Life science loves UPPMAX
An estimated 40% of all publications reported to SciLifeLab under 2020 involved work done on UPPMAX resources.
The proportion of Swedish life science publications where UPPMAX has played a role has been steadily increasing every year, and last year was no different.
The staff are proud to have been a part of literally hundreds of exciting research projects over the years, and we feel honoured by the trust and responsibility bestowed upon us by our user community. The fact that this community is growing both in share as well as absolute size and productivity is a sign that we are in fact meeting our goals — to offer a digital research environment of the highest possible quality that addresses the evolving needs of a cutting-edge scientific community.
2021 holds promise for continuing the trend. Among other things:
- With GPU capability added to Bianca, we are enabling machine learning methods on sensitive personal data, which will take multiomics on patient data to the next level.
- For Uppsala University general education, a new collaboration with Servicedesk means faster support for questions related to courses.
- A more transparent process for storage project administration will help staff and users keep Crex from being overburdened by old data.
For updates and information on current system status, please see the System Status page.
Bigger Bianca login nodesIncreasing resources of the Bianca login nodes has been much requested by ourSNIC-SENS users. We are thrilled to announce that we are bumping the specs forall Bianca login nodes and extending total number of compute nodes with anadditional 72x256GByte ("fat") nodes.
Undergraduate courses at UPPMAX
Uppsala University courses can request UPPMAX resources to use in teaching. Don't forget to apply soon for courses starting in Period 3.
Bianca and Rackham news
The SNIC board has approved about 10 MSEK in funding to procure more hardware for Bianca, including more GPU nodes, more storage, and more semi-fat compute nodes. With this increase in capacity and lifetime, we will be able to serve our growing community for several more years.
Additionally, an investment by the Kamerlin group has resulted in 144 nodes from the old NGI cluster, Irma, now added to Rackham. These resources, with 16 cores and 256 GB of RAM per node, amounting to about 1.5 million core-hours per month, are already available in the "core" partition (though the Kamerlin group naturally has priority over others). Look for nodes named "r1000" and higher!
Online workshop on Basic Singularity, 20 April 2022This online workshop is an introduction to the basic concepts of containerised software environment solutions within the Singularity framework https://sylabs.io/singularity/.During the workshop you will have the opportunity to follow the interactive guide on
To fully benefit from the workshop, basic Linux system administration experience is highly desirable i.e. knowledge of package management and common tools for building and managing software: git, pip, conda, wget, curl …For more information and access to registration please visit: https://www.uppmax.uu.se/support/courses-and-workshops/singularity-workshop-announcement
- how to run Singularity containers
- how to build your own
- good (and bad) practices on designing and building Singularity recipes
- build and/or host container remotely and what are the limitations
Open position: Technical system administrator
UPPMAX is hiring a new technical system administrator to expand the team and help us push the envelope of services that we can offer our users. We have many exciting tasks ahead of us and need competent, driven staff to reach our goals.
Open position: application expert in digital humanities
UPPMAX is hiring for a two-year position as an application expert in the field of digital humanities and social sciences. The position is split between CDHU and UPPMAX, and we are looking for people with experience in humanities or social sciences, and/or AI/ML methods that are used in these fields.
Lovande molekyl mot coronavirus på Uppmax
Uppsalaforskare har lyckats ta fram en molekyl som hämmar förökning av coronavirus och har stor potential att utvecklas till läkemedel mot covid-19. En del av arbetet utfördes på UPPMAX system.
Bianca to be upgraded in 2022
During the coming year, Bianca will get four really high-mem nodes, 48 cores each with 768GB RAM. We will also augment the number of 256GB nodes considerably, at least 50 more of those, for a total of more than 260 nodes compared to 204 today. This will also mean that we can give more memory (and possibly cores) to each login node.
More Rackham storage in Spring 2022
UPPMAX has laid an order for 3.75 PB of effective storage that will be added to the Crex storage system in the Spring of next year. This will bring the total volume of storage available on Rackham and Snowy to about 9.75 TB. Part of this space is reserved for system software and central databases, and available quota for projects is expected to increase by over 50%. This should be sufficient until the planned end-of-life of Rackham and Crex at the end of 2024.
Until the extension is in place, space on Crex is very tight. Please continue to delete unnecessary files, be patient with performance degradations, and please wait until Spring before generating significant amounts of new data.
Online training workshop: "Awk Workshop", Uppsala, January 17 (+18)*, 2022
This 1+1 days workshop aims to promote the awk tool for use in everyday research work and urges you to find solutions yourself rather than expecting ready-made ones. Thus, the material given during the seminar will not be a complete guide or manual. The purpose of the workshop is to give an overview of the capabilities of the awk language and to underline some of its particular strengths as well as its disadvantages.
When: January 17(+18)*, 2022
* During the workshop, you will be able to register for the second day of the workshop.
