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UPPMAX offline on October 4-5

Mon, 25 Sep 2023 07:28:00 GMT

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.

Welcome to UPPMAX 20 years

Mon, 15 May 2023 09:18:00 GMT

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

UPPMAX user in the news

Fri, 05 May 2023 08:44:00 GMT

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.

UPPMAX Celebrates 20 Years of High-Performance Computing and Storage Services

Fri, 28 Apr 2023 08:50:00 GMT

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.

Forskarfilm: UPPMAX och dess föreståndare

Tue, 28 Feb 2023 10:28:00 GMT

Upptech har gjort en kort film om Elisabeth Larsson och UPPMAX. Se filmen på Youtube.

Fat nodes to Bianca

Wed, 21 Dec 2022 12:52:00 GMT

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

Thu, 29 Sep 2022 07:49:00 GMT

Increasing resources of the Bianca login nodes has been much requested by our

SNIC-SENS users. We are thrilled to announce that we are bumping the specs for

all Bianca login nodes and extending total number of compute nodes with an

additional 72x256GByte ("fat") nodes.

Undergraduate courses at UPPMAX

Tue, 07 Jun 2022 07:33:00 GMT

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

Thu, 14 Apr 2022 07:59:00 GMT

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 2022

Tue, 08 Mar 2022 09:46:00 GMT

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

Tue, 22 Feb 2022 09:48:00 GMT

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

Tue, 22 Feb 2022 09:43:00 GMT

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.

Read the job ad for more information

Lovande molekyl mot coronavirus på Uppmax

Mon, 14 Feb 2022 14:44:00 GMT

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.

Läs hela artikeln för att veta mer

Bianca to be upgraded in 2022

Fri, 11 Feb 2022 15:05:00 GMT

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

Thu, 16 Dec 2021 13:31:00 GMT

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

Tue, 14 Dec 2021 10:09:00 GMT

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

Thu, 11 Nov 2021 10:25:00 GMT

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

Wed, 27 Oct 2021 08:50:00 GMT

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

Thu, 09 Sep 2021 12:30:00 GMT

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

Tue, 18 May 2021 09:21:00 GMT

Today, the 20 millionth job on Rackham was submitted.

Ny tjänst ger tillgång till superdator för utbildning

Wed, 24 Mar 2021 13:01:00 GMT

Avdelningen för universitetsgemensam IT (UIT) har lanserat en ny tjänst som tillgängliggör infrastruktur för stora databeräkningar inom hela universitetets utbildningsverksamhet.

Läs mer på nyhetssidan i MP

Ny Teknik: Tre år efter uppropet #teknisktfel – ”Kvinnor som är utsatta blir trodda nu”

Mon, 08 Mar 2021 07:23:00 GMT

(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

Tue, 02 Mar 2021 08:16:00 GMT

UPPMAX is expanding the team with two new staff members: one technical system administrator and one application expert.

SRC Survey on research data management

Tue, 23 Feb 2021 13:08:00 GMT

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

Wed, 13 Jan 2021 12:22:00 GMT

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

Wed, 28 Oct 2020 12:52:00 GMT

UPPMAX is gathering interest in user-funded GPU resources on Bianca. Users are invited to contact us.

New national HPC competence center launched

Tue, 27 Oct 2020 10:21:00 GMT

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

Tue, 29 Sep 2020 08:59:00 GMT

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

Thu, 14 May 2020 09:59:00 GMT

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

Thu, 02 Apr 2020 08:41:00 GMT

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

Thu, 27 Feb 2020 13:05:00 GMT

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

Application Expert (full time)

Application Expert (part time)

