For information about the status of the PDC computer systems, check the system alerts.
Our partner International Neuroinformatics Coordination Facility (INCF) has produced an information video about neuroinformatics and INCF with some footage from the PDC computer hall.
EASC2014: Solving Software Challenges for Exascale will be held in Stockholm from 2-4 April 2014. This conference aims to bring together all the developers and researchers involved in solving the software challenges of the exascale era. EASC2014 focuses on issues of applications for exascale and the associated tools, software programming models and libraries. The conference is being organized at KTH in association with SeRC and the CRESTA and EPiGRAM projects.
The Call for papers for EASC2014 is now open, with a final submission deadline of 12 January 2014. For details of the conference, please see
or contact Stefano Markidis (firstname.lastname@example.org) for additional information.
SNIC Training Survey
To plan future training activities within the Swedish National Infrastructure for Computing (SNIC), we would like to understand the training needs of both the user communities, and also of the staff at the SNIC centres. We therefore invite users and staff to participate in the training survey, which is accessible from:
The survey will be open until the 6th December 2013. We would really appreciate it if you would take a little of your time before the closing date to give us your input on training.
Lindgren, PDC's Cray XE6, is being used by Swedish researchers from the Science for Life Laboratory who are looking into causes of neurological conditions such as certain types of migraines and muscle cramps. For more information, see
Mikael Djurfeldt, an application expert at PDC, was recently interviewed on "Hjärnkontoret", a Swedish television programme for children. You can watch Mikael explaining how computers work, using an analogy based on how human brains see things, on SVT's website http://www.svt.se/barnkanalen/hjarnkontoret/. The interview with Mikael starts a little after the 5:30 timing mark and runs for just over 5 minutes.
PDC invites students with an interest in supercomputing to apply for a part-time position (40%) working at PDC until summer 2014 (preferably starting in October 2013). For details about this position, please see the PDC job openings page.
Supercomputer centres blossoming in Sweden thanks to the Swedish climate and distance heating/cooling technology
PDC has recently called for tenders for a new supercomputer intended for neuroscience research at KTH and KI. The new supercomputer is planned to be up and running at PDC by early 2014.
Information about the tendering process is available in Swedish here.
If you would like more information about the new neuroscience supercomputer system, please contact Gert Svensson, Deputy Director at PDC.
PDC invites candidates with suitable experience and qualifications to apply for a position as a Business Developer. For more details about this position, please see the PDC job openings page.
PDC has recently joined the Advanced Simulation Technologies (AST) University Partnership Program (UPP) - for more information about this program see:
There are now thirty (30) free UPP licenses available for using the simulation software AVL Fire at PDC for research and educational purposes. For more information about AVL FIRE, see:
If you are interested in running AVL FIRE at PDC, please contact email@example.com to request a license and include details of the research project or course(s) where you would like to use AVL FIRE.
The PRACE Advanced Training Center (http://www.prace-ri.eu/training) @ CSC - IT Center for Science Ltd. is offering a course on:
Data Staging and Data Movement with EUDAT
10-12 September, Helsinki (Espoo), Finland
With the rapid accumulation of research data, there is an ever-growing need to tackle the specific challenges of data management, and to ensure a coherent approach for accessing and preserving research data. This course will cover tools and techniques for moving data on, off and between high performance computers and community data repositories. As well as presenting the general principles, it will cover the data management tools and services developed by EUDAT, and focus specifically on their use within the PRACE infrastructure.
For more information and registration, please go to:
12th VI-HPS Tuning Workshop
7-11 October 2013
Juelich Supercomputing Centre, Forschungszentrum Juelich
VI-HPS and the German PRACE Advanced Training Centre (PATC) are organizing the 12th VI-HPS Tuning Workshop, the latest in a series of workshops given by tools developers for application developers. The Virtual Institute - High Productivity Supercomputing (VI-HPS) is an initiative to promote the development, integration and use of HPC tool - for further information about it, see http://www.vi-hps.org.
Participants are invited to bring their own application codes to the workshop to analyze and tune their performance with the help of experts.
The workshop will:
- give an overview of the VI-HPS programming tools suite,
- explain the functionality of individual tools, and how to use them effectively, and
- offer hands-on experience and expert assistance using the tools.
The workshop will be held in English and run from 09:00 to not later than 18:00 each day, with breaks for lunch and refreshments.
There is no fee for participation, however, participants are responsible for their own travel and accommodation.
Presentations and hands-on sessions are planned on the following topics:
- Score-P instrumentation and measurement,
- Scalasca automated trace analysis,
- Vampir interactive trace analysis,
- Periscope on-line automated analysis,
- Paraver trace analysis,
- TAU performance system,
- MUST correctness checking of MPI, and
- other tools.
For the full programme, see http://www.vi-hps.org/training/tws/tw12.html.
Classroom capacity is limited, therefore priority will be given to applicants with parallel codes already running on the workshop computer system (Juqueen BGQ), and those bringing codes from similar BlueGene systems to work on. Participants are therefore encouraged to prepare their own MPI, OpenMP and hybrid OpenMP/MPI parallel application codes for analysis.
Brian Wylie, JSC, firstname.lastname@example.org
PRACE's Preparatory Access Calls are intended for testing and developing code in order to prepare applications for PRACE Tier-0 project access. These are rolling calls, so researchers can apply for access at any time - proposals are then reviewed every third month and the next cut-off date is the 2nd of September 2013, at 11:00 CEST.
In particular, note that Preparatory Access Type C includes code development with support from PRACE experts.