For more information and registration, please visit:
Life of Rackham and Bianca extended through 2024
The SNIC Board has approved funding that will let UPPMAX not only continue to run Rackham and Bianca through the end of 2024, but also make some necessary investments to improve the user experience. Details are still being hammered out, but these investments will take place in early 2022, and will ensure that the user community can continue to grow and evolve.
VR invites comments on the future of HPC in Sweden
In June this year, the Swedish Research Council (SRC) decided to call off the process for renewed funding of the Swedish Infrastructure for Computing (SNIC). The process has begun to
find another form for a national research infrastructure and SRC wants
to hear from you about your compute and storage needs.
We ask all our users to leave feedback at the following link:
It is important that SRC gets input from all its users, so please take
this opportunity to make your needs heard.
GPUs now available in Bianca
UPPMAX is happy to announce that Bianca now offers GPUs! The GPUs that were provided by SNIC are available for all users. GPUs are a type of accelerator that may significantly increase performance for certain workloads, for instance, workloads that contain large amounts of identical operations on independent pieces of data.
20 million jobs on Rackham
Today, the 20 millionth job on Rackham was submitted.
Ny tjänst ger tillgång till superdator för utbildning
Avdelningen för universitetsgemensam IT (UIT) har lanserat en ny tjänst som tillgängliggör infrastruktur för stora databeräkningar inom hela universitetets utbildningsverksamhet.
Ny Teknik: Tre år efter uppropet #teknisktfel – ”Kvinnor som är utsatta blir trodda nu”
(This article is about a news article in Swedish)
Ny Teknik har intervjuat en av våra anställda i en artikel om effekterna av metoo-uppropet. För drygt tre år sedan synliggjorde metoo-uppropet #teknisktfel sexuella trakasserier inom teknikbranschen. Sedan dess har framsteg gjorts menar initiativtagarna. Men mycket återstår att förbättra på arbetsplatserna.
Läs artikeln här: https://www.nyteknik.se/ingenjorskarriar/tre-ar-efter-uppropet-teknisktfel-kvinnor-som-ar-utsatta-blir-trodda-nu-7011093
Two open positions at UPPMAX
SRC Survey on research data management
The Swedish Research Council is conducting a survey regarding current practises and available support functions for research data management. This work is part of a commissioned project to coordinate activities about Open Access data.
Answer the survey here: https://survey.vr.se/Survey/601
Life science loves UPPMAX
An estimated 40% of all publications reported to SciLifeLab under 2020 involved work done on UPPMAX resources.
Bianca users: report interest in GPUs on Bianca
UPPMAX is gathering interest in user-funded GPU resources on Bianca. Users are invited to contact us.
New national HPC competence center launched
The EuroCC National Competence Center Sweden (ENCCS) is an initiative to establish a support organisation for HPC competence in general and especially in large-scale applications running on EuroHPC systems (such as LUMI).
New SNIC system for AI/ML methods
A new resource for Artificial Intelligence and Machine Learning AI/ML research has recently opened at C3SE, the national centre for scientific and technical computing at Chalmers.
HPC cybersecurity issues
Several large European HPC-sites are reporting issues with cybersecurity and several SNIC centres have recently restricted access to some of its services.
UPPMAX contributions against the COVID-19 pandemic
While the main function of UPPMAX is to provide a world-class digital research environment, as a tax-funded resource we can and should keep public welfare in mind. In the current crisis, HPC resources can play a crucial role in contributing to the understanding of the virus itself as well as mitigation strategies and their impact.
Several positions open
User-paid GPU pool available
The UPPMAX board has decided to offer users an opportunity to
co-finance a pool of Nvidia Tesla T4 cards with 16 GB RAM each, at a price of
roughly 20 000 SEK/card. Read on if your research group may be interested in buying access to GPU capability at UPPMAX.
Rackham storage nearly full
The 6PB large storage system, called Crex, is nearly fully allocated. This is the storage system attached to Rackham and Snowy. When we have allocated all the space available on it, we cannot both grant new projects that need disk space and prolong old ones with large allocations. Please read on to learn more about the situation.
User-paid offload storage available at UPPMAX
Since this spring, we have been offering the Lutra offload storage system suitable for "cold" data which is not accessed or changed frequently, but which still has to be kept available on our clusters.
Due to the popularity of this service, the UPPMAX board wants to offer current
PIs at UPPMAX the possibility to sign up for additional storage. This time,
it will also be possible to buy storage suitable for sensitive personal data.
Read the full article for more details
10 million jobs on Rackham
Rackham just passed 10 million completed jobs. See the picture below
SNAC Chair to hold a seminar
Seminar by Philipp Schlatter, the chair of the SNIC Allocations Committee (SNAC), "SNIC and SNAC: Handling of large-scale computer time allocations in Sweden", to be held on in the afternoon on September 25th.
CONDA is updated
As of now, CONDA should work (module load conda) again, but please report anything weird (For CONDA, being slow is not weird).
CONDA is being updated
Due to some changes and external alterations, the entire CONDA installation is in need of being re-installed. This might cause some lag and even some failures in the near future. Hopefully we will have the systems and repositories up and running as soon as possible.
