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December 2024 Maintenance Details

Kristen Finch

Kristen Finch

HPC Staff Scientist

Hello Hyak Community,

Our December maintenance is complete. Thank you for your patience. The next maintenance will be Tuesday January 14, 2025.

Notable Updates#

  • Updated node images, ensuring the security and behavior you expect from Hyak klone.
  • We migrated LMOD modules and other tools and software stored in /mmfs1/sw/ to Solid State Drives (SSDs). Users may notice increased speed of modules.

Office Hours over Winter Break#

I will continue to hold Zoom office hours on Wednesdays at 2pm throughout December. Attendees need only register once and can attend any of the occurrences with the Zoom link that will arrive via email. Click here to Register for Zoom Office Hours.

December 12 will be the last in-person office hours for Fall term to be held at 2pm at the eScience Institute (address: WRF Data Science Studio, UW Physics/Astronomy Tower, 6th Floor, 3910 15th Ave NE, Seattle, WA 98195). In-person office hours will resume on Thursdays at 2pm starting January 9, 2025.

If you would like to request 1 on 1 help, please send an email to help@uw.edu with "Hyak Office Hour" in the subject line to coordinate a meeting.

Research Computing Club Officer Nominations#

The Research Computing Club (RCC) at UW is looking for nominations for Officer positions. The RCC provides essential computational resources to support students working on a wide range of research projects using high-performance computing through UW’s Hyak system and cloud platforms like AWS, Microsoft Azure, and Google Cloud. The RCC relies on student officers to continue providing these resources to the UW community and to organize community-driven events such as Hackathons and trainings. Officer positions are:

  • President
  • Director of AI/ML
  • Director of Outreach
  • Director of Hyak
  • Director of Cloud Computing

Please consider nominating yourself if you are interested, or nominating someone you know who is interested, by filling out the form linked HERE.

External Opportunities#

DOE Computational Science Graduate Fellowship- Applications are being accepted through January 16, 2025 for the Department of Energy Computational Science Graduate Fellowship (DOE CSGF). Candidates must be U.S. citizens or lawful permanent residents who plan full-time, uninterrupted study toward a Ph.D. at an accredited U.S. university.

The DOE CSGF is composed of two computational science tracks. Eligible fellowship candidates should carefully review the criteria for both tracks prior to initiating the application process:

  • The Science & Engineering Track accepts doctoral students engaged in computational science research with a science or engineering focus.
  • The Mathematics/Computer Science Track accepts students pursuing research in broadly applicable methods and technology for high-performance computing (HPC) systems.

Students applying to the Mathematics/Computer Science Track must be pursuing a doctoral degree in applied mathematics, statistics, computer science, computer engineering or computational science — in one of these departments or their academic equivalent. A departmental exception is made for students whose research is focused on algorithms or software for quantum information systems and who are enrolled in a science or engineering field. In all cases, research must contribute to more effective use of emerging HPC systems.

DOE NNSA Stewardship Science Graduate Fellowship- Applications are being accepted through January 14, 2025 for the Department of Energy National Nuclear Security Administration Stewardship Science Graduate Fellowship (DOE NNSA SSGF). Candidates must be U.S. citizens who plan full-time, uninterrupted study toward a Ph.D. at an accredited U.S. university.

The DOE NNSA SSGF provides doctoral students with in-depth training in areas relevant to stewardship of the nation's nuclear stockpile: high energy density physics, nuclear science, or materials under extreme conditions. Senior undergraduates and first- or second-year doctoral students are eligible to apply.

DOE NNSA Laboratory Residency Graduate Fellowship- As part of its science and national security missions, the U.S. Department of Energy National Nuclear Security Administration (DOE NNSA) supports a spectrum of basic and applied research in science and engineering at the agency's national laboratories, at universities and in industry.

