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Merge pull request #182 from MagneticResonanceImaging/nh/gpuSupport
Add GPU support to MRIReco.jl
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,99 @@ | ||
| steps: | ||
| - label: "Nvidia GPUs -- MRIReco.jl" | ||
| plugins: | ||
| - JuliaCI/julia#v1: | ||
| version: "1.10" | ||
| agents: | ||
| queue: "juliagpu" | ||
| cuda: "*" | ||
| command: | | ||
| julia --color=yes --project -e ' | ||
| using Pkg | ||
| Pkg.develop([PackageSpec(path=pwd(), subdir="MRIBase") | ||
| , PackageSpec(path=pwd(), subdir="MRIFiles") | ||
| , PackageSpec(path=pwd(), subdir="MRISampling") | ||
| , PackageSpec(path=pwd(), subdir="MRISimulation") | ||
| , PackageSpec(path=pwd(), subdir="MRIOperators") | ||
| , PackageSpec(path=pwd(), subdir="MRICoilSensitivities")]) | ||
| Pkg.add("TestEnv") | ||
| using TestEnv | ||
| TestEnv.activate(); | ||
| Pkg.add("CUDA") | ||
| Pkg.instantiate() | ||
| include("test/gpu/cuda.jl")' | ||
| timeout_in_minutes: 30 | ||
|
|
||
| #- label: "AMD GPUs -- MRIReco.jl" | ||
| # plugins: | ||
| # - JuliaCI/julia#v1: | ||
| # version: "1.10" | ||
| # agents: | ||
| # queue: "juliagpu" | ||
| # rocm: "*" | ||
| # rocmgpu: "*" | ||
| # command: | | ||
| # julia --color=yes --project -e ' | ||
| # using Pkg | ||
| # Pkg.develop([PackageSpec(path=pwd(), subdir="MRIBase") | ||
| # , PackageSpec(path=pwd(), subdir="MRIFiles") | ||
| # , PackageSpec(path=pwd(), subdir="MRISampling") | ||
| # , PackageSpec(path=pwd(), subdir="MRISimulation") | ||
| # , PackageSpec(path=pwd(), subdir="MRIOperators") | ||
| # , PackageSpec(path=pwd(), subdir="MRICoilSensitivities")]) | ||
| # Pkg.add("TestEnv") | ||
| # using TestEnv | ||
| # TestEnv.activate(); | ||
| # Pkg.add("AMDGPU") | ||
| # Pkg.instantiate() | ||
| # include("test/gpu/rocm.jl")' | ||
| # timeout_in_minutes: 30 | ||
|
|
||
| - label: "Nvidia GPUs -- MRIOperators.jl" | ||
| plugins: | ||
| - JuliaCI/julia#v1: | ||
| version: "1.10" | ||
| agents: | ||
| queue: "juliagpu" | ||
| cuda: "*" | ||
| command: | | ||
| julia --color=yes --project -e ' | ||
| using Pkg | ||
| Pkg.develop([PackageSpec(path=pwd(), subdir="MRIBase") | ||
| , PackageSpec(path=pwd(), subdir="MRIFiles") | ||
| , PackageSpec(path=pwd(), subdir="MRISampling") | ||
| , PackageSpec(path=pwd(), subdir="MRISimulation") | ||
| , PackageSpec(path=pwd(), subdir="MRIOperators") | ||
| , PackageSpec(path=pwd(), subdir="MRICoilSensitivities")]) | ||
| Pkg.add("TestEnv") | ||
| using TestEnv | ||
| TestEnv.activate("MRIOperators"); | ||
| Pkg.add("CUDA") | ||
| Pkg.instantiate() | ||
| include("MRIOperators/test/gpu/cuda.jl")' | ||
| timeout_in_minutes: 30 | ||
|
|
||
|
|
||
| - label: "AMD GPUs -- MRIOperators.jl" | ||
| plugins: | ||
| - JuliaCI/julia#v1: | ||
| version: "1.10" | ||
| agents: | ||
| queue: "juliagpu" | ||
| rocm: "*" | ||
| rocmgpu: "*" | ||
| command: | | ||
| julia --color=yes --project -e ' | ||
| using Pkg | ||
| Pkg.develop([PackageSpec(path=pwd(), subdir="MRIBase") | ||
| , PackageSpec(path=pwd(), subdir="MRIFiles") | ||
| , PackageSpec(path=pwd(), subdir="MRISampling") | ||
| , PackageSpec(path=pwd(), subdir="MRISimulation") | ||
| , PackageSpec(path=pwd(), subdir="MRIOperators") | ||
| , PackageSpec(path=pwd(), subdir="MRICoilSensitivities")]) | ||
| Pkg.add("TestEnv") | ||
| using TestEnv | ||
| TestEnv.activate("MRIOperators"); | ||
