Postdoc/PhD Positions, Parallel Computing, Extreme-Scale Systems, Umeå University

Department of Computing Science at Umea University, Sweden invites excellent candidates to apply for postdoctoral and PhD positions. The successful candidate(s) will join NLAFET, which is one of the high-profile extreme-scale computing projects funded by the European Commission within the recent FET-HPC call under Horizon 2020. NLAFET is coordinated by Umea University with international partners from INRIA (France), University of Manchester and STFC-RAL (UK).

Future extreme-scale supercomputers will be heterogeneous and lead to new and challenging demands for efficient numerical algorithms and parallel software libraries. The aim of NLAFET is to tackle these challenges and ultimately deliver new scalable numerical libraries for fundamental problems in numerical linear algebra, including the
solution of dense and sparse systems of equations and eigenvalue problems. Achieving this requires a co-design effort including developing novel algorithms, exploration of advanced scheduling strategies and runtime systems, offline and online autotuning, as well as avoiding communication and synchronization bottlenecks.

The positions will focus on design, implementation, and evaluation of parallel algorithms for matrix eigenvalue problems with regards to the extreme-scale challenges. The research will be done in close collaboration with recognized researchers and PhD students in the research group as well as with other partners in NLAFET.

For complete information of the positions see (dead-line for applications is August 17, 2015):

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
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Swedish e-Science Education graduate school (SeSE) courses: Autumn 2015

The Swedish e-Science Education graduate school (SeSE) now announces its graduate courses of autumn 2015.

The courses are listed at the SeSE website:

SeSE gives basic training in fields where the use of e-Science is emerging and where such education can have an immense impact on the research as well as advanced training for students in fields that are already computer-intensive. The course curriculum is tailored to meet a broad set of prerequisites and will foster collaborations between Swedish researchers, possibly opening up for new research fields utilising e-Science tools and methods and also making it possible for inter- disciplinary collaborations on a Nordic level.

Swedish e-Science Education graduate school (SeSE) courses: spring 2015

The Swedish e-Science Education graduate school (SeSE) now announces its graduate courses of spring 2015.

The courses are listed at the SeSE website:

SeSE gives basic training in fields where the use of e-Science is emerging and where such education can have an immense impact on the research as well as advanced training for students in fields that are already computer-intensive. The course curriculum is tailored to meet a broad set of prerequisites and will foster collaborations between Swedish researchers, possibly opening up for new research fields utilising e-Science tools and methods and also making it possible for inter- disciplinary collaborations on a Nordic level.

Postdoc in structural bioinformatics of GPCRs – Development of GPCR-ModSim

Postdoc opening in structural bioinformatics of GPCRs
Development of GPCR-ModSim,

The platform GPCR-ModSim is one of the first and most complete web-based solutions for the modeling and simulation of GPCRs (see The GPCR-ModSim project is now part of the Computational and Systems Biology program at the Cell and Molecular Biology department in Uppsala University, one of the most vibrant and dynamic Universities in Europe. Our research on G-protein coupled receptors (see ) is currently funded by several private and public sources. In particular, the development of GPCR-ModSim is supported by a grant from the Carl Trygger Foundation (Stockholm), and we are looking for a talented postdoc to join this project in the spring 2015. If you have recently finished your PhD (or you are about to in the very next future) in bioinformatics, computer science, computational chemistry or similar disciplines, you are encouraged to send us an application for this position. Simply send a CV and a motivation letter by e-mail to

You should:

  • Have experience in computer simulations and/or protein modeling and/or bioinformatics
  • Have programming skills in Python and be familiar with Unix systems,
    web servers and databases.
  • Be interested in the development and implementation of novel computational methodologies within structural biology and ligand design.
  • Have demonstrated capacity of collaboration and ability for multidisciplinary

We offer:

  • A one year, tax-free fixed postdoctoral position, with possibilities to extend our funding.
  • An extensive network of collaborations. We are part of the EU-COST action GLISTEN, which agglutinates the major GPCR research labs and industries in Europe, and maintain several collaborations with top medicinal chemists, structural biologists and pharmacologists in the field (see
  • A vibrant international environment in one of Europe’s top universities.

