Uppsala Multidisciplinary Center for Advanced Computational Science


High-performance computing resources for analyzing sensitive data in Sweden

SNIC-SENS is a SNIC project with the goals:

  • To set up and maintain an eInfrastructure for handling sensitive personal data at the National Genomics Infrastructure, NGI. Resources for this includes:
    • NGI production cluster - Irma
    • NGI production cluster storage - Lupus
    • NGI data delivery - Grus
  • To establish and maintain high-performance and data-intensive computational resources within SNIC for researchers that analyze sensitive personal data from large-scale molecular experiments. Resources for this includes:
    • Research cluster - Bianca
    • Research cluster storage - Castor

Project partners are SNIC, UPPMAX, PDC, NGI, and Science for Life Laboratory.

The project is funded by the Swedish Research Council, the Knut and Alice Wallenberg Foundation, Science for Life Laboratory, and Uppsala University.

Project owner: Ann-Charlotte Sonnhammer, SNIC

Team leader: Peter Ankerstål, UPPMAX

Progress report for the Bianca project 2017-01-18

Part 2 of the project is finished. We are setting up project clusters. each one meant to be similar in behaviour to Milou, but with only one research project on each cluster.

We have accomplished:

  • /home, /proj, and /proj/nobackup directories are working
  • Two factor ssh logins to project clusters are working
  •  A "wharf" for copying files between /proj/nobackup and Internet, with two factor authentication
  • Internet access is otherwise closed. Access between project clusters is not possible.
  • The module system is in place, together with a /sw file system and /sw/data
  • Slurm is working, with seven GB RAM available for each compute core, with up to 16 cores per compute node
  • A /scratch file system is set up on the compute nodes
  • Five pilot projects are already allowed access to project clusters. Two of these projects have already successfully run a substantial amount of Slurm jobs.
  • A logging system
  • Encrypted backups
  • An internal, secure e-mail system for feedback messages to users from Slurm (but with no user access to e-mail communications)

The 25th of January, we plan to allow a sixth pilot project to join.

Some of the current activities :

  • Increase the speed of the underlying OpenStack cloud system by installing SSD disks on some machines
  • Rebuild and upgrade the underlying OpenStack cloud system, for a tighter integration with other parts of Bianca's automation
  • Increase automation (this is the major work item)
  • Rebuild some subsystems, so they will scale up to 500 concurrent project clusters

The ultimate goal (part 3) is to put Bianca in normal production.