From the cut-off date for this 14th call (2 September 2013) onwards, the hybrid partition of MareNostrum is available for PA.
For further information and a list of the available systems, see the PRACE web page:
All researchers whose projects fit the criteria of the PRACE calls are cordially invited to take advantage of this opportunity and submit applications.
The criteria for the PRACE calls, as well as further details about the PRACE machines, application process and peer review process, can be found at:
If you need extra information please feel free to contact PRACE directly via
or feel free to contact the PRACE SNIC coordinator, Dr Michaela Barth, to get help you with your application.
The PRACE Regular Access Call 8 will open on 3 September 2013 at 12:00 (noon) CEST, Brussels time, and close on 15 October 2013 at 12:00 (noon) CET, Brussels time.
Please note that although the above information is what is currently on the PRACE website, the call probably ends at 12:00 CEST, not CET, so please put your applications in early.
Allocations awarded under this call will run from March 2014 to March 2015.
For more information about the call, see:
The "Introduction to High-Performance Computing" PDC Summer School started this week. On Monday there was a picnic at KTH and, on Tuesday, students visited the PDC Computer Hall. As well as seeing the supercomputer systems, students were also able to see the back-up batteries and fire protection system.
What do genomes, brains and earthquakes have in common?
They are just some of the many topics that will be addressed at the 2nd EUDAT Conference to be held in Rome from 28-30 October 2013.
EUDAT and EPOS are collaborating to provide safe back-up and service redundancy to the Italian seismological community (INGV). The challenge of daily copying and synchronizing the whole of the INGV community archive from its data centre in Rome to the EUDAT node in Bologna (CINECA) has been overcome through using the EUDAT Safe Replication service, which has been carefully tuned to the specific requirements of the community. The seismologists' data sets archived and registered in the EUDAT CDI will also form the base for the community services to be hosted by EUDAT.
This is just one of the data infrastructure and service success stories that you can learn about at the 2nd EUDAT Conference in Rome. There will be keynote presentations from Richard Frackowiak of the Human Brain flagship project, Ewan Birney on Annotating the Human Genome, and Maryline Lengert of the Helix-Nebula Science Cloud, with Bill Michener giving a view from across the Atlantic on DataONE. These presentations will be complimented by a series of parallel tracks and training sessions on the EUDAT services, along with associated workshops on topics that include humanities and social sciences, novel big data technologies and ultra-scalable data management technologies, as well as policies for the management of research data.
Check out the rich three day programme at
and register on-line.
Karolinska Institutet, Institutionen för kvinnors och barns hälsa
Karolinska Institutet, Women’s and Children’s Health.
Center of Neurodevelopmental Disorders at Karolinska Institutet (KIND - www.ki.se/kind).
KIND is a competence center for research, development and education within the area of developmental psychopathology. The center is established in collaboration between Karolinska Institutet and Stockholm County Council, and aims at improving clinical practice, generating basic research, and spreading new knowledge to stakeholders. The Roots of Autism Twin Study Sweden (RATSS) is a frontline research project within KIND, focusing on monozygotic twins being discordant for autism spectrum disorder and other neurodevelopmental disorders, e.g. ADHD. For the first time ever, twins are examined on multiple levels, among them functional and structural neuroimaging using MRI. Scanning is performed in the Karolinska Institutet MR Research Center, using a 3 Tesla MR scanner (GE MR750), and more than 45 pairs have now been examined.
As a post-doc, you will be mainly responsible for the acquisition and analyses of the multimodal neuroimaging data. This includes DTI, resting-state fMRI and structural T1, to be combined according to a brain connectome approach. This work will be done in close collaboration with the department of Clinical Neuroscience. The position also includes several other responsibilities, e.g. coordination of the neuroimaging works at KIND, involvement in international collaborations, administrative tasks, grant application and article writing.
A person is eligible for a postdoc position if he or she has obtained a PhD no more than seven years before the last date of employment as postdoc.
To qualify, the applicant must hold a doctor’s degree or a foreign qualification deemed equivalent to a doctorate. Applicants who have completed their degree no more than three years before the last date for applications should be given priority. Candidates who have completed their degree earlier than this should receive equal priority if special grounds exist.
The applicant should have a PhD (e.g. in psychology) and a profound experience in human cognitive neuroimaging. Education in mathematics and/or physics, interest in neuroscience and experience in multimodal imaging is preferred. The applicant should also be able to independently perform MR-scans (if not, Karolinska Institutet provides a MR driving license) and to analyze the data. Documented independent research and scientific drive is meriting. Good collaborative skills and handling of children/teenagers with neurodevelopmental disorders are also required.
An employment application must contain the following documents in English or Swedish:
- A complete curriculum vitae, including date of the thesis defence, title of the thesis, previous academic positions, academic title, current position, academic distinctions, and committee work
- A complete list of publications
- A summary of current work (no more than one page)
- Verifications for crediting of illness, military service, work for labour unions or student organisations, parental leave or similar circumstances
- Verification from the thesis defence committee or the equivalent (only if the thesis defence is scheduled within three months after the application deadline)
The application is to be submitted on the NetRecruiter system.
Registration for the 2nd EUDAT Conference, which will be held in Rome from 28-30 October 2013, is now open. We warmly invite data managers and researchers who are using EUDAT's common data infrastructure (or who are interested in using the CDI) to attend the conference – we welcome your valuable input and feedback in the discussion sessions and workshops. Other important topics, such as RDA developments and the implications of Horizon 2020 for e-infrastructures, will also be addressed in the broad range of seminars and presentations. For further information about the conference, see
and, to register now, go to