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memory allocations in tridiagonal LU factorization #648

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simonbyrne opened this issue Jul 14, 2022 · 3 comments · Fixed by #715
Closed

memory allocations in tridiagonal LU factorization #648

simonbyrne opened this issue Jul 14, 2022 · 3 comments · Fixed by #715
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@simonbyrne
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The call to lu! in the linear solve causes significant memory allocations. My guess is that it is caused by the allocation of the pivot array:
https://github.com/JuliaLang/julia/blob/v1.7.3/stdlib/LinearAlgebra/src/lu.jl#L500

Options:

  • write our own direct tridiagonal solver. @OsKnoth might have some code?
  • use BandedMatrices.jl, which wraps the general LAPACK banded solvers
@simonbyrne
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The best option is probably to implement the Thomas algorithm

@charleskawczynski
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Is there an issue open in Julia about the allocations? (not that we'll be able to leverage it yet)

@simonbyrne
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no idea: feel free to open one

@charleskawczynski charleskawczynski mentioned this issue Jul 19, 2022
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@simonbyrne simonbyrne mentioned this issue Jul 21, 2022
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@sriharshakandala sriharshakandala mentioned this issue Jul 28, 2022
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bors bot added a commit that referenced this issue Jul 28, 2022
@bors @sriharshakandala
Merge #715
0a3db74 
715: Adds Thomas algorithm for solving a tri-diagonal system of linear equations. r=sriharshakandala a=sriharshakandala



# PULL REQUEST

## Purpose and Content
Adds Thomas algorithm for solving a tri-diagonal system of linear equations. This replaces the pre-existing `lu!` solver in `linsolve`.

## Benefits and Risks
The Thomas algorithm computes the solution in-place and eliminates memory allocations noticed in the pre-existing `lu!` solver.

## Linked Issues
(Provide references to any link issues. Use closes #issuenum to automatically close an open issue)
- Fixes #648 
- Closes #648 

## PR Checklist
- [x] This PR has a corresponding issue OR is linked to an SDI.
- [x] I have followed CliMA's codebase [contribution](https://clima.github.io/ClimateMachine.jl/latest/Contributing/) and [style](https://clima.github.io/ClimateMachine.jl/latest/DevDocs/CodeStyle/) guidelines OR N/A.
- [x] I have followed CliMA's [documentation policy](https://github.com/CliMA/policies/wiki/Documentation-Policy).
- [x] I have checked all issues and PRs and I certify that this PR does not duplicate an open PR.
- [x] I linted my code on my local machine prior to submission OR N/A.
- [x] Unit tests are included OR N/A.
- [x] Code used in an integration test OR N/A.
- [x] All tests ran successfully on my local machine OR N/A.
- [x] All classes, modules, and function contain docstrings OR N/A.
- [x] Documentation has been added/updated OR N/A.


Co-authored-by: sriharshakandala <[email protected]>
@bors bors bot closed this as completed in 99a8f88 Jul 29, 2022
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Adds Thomas algorithm for solving a tri-diagonal system of linear equations. CliMA/ClimaAtmos.jl
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@simonbyrne @charleskawczynski