Scalable Software Services for Life Science

Member Partners & Work Packages

Scalalife has the following member sites:

Work Packages:

WP1: Management

  • Overall project management and reporting to the EU
  • Daily management of the project activities, resource allocation and monitoring, quality assurance
  • Conflict resolutions and corrective actions.

WP2: Dissemination and Trainings

This work package aims to engage actively with computational life scientists both in academic and related research as well as in industry with the aim to:

  • disseminate widely the results of this project
  • carry out training aimed at life scientists and Life Science (LS) software developers in: HPC and related technologies; in the software, tools and infrastructures developed by this project
  • ensure that this project has maximum impact in future activities and developments in the LS.

WP3: Software Integration & Maintenance

This workpackage will set up an infrastructure for porting and maintenance of a subset of these codes – in particular GROMACS and DALTON, but also DISCRETE which we are designing to use the research advances of the prior workpackages – on the large next-generation supercomputers planned in Europe, it will integrate reference implementations of new scaling techniques developed by WP6, and adapt software to new communication network topologies and new architectures. It will also coordinate the new data exchange standards developed in WP7 with the major software codes, and provide the program binaries used for the subsequent test case phase.

WP4: Application Validation

The objective of WP4 is to verify and validate the enhanced applications and assess their performance on various resources. This service enables developers and users to rely on a common set of data, software and hardware, which has been thoroughly tested and can be used as a "gold-standard". After validating the modified applications from WP3 against selected test examples a set of important and current test problems will be chosen in collaboration with a group of selected test users which serves as an alpha user community which will eventually be the seed for the user community of the competence centre in WP5.
Specifically, we will

  • Maintain and port the application examples and their validation
  • Perform performance assessment
  • Provide information on porting problems and a summary of performance results for each platform.
  • Establish an alpha-user community

WP5: Life Science Software Competence Center

The goal of WP5 is to establish a distributed Life Science Software Competence Centre to support European Life Science and provide support to the other work packages in the project by providing access to required tools and e-Infrastructures. It will collect the knowledge generated by the project and make it available to interested parties as best practices and also offer expert advise.

WP6: Scalable Techniques for Life Science Software

The aim of this workpackage is to connect the very latest research on scalability and hardware design with application software work, and to properly document algorithms and optimization techniques so they can also be applied to other life science applications. In particular, the workpackage will address

  • Analysis and performance profiling of current life science codes, in particular starting with the GROMACS, Dalton, and DISCRETE software packages included in the application.
  • Multi-level parallelization using different simultaneous approaches for scaling over multiple cores in chips, several sockets in a node, and large numbers of nodes connected with fast networks.
  • Ensemble computing techniques, to break the “impossible” performance barrier on machines where there will be significantly more cores (millions) than particles in the system simulated
  • Stream computing implementations of life science applications for data parallel architectures, e.g. GPUs

WP7: Interface Definitions & Data Exchange

The aim of this workpackage is to develop and push standards for handling both storage and exchange of the ever-increasing amount of simulation data in life science. This will include XML representations of input/output files formats for simulation data, standardized compressed file formats for simulation data, and high-level APIs. The developments will be promoted widely in related computational biology and computing initiatives (such as ELIXIR, PRACE, and EGI).