Winter 2018 Maintenance

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To accommodate updates to software, hardware, and operating systems, Flux, Armis, ConFlux, Flux Hadoop, and their storage systems (/home and /scratch) will be unavailable starting at 7 a.m. Tuesday, January 2nd and returning to service on Friday, January 5th.  These updates will improve the performance and stability of ARC-TS services.  We try to encapsulate the required changes into two maintenance periods per year and work to complete these tasks quickly, as we understand the impact of the maintenance on your research.

For up-to-date information on the maintenance, visit http://arc-ts.umich.edu/winter-2018-maintenance/

Service Disruption: MiStorage Silver (Value Storage) Maintenance

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The ITS Storage team will be applying an operating system patch on the MiStorage Silver (Value Storage) environment, which provides home directories for both Flux and Flux Hadoop.  The ITS maintenance window will be from December 2nd 11:00pm to December 3rd 7:00am (8 hours total) and ARC-TS will prepare Flux, Armis, and Flux Hadoop for the maintenance starting at 10:00pm.  This update might be potentially disruptive to the stability of the nodes and jobs running on them.

The ITS status page for this incident is here:  http://status.its.umich.edu/report.php?id=141155

For Flux and Armis users: we have created a reservation on Flux so no jobs will be running or impacted.  We will remove the reservation after we receive the update from the ITS storage team of a successful update.

For Flux Hadoop users:  The scheduler and user logins will be deactivated when the outage starts, and any user currently logged into the cluster will be logged out for the duration of the outage.  We will reactivate access when we have received the all-clear from the ITS storage team of a successful update.

Status updates will be posted on the ARC-TS Twitter feed: https://twitter.com/arcts_um  and if you have any questions, please email us at hpc-support@umich.edu.

U-M partners with Cavium on Big Data computing platform

By | Feature, General Interest, Happenings, HPC, News

A new partnership between the University of Michigan and Cavium Inc., a San Jose-based provider of semiconductor products, will create a powerful new Big Data computing cluster available to all U-M researchers.

The $3.5 million ThunderX computing cluster will enable U-M researchers to, for example, process massive amounts of data generated by remote sensors in distributed manufacturing environments, or by test fleets of automated and connected vehicles.

The cluster will run the Hortonworks Data Platform providing Spark, Hadoop MapReduce and other tools for large-scale data processing.

“U-M scientists are conducting groundbreaking research in Big Data already, in areas like connected and automated transportation, learning analytics, precision medicine and social science. This partnership with Cavium will accelerate the pace of data-driven research and opening up new avenues of inquiry,” said Eric Michielssen, U-M associate vice president for advanced research computing and the Louise Ganiard Johnson Professor of Engineering in the Department of Electrical Engineering and Computer Science.

“I know from experience that U-M researchers are capable of amazing discoveries. Cavium is honored to help break new ground in Big Data research at one of the top universities in the world,” said Cavium founder and CEO Syed Ali, who received a master of science in electrical engineering from U-M in 1981.

Cavium Inc. is a leading provider of semiconductor products that enable secure and intelligent processing for enterprise, data center, wired and wireless networking. The new U-M system will use dual socket servers powered by Cavium’s ThunderX ARMv8-A workload optimized processors.

The ThunderX product family is Cavium’s 64-bit ARMv8-A server processor for next generation Data Center and Cloud applications, and features high performance custom cores, single and dual socket configurations, high memory bandwidth and large memory capacity.

Alec Gallimore, the Robert J. Vlasic Dean of Engineering at U-M, said the Cavium partnership represents a milestone in the development of the College of Engineering and the university.

“It is clear that the ability to rapidly gain insights into vast amounts of data is key to the next wave of engineering and science breakthroughs. Without a doubt, the Cavium platform will allow our faculty and researchers to harness the power of Big Data, both in the classroom and in their research,” said Gallimore, who is also the Richard F. and Eleanor A. Towner Professor, an Arthur F. Thurnau Professor, and a professor both of aerospace engineering and of applied physics.