| Pkg.add("AMDGPU") | ||
| Pkg.instantiate() | ||
| include("MRIOperators/test/gpu/rocm.jl")' | ||
| timeout_in_minutes: 30 |
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110 changes: 110 additions & 0 deletions
110
MRIOperators/ext/MRIOperatorsGPUArraysExt/ExplicitOp.jl
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,110 @@ | ||
| function MRIOperators.produ!(out::vecTc, x::vecTc, shape::NTuple{2,Int64}, | ||
| nodes::matT, times::vecT, echoOffset::T, | ||
| disturbanceTerm::matTc) where {T, Tc <: Union{T, Complex{T}}, vecTc <: AbstractGPUArray{Tc}, matT <: AbstractGPUArray{T}, vecT <: AbstractGPUArray{T}, matTc <: AbstractGPUArray{Tc}} | ||
|
|
||
| factor = Tc(-2 * 1im * pi) | ||
| limit = prod(shape) | ||
| fill!(out, zero(Tc)) | ||
| gpu_call(out, reshape(x, shape), shape, nodes, times, echoOffset, disturbanceTerm; elements = size(nodes, 2)) do ctx, out_, x_, shape_, nodes_, times_, echoOffset_, disturbanceTerm_ | ||
| k = linear_index(ctx) | ||
| if !(1 <= k <= limit) | ||
| return nothing | ||
| end | ||
|
|
||
| for nx = 1:shape_[1] | ||
| for ny = 1:shape_[2] | ||
| phi = (nodes_[1, k] * (nx - shape_[1] / 2 - 1) + nodes_[2, k] * (ny - shape_[2] / 2 - 1)) | ||
| e = exp(factor * phi - (times_[k] - echoOffset_) * disturbanceTerm_[nx, ny]) | ||
| out_[k] += x_[nx, ny] * e | ||
| end | ||
| end | ||
| return nothing | ||
| end | ||
|
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||
| return out | ||
| end | ||
|
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| function MRIOperators.produ!(out::vecTc, x::vecTc, shape::NTuple{3,Int64}, | ||
| nodes::matT, times::vecT, echoOffset::T, | ||
| disturbanceTerm::arrTc) where {T, Tc <: Union{T, Complex{T}}, vecTc <: AbstractGPUArray{Tc}, matT <: AbstractGPUArray{T}, vecT <: AbstractGPUArray{T}, arrTc <: AbstractGPUArray{Tc, 3}} | ||
|
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| factor = Tc(-2 * 1im * pi) | ||
| limit = prod(shape) | ||
| fill!(out, zero(Tc)) | ||
| gpu_call(out, reshape(x, shape), shape, nodes, times, echoOffset, disturbanceTerm; elements = size(nodes, 2)) do ctx, out_, x_, shape_, nodes_, times_, echoOffset_, disturbanceTerm_ | ||
| k = linear_index(ctx) | ||
| if !(1 <= k <= limit) | ||
| return nothing | ||
| end | ||
|
|
||
| for nx = 1:shape_[1] | ||
| for ny = 1:shape_[2] | ||
| for nz = 1:shape_[3] | ||
| phi = (nodes_[1, k] * (nx - shape_[1] / 2 - 1) + nodes_[2, k] * (ny - shape_[2] / 2 - 1) + nodes_[3, k] * (nz - shape_[3] / 2 - 1)) | ||
| e = exp(factor * phi - (times_[k] - echoOffset_) * disturbanceTerm_[nx, ny, nz]) | ||
| out_[k] += x_[nx, ny, nz] * e | ||
| end | ||
| end | ||
| end | ||
| return nothing | ||
| end | ||
|
|
||
| return out | ||
| end | ||
|
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| function MRIOperators.ctprodu!(out::vecTc, x::vecTc, shape::NTuple{2,Int64}, | ||
| nodes::matT, times::vecT, echoOffset::T, | ||
| disturbanceTerm::matTc) where {T, Tc <: Union{T, Complex{T}}, vecTc <: AbstractGPUArray{Tc}, matT <: AbstractGPUArray{T}, vecT <: AbstractGPUArray{T}, matTc <: AbstractGPUArray{Tc}} | ||
|
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||
| factor = Tc(-2 * 1im * pi) | ||
| limit = prod(shape) | ||
| fill!(out, zero(Tc)) | ||
| gpu_call(reshape(out, shape), x, shape, nodes, times, echoOffset, disturbanceTerm; elements = limit) do ctx, out_, x_, shape_, nodes_, times_, echoOffset_, disturbanceTerm_ | ||