Because of its continuing needs, the NNSA seeks candidates who demonstrate the skills and potential to form the next generation of leaders in the following fields via the DOE NNSA LRGF program:

  • Engineering and Applied Sciences
  • Physics
  • Materials
  • Mathematics and Computational Science To meet its primary objective of encouraging the training of scientists, the DOE NNSA LRGF program provides financial support to talented students who accompany their study and research with practical work experience at one or more of the following DOE NNSA facilities: Lawrence Livermore National Laboratory, Los Alamos National Laboratory, Sandia National Laboratories or the Nevada National Security Site.

NSF ACCESS Student Training and Engagement Program (STEP) - Applications due February 15.

  • STEP 1: 2-week introductory experience - Join a dynamic two-week experience in Miami, FL in May! Travel, accommodations, and stipend included. This program is designed to help you:

    • Become more aware of the many areas of interest within the field: web programming, high performance computing, cybersecurity, networking, real use of AI.
    • Determine where your interests are.
    • Discover what areas of study you should pursue in the future.
    • Experience high levels of direct interaction with diverse people with diverse skill sets.
  • STEP-2: Full-time for the summer (in-person + virtual) - follows STEP-1 Travel and accommodations covered for in-person events as well as a stipend for participating plus includes travel to a national conference. This program is designed to help you:

    • Develop an intermediate understanding of one of the areas of interest within the field: web programming, high performance computing, cybersecurity, networking, real use of AI.
    • Provide opportunities for interactions with professionals in the field.
  • STEP-3: Part-time during the school year, follows STEP-2. Continue interacting (virtually) with your team on projects on a part-time basis during the academic year. Participants will receive a stipend and travel to the annual Supercomputing conference (SC25 in St. Louis, MO, USA). This program is designed to help you:

    • Develop a deep understanding of one of the areas of interest within the field: web programming, high performance computing, cybersecurity, networking, real use of AI.
    • Provide further opportunities for interactions with professionals in the field.

Understand how a career in cyberinfrastructure could fit with your future plans!

External Trainings#

Looking for FREE training on cutting-edge digital technologies for industry? Find out more about the Training from the Hartree Centre HERE!

Whether you’re looking to get to grips with the basics or searching for new tools and techniques to apply, Hartree Training supports both self-directed online learning as well as face-to-face practical sessions with badge certification available for you to share your new skills with your network. Currently offering courses covering a range of advanced digital technologies including:

  • Data Science
  • Artificial Intelligence and Modelling
  • High Performance and Exascale Computing
  • Software Engineering
  • Emerging Technologies

To enroll, create a FREE account or log in. Once you have created an account, you can log in and sign up for as many of our courses as you like.

NVIDIA Professional Workshops and Certificates Blog post HERE discusses NVIDIA Professional Workshops ($3000 each) and Certificate Exams ($400 each) in AI Infrastructure and AI Operations. Includes links to workshops and certificate programs in Generative AI LLMs and Generative AI Multimodal.

Happy Computing,

Hyak Team

November 2024 Maintenance Details

Kristen Finch

Kristen Finch

HPC Staff Scientist

Hello Hyak Community,

Our November maintenance is complete. Thank you for your patience while we make package updates to node images, ensuring the security and behavior you expect from Hyak klone.

The next maintenance will be Tuesday December 10, 2024.

Notable Updates#

  • We updated the GPU drivers to version 565.57.01 to patch security vulnerabilities CVE-2024-0117 through CVE-2024-0121 and CVE-2024-0126.
  • We migrated user Home directories to Solid State Drives (SSDs). Users may notice increased speed of software stored in Home directories.

Upcoming Training#

Hyak: Scheduling jobs with Slurm workshop is on Thursday, November 14th, from 10 a.m. to 12 p.m. in the WRF Data Science Studio (UW Physics/Astronomy Tower, 6th Floor; 3910 15th Ave NE, Seattle, WA 98195), and will cover Hyak’s job scheduler Slurm, interactive jobs, batch jobs, and array jobs. REGISTER HERE!

Hyak: Introduction to Deep Learning workshop is on Tuesday, December 3rd, from 10 to 11:50 a.m. in CSE2 (Gates Center) Room 371. Participants will start with a computer vision example, training a model on a sample dataset, and then learn how to execute the training process on Hyak. REGISTER HERE!

