SNIC joins iRODS Consortium
SNIC now implementing new iRODS-based infrastructure
The Swedish National Infrastructure for Computing (SNIC), a national research infrastructure hosted at universities across Sweden, is the newest member of the iRODS Consortium, the membership-based foundation that leads development and support of the integrated Rule-Oriented Data System (iRODS).
SNIC provides balanced and cost-effective resources and user support for large-scale computation and data storage to researchers in all scientific disciplines nationwide. The resources are made available through open application procedures so that the best Swedish research is supported.
SNIC services are provided by six university-based high performance computing (HPC) centres:
- the High Performance Computing Center North (HPC2N) at Umeå University,
- the Uppsala Multidisciplinary Center for Advanced Computational Science (UPPMAX) at Uppsala University,
- the PDC Center for High Performance Computing at the KTH Royal Institute of Technology,
- the National Supercomputer Centre (NSC) at Linköping University,
- the Chalmers Centre for Computational Science and Engineering (C3SE) at Chalmers University of Technology and
- LUNARC, the Center for Scientific and Technical Computing at Lund University.
These SNIC partner centres provide the expert services needed to ensure that researchers can make optimal use of national HPC resources, resolving problems that range from compiling code to data management.
As an iRODS Consortium member, SNIC is incorporating iRODS into its national service portfolio and deploying iRODS-based storage for research data. SNIC technical experts also plan to collaborate with iRODS developers and other consortium members to
- enable new iRODS features based on the needs of users,
- contribute to the development of the open source, graphical interface Kanki iRODS client, and
- contribute to the continuing integration of iRODS into HPC systems, including parallel file system integration and possible future high-performance transport mechanisms for iRODS.
“At SNIC, we look forward to serving the Swedish scientific research community with our new iRODS-based infrastructure and we are excited to be members of the consortium,” said Dejan Vitlacil, SNIC storage coordinator. “We see supporting the continuity of the development of iRODS as vitally important to our operation and we are happy to see a vibrant and growing community behind iRODS.”
In addition to SNIC, iRODS Consortium members include Bayer, Dell/EMC, DDN, HGST, IBM, Intel, MSC, the National Institute for Computational Science at the University of Tennessee, OCF, RENCI, the National Institute of Environmental Health Sciences (NIEHS), University College London, Utrecht University, and the Wellcome Trust Sanger Institute. Consortium members direct the technology and governance of iRODS, which is used by thousands of businesses, research institutes, universities, and governments worldwide. Consortium members also receive priority access to support, training, and consulting.
“With SNIC as a member of the consortium, iRODS becomes an important piece of the technology infrastructure that supports Swedish research endeavors,” said Jason Coposky, iRODS Consortium executive director. “We are thrilled to be the data management and storage solution for SNIC and to work with them to enable research and discovery across Sweden.”
To learn more about iRODS and the iRODS Consortium, please visit irods.org.
To learn more about SNIC, please visit www.snic.se.
For updates and information on current system status, please see the System Status page.
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