| linearIndex = linear_index(ctx) | ||
| if !(1 <= linearIndex <= limit) | ||
| return nothing | ||
| end | ||
|
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||
| cartIndex = CartesianIndices(shape)[linearIndex] | ||
|
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| nx = cartIndex[1] | ||
| ny = cartIndex[2] | ||
| for k = 1:size(nodes_, 2) | ||
| phi = (nodes_[1,k]*(nx-shape_[1]/2-1)+nodes_[2,k]*(ny-shape_[2]/2-1)) | ||
| e = exp(factor * phi - (times_[k]-echoOffset_)*disturbanceTerm_[cartIndex]) | ||
| out_[cartIndex] += x_[k] * conj(e) | ||
| end | ||
| return nothing | ||
| end | ||
|
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| return out | ||
| end | ||
|
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| function MRIOperators.ctprodu!(out::vecTc, x::vecTc, shape::NTuple{3,Int64}, | ||
| nodes::matT, times::vecT, echoOffset::T, | ||
| disturbanceTerm::arrTc) where {T, Tc <: Union{T, Complex{T}}, vecTc <: AbstractGPUArray{Tc}, matT <: AbstractGPUArray{T}, vecT <: AbstractGPUArray{T}, arrTc <: AbstractGPUArray{Tc, 3}} | ||
|
|
||
| factor = Tc(-2 * 1im * pi) | ||
| limit = prod(shape) | ||
| fill!(out, zero(Tc)) | ||
| gpu_call(reshape(out, shape), x, shape, nodes, times, echoOffset, disturbanceTerm; elements = limit) do ctx, out_, x_, shape_, nodes_, times_, echoOffset_, disturbanceTerm_ | ||
| linearIndex = linear_index(ctx) | ||
| if !(1 <= linearIndex <= limit) | ||
| return nothing | ||
| end | ||
|
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| cartIndex = CartesianIndices(shape)[linearIndex] | ||
|
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| nx = cartIndex[1] | ||
| ny = cartIndex[2] | ||
| nz = cartIndex[3] | ||
| for k = 1:size(nodes_, 2) | ||
| phi = (nodes_[1,k]*(nx-shape_[1]/2-1)+nodes_[2,k]*(ny-shape_[2]/2-1)+nodes_[3,k]*(nz-shape_[3]/2-1)) | ||
| e = exp(factor * phi - (times_[k]-echoOffset_)*disturbanceTerm_[cartIndex]) | ||
| out_[cartIndex] += x_[k] * conj(e) | ||
| end | ||
| return nothing | ||
| end | ||
|
|
||
| return out | ||
| end |
41 changes: 41 additions & 0 deletions
41
MRIOperators/ext/MRIOperatorsGPUArraysExt/FieldmapNFFTOp.jl
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,41 @@ | ||
| function MRIOperators.produ_inner!(K, C::matT, A::matT, shape, d::Vector{vecT}, s::vecT, sp, plan, idx, x_::vecT, p::Vector{arrT}) where {T, vecT <: AbstractGPUVector{T}, matT <: AbstractGPUMatrix{T}, arrT <: AbstractGPUArray{T}} | ||
| for κ=1:K | ||
| if !isempty(idx[κ]) | ||
| p[κ][:] .= C[κ,:] .* x_ | ||
| mul!(d[κ], plan[κ], p[κ]) | ||
| # Assumption: l is unique per idx[κ] | ||
| gpu_call(idx[κ], d[κ], view(A, :, κ), s) do ctx, indices, d_, A_, s_ | ||
| k = @linearidx(indices) | ||
| l = indices[k] | ||
| s_[l] += d_[k]*A_[l] | ||
| return nothing | ||
| end | ||
| end | ||
| end | ||
|
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| return | ||
| end | ||
|
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|
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| function MRIOperators.ctprodu_inner!(K, C::matT, A::matT, shape, d::Vector{vecT}, y::vecT, sp, plan, idx, x::vecT, p::Vector{arrT}) where {T, vecT <: AbstractGPUVector{T}, matT <: AbstractGPUMatrix{T}, arrT <: AbstractGPUArray{T}} | ||
|
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| for κ=1:K | ||
| if !isempty(idx[κ]) | ||