Pre-exascale system will be placed in Finland
A EuroHPC Joint Undertaking, involving Finland, Belgium, Czech Republic, Denmark, Norway, Poland, Sweden and Switzerland, will be placing a large HPC system at CSC in Finland. Scientists in member countries will be able to use the machine starting Q4 2020.
Survey on R training needs on SNIC resourcesThe SNIC Training team would appreciate your input regarding training requirements in the in the R language and environment for statistical computing and graphics. Please participate in a short survey. The survey will close on 22 June 2019.The survey is hosted by LUNARC on behalf of SNIC. It is available at this link: https://sunet.artologik.net/lu/Survey/24336
Top SciLifeLab AI poster award was deep learning research on Rackham
At the SciLifeLab Science Summit on the topic Artificial Intelligence for Life Science on May 15, the top 3 posters were given awards. The top position went to Kristiina Ausmees from Scientific Computing for "Nonlinear dimensionality reduction of genotype data using deep learning".
Wanted: Application Expert in cloud and container technology
The SciLifeLab Compute and Storage platform, a part of NBIS and hosted by UPPMAX, is looking for a person with experience working with cloud and/or container technology in order to support life science researchers. See below for a link to the job posting. Deadline is June 7th!
UPPMAX Offload Storage projects now available
For users who have purchased offload or glacial storage on our new system Lutra you may now start sending in your proposals from https://supr.snic.se.
Introductory Course Summer 2019 open for registration
UPPMAX application experts want to share their skills in a 4-day series of courses. We will help you move from being a Linux novice to an UPPMAX expert. If you already have the fundamentals down, you are still sure to enjoy the tips and tricks in the later parts of the course.
Dates: August 26-29.
Kin relations traced in ancient megalithic tombs
A research group used UPPMAX resources in a recent publication that has caused some popular interest. Around 4500 BCE, megalithic funerary monuments began to be built in northwestern Europe. The group's genomic investigation, published in the Proceedings of the National Academy of Sciences (PNAS), provides insight into the people associated with this long-standing megalith funerary tradition, including their social dynamics.
Technical Sysadmin position open
UPPMAX is looking for a new technical system administrator. If you enjoy working with Linux in a dynamic environment and contribute to a world-class research environment, please follow the url below.
Air Filter Research at UPPMAX on SR
Per Stenberg, a researcher at Umeå University and FOI, has used Rackham in a pilot study that explored the spread of organisms that were incidentally caught in more than 15,000 air filters that were archived for radioactivity measurements.
Introductory UPPMAX course winter 2019 open for registration
Dates: January 21-24.
CodeRefinery workshop in Uppsala
If you are writing code that is used in research, then this course is for you
Hands-on informal and interactive three-day event with type-along type of presentations, live coding and demos. Short tutorials alternate with practical exercises.
December 3-5, 2018, 9:00 am to 5:00 pm
Registration open to Hands on introduction to SNIC Science Cloud
Welcome to a short hands on introduction to SNIC Science Cloud from the “beginner’s user/developer” point of view.
SeSE Applied Cloud Computing Workshop open for registration
An application oriented introduction to cloud computing aimed mainly at PhD students. Basics of Service Oriented Architectures (SOA). Basic concepts of cloud computing such as virtualization and the service layers IaaS, PaaS and SaaS, dynamic provisioning, elasticity. Practical use of available public and private cloud stacks. Introduction to cloud security. Task based programming in cloud environments. Application of key technologies and design patterns to realize scientific applications in cloud computing environments.
The Large Fall 2018 call for large allocations is open
The Fall 2018 call for proposals for large allocations of computing time on the High Performance Computing resources of the Swedish National Infrastructure for Computing (SNIC) is open. Deadline 19 October 2018.
The allocations are for the period 1 January 2019 - 31 December 2019.
Welcome to the Scientific Visualisation Graduate Course 2018
This year's Scientific Visualisation course will be held from 26th to 30th of November in Uppsala, with specially invited guest-lecturer, Alex Telea, who is the author of the course book "Data Visualization: Principles and Practice" on which the course is based itself.
New system for home directories
With the retirement of Pica, a new storage system for home folders is being taken into production this week. This system is named Domus, which means "home" in Latin. In addition to home directories, the software library will also be located on Domus.
Rackham/Crex extensions fully in production
In order to replace the loss of the Milou cluster and Pica storage, Rackham and its storage system Crex have been extended. This new hardware is now fully in production.
Hearing and miniworkshop on AI/Machine Learning
The Knut and Alice Wallenberg Foundation (KAW) has launched an investigation into the needs and potential solutions for a Swedish infrastructure in support of AI, in particular Machine Learning, based research in Sweden.
Preliminary findings will be presented in a hearing in Stockholm on June 1st to which you are cordially invited. The hearing will include presentations from the panels as well a mini-workshop for feedback and open discussion around the presented topics.