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Merged
tkoskela merged 58 commits into from
Dec 12, 2025
Merged

Copy States Optimization #297

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40dfa12
slurm script
Jun 18, 2025
d0f9985
draft benchmarking scripts
Jun 30, 2025
0c125bf
reduce duplicated message
Angeladadd Jul 16, 2025
7075bad
update viz
Angeladadd Jul 17, 2025
fc6d16d
add measurement of overall execution time & pass flag whether to dedu…
Angeladadd Jul 17, 2025
a89684b
add slurm script
Jul 17, 2025
533e3d5
local copy/remote duplicate in parallel
Jul 24, 2025
58a56ee
optimize indices
Jul 31, 2025
e4e5e4a
stage viz
Angeladadd Jul 31, 2025
b283153
draft optimized indices
Angeladadd Jul 31, 2025
79fa663
add optimized resample flag to test
Angeladadd Aug 13, 2025
a14f88e
update test scripts
Aug 13, 2025
5025f6f
update viz
Angeladadd Aug 14, 2025
4092581
update test script
Aug 17, 2025
7bac387
update viz
Angeladadd Aug 17, 2025
7284b72
update timer naming
Angeladadd Aug 19, 2025
8f5bd9d
update code
Sep 1, 2025
e67c43f
update viz
Angeladadd Sep 1, 2025
5613111
remove serialization
Angeladadd Sep 1, 2025
fa12ab1
upgrade julia
Angeladadd Sep 1, 2025
26c0845
add TimerOutput
Angeladadd Sep 1, 2025
42801be
remove unused files
Sep 1, 2025
97ed1b3
update benchmark deps
Angeladadd Sep 1, 2025
af144b2
Revert "update benchmark deps"
Angeladadd Sep 3, 2025
097f2c8
downgrade julia
Angeladadd Sep 3, 2025
5570f1e
downgrade to 1.7
Angeladadd Sep 3, 2025
839e73e
fix ci
Angeladadd Sep 3, 2025
4791c84
add Test
Angeladadd Sep 3, 2025
05848bf
fix benchmark
Angeladadd Sep 3, 2025
8eaf224
upgrade benchmark julia to 1.10
Angeladadd Sep 3, 2025
33995ff
fix test depts
Angeladadd Sep 3, 2025
86c6e86
add tests
Angeladadd Sep 4, 2025
88ebb88
reduce modified files and update viz
Angeladadd Sep 4, 2025
888bb1d
update gitignore
Angeladadd Sep 4, 2025
bbe8830
update scripts
Sep 4, 2025
6bb81a5
use filter paramter
Angeladadd Sep 4, 2025
12796e7
update extra
Sep 4, 2025
2f71cab
add comments
Angeladadd Sep 4, 2025
b5be3c9
remove serialization pkg
Angeladadd Sep 4, 2025
5df8d31
update comment
Angeladadd Sep 4, 2025
9e19062
fix comments
Angeladadd Sep 4, 2025
c54afa3
replace unoptimized copy_states, put path to vars, set optimize optio…
Nov 1, 2025
1096973
fix integ test
Nov 1, 2025
cdbad91
remove output
Nov 1, 2025
3d70138
replace println with logging macros
Nov 1, 2025
ab1fda5
add logging
Angeladadd Nov 2, 2025
00c13b1
revert benchmark change
Angeladadd Nov 9, 2025
a02f3db
compat entry
Nov 9, 2025
8ee3a39
Update extra/weak_scaling/kathleen_slurm_weak_scaling.sh
Angeladadd Nov 9, 2025
9602190
Apply suggestions from code review
Angeladadd Nov 9, 2025
9a82a0e
add missing comments and changes
Nov 9, 2025
a3b4c0c
wip: add notes to notebook
Angeladadd Nov 9, 2025
e9c8d47
add comments to notebook
Angeladadd Nov 9, 2025
b8204ce
remove defined chdir
Nov 9, 2025
7a28c66
move testing script to extra
Nov 9, 2025
818c6d8
fix path issue
Nov 9, 2025
2c16667
Merge branch 'main' into cgsun/copy_states_refine
Angeladadd Nov 22, 2025
b4cc2ea
Merge branch 'main' into cgsun/copy_states_refine
tkoskela Dec 3, 2025
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1 change: 1 addition & 0 deletions .gitignore
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Original file line number Diff line number Diff line change
Expand Up @@ -5,3 +5,4 @@ Manifest-v*.toml
/docs/build/
/.benchmarkci
*.h5
slurm_log/
4 changes: 4 additions & 0 deletions Project.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,9 @@ version = "1.3.0"

[deps]
ChunkSplitters = "ae650224-84b6-46f8-82ea-d812ca08434e"
ExactOptimalTransport = "24df6009-d856-477c-ac5c-91f668376b31"
HDF5 = "f67ccb44-e63f-5c2f-98bd-6dc0ccc4ba2f"
HiGHS = "87dc4568-4c63-4d18-b0c0-bb2238e4078b"
LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
MPI = "da04e1cc-30fd-572f-bb4f-1f8673147195"
OpenMPI_jll = "fe0851c0-eecd-5654-98d4-656369965a5c"
Expand All @@ -19,7 +21,9 @@ YAML = "ddb6d928-2868-570f-bddf-ab3f9cf99eb6"

[compat]
ChunkSplitters = "3.1"
ExactOptimalTransport = "0.2.5"
HDF5 = "0.14, 0.15, 0.16, 0.17"
HiGHS = "1.19.0"
LinearAlgebra = "<0.0.1, 1"
MPI = "0.20.22"
OpenMPI_jll = "4"
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