARC and nationally. Attendees of the course will be introduced to recommended tools for data sharing and transfer both on campus, off campus, and cloud.  They will learn how to prepare data for archive, including special high performance versions of tar and compression allowing significant performance benefits over the standard versions of the tools.
Lastly we will cover the properties and selection process of the appropriate general purpose  storage for data that requires long term preservation and active archiving that supports the largest data volumes in a way that controls costs and ease of management.
Requirements are basic command line.

INSTRUCTOR

Brock Palen
Director for Advanced Research Computing – Technology Services (ARC-TS)
Information and Technology Services – Advanced Research Computing – Technology Services

Brock is the director for Advanced Research Computing – Technology Services at the University of Michigan, where he is responsible for implementing the overall strategy of research computing infrastructure, including high-performance computing (HPC), high-throughput computing, research storage, big data (Hadoop, Spark), private/public cloud services, and consulting for researchers at the University of Michigan..

MATERIALS

A Zoom link will be provided to the participants the day before the class. Registration is required.

Please note, this session will be recorded.  

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

Please register at https://ttc.iss.lsa.umich.edu/ttc/sessions/data-sharing-and-archiving-2/register/

Session Details


Location:
Your Desktop Remote
, Off Campus (view map) pop up map

 

Session level: All
Sponsor(s): Advanced Research Computing – Technology Services
Presenter(s): Brock Palen

 

 

This session is currently Open.
You are not enrolled.

 

Improving HPC IO with IME

By |

OVERVIEW

Supercomputers allow researchers to bring much more computational performance to their projects. One challenge of this additional performance is the increased rate that data may need to be accessed or written while the workloads are running.
This session will train users how to use the IME burst buffer on Great Lakes to reach IO performance potentially 10x greater than scratch or Turbo with their existing applications reaching over 80GBytes/s.
Requirements are basic command line and a Great Lakes user account.

INSTRUCTOR

Brock Palen
Director for Advanced Research Computing – Technology Services (ARC-TS)
Information and Technology Services – Advanced Research Computing – Technology Services

Brock is the director for Advanced Research Computing – Technology Services at the University of Michigan, where he is responsible for implementing the overall strategy of research computing infrastructure, including high-performance computing (HPC), high-throughput computing, research storage, big data (Hadoop, Spark), private/public cloud services, and consulting for researchers at the University of Michigan..

MATERIALS

A Zoom link will be provided to the participants the day before the class. Registration is required.

Please note, this session will be recorded.  

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

 

Session Details


Location:
Your Desktop Remote
, Off Campus (view map) pop up map

 

Session level: All
Sponsor(s): Advanced Research Computing – Technology Services
Presenter(s): Brock Palen

 

 

This session is currently Open.
You are not enrolled.

 

Data Sharing and Archiving

By |

OVERVIEW

For growing data volumes, how we manage data becomes more important. This session will cover the basics of managing data in a research environment such as those at ARC and nationally. Attendees of the course will be introduced to recommended tools for data sharing and transfer both on campus, off campus, and cloud.  They will learn how to prepare data for archive, including special high performance versions of tar and compression allowing significant performance benefits over the standard versions of the tools.
Lastly we will cover the properties and selection process of the appropriate general purpose  storage for data that requires long term preservation and active archiving that supports the largest data volumes in a way that controls costs and ease of management.
Requirements are basic command line.

INSTRUCTOR

Brock Palen
Director for Advanced Research Computing – Technology Services (ARC-TS)
Information and Technology Services – Advanced Research Computing – Technology Services

Brock is the director for Advanced Research Computing – Technology Services at the University of Michigan, where he is responsible for implementing the overall strategy of research computing infrastructure, including high-performance computing (HPC), high-throughput computing, research storage, big data (Hadoop, Spark), private/public cloud services, and consulting for researchers at the University of Michigan..

MATERIALS

A Zoom link will be provided to the participants the day before the class. Registration is required.

Please note, this session will be recorded.  

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

Please register at https://ttc.iss.lsa.umich.edu/ttc/sessions/data-sharing-and-archiving/register/

Session Details


Location:
Your Desktop Remote
, Off Campus (view map) pop up map

 

Session level: All
Sponsor(s): Advanced Research Computing – Technology Services
Presenter(s): Brock Palen

 

 

This session is currently Open.
You are not enrolled.

