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Fixes #141 and #142.
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@cncastillo
cncastillo committed Dec 30, 2022
1 parent 3f4e31a commit 6132e9d
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4 changes: 1 addition & 3 deletions Project.toml
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
name = "KomaMRI"
uuid = "6a340f8b-2cdf-4c04-99be-4953d9b66d0a"
authors = ["Carlos Castillo Passi <[email protected]>"]
version = "0.7.1"
version = "0.7.2"

[deps]
Adapt = "79e6a3ab-5dfb-504d-930d-738a2a938a0e"
Expand All @@ -12,7 +12,6 @@ Distributed = "8ba89e20-285c-5b6f-9357-94700520ee1b"
FileIO = "5789e2e9-d7fb-5bc7-8068-2c6fae9b9549"
Functors = "d9f16b24-f501-4c13-a1f2-28368ffc5196"
HDF5 = "f67ccb44-e63f-5c2f-98bd-6dc0ccc4ba2f"
Hwloc = "0e44f5e4-bd66-52a0-8798-143a42290a1d"
Interact = "c601a237-2ae4-5e1e-952c-7a85b0c7eef1"
Interpolations = "a98d9a8b-a2ab-59e6-89dd-64a1c18fca59"
JLD2 = "033835bb-8acc-5ee8-8aae-3f567f8a3819"
Expand All @@ -37,7 +36,6 @@ CUDA = "3"
FileIO = "1"
Functors = "0.4"
HDF5 = "0.16"
Hwloc = "2"
Interact = "0.10"
Interpolations = "0.13, 0.14"
JLD2 = "0.4"
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120 changes: 60 additions & 60 deletions examples/3.koma_paper/comparison_speed/Koma_rtx2080ti_gtx1650ti
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@@ -1,63 +1,63 @@
### KOMA Multi-Shot Spiral CPU ###
4.468904 seconds (348.87 k allocations: 7.061 GiB, 3.55% gc time, 0.74% compilation time)
4.445230 seconds (304.62 k allocations: 7.059 GiB, 3.22% gc time)
4.444298 seconds (304.62 k allocations: 7.059 GiB, 3.22% gc time)
4.438783 seconds (304.62 k allocations: 7.059 GiB, 3.23% gc time)
4.438602 seconds (304.62 k allocations: 7.059 GiB, 3.16% gc time)
4.421823 seconds (304.62 k allocations: 7.059 GiB, 3.17% gc time)
4.422771 seconds (304.49 k allocations: 7.059 GiB, 3.13% gc time)
4.418151 seconds (304.62 k allocations: 7.059 GiB, 3.05% gc time)
4.419588 seconds (304.62 k allocations: 7.059 GiB, 3.12% gc time)
4.423932 seconds (304.62 k allocations: 7.059 GiB, 3.05% gc time)
4.438833 seconds (304.62 k allocations: 7.059 GiB, 3.07% gc time)
4.438832 seconds (304.62 k allocations: 7.059 GiB, 3.04% gc time)
4.486883 seconds (304.62 k allocations: 7.059 GiB, 3.07% gc time)
4.700309 seconds (304.49 k allocations: 7.059 GiB, 2.98% gc time)
4.691741 seconds (304.62 k allocations: 7.059 GiB, 2.94% gc time)
4.752007 seconds (304.36 k allocations: 7.059 GiB, 2.83% gc time)
4.466893 seconds (304.49 k allocations: 7.059 GiB, 3.01% gc time)
4.464153 seconds (304.49 k allocations: 7.059 GiB, 3.03% gc time)
4.493246 seconds (304.62 k allocations: 7.059 GiB, 3.19% gc time)
4.457662 seconds (304.62 k allocations: 7.059 GiB, 3.00% gc time)
1.791288 seconds (348.88 k allocations: 7.061 GiB, 6.10% gc time, 2.04% compilation time)
1.788641 seconds (305.13 k allocations: 7.059 GiB, 3.22% gc time)
1.797306 seconds (305.01 k allocations: 7.059 GiB, 3.97% gc time)
1.760078 seconds (305.16 k allocations: 7.059 GiB, 3.21% gc time)
1.780291 seconds (304.88 k allocations: 7.059 GiB, 4.14% gc time)
1.803833 seconds (304.74 k allocations: 7.059 GiB, 4.24% gc time)
1.783240 seconds (305.01 k allocations: 7.059 GiB, 3.56% gc time)
1.779908 seconds (305.00 k allocations: 7.059 GiB, 3.28% gc time)
1.765165 seconds (304.60 k allocations: 7.059 GiB, 3.57% gc time)
1.797075 seconds (305.39 k allocations: 7.059 GiB, 3.16% gc time)
1.761110 seconds (305.29 k allocations: 7.059 GiB, 2.69% gc time)
1.771107 seconds (305.01 k allocations: 7.059 GiB, 2.82% gc time)
1.790191 seconds (304.60 k allocations: 7.059 GiB, 3.04% gc time)
1.743203 seconds (305.00 k allocations: 7.059 GiB, 2.63% gc time)
1.811720 seconds (305.14 k allocations: 7.059 GiB, 2.85% gc time)
1.775254 seconds (305.00 k allocations: 7.059 GiB, 3.58% gc time)
1.768405 seconds (304.86 k allocations: 7.059 GiB, 2.96% gc time)
2.550956 seconds (304.59 k allocations: 7.059 GiB, 35.09% gc time)
1.737120 seconds (305.14 k allocations: 7.059 GiB, 2.59% gc time)
1.774394 seconds (305.01 k allocations: 7.059 GiB, 3.46% gc time)
### KOMA Multi-Shot Spiral GPU0 ###
0.191547 seconds (377.14 k allocations: 23.680 MiB, 17.10% compilation time)
0.150679 seconds (332.70 k allocations: 21.300 MiB)
0.151408 seconds (332.65 k allocations: 21.297 MiB)
0.150065 seconds (332.85 k allocations: 21.309 MiB)
0.151362 seconds (332.89 k allocations: 21.311 MiB)
0.147650 seconds (332.80 k allocations: 21.305 MiB)
0.151219 seconds (332.80 k allocations: 21.306 MiB)
0.150325 seconds (332.70 k allocations: 21.300 MiB)
0.148065 seconds (332.84 k allocations: 21.308 MiB)
0.152075 seconds (332.94 k allocations: 21.314 MiB)
0.150261 seconds (332.70 k allocations: 21.300 MiB)
0.150011 seconds (332.94 k allocations: 21.314 MiB)
0.149172 seconds (332.80 k allocations: 21.306 MiB)
0.148890 seconds (332.75 k allocations: 21.302 MiB)
0.148253 seconds (332.94 k allocations: 21.315 MiB)
0.152094 seconds (332.75 k allocations: 21.303 MiB)
0.147646 seconds (332.75 k allocations: 21.302 MiB)
0.151022 seconds (332.94 k allocations: 21.315 MiB)
0.149571 seconds (332.75 k allocations: 21.303 MiB)
0.147972 seconds (332.80 k allocations: 21.306 MiB)
0.222617 seconds (410.00 k allocations: 24.362 MiB, 10.73% gc time, 26.09% compilation time)
0.149812 seconds (355.18 k allocations: 21.673 MiB)
0.150912 seconds (355.30 k allocations: 21.673 MiB)
0.154048 seconds (355.06 k allocations: 21.669 MiB)
0.153823 seconds (355.26 k allocations: 21.673 MiB)
0.150777 seconds (355.44 k allocations: 21.681 MiB)
0.151338 seconds (355.24 k allocations: 21.677 MiB)
0.155108 seconds (355.14 k allocations: 21.671 MiB)
0.152609 seconds (355.07 k allocations: 21.667 MiB)
0.152995 seconds (355.29 k allocations: 21.678 MiB)
0.149100 seconds (355.31 k allocations: 21.676 MiB)
0.148364 seconds (355.13 k allocations: 21.671 MiB)
0.147747 seconds (355.24 k allocations: 21.675 MiB)
0.152601 seconds (355.35 k allocations: 21.675 MiB)
0.148840 seconds (355.51 k allocations: 21.683 MiB)
0.150223 seconds (355.15 k allocations: 21.673 MiB)
0.151326 seconds (355.41 k allocations: 21.681 MiB)
0.149905 seconds (355.60 k allocations: 21.687 MiB)
0.150076 seconds (355.47 k allocations: 21.685 MiB)
0.152087 seconds (354.98 k allocations: 21.662 MiB)
### KOMA Multi-Shot Spiral GPU1 ###
0.383762 seconds (387.52 k allocations: 24.026 MiB, 3.61% gc time, 8.37% compilation time)
