SciML / SciML/JumpProcesses.jl
handling extinction for SSAs that use a running and updating sum_rate
Nobody has claimed this yet.
- Dominant language
- Julia
- Stars
- 150
- Forks
- 41
- Avg merge
- 1d 9h
- Merged PRs (30d)
- 28
Description
RSSA, RSSACR, DirectCR and SortingDirect all encounter the problem of the rates actually being zero but the current sum of the rates being a bit bigger than zero due to floating point errors in the running sum. This led to crashes for the first three when trying to sample the next reaction in a spatial A+B -> 0 system (SortingDirect ends up just sampling the last reaction, but this shouldn't matter since no further reaction should occur).
I'll put in a PR with a fix, but this is worth investigating more to make sure the fix doesn't hurt performance, and isn't missing any further cases.
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Locate the RSSA, RSSACR, DirectCR, and SortingDirect implementations and reproduce the spatial A+B -> 0 case described in the issue. Check how each handles a running sum that remains slightly positive when all rates are zero; done means no crash, no further reaction, and no unjustified performance regression.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- julia
- Domain
- backend
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100