Software

We make part of the software developed in the course of our research available to selected partners or the general public.

Disclaimer: Please note that any software written by the lab is intended as a proof-of-concept only, and thus carries no guarantees that it will work or that it will not damage your systems.

Projects

Publically available software from the lab includes:

  • Arrow-Street: a C++ library to aid vectorisation (via ExaScience github/arrow-street).
  • BWA-Cilk: a fork of BWA ALN that improves thread level scalability (via ExaScience github/bwa).
  • elPrep: a high-performance tool for preparing .sam/.bam files for variant calling in sequencing pipelines, drop-in replacement for SAMtools/Picard (via ExaScience github/elPrep and ExaScience github/demo
    • Demo file 1:  NA12878-chr22-10pct.bam (121 MB)
    • Demo file 2:  NA12878-chr22.bam (1.2 GB)
  • Halvade: a mapreduce implementation of the ‘best practices’ variant detection pipeline by Broad institute (available through its own github page).
  • High-performance BSP: a collection of BSP algorithms written using MulticoreBSP for C. Implements usable, high-performant, and highly scalable variants of real-world kernels. (via this page).
  • MulticoreBSP: a programming interface for C, C++, and Java that enables direct programming of parallel algorithms designed according to the Bulk Synchronous Parallel (BSP) model (via www.multicorebsp.com).
  • Pipelined Krylov Solvers (the KSPPIPECG, KSPPGMRES, and KPSPIPECR available through the PETSc library).
  • Shark: a C++11 library to simplify programming with large distributed grid data-types on clusters (via ExaScience github/shark).
  • Sniper: a fast architectural simulator (homepage).
  • The Sparse Library: various high-performance implementations of the sparse matrix—vector multiplication. Includes two of the fastest state-of-the-art methods (via this page).

Github

The lab’s public github page can be found here.

For access to non-public repositories for lab partners or other interested parties, please contact us directly to arrange this and get access details.

 

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