Applications or further inquiries are welcome until 31st January to the project leader:

Hugo Gutierrez de Teran, PhD.
Dept. of Cell and Molecular Biology
Uppsala University (SWEDEN)
Phone: +46(0)18 471 5056

Swedish Theoretical Chemistry Meeting, Uppsala, 27-29 Oct 2014

We invite you to participate in the following conference:

Swedish Theoretical Chemistry Meeting 2014 – New Horizons
at the Ångström Laboratory, Uppsala University, Sweden
27–29 October 2014 (lunch to lunch)

Room: Häggsalen at the Ångström Lab, Uppsala University
Deadline for abstracts and registration: 26 September 2014
Among the invited speakers are:

  • Prof. Roberto Car (Princeton U, USA)
    “Water, ice, dynamics and hybrids”
  • Prof. Martin Head-Gordon (UC Berkeley, USA)
    “The next generation of electronic structure theories”
  • Prof. Sally Price (UCL, UK)
    “Crystal-polymorphs prediction for pharmaceutical development – a challenge for force-field development and our understanding of crystallization”
  • Prof. Joost VandeVondele (ETH Zurich, CH)
    “Exploring the frontiers in sampling, large-scale models, and electroncorrelation using petascale computing and CP2K.”
  • Dr. Horst Weiss (BASF, DE)
    “Driving innovation for materials in the chemical industry – modelling needs and opportunities”

For this meeting we define theoretical chemistry in a broad sense, encompassing theory and computation from all fields of chemistry and its interfaces with physics, biology, materials science, and so on. The meeting is subtitled “New Horizons”, and the presentations will discuss new methods and directions, from fundamental concepts of bonding to calculations for industrial applications.

We welcome your participation and your oral or poster contributions!

/Kersti Hermansson and co-organisers

PRACE 10th Call for Proposals

PRACE 10th Call for Proposals for Project Access including Multi-year, and Programmatic Access is Open

Important dates:

  • Opening date: 10 September 2014
  • Closing date: 22 October 2014, 12:00 (noon) CEST
  • Response of applicants to reviews: 15– 21 January 2015
  • Anticipated allocation decisions: last week of February 2015
  • Allocation start date of awarded proposals: 10 March 2015
  • Allocation end date of award: 9 March 2016
  • Type of access: Project Access, Multi-Year Project Access, Programmatic

PRACE HPC systems available:

  • “Curie”, Bull Bullx cluster (GENCI@CEA, France)
  • “Fermi”, IBM Blue Gene/Q (CINECA, Italy)
  • “Hornet” – Cray XC30 (GCS@HLRS, Germany)
  • “MareNostrum”, IBM System X iDataplex (BSC, Spain)
  • “SuperMUC”, IBM System X iDataplex (GCS@LRZ, Germany)

The mission of PRACE is to enable high impact scientific discovery and engineering research and development across all disciplines to enhance European competitiveness for the benefit of society. PRACE seeks to realize this mission by offering world class computing and data management resources and services through a peer review process.

Scientists and researchers from around the world can apply for access to PRACE resources.

Industrial users can apply if they have their head offices or substantial R&D activity in Europe.

Project Access:

Proposals can be based on a 12-months schedule, or, for Multi-year Projects, on a 24- or 36-months schedule. The allocation of awarded resources is made for 1 year at a time with provisional allocations awarded for the 2nd and 3rd year.

Additionally, the Call:

  • includes a pilot test case for Programmatic Access for 12-months
    allocations schedule only.
  • reserves 0.5% of the total resources available for this call for Centres of Excellence (CoE) as selected by the EC under the E-INFRA-5-2015 call for proposals.