Along with applications in fields like manufacturing and transportation, the platform will enable researchers in the social, health and information sciences to more easily mine large, structured and unstructured datasets. This will eventually allow, for example, researchers to discover correlations between health outcomes and disease outbreaks with information derived from socioeconomic, geospatial and environmental data streams.

U-M and Cavium chose to run the cluster on Hortonworks Data Platform, which is based on open source Apache Hadoop. The ThunderX cluster will deliver high performance computer services for the Hadoop analytics and, ultimately, a total of three petabytes of storage space.

“Hortonworks is excited to be a part of forward-leading research at the University of Michigan exploring low-powered, high-performance computing,” said Nadeem Asghar, vice president and global head of technical alliances at Hortonworks. “We see this as a great opportunity to further expand the platform and segment enablement for Hortonworks and the ARM community.”

Potential service disruption for Value Storage maintenance — Dec. 2

By | Flux, General Interest, Happenings, HPC, News

The ITS Storage team will be applying an operating system patch on the MiStorage Silver environment, which provides home directories for both Flux and Flux Hadoop.  The ITS maintenance window will be from December 2nd 11:00pm to December 3rd 7:00am (8 hours total).  This update might be potentially disruptive to the stability of the nodes and jobs running on them.

The ITS status page for this incident is here:  http://status.its.umich.edu/report.php?id=141155

For Flux users: we have created a reservation on Flux so no jobs will be running or impacted.  We will remove the reservation after we receive the update from the ITS storage team of a successful update.

For Flux Hadoop users:  The scheduler and user logins will be deactivated when the outage starts, and any user currently logged into the cluster will be logged out for the duration of the outage.  We will reactivate access when we have received the all-clear from the ITS storage team of a successful update.

Status updates will be posted on the ARC-TS Twitter feed: https://twitter.com/arcts_um  and if you have any questions, please email us at hpc-support@umich.edu.

CSCAR provides walk-in support for new Flux users

By | Data, Educational, Flux, General Interest, HPC, News

CSCAR now provides walk-in support during business hours for students, faculty, and staff seeking assistance in getting started with the Flux computing environment.  CSCAR consultants can walk a researcher through the steps of applying for a Flux account, installing and configuring a terminal client, connecting to Flux, basic SSH and Unix command line, and obtaining or accessing allocations.  

In addition to walk-in support, CSCAR has several staff consultants with expertise in advanced and high performance computing who can work with clients on a variety of topics such as installing, optimizing, and profiling code.  

Support via email is also provided via hpc-support@umich.edu.  

CSCAR is located in room 3550 of the Rackham Building (915 E. Washington St.). Walk-in hours are from 9 a.m. – 5 p.m., Monday through Friday, except for noon – 1 p.m. on Tuesdays.

See the CSCAR web site (cscar.research.umich.edu) for more information.

Advanced batch computing on the Flux cluster

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Overview

This course will cover some more advanced topics in cluster computing on the U-M Flux Cluster. Topics to be covered include a review of common parallel programming models and basic use of Flux; dependent and array scheduling; advanced troubleshooting and analysis using checkjob, qstat, and other tools; and parallel debugging and profiling of C and Fortran code, including logging, gdb (line-oriented debugging), ddt (GUI-based debugging) and map (GUI-based profiling) of MPI and OpenMP programs. We will issue you a temporary allocation to use for the course, or you can use your existing Flux allocations, if any.

Prerequisites

Introduction to Batch Computing on Flux or equivalent. This course assumes familiarity with the Linux command line, text editing on Linux, and a basic understanding of Flux including how to submit and track jobs.

click here to register

Instructors

Dr. Charles J Antonelli
Advocacy and Research Support
LSA Information Technology

Charles is a High Performance Computing Consultant in the Advocacy and Research Support Group of LSAIT at the University of Michigan, where he is responsible for high performance computing support and education, and is 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.

Dr. Alexander Gaenko
Technical Services
Advanced Research Computing

Mark Champe
Advocacy and Research Support
LSA Information Technology

Materials

Course Preparation

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


Flux user account

A single Flux user account can be used to prepare and submit jobs using various allocations. If you already already possess a user account, you can use it for this course, you can skip to “Flux allocation” below. If not, please visit https://arc-ts.umich.edu/fluxform to obtain one. A user account is free to members of the University community. Please note that obtaining an account requires human processing, so be sure to do this at least two business days before class begins.