User-paid GPU pool available

Wed, 11 Dec 2019 11:47:00 GMT

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

Tue, 12 Nov 2019 10:58:00 GMT

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

Thu, 10 Oct 2019 12:21:00 GMT

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

Fri, 20 Sep 2019 10:45:00 GMT

Rackham just passed 10 million completed jobs. See the picture below

SNAC Chair to hold a seminar

Wed, 11 Sep 2019 07:53:00 GMT

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

Wed, 04 Sep 2019 11:52:00 GMT

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

Mon, 26 Aug 2019 13:05:00 GMT

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

Tue, 11 Jun 2019 09:47:00 GMT

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 resources

Wed, 29 May 2019 08:23:00 GMT

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

Wanted: Application Expert in cloud and container technology

Mon, 20 May 2019 09:40:00 GMT

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

Tue, 14 May 2019 15:00:00 GMT

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

Thu, 09 May 2019 07:14:00 GMT

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

Wed, 17 Apr 2019 13:22:00 GMT

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

Tue, 05 Feb 2019 10:32:00 GMT

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

Tue, 15 Jan 2019 12:54:00 GMT

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

Thu, 08 Nov 2018 08:30:00 GMT

Dates: January 21-24.

CodeRefinery workshop in Uppsala

Mon, 05 Nov 2018 10:12:00 GMT

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

Thu, 18 Oct 2018 18:23:00 GMT

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

Tue, 02 Oct 2018 08:21:00 GMT

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

Wed, 19 Sep 2018 08:05:00 GMT

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

Wed, 12 Sep 2018 09:34:00 GMT

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

Tue, 12 Jun 2018 12:16:00 GMT

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

Wed, 30 May 2018 12:15:00 GMT

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

Mon, 14 May 2018 08:57:00 GMT

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 1^st 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.

Paper published: Tracking the NGS revolution

Wed, 02 May 2018 14:56:00 GMT

Parts of the UPPMAX staff have written a paper that traces the growth and development of NGS (next generation sequencing) projects at UPPMAX, comparing these projects with those in other fields in a variety of different ways. The paper has now been published and is well worth reading.

Rackham and Crex extensions installed

Tue, 17 Apr 2018 09:16:00 GMT

The long-awaited extensions of the compute cluster Rackham, and its storage system, Crex, has been installed and will soon be ready to use.

SNAC Large Spring 2018 call open

Wed, 04 Apr 2018 08:43:00 GMT

The Spring 2018 call for LARGE SNIC projects is open. Users interested in more than 100,000 core-hours/month for 6 months or more are invited to apply.

17th PRACE Call for Proposals for Project Access

Wed, 21 Mar 2018 13:08:00 GMT

Partnership for Advanced Computing in Europe (PRACE) has opened another call for proposals. The closing date is 02 May 2018.

Upp till fyra tekniska systemadministratörer vid UPPMAX

Fri, 02 Feb 2018 08:09:00 GMT

Vill du vara med och driva och utveckla UPPMAX, så kan denna tjänst vara något för dig. Som teknisk systemadministratör vid UPPMAX kommer du arbeta i ett team på cirka tio systemexperter med UPPMAX lagrings- och beräkningssystem.

Teknisk koordinator sökes

Tue, 30 Jan 2018 11:58:00 GMT

UPPMAX söker en ny Teknisk Koordinator. Som Teknisk koordinator kommer du ha det övergripande tekniska ansvaret för UPPMAX IT-miljö. Du kommer ha en ledande roll i den strategiska planeringen av UPPMAX tekniska utveckling och en koordinerande roll när det gäller planering och samordning av upphandlingar av beräknings- och lagringssystem.

SNIC joins iRODS Consortium

Thu, 25 Jan 2018 09:00:00 GMT

SNIC now implementing new iRODS-based infrastructure

Newsworthy Uppsala research done at UPPMAX

Tue, 02 Jan 2018 08:02:00 GMT

Upsala Nya Tidning (UNT) has an article about the most newsworthy research performed by Uppsala researchers. Most of the science that is mentioned was done partially with the aid of the UPPMAX cluster Milou.

Update on the move from Milou: Crex is booked up in the short term

Thu, 14 Dec 2017 12:07:00 GMT

Because of the shutdown of Milou, the current storage resources on Rackham/Crex are now fully booked. New projects' allocations will be made available after we have expanded the size of the storage system, which should be by April 2018. Please continue to submit project proposals as per our earlier instructions.

