New Software Release: Arbor Library v0.2

Nora Abi Akar; John Biddiscombe; Benjamin Cumming; Felix Huber; Marko Kabic; Vasileios Karakasis; Wouter Klijn; Anne Küsters; Alexander Peyser; Stuart Yates. Doi: 10.5281/zenodo.1459678

Arbor is a library for implementing performance portable network simulations of multi-compartment neuron models.

An installation guide and library documentation are available online at Read the Docs.

Some key features include:

• Optimized back ends for CUDA, KNL, AVX2, ARM NEON intrinsics.
• Asynchronous spike exchange that overlaps compute and communication.
• Efficient sampling of voltage and current on all back ends.
• Efficient implementation of all features on GPU.
• Reporting of memory and energy consumption (when available on platform).
• An API for addition of new cell types, e.g. LIF and Poisson spike generators.

Change Log

Changes since v0.1:

• A new Hines matrix solver back end for the GPU that parallelises over cell branches, not cells, to increase the amount of parallelism. See #631.
• Support for describing and simulating electrical gap junctions. See #661 #686.
• An additional library libarborenv is now installed with useful helper functionality for managing the environment (e.g. detecting the number of available CPU cores). See #679.
• Detection and allocation of GPUs to MPI ranks on systems with more than one GPU per node in libarborenv. See #659 and #654.
• The miniapp example was removed and replaced with a simple single cell model that shows how to use morphologies. See #703 and #710.
• Support for ARM NEON intrinsics. See #698.
• Basic Python support. Full Python support is slated for v0.3. See #668.

Contributors

Nora Abi Akar John Biddiscombe Benjamin Cumming Felix Huber Marko Kabic Vasileios Karakasis Wouter Klijn Anne Küsters Alexander Peyser Stuart Yates

10.5281/zenodo.1459678