Flux allocation

We create an allocation 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 allocation 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 Flux allocation, you can use that, though if there are any issues with that allocation, we will ask you to use the workshop allocation.


Duo Authentication

Duo two-factor authentication is required to log in to the cluster. When logging in, you will need to type your UMICH password as well as authenticate through Duo in order to access Flux.

If you need to enroll in Duo, follow the instructions at Getting Started: How to Enroll in Duo.

Please enroll in Duo before you come to class.

Laptop Preparation

You do not need to bring your own laptop to class. The classroom contains Windows computers, which require your uniqname and UMICH password to login, and that have all necessary software pre-loaded.

If you want to use a laptop for the course, you are welcome to do so:  please see our web page on Preparing your laptop to use Flux. However, if there are problems connecting your laptop, you will be asked to switch to the provided computer for the class. We cannot stop to debug connection issues with personal or departmental laptops during the class.

More help

Please use our class mailing list hpc201course@umich.edu for questions, comments, or to seek further assistance.

Advanced batch computing on the Flux cluster

By |

Overview

This course will cover some more advanced topics in cluster computing on the U-M Flux Cluster. Topics to be covered include a review of common parallel programming models and basic use of Flux; dependent and array scheduling; advanced troubleshooting and analysis using checkjob, qstat, and other tools; and parallel debugging and profiling of C and Fortran code, including logging, gdb (line-oriented debugging), ddt (GUI-based debugging) and map (GUI-based profiling) of MPI and OpenMP programs. We will issue you a temporary allocation to use for the course, or you can use your existing Flux allocations, if any.

Prerequisites

Introduction to Batch Computing on Flux or equivalent. This course assumes familiarity with the Linux command line, text editing on Linux, and a basic understanding of Flux including how to submit and track jobs.

click here to register

Instructors

Dr. Charles J Antonelli
Advocacy and Research Support
LSA Information Technology

Charles is a High Performance Computing Consultant in the Advocacy and Research Support Group of LSAIT at the University of Michigan, where he is responsible for high performance computing support and education, and is 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.

Dr. Alexander Gaenko
Technical Services
Advanced Research Computing

Mark Champe
Advocacy and Research Support
LSA Information Technology

Materials

Course Preparation

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


Flux user account

A single Flux user account can be used to prepare and submit jobs using various allocations. If you already already possess a user account, you can use it for this course, you can skip to “Flux allocation” below. If not, please visit https://arc-ts.umich.edu/fluxform to obtain one. A user account is free to members of the University community. Please note that obtaining an account requires human processing, so be sure to do this at least two business days before class begins.


Flux allocation

We create an allocation 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 allocation 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 Flux allocation, you can use that, though if there are any issues with that allocation, we will ask you to use the workshop allocation.


Duo Authentication

Duo two-factor authentication is required to log in to the cluster. When logging in, you will need to type your UMICH password as well as authenticate through Duo in order to access Flux.

If you need to enroll in Duo, follow the instructions at Getting Started: How to Enroll in Duo.

Please enroll in Duo before you come to class.

Laptop Preparation

You do not need to bring your own laptop to class. The classroom contains Windows computers, which require your uniqname and UMICH password to login, and that have all necessary software pre-loaded.

If you want to use a laptop for the course, you are welcome to do so:  please see our web page on Preparing your laptop to use Flux. However, if there are problems connecting your laptop, you will be asked to switch to the provided computer for the class. We cannot stop to debug connection issues with personal or departmental laptops during the class.

More help

Please use our class mailing list hpc201course@umich.edu for questions, comments, or to seek further assistance.

Introduction to the Flux cluster and batch computing

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Overview

This workshop will provide a brief overview of the components of the Flux Cluster. The main body of the workshop will cover the resource manager and scheduler, creating submissions scripts to run jobs and the options available in them, and hands-on experience. By the end of the workshop, every participant should have created a submission script, submitted a job, tracked its progress, and collected its output. Participants will have several working examples from which to build their own submissions scripts in their own home directories.

