Skip to content
This repository was archived by the owner on Mar 20, 2023. It is now read-only.

Data structure development

Jump to bottom
Olli Lupton edited this page Apr 15, 2021 · 7 revisions

This page is intended to collect ideas and discussion points for the forthcoming development work on NEURON and CoreNEURON data structures, particularly in relation to host/device memory transfers and general memory management.

Goals

Improvements

The existing code managing data transfer to/from an accelerator/GPU is rather explicit and error prone, with a lot of hand-written code to ensure -- for example -- that structs containing pointers have those pointers updated to be valid on the device side too, and so on. Deallocation/cleanup is also managed by hand, and was only added rather recently in some cases. We would, therefore, like to improve in these areas as part of a re-write. For example:

  • Automatic lifetime management
  • Abstracting away the 2-part copy-data-and-then-manually-update-pointers-to-it pattern
  • ...

New features

Re-working this area of [Core]NEURON is also an opportunity to add support for new features and optimisations. Here is a list of possible improvements, please add to it as appropriate!

  • Support for placing data in different types of device/GPU memory (e.g. constants -- this can include mechanism properties and matrix elements)
  • Reducing device/GPU memory requirements by copying more selectively (there is data relating to artificial mechanisms that never needs to go onto the device/GPU)
  • Finer grained control over NUMA domains / locality (unclear how explicit this needs to be; it may be fine to just allocate from pinned threads)
  • Support for GPU programming models other than OpenACC (perhaps move to OpenMP if support is now better; would like Intel/AMD GPU support)
  • Support for multiple GPUs per process (this is probably not important to us)
  • Support for monitoring mechanism properties' evolution on GPU, probably by buffering per-time-step on the device and doing batched copies to the host CPU (this is getting into implementation detail, but good to be aware)
  • ...

Links

Useful resources

This GitHub repository

External

Clone this wiki locally