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Merge pull request #292 from Julia-Tempering/iss290
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Fix detection of target chain for VariationalDEO
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@miguelbiron
miguelbiron authored Oct 22, 2024
2 parents 7934673 + 0c8cea3 commit ff27c73
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Showing 7 changed files with 48 additions and 33 deletions.
22 changes: 11 additions & 11 deletions .github/workflows/CI.yml
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Expand Up @@ -39,13 +39,13 @@ jobs:
with:
distribution: 'temurin'
java-version: '11'
- uses: julia-actions/setup-julia@latest
- uses: julia-actions/setup-julia@v2
with:
version: ${{ matrix.version }}
- uses: julia-actions/cache@v2
- uses: julia-actions/julia-buildpkg@latest
- uses: julia-actions/julia-runtest@latest
- uses: julia-actions/julia-processcoverage@latest
- uses: julia-actions/julia-buildpkg@v1
- uses: julia-actions/julia-runtest@v1
- uses: julia-actions/julia-processcoverage@v1
- uses: codecov/codecov-action@v4
with:
files: lcov.info
Expand All @@ -71,7 +71,7 @@ jobs:
- name: Checkout
uses: actions/checkout@v4

- uses: julia-actions/setup-julia@latest
- uses: julia-actions/setup-julia@v2
with:
version: ${{ matrix.version }}
- uses: julia-actions/cache@v2
Expand All @@ -85,7 +85,7 @@ jobs:
MPIPreferences.use_jll_binary("OpenMPI_jll")
rm("test/Manifest.toml")
- uses: julia-actions/julia-runtest@latest
- uses: julia-actions/julia-runtest@v1


# # CI is getting too slow!
Expand Down Expand Up @@ -119,7 +119,7 @@ jobs:
distribution: 'temurin'
java-version: '11'

- uses: julia-actions/setup-julia@latest
- uses: julia-actions/setup-julia@v2
with:
version: ${{ matrix.version }}

Expand All @@ -137,7 +137,7 @@ jobs:
run(`sed -i.bu 's/unknown/MPICH/' test/LocalPreferences.toml`) # fix wrong abi detection for mpich
rm("test/Manifest.toml")
- uses: julia-actions/julia-runtest@latest
- uses: julia-actions/julia-runtest@v1


docs:
Expand All @@ -151,11 +151,11 @@ jobs:
with:
distribution: 'temurin'
java-version: '11'
- uses: julia-actions/setup-julia@latest
- uses: julia-actions/setup-julia@v2
with:
version: '1.10'
- uses: julia-actions/julia-buildpkg@latest
- uses: julia-actions/julia-docdeploy@latest
- uses: julia-actions/cache@v2
- uses: julia-actions/julia-docdeploy@v1
env:
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
- run: |
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2 changes: 1 addition & 1 deletion Project.toml
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@@ -1,7 +1,7 @@
name = "Pigeons"
uuid = "0eb8d820-af6a-4919-95ae-11206f830c31"
authors = ["Alexandre Bouchard-Côté <[email protected]>, Nikola Surjanovic <[email protected]>, Paul Tiede <[email protected]>, Trevor Campbell, Miguel Biron-Lattes, Saifuddin Syed"]
version = "0.4.6"
version = "0.4.7"

[deps]
DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
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18 changes: 9 additions & 9 deletions src/pt/process_sample.jl
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Expand Up @@ -19,12 +19,12 @@ and pair plots (via [PairPlots](https://sefffal.github.io/PairPlots.jl/dev/chain
function sample_array(pt::PT)
chains = chains_with_samples(pt)
dim, size = sample_dim_size(pt, chains)
result = zeros(size, dim, length(chains))
for chain_index in eachindex(chains)
t = chains[chain_index]
n_chains_with_samples = count(!isnothing, chains) # iterators have no `length` method
result = zeros(size, dim, n_chains_with_samples)
for (chain_index, t) in enumerate(chains)
sample = get_sample(pt, t)
for i in 1:size
vector = sample[i]
for i in 1:size
vector = sample[i]
result[i, :, chain_index] .= vector
end
end
Expand All @@ -34,13 +34,13 @@ end
chains_with_samples(pt) = pt.inputs.extended_traces ? (1:n_chains(pt.inputs)) : target_chains(pt)

function sample_dim_size(pt::PT, chains)
sample = get_sample(pt, chains[1])
return length(sample[1]), length(sample)
sample = get_sample(pt, first(chains))
return length(first(sample)), length(sample)
end

function target_chains(pt::PT)
n = n_chains(pt.inputs)
return filter(i -> is_target(pt.shared.tempering.swap_graphs, i), 1:n)
return (i for i in 1:n if is_target(pt.shared.tempering.swap_graphs, i))
end

"""
Expand Down Expand Up @@ -84,7 +84,7 @@ The `chain` option can be omitted and by default the
first chain targetting the distribution of interest will be used
(in many cases, there will be only one, in variational cases, two).
"""
get_sample(pt::PT, chain = target_chains(pt)[1]) = SampleArray(pt, chain)
get_sample(pt::PT, chain = first(target_chains(pt))) = SampleArray(pt, chain)

function Base.show(io::IO, s::SampleArray{T,PT}) where {T,PT}
println(io, "SampleArray{$T}")
Expand Down
2 changes: 1 addition & 1 deletion src/swap/VariationalDEO.jl
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Expand Up @@ -18,4 +18,4 @@ create_swap_graph(deo::VariationalDEO, shared) =
iseven(shared.iterators.scan) ? even(deo.n_chains_fixed, deo.n_chains_var) : odd(deo.n_chains_fixed, deo.n_chains_var)

is_reference(deo::VariationalDEO, chain::Int) = (chain == 1) || (chain == n_chains(deo))
is_target(deo::VariationalDEO, chain::Int) = (chain == deo.n_chains_fixed) || (chain == deo.n_chains_fixed + 1)
is_target(deo::VariationalDEO, chain::Int) = (chain == deo.n_chains_var) || (chain == deo.n_chains_var + 1)
1 change: 1 addition & 0 deletions test/supporting/setup.jl
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Expand Up @@ -7,6 +7,7 @@ using Pigeons,
Distributions,
DynamicPPL,
Enzyme,
FillArrays,
ForwardDiff,
HypothesisTests,
LinearAlgebra,
Expand Down
1 change: 1 addition & 0 deletions test/test_mala.jl
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Expand Up @@ -8,6 +8,7 @@ which also cover checks of the Hamiltonian dynamics.
target = toy_mvn_target(2),
n_chains = 2,
explorer = MALA(),
n_chains_variational = 4,
record = [Pigeons.online],
n_rounds = 10);
for var_name in Pigeons.continuous_variables(pt)
Expand Down
35 changes: 24 additions & 11 deletions test/test_two_legs.jl
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@@ -1,10 +1,11 @@
@testset "Two legs schedule adaptation" begin
@testset "Test StabilizedPT machinery" begin
n_rounds = 10
n_chains = 10
n_chains = 8
n_chains_variational = 7
pt_2_legs = pigeons(;
target = Pigeons.toy_turing_unid_target(),
variational = GaussianReference(first_tuning_round = n_rounds + 1), # never activate
n_chains_variational = n_chains,
n_chains_variational = n_chains_variational,
n_chains,
n_rounds)

Expand All @@ -15,14 +16,26 @@
n_chains,
n_rounds)


@show gcb_1 = Pigeons.global_barrier(pt_1_leg.shared.tempering)
@show gcb_2_1 = Pigeons.global_barrier(pt_2_legs.shared.tempering)
@show gcb_2_2 = Pigeons.global_barrier_variational(pt_2_legs.shared.tempering)
@testset "Two legs schedule adaptation" begin
@show gcb_1 = Pigeons.global_barrier(pt_1_leg.shared.tempering)
@show gcb_2_1 = Pigeons.global_barrier(pt_2_legs.shared.tempering)
@show gcb_2_2 = Pigeons.global_barrier_variational(pt_2_legs.shared.tempering)
truth = 3.5 # based on 15 rounds
for approx in [gcb_1, gcb_2_1, gcb_2_2]
@test isapprox(approx, truth, rtol = 0.1)
end
end

truth = 3.5 # based on 15 rounds

for approx in [gcb_1, gcb_2_1, gcb_2_2]
@test isapprox(approx, truth, atol = 0.1)
@testset "Issue #290" begin
n = Pigeons.n_chains(pt_2_legs.inputs)
idxs_targets = Pigeons.target_chains(pt_2_legs)
idxs_refs = (i for i in 1:n if Pigeons.is_reference(pt_2_legs.shared.tempering.swap_graphs, i))
indexer = pt_2_legs.shared.tempering.indexer
@test isempty(intersect(idxs_refs, idxs_targets)) # targets and references should be different
# test: if multiple references/targets exist, they should live on different legs
for idxs in (idxs_targets, idxs_refs)
n_distinct_legs = length(Set(last(indexer.i2t[idx]) for idx in idxs))
@test length(collect(idxs)) == n_distinct_legs
end
end
end

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Registration pull request created: JuliaRegistries/General/117796

Tip: Release Notes

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## Breaking changes

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Tagging

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This will be done automatically if the Julia TagBot GitHub Action is installed, or can be done manually through the github interface, or via:

git tag -a v0.4.7 -m "<description of version>" ff27c73b79bb11fd66870757896fc9a6b21c1ebc
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