SNIC joins iRODS Consortium

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.

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".

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! 

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.

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.

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.

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.

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.

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.

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

Welcome to a short hands on introduction to SNIC Science Cloud from the “beginner’s user/developer” point of view.

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 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.
 

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.

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.

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.

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.

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.

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

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.

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

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.

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 now implementing new iRODS-based infrastructure

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. 

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.

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

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. 

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 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. 

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.

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.

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

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.

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

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.

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.

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.

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

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

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.

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.

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.

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.

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.

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