| gpu_call(idx[κ], d[κ], view(A, :, κ), x) do ctx, indices, d_, A_, x_ | ||
| k = @linearidx(indices) | ||
| l = indices[k] | ||
| d_[k] = conj(A_[l]) * x_[l] | ||
| return nothing | ||
| end | ||
| mul!(p[κ], adjoint(plan[κ]), d[κ]) | ||
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| gpu_call(p[κ], view(C, κ, :), y) do ctx, p_, C_, y_ | ||
| k = @linearidx(p_) | ||
| y_[k] += conj(C_[k]) * p_[k] | ||
| return nothing | ||
| end | ||
| end | ||
| end | ||
|
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||
| return | ||
| end |
13 changes: 13 additions & 0 deletions
13
MRIOperators/ext/MRIOperatorsGPUArraysExt/MRIOperatorsGPUArraysExt.jl
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|---|---|---|
| @@ -0,0 +1,13 @@ | ||
| module MRIOperatorsGPUArraysExt | ||
|
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| using MRIOperators, GPUArrays, MRIOperators.FFTW, MRIOperators.LinearAlgebra | ||
|
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| include("ExplicitOp.jl") | ||
| include("Shutter.jl") | ||
| include("SensitivityOp.jl") | ||
| include("FieldmapNFFTOp.jl") | ||
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| MRIOperators.fftParams(::Type{<:AbstractGPUArray}) = (;) | ||
|
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| end # module |
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@JuliaRegistrator release subdir=MRIBase
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Error while trying to register: Action not recognized: release
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@JuliaRegistrator register subdir=MRIBase
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Registration pull request created: JuliaRegistries/General/113065
Tip: Release Notes
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@JuliaRegistrator register subdir=MRIOperators
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Registration pull request created: JuliaRegistries/General/113066
Tip: Release Notes
Did you know you can add release notes too? Just add markdown formatted text underneath the comment after the text
"Release notes:" and it will be added to the registry PR, and if TagBot is installed it will also be added to the
release that TagBot creates. i.e.
To add them here just re-invoke and the PR will be updated.
Tagging
After the above pull request is merged, it is recommended that a tag is created on this repository for the registered package version.
This will be done automatically if the Julia TagBot GitHub Action is installed, or can be done manually through the github interface, or via:
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@JuliaRegistrator register
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Registration pull request created: JuliaRegistries/General/113070
Tip: Release Notes
Did you know you can add release notes too? Just add markdown formatted text underneath the comment after the text
"Release notes:" and it will be added to the registry PR, and if TagBot is installed it will also be added to the
release that TagBot creates. i.e.
To add them here just re-invoke and the PR will be updated.
Tagging
After the above pull request is merged, it is recommended that a tag is created on this repository for the registered package version.
This will be done automatically if the Julia TagBot GitHub Action is installed, or can be done manually through the github interface, or via: