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Update to Julia 1.3.0 #11

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12 changes: 6 additions & 6 deletions Dockerfile
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
# Start with 0.5.0 which is also latest at the moment
FROM julia:0.5.0
FROM julia:1.3.0

# Install stuff needed by the HttpParser package
RUN apt-get update && apt-get install -y \
Expand All @@ -12,9 +12,9 @@ RUN apt-get update && apt-get install -y \

# Make package folder and install everything in require
ENV JULIA_PKGDIR=/opt/julia
RUN julia -e "Pkg.init()"
COPY REQUIRE /opt/julia/v0.5/REQUIRE
RUN julia -e "Pkg.resolve()"
RUN julia -e "Pkg.activate()"
COPY Project.toml /opt/julia/v1.3.0/Project.toml
RUN julia -e "Pkg.instantiate()"

# Build all the things
RUN julia -e 'Pkg.build()'
Expand All @@ -23,10 +23,10 @@ RUN julia -e 'Pkg.build()'
RUN julia -e 'Pkg.build("Plots"); Pkg.build("SymEngine"); Pkg.rm("Conda")'

# Clone WebBase
RUN julia -e 'Pkg.clone("https://github.com/JuliaDiffEq/DiffEqWebBase.jl");'
RUN julia -e 'Pkg.add(PackageSpec(url="https://github.com/JuliaDiffEq/DiffEqWebBase.jl", rev="master"));'

# Check out master until patches
RUN julia -e 'Pkg.checkout("DiffEqBase"); Pkg.checkout("OrdinaryDiffEq"); Pkg.checkout("StochasticDiffEq"); Pkg.checkout("ParameterizedFunctions");'
RUN julia -e 'Pkg.add(PackageSpec(name="DiffEqBase", rev="master")); Pkg.add(PackageSpec(name="OrdinaryDiffEq", rev="master")); Pkg.add(PackageSpec(name="StochasticDiffEq", rev="master")); Pkg.add(PackageSpec(name="ParameterizedFunctions", rev="master"));'

# Force precompile of all modules -- this should greatly improve startup time
RUN julia -e 'using DiffEqBase, DiffEqWebBase, OrdinaryDiffEq, StochasticDiffEq, ParameterizedFunctions, Plots, Mux, JSON, HttpCommon'
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12 changes: 12 additions & 0 deletions Project.toml
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@@ -0,0 +1,12 @@
[deps]
Calculus = "49dc2e85-a5d0-5ad3-a950-438e2897f1b9"
DiffEqBase = "2b5f629d-d688-5b77-993f-72d75c75574e"
DiffEqWebBase = "199ddbe7-5660-5d34-ad45-164698b1b2b3"
HttpCommon = "77172c1b-203f-54ac-aa54-3f1198fe9f90"
JSON = "682c06a0-de6a-54ab-a142-c8b1cf79cde6"
Mux = "a975b10e-0019-58db-a62f-e48ff68538c9"
OrdinaryDiffEq = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed"
ParameterizedFunctions = "65888b18-ceab-5e60-b2b9-181511a3b968"
Plotly = "58dd65bb-95f3-509e-9936-c39a10fdeae7"
PlotlyJS = "f0f68f2c-4968-5e81-91da-67840de0976a"
StochasticDiffEq = "789caeaf-c7a9-5a7d-9973-96adeb23e2a0"
175 changes: 89 additions & 86 deletions api/mux_server.jl
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Original file line number Diff line number Diff line change
@@ -1,27 +1,29 @@
tic()
using DiffEqBase, DiffEqWebBase, OrdinaryDiffEq, StochasticDiffEq, Calculus, ParameterizedFunctions, Plots, Mux, JSON, HttpCommon
include("sanitation.jl")
plotly()

