Rackham End of Life 2024-12-31
2023-10-13
After many years of service, the time is approaching when Rackham will be too old to keep running. Rackham will be shut down on 2024-12-31. Before we say anything else, we want to express a deep appreciation for each of our users — it is you that made this system so meaningful and pushed us to the limit in so many ways.
This is why we have made plans for your future, and why the UPPMAX staff are contacting you now. Please continue reading to learn about what will happen to your compute and storage projects and how we plan to help you transition to a new system.
The NAISS system that we believe is the best choice for most of our users is Dardel, at PDC (KTH) in Stockholm. UPPMAX and PDC have, with blessing from NAISS, started a collaboration to ensure that Dardel will host a suitable environment for your work, and that the move is as smooth as possible.
The plan is as follows:
- Starting in October 2023, new and continuation projects on Rackham and Crex will automatically receive accompanying allocations on Dardel and Klemming.
- PI:s receiving such allocations will receive instructions and guides for moving their data and on how Dardel works.
- Starting 2024-01-01, no Rackham projects will be granted for the full 12 months. No allocations or extensions are possible after 2025-01-01. Your project on Rackham, and all remaining data on Crex, will be completely gone at the end of next year.
- Around February or March 2024, we will grant Dardel and Klemming allocations to all active Rackham projects.
- By November 2024, we expect that nearly all users will have moved their data from Crex.
- On December 31, 2024, we shut down Rackham and Crex, and anything that remains there will be lost.
Dear friends, there are hundreds of projects on Rackham and Crex. UPPMAX staff will have their hands full keeping the old systems running, while helping PDC prepare Dardel for you and set up a new system for Uppsala University. We will rely on you to help us help you.
To help us and to make your own lives easier, please read your emails from UPPMAX and PDC. Please be proactive and, when you receive your project on Dardel, start moving your data early. Use the guides and follow the instructions that we will send you.
FAQ:
What about UU researchers? UPPMAX has been assigned the task to acquire and set up a moderately sized system like Rackham to meet needs of local users. If you, as a Uppsala University researcher, do not wish to move to Dardel and instead wish to use the new local system, then please let us know in your proposal.
What about Snowy? The system mentioned above will replace Snowy. It will meet the needs of education and local compute and storage for research, plus cloud-like services.
What about Bianca users? While NAISS has decided on a 10 MSEK investment to guarantee continued sensitive data capacity, the exact use of these funds is currently still under discussion. UPPMAX, together with the support team at NBIS, will continue to maintain an environment that is as similar as possible on all NAISS systems with many life science users, so that, e.g., pipelines running on mice or cell lines will also work on clinical data. The same is true for the NGI system, Miarka — our ambition is that things should keep working as usual.
What about Lutra/Offload Storage? Lutra will continue to be available to everyone who has purchased space, at the very least through SSH. Since NAISS-funded (free to use) compute and storage will no longer be available at UPPMAX after 2024, we understand that some use-cases for Lutra will no longer be possible for groups outside of Uppsala, and we are prepared to discuss options with you if you contact us.
What about software/pipelines/long single-core jobs/etc on Dardel? Both UPPMAX and PDC are probably already working on it. When you get on Dardel, let us know what you need in order to work, and we will make sure it is done by the time Rackham is shut down. In the meantime, use Rackham to do research, move your data to Dardel, and adapt your workflows.
For updates and information on current system status, please see the System Status page.
UPPMAX News
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New procurement at UPPMAX
UPPMAX has received instructions to start procuring a system to meet Uppsala University's local needs for sensitive and non-sensitive HPC and cloud services in both research and general education. Funding is supplied by the disciplinary domains and from the Vice-Chancellor.
Any research group with an interest is welcome to contact the Director (director@uppmax.uu.se) and/or UPPMAX support (support@uppmax.uu.se) to discuss collaboration or co-investment.Read on for some more details.
