UPPMAX and Uppsala University strengthen the status of Application Experts
For a long time, Application Experts have filled a crucial role in supporting research at UPPMAX and other SNIC centers. Their importance was hitherto belied by the fact that "Application Expert" did not exist as a job title, and Application Experts always had to be employed in another role or title.
Today, Uppsala University has officially made Application Experts a job title. This is an excellent step towards creating new career paths for research support staff in academia, making it easier to recruit and retain highly skilled personnel in many essential functions.
For updates and information on current system status, please see the System Status page.
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.
CodeRefinery workshop in Uppsala
If you are writing code that is used in research, then this course is for you
Hands-on informal and interactive three-day event with type-along type of presentations, live coding and demos. Short tutorials alternate with practical exercises.
December 3-5, 2018, 9:00 am to 5:00 pm
Registration open to Hands on introduction to SNIC Science Cloud
Welcome to a short hands on introduction to SNIC Science Cloud from the “beginner’s user/developer” point of view.
SeSE Applied Cloud Computing Workshop open for registration
An application oriented introduction to cloud computing aimed mainly at PhD students. Basics of Service Oriented Architectures (SOA). Basic concepts of cloud computing such as virtualization and the service layers IaaS, PaaS and SaaS, dynamic provisioning, elasticity. Practical use of available public and private cloud stacks. Introduction to cloud security. Task based programming in cloud environments. Application of key technologies and design patterns to realize scientific applications in cloud computing environments.
The Large Fall 2018 call for large allocations is open
The Fall 2018 call for proposals for large allocations of computing time on the High Performance Computing resources of the Swedish National Infrastructure for Computing (SNIC) is open. Deadline 19 October 2018.
The allocations are for the period 1 January 2019 - 31 December 2019.
Welcome to the Scientific Visualisation Graduate Course 2018
This year's Scientific Visualisation course will be held from 26th to 30th of November in Uppsala, with specially invited guest-lecturer, Alex Telea, who is the author of the course book "Data Visualization: Principles and Practice" on which the course is based itself.
New system for home directories
With the retirement of Pica, a new storage system for home folders is being taken into production this week. This system is named Domus, which means "home" in Latin. In addition to home directories, the software library will also be located on Domus.
Rackham/Crex extensions fully in production
In order to replace the loss of the Milou cluster and Pica storage, Rackham and its storage system Crex have been extended. This new hardware is now fully in production.
Hearing and miniworkshop on AI/Machine Learning
The Knut and Alice Wallenberg Foundation (KAW) has launched an investigation into the needs and potential solutions for a Swedish infrastructure in support of AI, in particular Machine Learning, based research in Sweden.
Preliminary findings will be presented in a hearing in Stockholm on June 1st to which you are cordially invited. The hearing will include presentations from the panels as well a mini-workshop for feedback and open discussion around the presented topics.
Paper published: Tracking the NGS revolution
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
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
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
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
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
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
SNIC now implementing new iRODS-based infrastructure
Newsworthy Uppsala research done at UPPMAX
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
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
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
Time to start moving your research from Milou
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
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
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
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
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
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
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
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
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.
Reduced support staff during summer
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
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
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
UPPMAX welcomes its newest member of staff, Niharika Gauraha, to the team as a bioinformatics application expert.
NeIC 2017 in Umeå registration still open
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.
Photo report from Systems Inauguration event
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
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
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
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
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
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
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
on March 30th (10:15 – 12:00, Room 2347, ITC, Uppsala) by Stig Telfer.
Rackham/Bianca Inauguration April 24th
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
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
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
UPPMAX resources used for Science publication on Darwin's finches
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
UPPMAX publishes report on hadoop for NGS data analysis
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
UPPMAX resources used for PNAS publication on Capsella bursa-pastoris
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
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
UPPMAX used by Erik Larsson lab in Nature publication
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