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News

Mailing List

Sign up for the Hyak-users mailing list to stay up to date with the latest news: https://mailman1.u.washington.edu/mailman/listinfo/hyak-users

This list is used for ALL announcements to Hyak users, so please sign up. Important Hyak announcements are ONLY sent to this list, not to the individual Hyak accounts.

Announcements

September 1, 2016

The Hyak User Wiki has moved to a new wiki service. All the formatting may not be 100%, but we do hope to dedicate resources to reorganizing the wiki, both content and formatting, in the coming months.

January 14, 2016

You can now get to this top level page using the address: http://wiki.hyak.uw.edu

System Status

Current Status

December 13, 2016 5:29pm

Hyak is operating normally. The lolo archive filesystem will be back up as soon as possible.

Monthly Scheduled Maintenance

Hyak will be offline from 9:00 am - 5:00 pm for scheduled maintenance the second Tuesday of every month. Every third month (Feb, May, Aug, Nov), the maintenance window will last from 9:00 am to 9:00 the following morning. More on the Maintenance schedule.

Other maintenance performed on Hyak is relatively rare, short (30 - 60 minutes), and does not impact running jobs. This type of maintenance is announced to the hyak-users list.

Cluster Node Status

We run the Ganglia cluster status tool. Here you can find out the details about the CPU, memory, and network usage of the nodes in your allocation.

http://status.hyak.uw.edu/

Hyak Overview

Hyak is a service of UW-IT. You can read more about it in the Service Catalog.

Hyak contains two partitions, "p1" and "p2". Both partitions contain hundreds of nodes, each comparable to a high-end PC. A typical node has 16 processor cores and 128GB of memory. All the nodes run CentOS 6 Linux, and they are tied together by the Moab cluster software. The user tasks are typically submitted through TORQUE scheduler although simple programs can also be run directly. Hyak is made of several generations of hardware with different levels of performance, see Hyak Node Hardware for more details. Most of the nodes are devoted for computing but the cluster also includes a few "login-nodes", dedicated to logins, file transfers, and similar communication tasks. There are also nodes that belong to the sponsoring institutions, and nodes for compiling and testing the programs.

Purchasing Hyak Capacity

CPU and storage options are available for purchase to Hyak users associated with sponsored campus units.

This information is provided for preliminary planing purposes only. Please contact help@uw.edu for assistance in preparing actual Hyak hardware configurations.

https://itconnect.uw.edu/service/shared-scalable-compute-cluster-for-research-hyak/

Getting Started

Please review everything in this section before contacting Hyak support for help with new accounts.
This section also contains useful information on life with two-factor authentication, including setting up SSH tunnels to reduce hassles.

Using Hyak

First Steps

Knowledge Pre-requisites:

You should be familiar with the Linux command line. Hyak's default shell is bash which is also the default shell on a Mac computer. Here is a link to Software Carpentry's lessons on the bash shell, Python, git etc. (Scroll down for videos of their courses.)

http://software-carpentry.org/lessons/

Software Carpentry also conducts workshops at UW. See below link for the next workshop at UW:

http://software-carpentry.org/workshops/

Code Pre-requisites:

Before you start running your code to hyak, ensure it works on your own computer, or even better, in your lab network. Be sure you know how to keep all the cores busy. For example, using GNU Parallel for weak-scaling, or MPI for strong-scaling.

Software and Development Tools

Hyak provides software development tools and libraries for HPC and data intensive computing.

Filesystems and Data Transfer

Hyak offers a variety of filesystems, each best suited for a different set of circumstances.
Along with selecting the best filesystem for the job, this section includes instructions for moving your data to and from Hyak.

Submitting and Running Jobs

All Hyak use is mediated by the system scheduler.
This section provides details on using the scheduler to run interactive, batch, and parallel jobs.
It also includes instructions for using the scheduler to monitor your
jobs and the cluster status.

Hyak uses TORQUE scheduler. It is controlled through several commands like qsub for
starting a job or qdel for canceling a job.

The jobs are supposed to be submitted via login nodes. Submissions
from other nodes will most likely fail with an error message, telling that you don't have the right to submit a jobs from that node.

Getting Help

If you use the STF (Student Technology Fee) allocation, please join the mailing list for the HPC club
(http://students.washington.edu/hpcc/) and direct all questions there. Do not contact UW-IT for support.

The principle means of support we provide is this Wiki - a comprehensive set of documentation covering all basic Hyak functions. If you encounter problems with one of Hyak's basic functions send an e-mail to help@u.washington.edu with 'hyak' as the first word in the subject and a brief description of your issue. If you do not use your UW provided e-mail account, please include your UW NetID in your e-mail. If you're reporting a problem with a job or the job scheduler, please include at least one affected jobid as well as paths to the job script and job stdout (<jobname>.o<jobid>).

We operate Hyak as a campus resource for research computing at scale. It provides a capable, stable platform upon which users can build complex, domain specific software environments and workflows. Our end-user support resources are limited, covering the system hardware, operating system, filesystems, networks, job scheduler, and a defined set of development tools and applications. Users are responsible for building, installing, maintaining and running any other applications.

To have a good experience using Hyak, or any other HPC/supercomputer system, [ we offer these general recommendations|WIKI for Hyak users-Guidelines]

For users building complex codes from sources, please read this.

Hyak Tutorials

Here are a few tutorials written for different tasks. While not directly applicable to all users' work, they're worth taking a look at to get an idea about how some common tasks are accomplished using Hyak.

  • Compiling HDF5: compiling a non-parallel application with the Intel compilers
  • Compiling an MPI application: compiling a test program with the Intel compilers and Intel MPI and then submitting a job to the scheduler

Hyak How-tos

  • Hyak HOWTO is a list of recipies for different tasks, including how to use R, Python and Matlab, and how to run Windows on hyak.

Hyak wiki pages Index

Hyak_wiki_Index

 

Below is a list of Hyak wiki pages which do not start with the word Hyak.

Managing your Files

Logging In

preemption

WIKI for Hyak users Guidelines

Other Tutorials

Please review this online course if you are not already familiar with *nix systems:

The Teragrid offers an excellent online tutorial series on more advanced HPC topics. You must create an account before accessing content. Just follow the instructions on the main page.

Troubleshooting

Feature Requests

Citing Hyak in Publications and Proposals

Please remember to acknowledge Hyak in any publications or posters with results Hyak contributed to generating. When citing Hyak please use the following language:

  • This work was facilitated though the use of advanced computational, storage, and networking infrastructure provided by the Hyak supercomputer system at the University of Washington

When you cite Hyak, please let us know! Send mail to help@uw.edu with Hyak as the first word in the subject along with a citation we can use in the body of the message. Likewise please let know of successful funding proposals and research collaborations which relied, at least in part, on Hyak for their success.

Here's a current list of publications citing Hyak.

Help for Hyak Node Sponsors

  • Hyak Account Creation - Information for Node Sponsors about how to create Hyak accounts
  • Hyak UNIX Groups - Information for node sponsors about how to create additional filesystem permission groups.
  • Hyak Quotas - Information for Node Sponsors about how to manage user, group, and fileset quotas.
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