Prerequisites

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

Register for Duo authentication. See below for details.

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.

click here to register

Instructor

Bennet Fauber
Scientific Applications Analyst
Advanced Research Computing — Technology Services

Bennet Fauber is a member of the technical team that administers the Flux cluster.

Materials

In-class handouts

Supplementary materials

Course Preparation

In order to participate successfully in the workshop exercises, you must have a Flux user account and be registered for the Duo authentication service. The user account allows you to log in to the cluster, create, compile, and test applications, and prepare Flux jobs for submission. Information about registering for Duo is at the ITS Two Factor Authentication web page.

Flux user account

A single Flux user account can be used to prepare and submit jobs using various allocations. If you already already possess a user account, you can use it for this course, you can skip to “Flux allocation” below. If not, please visit https://arc-ts.umich.edu/fluxform to obtain one. A user account is free to members of the University community. Please note that obtaining an account requires human processing, so be sure to do this at least two business days before class begins.

Flux allocation

We create an allocation 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 allocation 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 Flux allocation, you can use that, though if there are any issues with that allocation, we will ask you to use the workshop allocation.

Laptop Preparation

The classroom contains Windows computers, which require your uniqname and UMICH password to login, and which have all necessary software preloaded.

If you want to use a laptop for the course, you are welcome to do so. However, if there are problems connecting your laptop, you will be asked to switch to the provided computer for the class. We will try to help resolve issues after the workshop.

If you want to try to prepare your laptop for use in the class, please see our web page on Preparing your laptop to use Flux. If you have a Windows computer, we recommend that you install PuTTY/WinSCP from the Blue Disc web site. Macintosh computers typically have the minimum requirements installed as part of the system.

More help

Please use our class mailing list hpc101course@umich.edu for questions, comments, or to seek further assistance.

Introduction to the Flux cluster and batch computing

By |

Overview

This workshop will provide a brief overview of the components of the Flux Cluster. The main body of the workshop will cover the resource manager and scheduler, creating submissions scripts to run jobs and the options available in them, and hands-on experience. By the end of the workshop, every participant should have created a submission script, submitted a job, tracked its progress, and collected its output. Participants will have several working examples from which to build their own submissions scripts in their own home directories.

Prerequisites

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

Register for Duo authentication. See below for details.

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.

click here to register

Instructor

Bennet Fauber
Scientific Applications Analyst
Advanced Research Computing — Technology Services

Bennet Fauber is a member of the technical team that administers the Flux cluster.

Materials

In-class handouts

Supplementary materials

Course Preparation

In order to participate successfully in the workshop exercises, you must have a Flux user account and be registered for the Duo authentication service. The user account allows you to log in to the cluster, create, compile, and test applications, and prepare Flux jobs for submission. Information about registering for Duo is at the ITS Two Factor Authentication web page.

Flux user account

A single Flux user account can be used to prepare and submit jobs using various allocations. If you already already possess a user account, you can use it for this course, you can skip to “Flux allocation” below. If not, please visit https://arc-ts.umich.edu/fluxform to obtain one. A user account is free to members of the University community. Please note that obtaining an account requires human processing, so be sure to do this at least two business days before class begins.

Flux allocation

We create an allocation 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 allocation 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 Flux allocation, you can use that, though if there are any issues with that allocation, we will ask you to use the workshop allocation.

Laptop Preparation

The classroom contains Windows computers, which require your uniqname and UMICH password to login, and which have all necessary software preloaded.

If you want to use a laptop for the course, you are welcome to do so. However, if there are problems connecting your laptop, you will be asked to switch to the provided computer for the class. We will try to help resolve issues after the workshop.

If you want to try to prepare your laptop for use in the class, please see our web page on Preparing your laptop to use Flux. If you have a Windows computer, we recommend that you install PuTTY/WinSCP from the Blue Disc web site. Macintosh computers typically have the minimum requirements installed as part of the system.

More help

Please use our class mailing list hpc101course@umich.edu for questions, comments, or to seek further assistance.

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.

click here to register

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.