https://github.com/juliasmoothoptimizers/suitesparsematrixcollection.jl
A straightforward interface to the SuiteSparse Matrix Collection
https://github.com/juliasmoothoptimizers/suitesparsematrixcollection.jl
Last synced: about 1 year ago
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A straightforward interface to the SuiteSparse Matrix Collection
- Host: GitHub
- URL: https://github.com/juliasmoothoptimizers/suitesparsematrixcollection.jl
- Owner: JuliaSmoothOptimizers
- License: other
- Created: 2019-02-18T23:46:02.000Z (over 7 years ago)
- Default Branch: main
- Last Pushed: 2025-03-01T23:08:39.000Z (over 1 year ago)
- Last Synced: 2025-06-06T18:12:29.078Z (about 1 year ago)
- Language: Julia
- Size: 1.79 MB
- Stars: 10
- Watchers: 3
- Forks: 4
- Open Issues: 1
-
Metadata Files:
- Readme: README.md
- License: LICENSE.md
- Citation: CITATION.bib
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README
# SuiteSparseMatrixCollection.jl
| **Documentation** | **Linux/macOS/Windows/FreeBSD** | **Coverage** | **DOI** |
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[docs-stable-img]: https://img.shields.io/badge/docs-stable-blue.svg
[docs-stable-url]: https://JuliaSmoothOptimizers.github.io/SuiteSparseMatrixCollection.jl/stable
[docs-dev-img]: https://img.shields.io/badge/docs-dev-purple.svg
[docs-dev-url]: https://JuliaSmoothOptimizers.github.io/SuiteSparseMatrixCollection.jl/dev
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[build-gh-url]: https://github.com/JuliaSmoothOptimizers/SuiteSparseMatrixCollection.jl/actions
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[build-cirrus-url]: https://cirrus-ci.com/github/JuliaSmoothOptimizers/SuiteSparseMatrixCollection.jl
[codecov-img]: https://codecov.io/gh/JuliaSmoothOptimizers/SuiteSparseMatrixCollection.jl/branch/main/graph/badge.svg
[codecov-url]: https://app.codecov.io/gh/JuliaSmoothOptimizers/SuiteSparseMatrixCollection.jl
[doi-img]: https://img.shields.io/badge/DOI-10.5281%2Fzenodo.4324340-blue.svg
[doi-url]: https://doi.org/10.5281/zenodo.4324340
A straightforward interface to the [SuiteSparse Matrix Collection](https://sparse.tamu.edu/).
## References
> Davis, Timothy A. and Hu, Yifan (2011).
> The University of Florida sparse matrix collection.
> ACM Transactions on Mathematical Software, 38(1), 1--25.
> [10.1145/2049662.2049663](https://doi.org/10.1145/2049662.2049663)
## How to Cite
If you use SuiteSparseMatrixCollection.jl in your work, please cite using the format given in [CITATION.bib](https://github.com/JuliaSmoothOptimizers/SuiteSparseMatrixCollection.jl/blob/main/CITATION.bib).
## How to install
```julia
pkg> add SuiteSparseMatrixCollection
pkg> test SuiteSparseMatrixCollection
```
## Updating the database
Clone this repository, activate the `utils` environment and run `gen_db.jl` to check if the database needs to be updated.
## Updating `Artifacts.toml`
Clone this repository, activate the `utils` environment and run `gen_artifacts.jl` to check if `Artifacts.toml` needs to be updated.
