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.
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).
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.
- Invited talk on elPrep at the (IB)² Seminar on March 20, 2015
- New results and software on HPC sparse computation published
- Videos from the “High Performance Computing (HPC) for Life Sciences” event now available
- Jörg Kurt Wegner (Johnson & Johnson) giving closing keynote at EuroQSAR 2014
- Tutorial on GASPI, the PGAS API