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    Opportunity: High Performance Computing Architect & Systems Administrator (#1308-IT) @ H3 Biomedicine -- Cambridge, MA (US)
    Submitted by JT Rynak; posted on Tuesday, April 09, 2013


    High Performance Computing Architect and Systems Administrator will work with our IT group to support the bioinformatics needs of H3 Biomedicine. This position will have a broad range of responsibilities including: innovation of the overall HPC architecture, working within and improving large HPC systems; interaction with bioinformaticians in consulting and integrating their applications/algorithms into the HPC environment. Scientific areas include genetic analysis, next-gen sequencing; and troubleshooting and tuning informatics pipelines for their efficient use within the HPC systems. Typical applications include large-scale genetic/genomic sequencing analysis (Cancer Genomes), image analysis and visualization using various in-house developed or commercial parallel computing applications.

    The characteristics of the position are an eagerness to quickly learn, apply and integrate innovative technologies and techniques of High-Performance and Parallel Computing with Bioinformatics to support H3 Biomedicine in its mission. Versatility and breadth in computationally intense scientific and informatics skills, ability to work independently, outstanding customer service and training skills, and the ability to help teams and projects successfully accomplish their research objectives will be the successful qualities in this role.


    • Participate in and support capacity planning and the development of long-term strategic goals for HPC systems and software in conjunction with end-users and department managers.
    • Ability to work independently and demonstrate excellent project management and communication skills with strong commitment to customer service.
    • Work directly with developers and bioinformaticians as a member of their team in designing, prototyping/testing, tuning for parallelization, problem analysis, and documenting HPC pipelines.
    • Develop relationship with and work closely with developers and bioinformaticians for enabling the HPC-informatics ecosystem, including applications, algorithms and tools.
    • Work within the IT team to support colleagues in all aspects of HPC computing hardware, techniques and software for biomedical research.
    • Linux, UNIX administration and Windows administration or other responsibilities as appropriate.
    • Design, build and maintain unix, linux infrastructure supporting scientific data system and computation environment.
    • Architect and implement software development environment.
    • System engineering for complex parallel systems and software.
    • Assist users to install, configure and/or script informatics tools and applications, understanding and guiding work and data flows for their analysis.
    • Perform standard configuration, management, and maintenance tasks for related file systems, input/output systems, networking, clustering, storage, and applications.
    • Learn new programming languages, libraries, techniques, API documentation as needed.
    • Perform and test system configuration backups and restores to ensure system recovery from error or outage.
    • Understand the research process and be comfortable working in a dynamic environment, with flexibility to meet evolving requirements with minimal supervision.
    • Review and deploy HPC system releases and vendor-supplied patches according to best practices.
    • Anticipate, mitigate, identify, troubleshoot, and resolve hardware and software problems on all HPC systems.
    • Monitor, test, and tune system performance; preserve and provide system log files as needed.
    • Recommend and execute modifications to HPC systems in order to improve efficiency, reliability, and performance.
    • Conduct research on HPC-related hardware and software in support of procurement and system development efforts.
    • Remain informed on laws, trends, and issues, including current and emerging technologies and best practices.
    • Ensure HPC-based systems comply with policies, standards, licensing agreements, configuration guidelines, and best-practices for maintaining regulatory compliance.
    • Ensure secure user access and role validation processes.
    • Create required reports in response to business user needs.
    • Develop, document, and maintain HPC system documentation for educating end users and IT staff.


    • BS/MS in of Computer Science, Computational Science, or Bioinformatics required.
    • Expert knowledge of linux/unix systems, Windows (HPC) Server also desirable.
    • 5+ years of experience building and maintaining linux/unix systems.
    • 3+ years of demonstrated experience building and maintaining computational clusters, HPC and/or grid computing environments.
    • 3+ years' experience supporting informatics systems in biological, medical, or basic science research environments strongly preferred.
    • Experience of development and management of informatics applications and web services including database development on unix/linux systems preferred.
    • Demonstrated knowledge and experience with cloud technologies and platforms such as Amazon Web Services and S3.
    • Familiarity with Oracle Database Administration and appliances is a plus.


    H3 Biomedicine Inc. is a privately-held, uniquely-structured oncology discovery enterprise whose sole mission is to become a prolific source of new drugs that treat more human cancers with greater success. H3 Biomedicine is applying the expertise of leading scientists to the integration of insights from cancer genomics with innovative capabilities in synthetic chemistry and tumor biology to pursue the most promising current opportunity in cancer therapeutics: patient-based, genomics-driven, small molecule drugs.


    Cambridge, MA


    Interested candidates may forward a CV to h3_career[at]

    Job Code 1308-IT

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