0.326810 seconds (343.31 k allocations: 21.657 MiB, 2.48% gc time)
0.317470 seconds (343.31 k allocations: 21.658 MiB, 2.54% gc time)
0.315657 seconds (343.32 k allocations: 21.659 MiB, 2.59% gc time)
0.312953 seconds (343.41 k allocations: 21.663 MiB, 2.58% gc time)
0.317549 seconds (343.50 k allocations: 21.669 MiB, 2.56% gc time)
0.316872 seconds (343.41 k allocations: 21.663 MiB, 2.57% gc time)
0.318535 seconds (343.50 k allocations: 21.669 MiB, 2.54% gc time)
0.317094 seconds (343.45 k allocations: 21.666 MiB, 2.54% gc time)
0.317818 seconds (343.45 k allocations: 21.666 MiB, 2.57% gc time)
0.319701 seconds (343.45 k allocations: 21.666 MiB, 2.51% gc time)
0.320600 seconds (343.36 k allocations: 21.660 MiB, 2.50% gc time)
0.316938 seconds (343.36 k allocations: 21.660 MiB, 2.56% gc time)
0.318238 seconds (343.31 k allocations: 21.657 MiB, 2.51% gc time)
0.316747 seconds (343.45 k allocations: 21.666 MiB, 2.58% gc time)
0.323734 seconds (343.40 k allocations: 21.663 MiB, 2.49% gc time)
0.320136 seconds (343.40 k allocations: 21.663 MiB, 2.52% gc time)
0.316931 seconds (343.50 k allocations: 21.669 MiB, 2.55% gc time)
0.316066 seconds (343.40 k allocations: 21.663 MiB, 2.53% gc time)
0.315290 seconds (343.37 k allocations: 21.663 MiB, 2.57% gc time)
0.375906 seconds (410.02 k allocations: 24.403 MiB, 6.18% gc time, 8.52% compilation time)
0.328961 seconds (365.91 k allocations: 22.043 MiB, 2.27% gc time)
0.324912 seconds (365.93 k allocations: 22.044 MiB, 2.21% gc time)
0.317966 seconds (365.93 k allocations: 22.043 MiB, 2.31% gc time)
0.317574 seconds (365.99 k allocations: 22.047 MiB, 2.41% gc time)
0.316693 seconds (365.93 k allocations: 22.043 MiB, 2.25% gc time)
0.318666 seconds (365.97 k allocations: 22.047 MiB, 2.37% gc time)
0.316730 seconds (365.83 k allocations: 22.038 MiB, 2.29% gc time)
0.317443 seconds (365.69 k allocations: 22.031 MiB, 2.33% gc time)
0.318769 seconds (365.94 k allocations: 22.044 MiB, 2.36% gc time)
0.320683 seconds (365.92 k allocations: 22.043 MiB, 2.22% gc time)
0.319358 seconds (365.88 k allocations: 22.041 MiB, 2.38% gc time)
0.318528 seconds (365.78 k allocations: 22.035 MiB, 2.33% gc time)
0.322693 seconds (365.73 k allocations: 22.034 MiB, 2.31% gc time)
0.323850 seconds (365.83 k allocations: 22.038 MiB, 2.66% gc time)
0.320972 seconds (365.85 k allocations: 22.040 MiB, 2.41% gc time)
0.324835 seconds (365.77 k allocations: 22.035 MiB, 2.22% gc time)
0.322921 seconds (365.93 k allocations: 22.044 MiB, 2.19% gc time)
0.320311 seconds (365.80 k allocations: 22.037 MiB, 2.24% gc time)
0.324080 seconds (365.67 k allocations: 22.031 MiB, 2.23% gc time)
8 changes: 3 additions & 5 deletions examples/3.koma_paper/comparison_speed/MRiLab_speed.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -39,22 +39,20 @@ if (ARGS == String[]) #No arguments, use defaults
simParams = Dict{String,Any}(
"Nblocks" => 20,
"gpu" => true,
"gpu_device" => 0,
"Nthreads" => 1
"gpu_device" => 0
)
else
simParams = Dict{String,Any}(
"Nblocks" => 20,
"gpu" => ARGS[1] == "gpu" ? true : false,
"gpu_device" => parse(Int64, ARGS[2]),
"Nthreads" => parse(Int64, ARGS[3])
"gpu_device" => parse(Int64, ARGS[2])
)
end

