Computational Systems Biology Researcher R2-3 – Codesign activities LS & CS

Context And Mission

The Laboratory of Open Computer Architecture (LOCA) at Barcelona Supercomputing Center aims to break through traditional disciplinary silos and lead the research and development of European open software and hardware stacks based on the RISC-V Instruction Set Architecture for Exascale and beyond. This will be done with BSC's scientific departments to produce highly optimized grand challenge scientific applications in climate modelling, personalized medicine and energy. LOCA spans topics ranging from Computer Architecture to System Software to Applications, in both traditional HPC and emerging High-Performance Data Analytics (HPDA) and is working towards EU autonomy in HPC technologies. BSC is looking for one domain expert for each of the centre's application departments (Earth Science, Life and Engineering Sciences) to contribute to this aim.

In the Life Sciences area, we are looking for a Researcher to work in the computational systems biology approaches to simulate biological networks at different time-scales (Ponce-de-Leon et al., 2023). In particular, we are interested in the development of efficient multi-scale simulators that could leverage all the potential of parallel and distributed environments at the BSC and at other HPC centres in Europe. These agent-based tools will enable the simulation of real-sized organs with complex, heterogeneous microenvironmental architectures and will bridge from intracellular pathways to the organ-level.

The Researcher will work providing efficient HPC solutions to scale-up multi-scale simulation tools aimed at providing digital twins of patients. The specific tasks involve the development and implementation of parallel and distributed programming tools that leverage different heterogeneous HPC centres, as well as the co-design of these simulation tools to BSC's RISC-V and other diverse architectures and accelerators.

The candidate will be working in close collaboration with all the different groups and departments to co-design these novels tools to new computer architectures (Kreuzer et al., 2021) in the context of the BSC's Severo Ochoa award for the 2023-26 period, which aims to boost BSC capacities to codesign hardware and software, maximise internal and external synergies, expand international leadership, provide best-practice career development with strong gender actions, and enhance societal engagement and technology transfer (
/bsc.es/discover-bsc/research-excellence/severo-ochoa).

Key Duties

Design and implement efficient HPC solutions to simulate multi-scale biological processes using hundreds of thousands of CPUs in BSC clusters.
Optimize code for HPC platforms and maintain software performance.
Co-design multi-scale simulation tools to BSC's RISC-V and other heterogeneous architectures.
Co-design multi-scale simulation tools to different accelerators such as GPUs, vectorisation and stencil.
Design, implement and deploy a set of unit tests to study the scalability and efficiency of the optimised and co-designed code.
Design and implement a CI/CD suite to test and deploy the code in several EuroHPC centres.
Provide technical expertise in the areas of parallel computing, distributed computing, and software performance.
Help to characterize the core applications for the department by using the resources available at BSC and contribute to the definition of Key Performance Indicators (KPI) for improving their performance.
Work to optimize domain applications for BSC-designed RISC-V HPC processors in collaboration with the multi-disciplinary team and contribute to enhancing the full HPC stack.

Requirements
• Education
PhD in Computer Science or similar topic, with strong background on parallel and distributed computing.
• Essential Knowledge and Professional Experience
Proved experience on computer science.
Strong background on scientific computing, scaling up of tools and performance analysis in HPC.
Very strong programming skills, in particular on C+ and Python language.
Administration level in Linux/Unix systems.
• Additional Knowledge and Professional Experience
Interest in computational biology and the simulation of biological processes.
Experience in the preparation and presentation of scientific projects.
Experience in reporting progress.
Experience in mentoring/advising PhD students.
Good communication skills (verbal and written) in English.
• Competences
Ability to effectively communicate technical concepts to non-experts.
Proactive and able to take the initiative when needed.
Creative thinking.
Operate independently but love being part of a collaborative team.

Conditions
• The position will be located at BSC within the Life Sciences Department
We offer a full-time contract (37.5h/week), a good working environment, a highly stimulating environment with state-of-the-art infrastructure, flexible working hours, extensive training plan, restaurant tickets, private health insurance, support to the relocation procedures
Duration:
Open-ended contract due to technical and scientific activities linked to the project and budget duration
Holidays:
23 paid vacation days plus 24th and 31st of December per our collective agreement
Salary:
we offer a competitive salary commensurate with the qualifications and experience of the candidate and according to the cost of living in Barcelona
Starting date:
asap
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