 

Advanced research computing on the Great Lakes Cluster

By |

OVERVIEW

This workshop will cover some more advanced topics in 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; workflow scripting using bash; high-throughput computing using launcher; parallel processing in one or more of Python, R, and MATLAB; and profiling of parallel code using Allinea Performance Reports and Allinea MAP.

PRE-REQUISITES

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.

INSTRUCTORS

Dr. Charles J Antonelli
Research Computing Services
LSA Technology Services

Charles is a member of the LSA Technology Services Research team at the University of Michigan, where he is responsible for high performance computing support and education, and was an Advocate to the Departments of History and Communications. Prior to this, he built a parallel data ingestion component of a novel earth science data assimilation system, a secure packet vault, and worked on the No. 5 ESS Switch at Bell Labs in the 80s. He has taught courses in operating systems, distributed file systems, C++ programming, security, and database application design.

John Thiels
Research Computing Services
LSA Technology Services

MATERIALS

COURSE PREPARATION

In order to participate successfully in the workshop exercises, you must have a user login, a Slurm account, and be enrolled in Duo. The user login allows you to log in to the cluster, create, compile, and test applications, and prepare jobs for submission. The Slurm account allows you to submit those jobs, executing the applications in parallel on the cluster and charging their resource use to the account. Duo is required to help authenticate you to the cluster.

USER LOGIN

If you already have a Great Lakes user login, you don’t need to do anything.  Otherwise, go to the Great Lakes user login application page at: http://arc-ts.umich.edu/login-request/ .

Please note that obtaining a user account requires human processing, so be sure to do this at least two business days before class begins.

SLURM ACCOUNT

We create a Slurm account for the workshop so you can run jobs on the cluster during the workshop and for one day after for those who would like additional practice. The workshop job account is quite limited and is intended only to run examples to help you cement the details of job submission and management. If you already have an existing Slurm account, you can use that, though if there are any issues with that account, we will ask you to use the workshop account.

DUO AUTHENTICATION

Duo two-factor authentication is required to log in to the cluster. When logging in, you will need to type your UMICH (AKA Level 1) password as well as authenticate through Duo in order to access Great Lakes.

If you need to enroll in Duo, follow the instructions at Enroll a Smartphone or Tablet in Duo.

Please enroll in Duo before you come to class.

LAPTOP PREPARATION

You will need VPN software to access the U-M network.  If you do not have VPN software already installed, please download and install the Cisco AnyConnect VPN software following these instructions.  You will need VPN to be able to use the ssh client to connect to Great Lakes. Please use the ‘Campus All traffic’ profile in the Cisco client.

You will need an ssh client to connect to the Great Lakes cluster. Mac OS X and Linux platforms have this built-in. Here are a couple of choices for Windows platforms:

  • Download and install U-M PuTTY/WinSCP from the Compute at the U website. This includes both the PuTTY ssh client and terminal emulator and a graphical file transfer tool in one installer.  This document describes how to download and use this software, except please note you will be connecting to greatlakes.arc-ts.umich.edu instead of the cited host.  You must have administrative authority over your computer to install this software.
  • Download PuTTY directly from the developer. Download the putty.exe application listed under “Alternative binary files,”, then execute the application.  You do not need administrative authority over your computer to use this software.

Our Great Lakes User Guide in Section 1.2 describes in more detail how to use PuTTY to connect to Great Lakes.

Please prepare and test your computer’s ability to make remote connections before class; we cannot stop to debug connection issues during the class.

A Zoom link will be provided to the participants the day before the class. Registration is required.Please note this session will be recorded.

 

Please register at https://ttc.iss.lsa.umich.edu/ttc/sessions/advanced-research-computing-on-the-great-lakes-cluster-8/register/

Advanced research computing on the Great Lakes Cluster

By |

OVERVIEW

This workshop will cover some more advanced topics in 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; workflow scripting using bash; high-throughput computing using launcher; parallel processing in one or more of Python, R, and MATLAB; and profiling of parallel code using Allinea Performance Reports and Allinea MAP.

PRE-REQUISITES

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.

