SNIC joins iRODS Consortium
2018-01-25
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.
UPPMAX News
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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.
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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
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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SNIC joins iRODS Consortium
SNIC now implementing new iRODS-based infrastructure
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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.
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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.
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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
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UPPMAX and Uppsala University strengthen the status of Application Experts
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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.
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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!
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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.
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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.
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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.
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Registration open to Swedish e-Science Academy 2017
Date: 11-12 October, 2017
Place: Umeå UniversityFIRM deadline for registration 25 September, 2017 at 12 hrs. Click the news for links to website and registration.
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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.