User-paid offload storage available at UPPMAX
2019-10-10
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
Since this spring, we have been offering the Lutra offload storage system at
UPPMAX. This solution is intended for "cold" data which is not accessed or
changed frequently, but which still has to be kept available on our clusters.
This is in contrast to the active project storage provided by SNIC, which
is only intended for current analyses.
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.
For data mounted at Rackham, the price will be 500 SEK/TB/year, and users
will have to commit in units of 50 TB for a period of 4 years. That is, the
minimum cost is 100 000 SEK for storing 50 TB for 4 years (paid in multiple
installments per year).
The Rackham cluster, and hence its offload storage, is unsuitable for
sensitive data of the sort processed on Bianca. The processing of sensitive
data is more time-consuming for our staff. It also requires different service
contracts with our vendors, and includes a more expensive encrypted and
physically secured solution for tape backup. Thus, the price will be
800 SEK/TB/year for the sensitive system, i.e. a minimum of 160 000 SEK for
50 TB over 4 years.
The intent is to order the hardware in late December with the systems online in
February. A signed agreement with approval from your head of department will
be needed before we order the hardware.
If you are interested, contact support@uppmax.uu.se, UPPMAX Technical
Coordinator carl.nettelblad@uppmax.uu.se, or UPPMAX Director
elisabeth.larsson@uppmax.uu.se
FREQUENTLY ASKED QUESTIONS
--------------------------
Q: How is this storage different from existing storage, e.g. Crex and Castor?
A: The normal UPPMAX storage systems are intended for active project data,
i.e. the data which is needed during the course of a project. You have to
justify your storage needs in your project applications and storage can be
rationed when we run out. The storage itself is paid for through SNIC in
that case. When we run out of space on these resources, we have to be more
aggressive in urging users to limit their storage needs.
This storage solution is provided by us, but paid for by its users. We will
not question your needs to store data up to your quota. However, since it is
not intended for active project data, the performance of the solution is
tuned for large capacity, not a high amount of write operations. If you need
that, you should still apply for project storage.
Q: What kind of data can I put there?
A: The kind of use cases we see are storing various large data sets from old
projects. This can include the primary results from specific experiments.
If you ever need to re-analyze the data, you'll have it readily available
on our clusters. On the resource mounted on Rackham, you are not allowed to
store sensitive data, with the same interpretation of that concept as is
currently used for computation and storage projects allocations. Typical
examples of sensitive data we encounter are personally identifiable data
from population registries, health information systems, and biomolecular
assays (including genomic data).
Q: I don't need 50 TB. Why don't you offer a smaller volume?
A: We have chosen this limit to keep both the technical and financial
administration cost-efficient. Even at this price point, a substantial part
of our costs are staff costs for maintaining the solution and providing user
support.
Q: What will the availability be like? My data is super-critical.
A: We will maintain the same level of availability we do for other UPPMAX
resources, that is a best effort intent to maintain continuous operations,
with monthly service windows. An outage outside of office hours will in
general not start to be addressed until the next working day. If you need to
ensure immediate access to the data under all circumstances, we recommend
that you choose another solution.
Q: What happens if the hardware breaks down?
A: We will have redundancy within the solution, so failure of individual disks
will not affect user data. In addition, data will be backed up on tape at an
off-site location.
Q: My budget is already set, I can't pay for this now, but I want to join. What
do I do?
A: This is our second call of this sort. For now, we plan to continue making
such calls once a year. Come back in the end of 2020.
Q: How does this relate to other storage offerings and future rules and
solutions for long-term research data storage?
A: We are currently trying to serve a very concrete need for users that have
data that cannot easily be considered active project data, but where the
natural place to access the data, if it is ever needed again, would be
UPPMAX. In those cases, we think it is better to provide a common solution,
rather than individual groups buying and maintaining smaller storage systems.
In addition, our solution will be directly connected to our core network.
Even though it's a high-capacity solution, rather than a high-performance
solution, it will give higher bandwidth to our clusters than any solution
placed outside of our computer room.
The technical and organizational frameworks for true long-term storage of
research data will hopefully be clarified in the coming years, but we
believe there will still be some need for keeping data close to
computational resources, but outside of truly active project storage.
This should not be considered a replacement for permanent archival and
metadata tagging of data.
Q: When will this be available?
A: We intend to get agreements signed with all users and order the hardware
during December. The solution should be fully online during February, if
there are no significant delays from our vendors. Since this is the second
time we are doing this, the process is expected to be smooth.
Q: Can we be sure that the storage is going to be installed?
A: We assess the total interest for the two classes of data (sensitive and
non-sensitive) separately, since the hardware and software setup is
different. We will need to collect allocations in the range of 1 PB
in order to be able to go ahead with each system. This ensures that we
achieve a sufficient economy of scale to be able to offer our pricing model.
Judging from previous interest, we believe it is likely that we will
reach that point.
Q: What happens after four years?
A: The technology and organization landscape is always fluid, but after four
years the hardware will have reached its lifetime. At that point, you will
be free to retrieve the data over e.g. ssh. If there is no obvious
replacement solution provided by another entity, it is likely that we will
offer another 4-year contract at a similar price point.
For updates and information on current system status, please see the System Status page.
UPPMAX News
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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.
-
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
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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.
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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
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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.