Skip to content

Reduce memory usage of the block tally step #137

@GertjanBisschop

Description

@GertjanBisschop

Concatenating all blocks into a huge array prior to counting can lead to excessive memory usage, see #132.
Potential solutions (not mutually exclusive):

  1. Specify correct dtype instead of always using 64-bit integers.
  2. Use for loops over windows while tallying. This would allow us to skip having to allocate memory for the concatenated array entirely. Numba could be used to speed up the for loop if speed becomes an issue because of it.

Metadata

Metadata

Assignees

No one assigned

    Labels

    No labels
    No labels

    Type

    No type

    Projects

    No projects

    Milestone

    No milestone

    Relationships

    None yet

    Development

    No branches or pull requests

    Issue actions