PhD candidate in High Performance Multiscale Computing, Faculty of Science – Informatics Institute

The Faculty of Science of the Universiteit van Amsterdam (UvA) is one of Europe’s foremost institutions of higher education and research in its chosen fields of specialization. It plays an active role in international science networks and collaborates with universities and industry. The Faculty has approximately 4,000 students and 1,500 staff members spread over four departments and ten research institutes. Each institute has its own research programme, a substantial part of which is externally funded by the Netherlands Organization for Scientific Research (NWO), the Dutch government, the EU and various private enterprises.

The  Informatics Institute is one of the large research institutes with the faculty, with a focus on complex information systems divided in two broad themes: ‘Computational Systems’ and ‘Intelligent Systems.‘ The institute has a prominent international standing and is active in a dynamic scientific area, with a strong innovative character and an extensive portfolio of externally funded projects.

Project description — Background

Multiscale phenomena are everywhere around us. If we study the origin and evolution of the universe or fracture of materials, if we try to understand health and disease or develop fusion as a potential energy source of the future, in all these cases we find that processes on quite disparate length and time scales interact in strong and non-linear ways. To progress from the current state of the art requires new developments in multiscale computing, as well as at least a factor 100 to 1000 increase in computing capabilities. Advanced multiscale algorithms in combination with petascale resources will help us transition to predictive multiscale science.

To make this possible, we have to develop generic multiscale computing algorithms capable of producing high-fidelity scientific results and scalable to petascale and emerging exascale computing systems. We call this High Performance Multiscale Computing (HPMC). One can identify generic multiscale computing patterns arising in multiscale applications that dictate the scope for novel multiscale algorithms at the petascale. We will investigate three such multiscale computing patterns, and their generic mapping to High Performance Computing on petascale and emerging exascale computing infrastructures. In previous projects we developed the Multiscale Modelling and Simulation Framework, which entails a theoretical approach toward multiscale modelling, a simulation framework to develop and run multiscale simulations and a set of tools and middleware to execute and manage multiscale computations on a broad array of computing infrastructure, from the desktop, via clusters and the cloud, to HPC environments.

In close collaboration with a postdoctoral researcher, and embedded in a broader collaboration with a large number of European labs, you will develop multiscale computing patterns for High Performance Multiscale Computing. This will require specifications in the Multiscale Modelling Language (and maybe extensions to this language), implementations in MUSCLE2 (and most probably extensions of this multiscale computing library with HPC capabilities leading to MUSCLE3), development of advanced algorithms for large, dynamic and failure-resistant simulations with automatic load balancing, and finally measuring and predicting the performance of multiscale applications using multiscale computing patterns on HPC systems.

Your research will be driven by a set of different applications from science & engineering. The most relevant for your research will be cell-based models of blood flow, with applications in thrombosis modelling. The challenge will be to simulate billions of red blood cells and platelets, and glue this to continuum descriptions of blood flow. A PostDoc in Amsterdam will develop this application in the context of your multiscale computing patterns, allowing you to test your algorithms on real multiscale applications. You will develop comparable collaborations with other labs in Europe, thus building a larger portfolio of applications of your multiscale computing patterns.


The candidates should have a Masters degree in Computational Science, High Performance Computing, Computer Science, or related disciplines. The applicants should have experience in high performance computing, with good knowledge of MPI and insight in architectures of modern massively parallel computers. Experience with multiscale modelling and simulation is not immediately needed, but a strong interest is clearly required and candidates with experience in this field will be preferred. The same applies to experience with High Performance Computing or distributed computing. The PhD candidate should also form a bridge between the HPC community and the multiscale applications community, and should therefore be capable to ‘speak both languages’. Candidates should be able to work in an international multidisciplinary team.

Further information


The appointment will be full-time (38 hours a week) for a period of four years (initial employment is 18 months and after a positive evaluation, the appointment will be extended further with 30 months) and should lead to a dissertation (PhD thesis). An educational plan that includes attendance of courses and national and international meetings will be drafted. The PhD candidate is also expected to assist in teaching of undergraduates. The salary is in accordance with the university regulations for academic personnel. The salary will range from €2,125 (first year) up to a maximum of €2,717 (last year) before tax per month (scale P) based on a full-time appointment. There are also secondary benefits, such as 8% holiday allowance per year and the end of year allowance of 8.3%. The Collective Labour Agreement for Dutch Universities is applicable.

English is the working language within the Informatics Institute. Moreover, since Amsterdam is a very international city where almost everybody speaks and understands English, candidates need not be afraid of the language barrier.

Some of the things we have to offer:

  • very friendly, interactive and international working environment;
  • new building located near the city center (20 minutes by bicycle) of one of Europe’s most beautiful and lively cities;
  • access to high-end computing facilities (e.g., cluster with 4,000+ cores).

Job application

Applications should include the following information, in separate PDF files (not zipped), using surname, initials and a self-evident word as file names, e.g. , Smith J CV:

  • a curriculum vitae (including an url allowing download of pdf of M.Sc. thesis — if relevant);
  • a letter of motivation (at most 1 page) explaining why you are interested in this position;
  • a research statement (at most 2 pages), explaining your research interests and how you think they can be related to the topics mentioned in the Job description above;
  • a list of all university courses taken, including a transcript of grades;
  • the name and contact details (including email address) of two – three referees who can provide details about your profile (one of whom should be the main supervisor of your Master thesis).

Completed applications should only  be submitted via and should state your name, vacancy number 15-234 and the position you are applying for in the subject field. The committee does not guarantee that late or incomplete applications will be considered.

Applications will be accepted until 31 July 2015.

Publication date

18 June 2015
Level of education
Salary indication
€2,125 to €2,717 gross per month
Closing date
31 July 2015
38 hours per week
Vacancy number

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