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ARCHER2 Weekly Newsletter

By ARCHER2 Service on June 23, 2021

Tags: newsletters 

Reproducible computational environments using containers - Introduction to Docker and Singularity

Andy Turner and Jeremy Cohen

28 - 29 July 2021 10:00 - 16:00 BST

This course aims to introduce the use of containers with the goal of using them to effect reproducible computational environments. Such environments are useful for ensuring reproducible research outputs and for simplifying the setup of complex software dependencies across different systems. The course will introduce the use of Docker and Singularity containers but the material will be of use for whatever container technology you plan to, or end up, using. On completion of this course attendees should:

  • Understand what containers are and what they are used for
  • Understand how to manage and create Docker containers
  • Appreciate decisions that need to be made around containerising research workflows
  • Understand the differences between Docker and Singularity containersand why Singularity is more suitable for multi-user systems (e.g. HPC)
  • Understand how to manage and create Singularity containers
  • Appreciate how containers can be used to enable and improve reproducibility in research

Further details and registration : https://www.archer2.ac.uk/training/#upcoming-training

Advanced MPI

14 and 16 July 2021 09:30 - 17:00 BST

This course is aimed at programmers seeking to deepen their understanding of MPI and explore some of its more recent and advanced features. We cover topics including exploiting shared-memory access from MPI programs, communicator management and neighbourhood collectives. We also look at performance aspects such as which MPI routines to use for scalability, MPI internal implementation issues and overlapping communication and calculation. Intended learning outcomes

  • Understanding of how internal MPI implementation details affect performance
  • Techniques for overlapping communications and calculation
  • Knowledge of MPI memory models for RMA operations
  • Understanding of best practice for MPI+OpenMP programming
  • Familiarity with neighbourhood collective operations in MPI

Further details and registration : https://www.archer2.ac.uk/training/#upcoming-training

ARCHER2 Maintenance 29th June

Tuesday 29th June 0600 - late evening (TBC)

There will be a full ARCHER2 maintenance session for essential power work at the Advanced Computing Facility. The full shutdown will start on Tuesday 29th June at 0600. We expect the system to be returned on Tuesday 29th June by late evening. Users will be notified once the system is available again.

At 1900 Monday 28th June:

Access to the User Access Nodes (UANs) will be disabled to allow the prepartory work to take place. Any users logged into the system at this time will be logged off and the UANs will be unavailable. Jobs will continue to run until 0600 on Tuesday 29th June and users can submit jobs to the queue ready for the system to return to service.

At 0600 Tuesday 29th June:

The compute nodes will be unavailable from 0600. Any jobs that were submitted to the batch will be queued and jobs will start once the system is returned to service.

We apologise for the inconvenience of this planned essential work and please contact support@archer2.ac.uk if you require any further information.

Research Software Engineers in HPC: Creating Community, Building Careers, Addressing Challenges (RSE-HPC-2021)

To be held in conjunction with SC21, St. Louis, MO & virtual - Monday, 15 November, 2021

Research software engineers (RSEs) are critical to the impact of HPC, data science, and the larger scientific community. They have existed for decades, though often not under that name. However, the past few years have seen the development of the RSE concept, common job titles, and career paths; the creation of professional networks to connect RSEs; and the emergence of RSE groups at universities, national laboratories, and industry. This workshop will bring together RSEs and allies involved in HPC, from all over the world, to grow the RSE community by establishing and strengthening professional networks of current RSEs and RSE leaders. We’ll discuss the current activities and plans of national RSE organizations, discuss the needs of RSEs and RSE groups, and write a report on ways RSE organizations can help address these. Most of the workshop time will be spent in interactive discussions, preceded by a keynote address and several shorter talks to establish context.

Submissions

We encourage prospective participants to submit position papers (limit of 2 pages, not counting references; no format prescribed) on topics related to RSE issues. We particularly encourage submissions on the keynote topic:

  • Do RSEs need to change for exascale? Other possible topics include (but are not limited to):
  • Career paths: how do RSEs want to be hired, promoted and evaluated?
  • Building RSE organizations: how to find RSEs in your country/region and how to motivate them to join the network and engage?
  • Supporting RSE organizations: what can be done to help RSEs (and those supporting RSEs) at international, national, regional, and local levels?
  • Making the business case for RSEs and RSE groups: evidence, case studies, tactics?
  • How do we want funders to support RSE roles and activities?
  • Building in RSE requirements as part of wider research infrastructure
  • Providing mentoring and training for RSEs These papers will not be part of the SC proceedings, but we will ask the authors of accepted submissions to self-publish their submissions (after revisions, if they so choose) to an archival repository (e.g. Zenodo, figshare, OSF). Our website will then provide links to those self-published documents. Some submitters will be invited to present their papers at the workshop as lightning talks or to participate as panelists where appropriate.

We particularly encourage submissions from first-time conference presenters, and from members of groups that have historically been underrepresented in the HPC community.

Papers and discussion topics should be submitted using the link below. The deadline for submissions is Friday, August 6, 2021, at 11:59 PM AoE (UTC-12).

Submission website: https://submissions.supercomputing.org/?page=Submit&id=SC21WorkshopRSEHPC2021Submission&site=sc21

Timeline

  • Submissions open: Monday, June 7, 2021
  • Submissions due: Friday, August 6, 2021 - NO EXTENSIONS
  • Notifications sent: Friday, September 3, 2021
  • Program finalized: Friday, September 17, 2021
  • Workshop date: Monday, November 15, 2021 For more information See the workshop website: https://us-rse.org/rse-hpc-2021/ Or contact the organizers: sc-ws-rse-hpc@info.supercomputing.org

Upcoming ARCHER2 Training

  • Advanced MPI, Online, 14 and 16 July 2021 09:30 - 17:00 BST
  • Parallel Performance Analysis using Scalasca, Online, Tues 27 and Thurs 29 July 09:30 - 16:30 BST
  • Reproducible computational environments using containers - Introduction to Docker and Singularity, Online, 28 - 29 July 2021 10:00 - 16:00 BST
  • Message-passing Programming with MPI, Online, always-open self-service course
  • Shared Memory Programming with OpenMP, Online, always-open self-service course

Further details https://www.archer2.ac.uk/training/#upcoming-training

New virtual tutorials will be announced soon via: ARCHER2 website: https://www.archer2.ac.uk/training/#upcoming-training

Twitter: https://twitter.com/ARCHER2_HPC

Recordings of past virtual tutorials can be found here: https://www.archer2.ac.uk/training/materials/