INSTRUCTORS

Dr. Charles J Antonelli
Research Computing Services
LSA Technology Services

Charles is a member of the LSA Technology Services Research team at the University of Michigan, where he is responsible for high performance computing support and education, and was an Advocate to the Departments of History and Communications. Prior to this, he built a parallel data ingestion component of a novel earth science data assimilation system, a secure packet vault, and worked on the No. 5 ESS Switch at Bell Labs in the 80s. He has taught courses in operating systems, distributed file systems, C++ programming, security, and database application design.

John Thiels
Research Computing Services
LSA Technology Services

MATERIALS

COURSE PREPARATION

In order to participate successfully in the workshop exercises, you must have a user login, a Slurm account, and be enrolled in Duo. The user login allows you to log in to the cluster, create, compile, and test applications, and prepare jobs for submission. The Slurm account allows you to submit those jobs, executing the applications in parallel on the cluster and charging their resource use to the account. Duo is required to help authenticate you to the cluster.

USER LOGIN

If you already have a Great Lakes user login, you don’t need to do anything.  Otherwise, go to the Great Lakes user login application page at: http://arc-ts.umich.edu/login-request/ .

Please note that obtaining a user account requires human processing, so be sure to do this at least two business days before class begins.

SLURM ACCOUNT

We create a Slurm account for the workshop so you can run jobs on the cluster during the workshop and for one day after for those who would like additional practice. The workshop job account is quite limited and is intended only to run examples to help you cement the details of job submission and management. If you already have an existing Slurm account, you can use that, though if there are any issues with that account, we will ask you to use the workshop account.

DUO AUTHENTICATION

Duo two-factor authentication is required to log in to the cluster. When logging in, you will need to type your UMICH (AKA Level 1) password as well as authenticate through Duo in order to access Great Lakes.

If you need to enroll in Duo, follow the instructions at Enroll a Smartphone or Tablet in Duo.

Please enroll in Duo before you come to class.

LAPTOP PREPARATION

You will need VPN software to access the U-M network.  If you do not have VPN software already installed, please download and install the Cisco AnyConnect VPN software following these instructions.  You will need VPN to be able to use the ssh client to connect to Great Lakes. Please use the ‘Campus All traffic’ profile in the Cisco client.

You will need an ssh client to connect to the Great Lakes cluster. Mac OS X and Linux platforms have this built-in. Here are a couple of choices for Windows platforms:

  • Download and install U-M PuTTY/WinSCP from the Compute at the U website. This includes both the PuTTY ssh client and terminal emulator and a graphical file transfer tool in one installer.  This document describes how to download and use this software, except please note you will be connecting to greatlakes.arc-ts.umich.edu instead of the cited host.  You must have administrative authority over your computer to install this software.
  • Download PuTTY directly from the developer. Download the putty.exe application listed under “Alternative binary files,”, then execute the application.  You do not need administrative authority over your computer to use this software.

Our Great Lakes User Guide in Section 1.2 describes in more detail how to use PuTTY to connect to Great Lakes.

Please prepare and test your computer’s ability to make remote connections before class; we cannot stop to debug connection issues during the class.

A Zoom link will be provided to the participants the day before the class. Registration is required.Please note this session will be recorded.

 

Please register at https://ttc.iss.lsa.umich.edu/ttc/sessions/advanced-research-computing-on-the-great-lakes-cluster-7/register/

Introduction to Research Computing on the Great Lakes Cluster

By |

OVERVIEW

This workshop will introduce you to high performance computing on the Great Lakes cluster.  After a brief overview of the components of the cluster and the resources available there, the main body of the workshop will cover creating batch scripts and the options available to run jobs, and hands-on experience in submitting, tracking, and interpreting the results of submitted jobs. By the end of the workshop, every participant should have created a submission script, submitted a job, tracked its progress, and collected its output. Additional tools including high-performance data transfer services and interactive use of the cluster will also be covered.

PRE-REQUISITES

This course assumes familiarity with the Linux command line as might be obtained from the 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, and be able to create and remove files and folders.  Some exposure to shell input and output redirection and pipes would also be useful.

INSTRUCTORS

Dr. Charles J Antonelli
Research Computing Services
LSA Technology Services

Charles is a member of the LSA Technology Services Research team at the University of Michigan, where he is responsible for high performance computing support and education, and was an Advocate to the Departments of History and Communications. Prior to this, he built a parallel data ingestion component of a novel earth science data assimilation system, a secure packet vault, and worked on the No. 5 ESS Switch at Bell Labs in the 80s. He has taught courses in operating systems, distributed file systems, C++ programming, security, and database application design.