Job posting: UPPMAX seeks a new Application Expert

Tue, 05 Dec 2017 11:57:00 GMT

The UPPMAX Application Expert group is growing! A new application expert is needed to help with software installations and advanced user support in a variety of possible areas. See the job posting at the URL below. http://www.uu.se/jobb/detaljsida/?positionId=181543

UPPMAX and Uppsala University strengthen the status of Application Experts

Fri, 24 Nov 2017 15:16:00 GMT

Time to start moving your research from Milou

Wed, 08 Nov 2017 12:37:00 GMT

The dedicated bioinformatics/life science compute resource Milou and its storage system Pica have reached their end of life. If you use Milou and will continue research into 2018 and beyond, then it is time for you to plan your move.

Register now to UPPMAX Introductory courses Winter 2018

Tue, 07 Nov 2017 13:04:00 GMT

Registration is now open for the UPPMAX Introductory Course and the Awk Workshop to be held in January 2018. These courses are very popular, reserve a place now!

UPPMAX rejoins the SNIC Science Cloud

Tue, 07 Nov 2017 08:27:00 GMT

UPPMAX happily rejoins the HPC2N and C3SE cloud regions in the SNIC Science Cloud (SSC) project. SSC offer Infrastructure-as-a-service (IaaS) free of charge for Swedish PIs and their collaborators.

New hardware for SENS purchased

Tue, 03 Oct 2017 12:15:00 GMT

The storage systems for SNIC-SENS are being upgraded and extended by a total of about 5 PB, bringing the total disk surface for sensitive data at UPPMAX to nearly 12 PB. The new hardware could be in place already by the end of 2017.

SSC training workshop at HPC2N on Oct 10

Tue, 03 Oct 2017 12:03:00 GMT

We would like to invite all interested current and future users to a training workshop on introductory level at HPC2N, Umeå, on Oct 10. We will introduce cloud computing in general, including covering best practices around security. The majority of time will be spent in lab sessions on basic usage of the IaaS cloud.

Registration open to Swedish e-Science Academy 2017

Tue, 12 Sep 2017 09:25:00 GMT

Date: 11-12 October, 2017
Place: Umeå University

FIRM deadline for registration 25 September, 2017 at 12 hrs. Click the news for links to website and registration.

A female Viking warrior confirmed by genomics at UPPMAX

Fri, 08 Sep 2017 18:05:00 GMT

A genomics study performed on Milou has concluded that a high-standing Viking warrior was indeed female, confirming earlier osteological findings that were deemed controversial.

SNIC Science Cloud at IEEE eScience

Wed, 30 Aug 2017 11:53:00 GMT

The thirteenth IEEE eScience Conference will be held in Auckland, New Zealand from 24 – 27 October 2017. A paper describing the SNIC Science Cloud has been accepted to the conference. Co-authors from UPPMAX include Salman Toor, Andreas Vallin, Pontus Freyhult, Linus Nilsson, Martin Agback and Ola Spjuth.

Article in PDC Newsletter about SNIC-SENS

Tue, 11 Jul 2017 07:24:00 GMT

SNIC-SENS, the project where UPPMAX provides compute and storage resources to make large-scale computation on sensitive human data possible for Swedish academia, is described in an article in the bi-annual newsletter put out by PDC, the SNIC HPC center hosted by KTH.

https://www.pdc.kth.se/newsletter/2017-1/pdc-newsletter-2017-no.-1

Reduced support staff during summer

Thu, 29 Jun 2017 09:24:00 GMT

During the summer holidays, the availability of support staff will be reduced. Expect longer waiting times for non-critical support requests, especially during the month of July.

Application Expert position available at PDC

Fri, 02 Jun 2017 10:12:00 GMT

PDC is the supercomputing center hosted by KTH. They are looking for a full-time application expert with a background in either CFD or molecular dynamics.