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Rackham End of Life 2024-12-31
After many years of service, the time is approaching when Rackham will be too old to keep running. Rackham will be shut down on 2024-12-31. Before we say anything else, we want to express a deep appreciation for each of our users — it is you that made this system so meaningful and pushed us to the limit in so many ways.
This is why we have made plans for your future, and why the UPPMAX staff are contacting you now. Please continue reading to learn about what will happen to your compute and storage projects and how we plan to help you transition to a new system. -
UPPMAX offline on October 4-5
The Ångström Laboratory houses the UPPMAX compute hall, and the property manager, Akademiska Hus, will be performing work on the cooling system as part of an energy-saving project called “Project Bläckfisken.”
To facilitate this process, Akademiska Hus kindly requests a 48-hour power-down period for the compute hall between October 4 and 5. During this time, all systems will be unavailable.
We apologize for any inconvenience this may cause and appreciate your understanding as we aim to inform you well in advance.
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Welcome to UPPMAX 20 years
On Tuesday (2023-05-16) at 13:00 we will celebrate 20 years with UPPMAX. You are welcome to drop by on the ground floor of Ångström building 10! There will be some coffee and cake.
- 13:00 - Start
- 13:15 - Welcome - UPPMAX director, Elisabeth Larsson
- 13:30 - UPPMAX history - Linus
- 14:00 - User presentations: Mattias Jakobsson
- 14:30 - User presentation: Tove Fall
- 14:45 - Q&A session
- ~14:50 - UPPMAX compute hall visit
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UPPMAX user in the news
Kerstin Lindblad-Toh, a long-time user of UPPMAX systems, has made a big splash in the news lately with her Zoonomia project, which has resulted in 11 articles published in a special issue of Science. The project began at UPPMAX in 2015 under the title "200 Mammals", on Milou. Today, the project title reads "242 Mammals" and is still going strong. Read more in the Uppsala University news article.
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UPPMAX Celebrates 20 Years of High-Performance Computing and Storage Services
This year, UPPMAX celebrates 20 years of providing high-performance compute and storage services to the Swedish research community. During the past two decades, UPPMAX has witnessed a remarkable development in technical platforms, hardware, and the scientific landscape.
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Forskarfilm: UPPMAX och dess föreståndare
Upptech har gjort en kort film om Elisabeth Larsson och UPPMAX. Se filmen på Youtube.
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Fat nodes to Bianca
Twelve brand-new fat nodes with 512 GB of RAM have been added to Bianca and are accessible for use. To run a job on these nodes, add the flag
-C mem512GB
. For more information on using Bianca, see the Bianca user guide. -
Bigger Bianca login nodes
Increasing 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.
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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!
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Online workshop on Basic Singularity, 20 April 2022
This 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- 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
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 -
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.
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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.
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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.
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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.
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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.
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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:
https://www.uppmax.uu.se/support/courses-and-workshops/awk-workshop-winter-2022/
Registration: https://forms.gle/widJo8somBiPJSss7 -
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.
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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:
https://www.vr.se/english/just-now/news/news-archive/2021-10-21-give-us-your-views-on-new-research-infrastructure-for-large-scale-computing-resources.html
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.
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20 million jobs on Rackham
Today, the 20 millionth job on Rackham was submitted.
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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.
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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
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Two open positions at UPPMAX
UPPMAX is expanding the team with two new staff members: one technical system administrator and one application expert.
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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
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Life science loves UPPMAX
An estimated 40% of all publications reported to SciLifeLab under 2020 involved work done on UPPMAX resources.
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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.
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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).
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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.
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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.
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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.
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Several positions open
UPPMAX is growing and needs a new Technical Sysadmin as well as several Application Experts. Follow the links below to the job ads!
Technical System Administrator
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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.
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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
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10 million jobs on Rackham
Rackham just passed 10 million completed jobs. See the picture below
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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.
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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).
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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.
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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.
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Survey on R training needs on SNIC resources
The 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".
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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!
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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.
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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.
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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.
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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.
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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.
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Introductory UPPMAX course winter 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: January 21-24.