Office Hours#

Zoom office hours will be held on Wednesdays at 2pm. Attendees need only register once and can attend any of the occurrences with the Zoom link that will arrive via email. Click here to Register for Zoom Office Hours

In-person office hours will be held on Thursdays at 2pm at the eScience Institute (address: WRF Data Science Studio, UW Physics/Astronomy Tower, 6th Floor, 3910 15th Ave NE, Seattle, WA 98195).

The Research Computing Club will be holding office hours fall term. In-person office hours will be held at the eScience Institute, WRF Data Science Studio.

OfficerDateTime
Sam Shin19 Nov2pm
Teerth Mehta3 Dec2pm

If you would like to request 1 on 1 help, please send a ticket to help@uw.edu with "Hyak Office Hour" in the subject line to coordinate a meeting.

October 2024 Maintenance Details

Kristen Finch

Kristen Finch

HPC Staff Scientist

Hello Hyak Community,

Our October maintenance is complete. Thank you for your patience while we make package updates to node images, ensuring the security and behavior you expect from Hyak klone.

The next maintenance will be Tuesday November 12, 2024.

New Tools Documentation#

Our research computing interns have been hard at work adding documentation for new user tools that might help optimize your research computing. Click the links below to review the docs for these tools.

Squash Fuse - SquashFS packages multiple small files into a single read-only, compressed filesystem, reducing metadata calls and improving performance. This minimizes server load, enhancing throughput and efficiency in handling storage requests.

Use case on Hyak: In HPC, datasets often consist of numerous small files, which can lead to performance bottlenecks due to excessive metadata operations. By utilizing SquashFS, HPC applications can significantly reduce metadata overhead, improving data access speeds and enhancing overall system performance, particularly in large-scale distributed storage systems.

Checkpointing with DMTCP - DMTCP is a tool to transparently checkpoint and restart jobs, saving it to disk to be resumed at a later time. It requires no changes to application code, allowing easy use. Using DMTCP with your code allows checkpointing at regular intervals so if your job is pre-empted or reaches the time limit, it will resume from its last checkpoint.

Use case on Hyak: DMTCP offers a solution for folks who would like to use Hyak's ckpt partitions, but have jobs that exceed the ckpt time limits of 5 hours for CPU-noly jobs and 8 hours for GPU-only jobs. Checkpointing with DMTCP facilitates efficient use of ckpt resources, allowing higher throughput for your jobs.

Tools for Kopah Storage Users - We have installed Command Line Interface tools like s3cmd and s5cmd on klone and provide insctructions for using Python library boto3 for Kopah interaction and retreival to build Kopah S3 storage usage into your research computing applciations on Hyak.

If you have any issue using these tools, please open a ticket by emailing help@uw.edu with "Hyak" in the subject line. We appreciate any feedback about how to improve ease of use for tools presented in our documentation.

Upcoming Training#

We have planned 2 Hyak-specific trainings for this Fall (more to come, stay tuned). These trainings will be held in person and will not be recorded since recorded materials are already publicly accessible. Capacity is limited, follow the links below to register today to guarantee your spot.

Hyak: Containers are your friend - Monday October 28 10am - 12pm.

Hyak: Scheduling Jobs with Slurm - Thursday November 14 10am - 12pm

In the first hour and a half, we will go over content. The last 30 minutes will be reserved for questions.

Location: eScience Classroom; WRF Data Science Studio, UW Physics/Astronomy Tower, 6th Floor; 3910 15th Ave NE, Seattle, WA 98195

Keep an eye on your inbox for updates about additional trainings this fall.

Fall Office Hours#

Hyak HPC Staff Scientist and Facilitator, Kristen Finch, will be holding office hours fall term.

Zoom office hours will be held on Wednesdays at 2pm. Attendees need only register once and can attend any of the occurrences with the Zoom link that will arrive via email.

Click here to Register for Zoom Office Hours

In-person office hours will be held on Thursdays at 2pm at the eScience Institute (address: WRF Data Science Studio, UW Physics/Astronomy Tower, 6th Floor, 3910 15th Ave NE, Seattle, WA 98195). Click here to RSVP for in-person Office Hours.