Registration open to UPPMAX courses

Mon, 29 May 2017 12:51:00 GMT

In the last week of August, UPPMAX will offer a 4-day course on everything you need to know to be a productive HPC user, and a 1-day advanced course in Awk.

New Application Expert — Niharika Gauraha

Wed, 17 May 2017 08:06:00 GMT

UPPMAX welcomes its newest member of staff, Niharika Gauraha, to the team as a bioinformatics application expert.

NeIC 2017 in Umeå registration still open

Tue, 09 May 2017 09:45:00 GMT

Registration is still open to the third Nordic e-Infrastructure Conference, in Umeå May 29 – June 1. Four days of workshops and conference program, with topics ranging from security and bioethics to deep learning and emerging technologies.

Come here about (and influence) the future of e-infrastructure in the Nordics.

NeIC 2017 webpage

Photo report from Systems Inauguration event

Wed, 03 May 2017 07:59:00 GMT

On April 24th, UPPMAX inaugurated the new systems, Rackham and Bianca, with an event at SciLifeLab. Around 80 people attended, hearing speakers talk and mingling in a uniquely broad poster session.

Rackham popular in SNAC Large Spring 2017

Wed, 03 May 2017 07:51:00 GMT

The current SNAC Large round closed with requests for nearly 2 million core-hours/month on Rackham, three times more than what is available for this round. Proposed projects are split between bioinformatics and biochemistry. Scientific and technical reviews are due in mid-May, and allocation decisions will follow shortly afterwards.

Rackham to be expanded

Wed, 19 Apr 2017 09:13:00 GMT

On Friday, April 21st, 30 new Rackham nodes will be physically installed by the vendor, SouthPole. 24 nodes have been paid for by David Black-Schaffer, in Uppsala University's Department of Information Technology, and will provide a priority resource for his group's research in multicore processing. After installation, testing, and configuration, Rackham will boast a total of 334 compute nodes.

Bianca is now in production

Fri, 07 Apr 2017 13:03:00 GMT

The beta or pilot phase of the project is now over, and Bianca is now in a fully functional production mode. Sensitive data, e.g. genomes of living human beings, can now be analysed in a secure manner that complies with data privacy regulations. Apply for a project in SUPR.

Två nya superdatorer stärker viktig forskning

Wed, 05 Apr 2017 08:33:00 GMT

De två nya superdatorerna Bianca och Rackham invigs på UPPMAX vid Uppsala universitet den 24 april. De är båda unika på olika sätt och tillsammans ökar de möjligheterna för ny banbrytande forskning inom bland annat bioinformatik och materialvetenskap.

Now available: Two types of storage projects on Crex

Thu, 30 Mar 2017 07:41:00 GMT

Crex is a 2 PB storage system attached to Rackham. Anyone who uses Rackham and needs more than 128 GB of space can apply to one of two rounds in SUPR. Read on for more details.

The SNIC Science Cloud service is now in preproduction and accepting projects

Wed, 22 Mar 2017 08:52:00 GMT

The SNIC Science Cloud is now in preproduction, see https://cloud.snic.se/index.php/2017/03/21/ssc-in-pre-production/ for more information.

Seminar: Cloud Infrastructures for HPC and big data

Tue, 21 Mar 2017 11:56:00 GMT

on March 30th (10:15 – 12:00, Room 2347, ITC, Uppsala) by Stig Telfer.

Rackham/Bianca Inauguration April 24th

Thu, 09 Mar 2017 13:42:00 GMT

It is a tradition to inaugurate new HPC systems, and this time UPPMAX can proudly present two systems at once.

HATSID project funded by SSF

Wed, 01 Mar 2017 08:57:00 GMT

A group of UPPMAX users have received funding from the Swedish Foundation for Strategic Research (SSF) as part of an initiative on Big Data.

UPPMAX resources used for eLife publication on herring genome

Tue, 10 May 2016 11:34:00 GMT

UPPMAX resources were used for a publication in eLife on ecological adaptations of the Atlantic herring when the species expanded to the brackish waters of the Baltic Sea. The study was published on May 03, 2016.