The PRACE Access Committee, composed of leading European scientists and engineers, ranks the project proposals that will be awarded access to PRACE resources.

For more information and application forms see:

If you need some extra information please feel free to contact PRACE directly via


The following people at SNIC centers:

  • PDC – Lilit Axner
  • NSC – Chandan Basu, Soon-Heum “Jeff” Ko
  • HPC2N – Mikael Rännar, Jerry Eriksson

SeSE course Autumn 2014

Please see the attached call for participation in the SeSE courses this autumn.

The courses are free for PhD students (in Sweden) and it is possible to get a travel grant of 6000skr.

These courses are so far scheduled:

  • Introduction to high performance computing/PDC summer school, August
  • Matrix Computations in Statistics and with Applications, September, v39
  • Introduction to programming in science and technology, September
  • Computational Python, October, v42
  • Numerical Linear Algebra, October, v42
  • Scientific Visualisation, November 3-21
  • Scientific Software Development Toolbox, December
  • Topics in CFD, December 1-19

Kind regards
Anders Hast
Director of SeSE
ps. Please note that it is possible to register to get news about courses via our subscribe function:

Call for participation: SeSECall2014A.pdf

2014 IEEE 10th International Conference on e-Science


The way in which scientific research is carried out is undergoing a series of radical changes as a result of the digital revolution. Researchers in all disciplines are increasingly adopting digital tools, techniques and practices in communities and projects that span multiple disciplines, laboratories, organizations, and national boundaries. The e-Science 2014 conference is designed to bring together leading international and interdisciplinary research communities, developers, and users of e-Science applications and enabling IT technologies. The conference aims to serve as a forum to present recent research advances in e-Science and highlight associated activities worldwide, providing an outlook of challenges and opportunities we will face in the future.

e-Science 2014 will follow the previous e-Science conferences in encouraging submissions that explore advances in the application of technology in particular disciplines, covering both data-oriented and compute-oriented approaches, as well as extreme scale approaches and applications. Major topics include, but are not limited to

  • Arts, humanities (including Digital Humanities) and e-Social science
  • Bioinformatics and e-Health
  • Physical Sciences and Engineering
  • Climate, Environmental & Earth Sciences
  • Data science, data management and digital repositories
  • Cyberinfrastructure to support eScience, including novel hardware, software and services
  • eScience in the cloud
  • Education and eScience practice

Important Dates

  • Abstract submission deadline: 6 May 2014
  • Paper Submission Deadline: 12 May 2014
  • Notification of Acceptance: 7 July 2014
  • Camera Ready Papers Due: 4 August 2014
  • Conference Dates: 20-24 October 2014

The conference proceedings will be made available online through the IEEE Digital Library.
The proceedings of previous e-Science conferences are indexed by EI

Submission Process

Authors are invited to submit papers with unpublished, original work of not more than 10 pages of double column text using single spaced 10 point size on 8.5 x 11 inch pages, as per IEEE 8.5 x 11 manuscript guidelines. (Up to 2 additional pages may be purchased for US$150/page)

Templates are available from

Authors should submit a PDF file that will print on a postscript printer to

It is a requirement that at least one author of each accepted paper attend the conference.
For news, and updates, check (


PhD positions in Parallel and High-Performance Computing, Umeå University, Sweden

We are seeking outstanding candidates for PhD student positions within the field of Parallel and High-Performance Computing.

The research group is focused on the design, analysis, and implementation of efficient and robust algorithms, and library software for parallel dense and structured matrix computations. The research is performed in an international and creative environment. Locally, the research group is collaborating with the High Performance Computing Center North (HPC2N) and the UMIT Research Lab.

For further information of the positions, please contact Professor Bo Kagstrom ( or Ass. Professor Lars Karlsson ( at the Department of Computing Science and HPC2N.

Dead-line for applications is August 20, 2013.
For the complete announcement, visit