Click here to visit the eScience Office Hours page to see additional eScience office hours including AI/ML, R, Earth Data, and Python (not available to help with Homework).

The Research Computing Club will be holding office hours fall term. In-person office hours will be held at the eScience Institute (address: WRF Data Science Studio, UW Physics/Astronomy Tower, 6th Floor, 3910 15th Ave NE, Seattle, WA 98195).

OfficerDateTime
Brenden Pelkie16 Oct1pm
Nels Schimek23 Octipm
Nels Schimek6 Nov1pm
Sam Shin19 Nov2pm
Teerth Mehta3 Dec2pm

If you would like to request 1 on 1 help, please send a ticket to help@uw.edu with "Hyak Office Hour" in the subject line to coordinate a meeting with Kristen.

Please don't hesitate to reach out to the Hyak team with issues and feedback by opening a tickey by emailing help@uw.edu with "Hyak" in the subject.

Have a great October!

Happy computing,

Hyak Team

September 2024 Maintenance Details

Kristen Finch

Kristen Finch

HPC Staff Scientist

Hello Hyak Community,

Thanks again for your patience with our monthly scheduled maintenance. During this maintenance session, we were able to provide package updates to node images to ensure compliance with the latest operating system level security fixes and performance optimizations. Of note, the Nvidia GPU driver on Klone has been updated to the latest production datacenter release, version 560.35.03.

The next maintenance will be Tuesday October 8, 2024.

AMD Math libraries#

In June we announced the addition of AMD Nodes and Slices to klone which make up our generation 2 or g2 collection of resources. Click here to read more about the difference between our g1 and g2 resources. During August, we installed a new AMD compiler suite, AOCC, along with specialized math libraries like AOCL, OpenBLAS, and ScaLAPACK as modules to make the most of this upgade. The new modules are useful on all partitions. The AOCC and AOCL modules are particularly relevant for partitions cpu-g2, cpu-g2-mem2x, and ckpt-g2. These tools are designed to optimize performance on AMD processors, speeding up complex mathematical computations. Whether you're working on simulations, data analysis, or any number-crunching tasks, these libraries may help ensure you get faster, more efficient results. If you're looking to boost your workflow, it's worth exploring how these libraries can benefit your projects. Here are the names of the new modules:

aocc/4.2.0
aocl/4.2.0
openblas/0.3.28
scalapack/2.2.0

In our benchmarking tests, performance of these libraries was similar on g1 and g2 CPUs for each math library, regardless of architecture. The best library performer on AMD CPUs is AOCC+AOCL, and for Intel CPUs it’s OpenBLAS+ScaLAPACK:

Image displays graph indicating that the best library performer on AMD CPUs is AOCC plus AOCL, and for Intel CPUs it’s OpenBLAS plus ScaLAPACK

Fall Office Hours#

Hyak HPC Staff Scientist and Facilitator, Kristen Finch, will be holding office hours fall term. Zoom office hours will be held on Wednesdays at 2pm. Attendees need only register once and can attend any of the occurrences with the Zoom link that will arrive via email.

Click here to Register

In-person office hours will be held on Thursdays at 2pm at the eScience Institute (address: WRF Data Science Studio, UW Physics/Astronomy Tower, 6th Floor, 3910 15th Ave NE, Seattle, WA 98195). Click here to RSVP for in-person Office Hours.

Click here to visit the eScience Office Hours page to see additional eScience office hours including AI/ML, R, Earth Data, and Python (not available to help with Homework).

If you would like to request 1 on 1 help, please send a ticket to help@uw.edu with "Hyak Office Hour" in the subject line to coordinate a meeting with Kristen.

August 2024 Training Videos#

In case you missed it, we recorded the August 2024 Wednesday training sessions and posted them on the UW-IT YouTube channel under the playlist, "Hyak Training." Here are the links:

Keep an eye on your indox for updates about our Fall training schedule; training sessions are currently TBA. Trainings will be announced via the Hyak mailing list, click here to join the mailing list.