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

10 Apr 2024
Job Information

Organisation/Company

BARCELONA SUPERCOMPUTING CENTER

Research Field

Computer science

Researcher Profile

Recognised Researcher (R2)
Established Researcher (R3)

Country

Spain

Application Deadline

16 Apr 2024 - 23:59 (Europe/Madrid)

Type of Contract

Permanent

Job Status

Full-time

Hours Per Week

37,5

Offer Starting Date

10 Apr 2024

Is the job funded through the EU Research Framework Programme?

Not funded by an EU programme

Reference Number

211_24_LS_CB_R2

Is the Job related to staff position within a Research Infrastructure?

No

Offer Description
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 (https://www.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

Research Field

Computer science

Education Level

PhD or equivalent

Skills/Qualifications

 

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.

Languages

ENGLISH

Level

Good

Additional Information
Benefits
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

Website for additional job details

https://www.bsc.es/join-us/job-opportunities/21124lscbr2

Work Location(s)

Number of offers available

1

Company/Institute

Barcelona Supercomputing Center

Country

Spain

Geofield

Where to apply

Website

https://www.bsc.es/join-us/job-opportunities/21124lscbr2

Contact

City

Barcelona

Website

http://www.bsc.es/

Street

c/ Jordi Girona nº31

Postal Code

08034

STATUS: EXPIRED