MATERIALS

COURSE PREPARATION

In order to participate successfully in the workshop exercises, you must have a user login, a Slurm account, and be enrolled in Duo. The user login allows you to log in to the cluster, create, compile, and test applications, and prepare jobs for submission. The Slurm account allows you to submit those jobs, executing the applications in parallel on the cluster and charging their resource use to the account. Duo is required to help authenticate you to the cluster.

USER LOGIN

If you already have a Great Lakes user login, you don’t need to do anything.  Otherwise, go to the Great Lakes user login application page at: http://arc-ts.umich.edu/login-request/

Please note that obtaining a user account requires human processing, so be sure to do this at least two business days before class begins.

SLURM ACCOUNT

We create a Slurm account for the workshop so you can run jobs on the cluster during the workshop and for one day after for those who would like additional practice. The workshop job account is quite limited and is intended only to run examples to help you cement the details of job submission and management. If you already have an existing Slurm account, you can use that, though if there are any issues with that account, we will ask you to use the workshop account.

DUO AUTHENTICATION

Duo two-factor authentication is required to log in to the cluster. When logging in, you will need to type your UMICH (AKA Level 1) password as well as authenticate through Duo in order to access Great Lakes.

If you need to enroll in Duo, follow the instructions at Enroll a Smartphone or Tablet in Duo.

Please enroll in Duo before you come to class.

LAPTOP PREPARATION

You will need VPN software to access the U-M network on which Great Lakes is located.  If you do not have VPN software already installed, please download and install the Cisco AnyConnect VPN software following these instructions.  Please use the ‘Campus All traffic’ profile in the Cisco client.

You will need an ssh client to connect to the Great Lakes cluster. Mac OS X and Linux platforms have this built-in. Here are a couple of choices for Windows platforms:

Download and install U-M PuTTY/WinSCP from the Compute at the U website. This includes both the PuTTY ssh client and terminal emulator and a graphical file transfer tool in one installer.  This document describes how to download and use this software, except please note you will be connecting to greatlakes.arc-ts.umich.edu instead of the cited host.  You must have administrative authority over your computer to install this software.
Download PuTTY directly from the developer. Download the putty.exe application listed under “Alternative binary files,”, then execute the application.  You do not need administrative authority over your computer to use this software.
Our Great Lakes User Guide in Section 1.2 describes in more detail how to use PuTTY to connect to Great Lakes.

Please prepare and test your computer’s ability to make remote connections before class; we cannot stop to debug connection issues during the class.

A Zoom link will be provided to the participants the day before the class. Registration is required.  Please note this session will be recorded.

 

If you have questions about this workshop, please send an email to the instructors at hpc-course@umich.edu

Please register at https://ttc.iss.lsa.umich.edu/ttc/sessions/introduction-to-research-computing-on-the-great-lakes-cluster-4/register/

DNA sequencing productivity increases with ARC-TS services

By | HPC, News, Research, Systems and Services
NovaSeq, the DNA sequencer that is about the size of large laser printer.

The Advanced Genomics Core’s Illumina NovaSeq 6000 sequencing platform. It’s about the size of large laser printer.

On the cutting-edge of research at U-M is the Advanced Genomics Core’s Illumina NovaSeq 6000 sequencing platform. The AGC is one of the first academic core facilities to optimize this exciting and powerful instrument, that is about the size of a large laser printer. 

The Advanced Genomics Core (AGC), part of the Biomedical Research Core Facilities within the Medical School Office of Research, provides high-quality, low-cost next generation sequencing analysis for research clients on a recharge basis. 

One NovaSeq run can generate as much as 4TB of raw data. So how is the AGC able to generate, process, analyze, and transfer so much data for researchers? They have partnered with Advanced Research Computing – Technology Services (ARC-TS) to leverage the speed and power of the Great Lakes High-Performance Computing Cluster

With Great Lakes, AGC can process the data, and then store the output on other ARC-TS services: Turbo Research Storage and Data Den Research Archive, and share with clients using Globus File Transfer. All three services work together. Turbo offers the capacity and speed to match the computational performance of Great Lakes, Data Den provides an archive of raw data in case of catastrophic failure, and Globus has the performance needed for the transfer of big data. 

