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HPC System Engineer (f/m)

Job Code




The Berlin Institute of Health (BIH) is a joint venture of the Charite University Medicine and the Max Delbrueck Center for Molecular Medicine (MDC) for interdisciplinary translational system medicine.

The BIH HPC IT team is looking for a highly-motivated and detail-oriented individual to join us. As HPC System Engineer you will be responsible for the BIH high-performance compute cluster, connected servers and networking. In this position, you will drive the course of change and improvement while retaining stability of our systems and support bioinformatics and data science researchers.

Working in the BIH gives you the opportunity to support world-class scientific facilities in their interesting projects with the aim of translational biomedical research and bringing research results closer to the patient for diagnostics or treatment.

  • Administration, monitoring, tuning and extension of the Linux-based HPC cluster (6000+ cores plus GPUs, 2PB GPFS), and connected systems, such as job queue (Grid Engine), storage (DDN)
  • Perform root-cause analysis and fixing of errors and performance problems
  • Plan and deploy patches, upgrades and configuration changes
  • Monitor and adjust the queuing system
  • Realize seamless data flow from sequencing and mass spectometry devices with scripting and monitoring
  • Support virtualization and containerization of servers and workflows; work with MDC IT on topics such as networking, data backup and archiving
  • Contribute to user support and user documentation
  • Contribute to evaluation of new technologies and planning and realization clusters extensions


  • At least three years experience as a professional HPC System Engineer is required with excellent demonstrable skill set
  • Proven ability to create versioned, well-structured configuration and deployment systems
  • Ability to write technical and user-targeted documentation required
  • Experience with CentOS, OpenLDAP, Ansible, Git, SGE, Ganglia, CheckMK, GPFS, ZFS, KVM are a plus but not required if you are willing to quickly learn these skills
  • Team-oriented with good communication skills in German and English
  • Willingness to keep on learning

The MDC is an equal opportunity employer and supports gender equality.

Please send your application by 31.01.2019 indicating the registration number 11015/2018 preferably as one PDF file to


Salaries are set according to TVöD up to level 12 (payment range 43 to 68 thousand euro), according to qualification and experience. Appointments are made for an initial period of 2 years with option for becoming permanent.

Start date

the soon as possible

Application Period


Apply now


Dr. Dieter Beule