The genetic basis for ecological adaptation of the Atlantic herring revealed by genome sequencing

Alvaro Martinez Barrio, Sangeet Lamichhaney, Guangyi Fan, Nima Rafati, Mats Pettersson, He Zhang, Jacques Dainat, Diana Ekman, Marc Höppner, Patric Jern, Marcel Martin, Björn Nystedt, Xin Liu, Wenbin Chen, Xinming Liang, Chengcheng Shi, Yuanyuan Fu, Kailong Ma, Xiao Zhan, Chungang Feng, Ulla Gustafson, Carl-Johan Rubin, Markus Sällman Almén, Martina Blass, Michele Casini, Arild Folkvord, Linda Laikre, Nils Ryman, Simon Ming-Yuen Lee, Xun Xu, Leif Andersson

DOI: 10.7554/eLife.12081

UPPMAX resources used for Science publication on Darwin's finches

Tue, 10 May 2016 11:14:00 GMT

UPPMAX resources were used for a publication in Science on the the discovery of a major gene locus associated with changes in beak size that apparently facilitated a rapid ecological diversification in the adaptive radiation of Darwin's finches.

A beak size locus in Darwin’s finches facilitated character displacement during a drought

Sangeet Lamichhaney, Fan Han, Jonas Berglund, Chao Wang, Markus Sällman Almén, Matthew T. Webster, B. Rosemary Grant, Peter R. Grant, Leif Andersson

doi: 10.1126/science.aad8786

UPPMAX publishes report on hadoop for NGS data analysis

Wed, 10 Jun 2015 08:18:00 GMT

Researchers affiliated with UPPMAX and financed by the Strategic Research Program eSSENCE published a report on the applicability of Hadoop for analyzing next-generation sequencing data.

Siretskiy A, Sundqvist T, Voznesenskiy M, Spjuth O.
A quantitative assessment of the Hadoop framework for analyzing massively parallel DNA sequencing data.
Gigascience. 2015 Jun 4; 4:26. doi: 10.1186/s13742-015-0058-5
http://www.gigasciencejournal.com/content/4/1/26

UPPMAX resources used for PNAS publication on Capsella bursa-pastoris

Mon, 23 Feb 2015 09:17:00 GMT

UPPMAX resources were used for a PNAS publication on the tetraploid Capsella bursa-pastoris.

Hybrid origins and the earliest stages of diploidization in the highly successful recent polyploid Capsella bursa-pastoris
Gavin M. Douglas, Gesseca Gos, Kim A. Steige, Adriana Salcedo, Karl Holm, Emily B. Josephs, Ramesh Arunkumar, J. Arvid Ågren, Khaled M. Hazzouri, Wei Wang, Adrian E. Platts, Robert J. Williamson, Barbara Neuffer, Martin Lascoux, Tanja Slotte, and Stephen I. Wright

UPPMAX resources used for a Nature publication on Darwin's finches

Tue, 17 Feb 2015 09:16:00 GMT

UPPMAX resources were used for a Nature publication on Darwin's finches. The article was published online on the 11th of February:

Evolution of Darwin’s finches and their beaks revealed by genome sequencing

Sangeet Lamichhaney, Jonas Berglund, Markus Sällman Almén, Khurram Maqbool, Manfred Grabherr, Alvaro Martinez-Barrio, Marta Promerová, Carl-Johan Rubin, Chao Wang, Neda Zamani, B. Rosemary Grant, Peter R. Grant, Matthew T. Webster & Leif Andersson

http://www.nature.com/nature/journal/vaop/ncurrent/full/nature14181.html

UPPMAX used by Erik Larsson lab in Nature publication

Wed, 07 Jan 2015 09:15:00 GMT

Erik Larsson's Lab have a couple of recent publications that was made possible by UPPMAX resources:

Nature Genetics: Systematic analysis of noncoding somatic mutations and gene expression alterations across 14 tumor types
International Journal of Cancer: Absence of cytomegalovirus in high-coverage DNA sequencing of human glioblastoma multiforme