“Thanks to Great Lakes, we were able to process dozens of large projects simultaneously, instead of being limited to just a couple at a time with our in-house system,” said Olivia Koues, Ph.D., AGC managing director. 

“In calendar year 2020, the AGC delivered nearly a half petabyte of data to our research community. We rely on the speed of Turbo for storage, the robustness of Data Den for archiving, and the ease of Globus for big data file transfers. Working with ARC-TS has enabled incredible research such as making patients resilient to COVID-19. We are proudly working together to help patients.”

“Our services process more than 180,000GB of raw data per year for the AGC. That’s the same as streaming the three original Star Wars movies and the three prequels more than 6,000 times,” said Brock Palen, ARC-TS director. “We enjoy working with AGC to assist them into the next step of their big data journey.”

ARC-TS is a division of Information and Technology Services (ITS). The Advanced Genomics Core (ACG) is part of the Biomedical Research Core Facilities (BRCF) within the Medical School Office of Research.

Advanced research computing on the Great Lakes Cluster

By |

OVERVIEW

This workshop will cover some more advanced topics in 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; workflow scripting using bash; high-throughput computing using launcher; parallel processing in one or more of Python, R, and MATLAB; and profiling of parallel code using Allinea Performance Reports and Allinea MAP.

PRE-REQUISITES

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.

INSTRUCTORS

Dr. Charles J Antonelli
Research Computing Services
LSA Technology Services

Charles is a member of the LSA Technology Services Research team at the University of Michigan, where he is responsible for high performance computing support and education, and was an Advocate to the Departments of History and Communications. Prior to this, he built a parallel data ingestion component of a novel earth science data assimilation system, a secure packet vault, and worked on the No. 5 ESS Switch at Bell Labs in the 80s. He has taught courses in operating systems, distributed file systems, C++ programming, security, and database application design.

John Thiels
Research Computing Services
LSA Technology Services

MATERIALS

COURSE PREPARATION

In order to participate successfully in the workshop exercises, you must have a user login, a Slurm account, and be enrolled in Duo. The user login allows you to log in to the cluster, create, compile, and test applications, and prepare jobs for submission. The Slurm account allows you to submit those jobs, executing the applications in parallel on the cluster and charging their resource use to the account. Duo is required to help authenticate you to the cluster.

USER LOGIN

If you already have a Great Lakes user login, you don’t need to do anything.  Otherwise, go to the Great Lakes user login application page at: http://arc-ts.umich.edu/login-request/ .

Please note that obtaining a user account requires human processing, so be sure to do this at least two business days before class begins.

SLURM ACCOUNT

We create a Slurm account for the workshop so you can run jobs on the cluster during the workshop and for one day after for those who would like additional practice. The workshop job account is quite limited and is intended only to run examples to help you cement the details of job submission and management. If you already have an existing Slurm account, you can use that, though if there are any issues with that account, we will ask you to use the workshop account.

DUO AUTHENTICATION

Duo two-factor authentication is required to log in to the cluster. When logging in, you will need to type your UMICH (AKA Level 1) password as well as authenticate through Duo in order to access Great Lakes.

If you need to enroll in Duo, follow the instructions at Enroll a Smartphone or Tablet in Duo.

Please enroll in Duo before you come to class.

LAPTOP PREPARATION

You will need VPN software to access the U-M network.  If you do not have VPN software already installed, please download and install the Cisco AnyConnect VPN software following these instructions.  You will need VPN to be able to use the ssh client to connect to Great Lakes. Please use the ‘Campus All traffic’ profile in the Cisco client.

You will need an ssh client to connect to the Great Lakes cluster. Mac OS X and Linux platforms have this built-in. Here are a couple of choices for Windows platforms:

  • Download and install U-M PuTTY/WinSCP from the Compute at the U website. This includes both the PuTTY ssh client and terminal emulator and a graphical file transfer tool in one installer.  This document describes how to download and use this software, except please note you will be connecting to greatlakes.arc-ts.umich.edu instead of the cited host.  You must have administrative authority over your computer to install this software.
  • Download PuTTY directly from the developer. Download the putty.exe application listed under “Alternative binary files,”, then execute the application.  You do not need administrative authority over your computer to use this software.