Nexp = 20
raw = @suppress simulate(phantom, seq, sys; simParams) #warmup
for i = 1:Nexp
raw = simulate(phantom, seq, sys; simParams)
local raw = simulate(phantom, seq, sys; simParams)
end
# plot_signal(raw; range=[50.5, 54]) #; show_sim_blocks=true)

Expand Down
6 changes: 3 additions & 3 deletions examples/3.koma_paper/comparison_speed/run_test.sh
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@@ -1,7 +1,7 @@
#!/bin/bash
echo "### KOMA Multi-Shot Spiral CPU ###" | tee .out
julia $1 ./MRiLab_speed.jl cpu 0 8 | tee -a .out #CPU
julia -t 8 $1 ./MRiLab_speed.jl cpu 0 | tee -a .out #CPU
echo "### KOMA Multi-Shot Spiral GPU0 ###" | tee -a .out
julia $1 ./MRiLab_speed.jl gpu 0 1 | tee -a .out #GPU0
julia -t 8 $1 ./MRiLab_speed.jl gpu 0 | tee -a .out #GPU0
echo "### KOMA Multi-Shot Spiral GPU1 ###" | tee -a .out
julia $1 ./MRiLab_speed.jl gpu 1 1 | tee -a .out #GPU1
julia -t 8 $1 ./MRiLab_speed.jl gpu 1 | tee -a .out #GPU1
2 changes: 1 addition & 1 deletion src/KomaMRI.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,7 @@ using Scanf, ProgressMeter
#Datatypes
using Parameters
#Simulation
using CUDA, Interpolations, Hwloc
using CUDA, Interpolations
#Reconstruction
using MRIReco, MRIFiles
@reexport using MRIReco: RawAcquisitionData, AcquisitionData, reconstruction
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15 changes: 6 additions & 9 deletions src/simulation/SimulatorCore.jl
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Original file line number Diff line number Diff line change
@@ -1,5 +1,3 @@
const Nphyscores = Hwloc.num_physical_cores()

abstract type SimulationMethod end #get all available types by using subtypes(KomaMRI.SimulationMethod)
abstract type SpinStateRepresentation{T<:Real} end #get all available types by using subtypes(KomaMRI.SpinStateRepresentation)

Expand Down Expand Up @@ -28,7 +26,7 @@ separating the spins of the phantom `obj` in `Nthreads`.
"""
function run_spin_precession_parallel!(obj::Phantom{T}, seq::DiscreteSequence{T}, sig::AbstractArray{Complex{T}},
Xt::SpinStateRepresentation{T}, sim_method::SimulationMethod;
Nthreads=Nphyscores) where {T<:Real}
Nthreads=Threads.nthreads()) where {T<:Real}

parts = kfoldperm(length(obj), Nthreads, type="ordered")

Expand Down Expand Up @@ -60,7 +58,7 @@ different number threads to excecute the process.
"""
function run_spin_excitation_parallel!(obj::Phantom{T}, seq::DiscreteSequence{T},
Xt::SpinStateRepresentation{T}, sim_method::SimulationMethod;
Nthreads=Nphyscores) where {T<:Real}
Nthreads=Threads.nthreads()) where {T<:Real}

parts = kfoldperm(length(obj), Nthreads; type="ordered")

Expand Down Expand Up @@ -98,7 +96,7 @@ take advantage of CPU parallel processing.
"""
function run_sim_time_iter!(obj::Phantom, seq::DiscreteSequence, sig::AbstractArray{Complex{T}},
Xt::SpinStateRepresentation{T}, sim_method::SimulationMethod;
Nblocks=1, Nthreads=Nphyscores, parts=[1:length(seq)], w=nothing) where {T<:Real}
Nblocks=1, Nthreads=Threads.nthreads(), parts=[1:length(seq)], w=nothing) where {T<:Real}
# Simulation
rfs = 0
samples = 1
Expand Down Expand Up @@ -168,16 +166,15 @@ julia> plot_signal(ismrmrd)
"""
function simulate(obj::Phantom, seq::Sequence, sys::Scanner; simParams=Dict{String,Any}(), w=nothing)
#Simulation parameter parsing, and setting defaults
enable_gpu = get(simParams, "gpu", true)
enable_gpu = get(simParams, "gpu", true); if enable_gpu check_use_cuda(); enable_gpu &= use_cuda[] end
gpu_device = get(simParams, "gpu_device", 0)
Nthreads = get(simParams, "Nthreads", enable_gpu ? 1 : Nphyscores)
Nthreads = get(simParams, "Nthreads", enable_gpu ? 1 : Threads.nthreads())
Nblocks = get(simParams, "Nblocks", 20)
Δt = get(simParams, "Δt", 1e-3)
Δt_rf = get(simParams, "Δt_rf", 5e-5)
sim_method = get(simParams, "sim_method", Bloch())
precision = get(simParams, "precision", "f32")
return_type = get(simParams, "return_type", "raw")
if enable_gpu check_use_cuda(); enable_gpu &= use_cuda[] end
return_type = get(simParams, "return_type", "raw")
# Simulation init
t, Δt = get_uniform_times(seq, Δt; Δt_rf)
t = [t; t[end]+Δt[end]]
Expand Down

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Registration pull request created: JuliaRegistries/General/74821

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:

git tag -a v0.7.2 -m "<description of version>" 6132e9d6b9da06b8504ed2b5d0359a4e04346e91
git push origin v0.7.2

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