## Examples
```julia
julia> using SuiteSparseMatrixCollection
julia> # name-based selection can be done with `ssmc_matrices()`
julia> ssmc = ssmc_db()
julia> ssmc_matrices(ssmc, "HB", "bcsstk") # all matrices whose group contains "HB" and name contains "bcsstk"
julia> ssmc_matrices(ssmc, "", "bcsstk") # all matrices whose name contains "bcsstk"
julia> ssmc_matrices(ssmc, "HB", "") # all matrices whose group contains "HB"
julia> # select symmetric positive definite matrices with ≤ 100 rows and columns
julia> tiny = ssmc[(ssmc.numerical_symmetry .== 1) .& (ssmc.positive_definite.== true) .&
(ssmc.real .== true) .& (ssmc.nrows .≤ 100), :]
julia> # fetch the matrices selects in MatrixMarket format
julia> paths = fetch_ssmc(tiny, format="MM") # matrices are downloaded in paths
julia> downloaded_matrices = installed_ssmc() # name of all downloaded matrices
julia> delete_ssmc("HB", "bcsstk02") # delete the matrix "bcsstk02" of group "HB"
julia> delete_all_ssmc() # delete all matrices from the SuiteSparseMatrixCollection
```
Matrices are available in formats:
* `"RB"`: the [Rutherford-Boeing format](https://www.cise.ufl.edu/research/sparse/matrices/DOC/rb.pdf);
* `"MM"`: the [MatrixMarket format](http://math.nist.gov/MatrixMarket/formats.html#MMformat).
Use `DataFrames` syntax to further examine a list of selected matrices:
```julia
julia> tiny[!, [:name, :nrows, :ncols, :positive_definite, :lower_bandwidth]]
12×5 DataFrame
│ Row │ name │ nrows │ ncols │ positive_definite │ lower_bandwidth │
│ │ String │ Int64 │ Int64 │ Bool │ Int64 │
├─────┼───────────────┼───────┼───────┼───────────────────┼─────────────────┤
│ 1 │ bcsstk01 │ 48 │ 48 │ 1 │ 35 │
│ 2 │ bcsstk02 │ 66 │ 66 │ 1 │ 65 │
│ 3 │ bcsstm02 │ 66 │ 66 │ 1 │ 0 │
│ 4 │ nos4 │ 100 │ 100 │ 1 │ 13 │
│ 5 │ ex5 │ 27 │ 27 │ 1 │ 20 │
│ 6 │ mesh1e1 │ 48 │ 48 │ 1 │ 47 │
│ 7 │ mesh1em1 │ 48 │ 48 │ 1 │ 47 │
│ 8 │ mesh1em6 │ 48 │ 48 │ 1 │ 47 │
│ 9 │ LF10 │ 18 │ 18 │ 1 │ 3 │
│ 10 │ LFAT5 │ 14 │ 14 │ 1 │ 5 │
│ 11 │ Trefethen_20b │ 19 │ 19 │ 1 │ 16 │
│ 12 │ Trefethen_20 │ 20 │ 20 │ 1 │ 16 │
```
Matrices in Rutherford-Boeing format can be opened with [`HarwellRutherfordBoeing.jl`](https://github.com/JuliaSparse/HarwellRutherfordBoeing.jl):
```julia
pkg> add HarwellRutherfordBoeing
julia> using HarwellRutherfordBoeing
julia> matrix = ssmc[ssmc.name .== "bcsstk01", :]
1×30 DataFrame. Omitted printing of 17 columns
│ Row │ group │ nnzdiag │ nrows │ numerical_symmetry │ amd_vnz │ binary │ structural_rank │ is_nd │ is_graph │ RB_type │ lower_bandwidth │ explicit_zeros │ amd_flops │
│ │ String │ Int64 │ Int64 │ Float64 │ Int64 │ Bool │ Int64 │ Bool │ Bool │ String │ Int64 │ Int64 │ Float64 │
├─────┼────────┼─────────┼───────┼────────────────────┼─────────┼────────┼─────────────────┼───────┼──────────┼─────────┼─────────────────┼────────────────┼───────────┤
│ 1 │ HB │ 48 │ 48 │ 1.0 │ 651 │ 0 │ 48 │ 1 │ 0 │ rsa │ 35 │ 0 │ 6009.0 │
julia> path = fetch_ssmc(matrix, format="RB")
1-element Array{String,1}:
"/Users/dpo/dev/JSO/SuiteSparseMatrixCollection.jl/src/../data/RB/HB/bcsstk01"
julia> A = RutherfordBoeingData(joinpath(path[1], "$(matrix.name[1]).rb"))
Rutherford-Boeing data 23 of type rsa
48 rows, 48 cols, 224 nonzeros
```
Matrices in MM format can be opened with [`MatrixMarket.jl`](https://github.com/JuliaSparse/MatrixMarket.jl).