Our Great Lakes User Guide in Section 1.2 describes in more detail how to use PuTTY to connect to Great Lakes.

Please prepare and test your computer’s ability to make remote connections before class; we cannot stop to debug connection issues during the class.

A Zoom link will be provided to the participants the day before the class. Registration is required.Please note this session will be recorded.

Introduction to Research Computing on the Great Lakes Cluster

By |

OVERVIEW

This workshop will introduce you to high performance computing on the Great Lakes cluster.  After a brief overview of the components of the cluster and the resources available there, the main body of the workshop will cover creating batch scripts and the options available to run jobs, and hands-on experience in submitting, tracking, and interpreting the results of submitted jobs. By the end of the workshop, every participant should have created a submission script, submitted a job, tracked its progress, and collected its output. Additional tools including high-performance data transfer services and interactive use of the cluster will also be covered.

PRE-REQUISITES

This course assumes familiarity with the Linux command line as might be obtained from the 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, and be able to create and remove files and folders.  Some exposure to shell input and output redirection and pipes would also be useful.

INSTRUCTORS

Dr. Charles J Antonelli
Research Computing Services
LSA Technology Services

Charles is a member of the LSA Technology Services Research team at the University of Michigan, where he is responsible for high performance computing support and education, and was an Advocate to the Departments of History and Communications. Prior to this, he built a parallel data ingestion component of a novel earth science data assimilation system, a secure packet vault, and worked on the No. 5 ESS Switch at Bell Labs in the 80s. He has taught courses in operating systems, distributed file systems, C++ programming, security, and database application design.

MATERIALS

COURSE PREPARATION

In order to participate successfully in the workshop exercises, you must have a user login, a Slurm account, and be enrolled in Duo. The user login allows you to log in to the cluster, create, compile, and test applications, and prepare jobs for submission. The Slurm account allows you to submit those jobs, executing the applications in parallel on the cluster and charging their resource use to the account. Duo is required to help authenticate you to the cluster.

USER LOGIN

If you already have a Great Lakes user login, you don’t need to do anything.  Otherwise, go to the Great Lakes user login application page at: http://arc-ts.umich.edu/login-request/

Please note that obtaining a user account requires human processing, so be sure to do this at least two business days before class begins.

SLURM ACCOUNT

We create a Slurm account for the workshop so you can run jobs on the cluster during the workshop and for one day after for those who would like additional practice. The workshop job account is quite limited and is intended only to run examples to help you cement the details of job submission and management. If you already have an existing Slurm account, you can use that, though if there are any issues with that account, we will ask you to use the workshop account.

DUO AUTHENTICATION

Duo two-factor authentication is required to log in to the cluster. When logging in, you will need to type your UMICH (AKA Level 1) password as well as authenticate through Duo in order to access Great Lakes.

If you need to enroll in Duo, follow the instructions at Enroll a Smartphone or Tablet in Duo.

Please enroll in Duo before you come to class.

 

LAPTOP PREPARATION

You will need VPN software to access the U-M network on which Great Lakes is located.  If you do not have VPN software already installed, please download and install the Cisco AnyConnect VPN software following these instructions.  Please use the ‘Campus All traffic’ profile in the Cisco client.

You will need an ssh client to connect to the Great Lakes cluster. Mac OS X and Linux platforms have this built-in. Here are a couple of choices for Windows platforms:

Download and install U-M PuTTY/WinSCP from the Compute at the U website. This includes both the PuTTY ssh client and terminal emulator and a graphical file transfer tool in one installer.  This document describes how to download and use this software, except please note you will be connecting to greatlakes.arc-ts.umich.edu instead of the cited host.  You must have administrative authority over your computer to install this software.
Download PuTTY directly from the developer. Download the putty.exe application listed under “Alternative binary files,”, then execute the application.  You do not need administrative authority over your computer to use this software.
Our Great Lakes User Guide in Section 1.2 describes in more detail how to use PuTTY to connect to Great Lakes.

Please prepare and test your computer’s ability to make remote connections before class; we cannot stop to debug connection issues during the class.

A Zoom link will be provided to the participants the day before the class. Registration is required.  Please note this session will be recorded.

Instructor will be available at the Zoom link, to be provided, from 12 -1 PM for computer setup assistance.

If you have questions about this workshop, please send an email to the instructors at hpc-course@umich.edu