const algs = Dict{Symbol,DEAlgorithm}(
:Tsit5 => Tsit5(),
:Vern6 => Vern6(),
:Vern7 => Vern7(),
:BS3 => BS3(),
:Rosenbrock23 => Rosenbrock23(),
:SRIW1 => SRIW1(),
:SRA1 => SRA1())
const opts = Dict{Symbol,Bool}(
:build_tgrad => false,
:build_jac => false,
:build_expjac => false,
:build_invjac => false,
:build_invW => false,
:build_hes => false,
:build_invhes => false,
:build_dpfuncs => false)

println("Package loading took this long: ", toq())
time = @elapsed begin
using DiffEqBase, DiffEqWebBase, OrdinaryDiffEq, StochasticDiffEq, Calculus, ParameterizedFunctions, Plots, Mux, JSON, HttpCommon
include("sanitation.jl")
plotly()

const algs = Dict{Symbol,DEAlgorithm}(
:Tsit5 => Tsit5(),
:Vern6 => Vern6(),
:Vern7 => Vern7(),
:BS3 => BS3(),
:Rosenbrock23 => Rosenbrock23(),
:SRIW1 => SRIW1(),
:SRA1 => SRA1())
const opts = Dict{Symbol,Bool}(
:build_tgrad => false,
:build_jac => false,
:build_expjac => false,
:build_invjac => false,
:build_invW => false,
:build_hes => false,
:build_invhes => false,
:build_dpfuncs => false)

end

println("Package loading took this long: ", time)

# Headers -- set Access-Control-Allow-Origin for either dev or prod
function withHeaders(res, req)
Expand Down Expand Up @@ -69,70 +71,71 @@ function solveit(req::Dict{Any,Any})
end

function solveit(b64::String)
tic()

setup_time = @elapsed begin
strObj = String(base64decode(b64))
obj = JSON.parse(strObj)
title = obj["title"]
println("Title: ", title)
exstr = string("begin\n", obj["diffEqText"], "\nend")
sanitize_string(exstr)
ex = parse(exstr)
# Need a way to make sure the expression only calls "safe" functions here!!!
println("Diff equ: ", ex)
name = Symbol(strObj)
[sanitize_string(p) for p in obj["parameters"]]
params = [parse(p) for p in obj["parameters"]]
println("Params: ", params)

# Make sure these are always floats
tspan = (Float64(obj["timeSpan"][1]),Float64(obj["timeSpan"][2]))
println("tspan: ", tspan)
u0 = [parse(Float64, u) for u in obj["initialConditions"]]
println("u0: ", u0)
# Also need sanitization here!
sanitize_string(obj["vars"])
vars = eval(parse(obj["vars"]))
println("vars: ", vars, " type: ", typeof(vars))
algstr = obj["solver"] #Get this from the reqest in the future!
f = ode_def_opts(name, opts, ex, params...)

if haskey(obj,"noiseText")
noise_name = Symbol(strObj*"noise")
exstr = string("begin\n", obj["noiseText"], "\nend")
time = @elapsed begin

setup_time = @elapsed begin
strObj = String(base64decode(b64))
obj = JSON.parse(strObj)
title = obj["title"]
println("Title: ", title)
exstr = string("begin\n", obj["diffEqText"], "\nend")
sanitize_string(exstr)
noise_ex = parse(exstr)
println("Noise equ: ", noise_ex)
[sanitize_string(p) for p in obj["noiseParameters"]]
noise_params = [parse(p) for p in obj["noiseParameters"]]
g = ode_def_opts(noise_name, opts, noise_ex, noise_params...)
prob = QuickSDEProblem{Vector{Float64},Float64,true,:Diagonal,typeof(randn)}(f,g,u0,tspan,DiffEqBase.WHITE_NOISE)
else
prob = QuickODEProblem{Vector{Float64},Float64,true}(f,u0,tspan)
end
alg = algs[parse(algstr)]
ex = parse(exstr)
# Need a way to make sure the expression only calls "safe" functions here!!!
println("Diff equ: ", ex)
name = Symbol(strObj)
[sanitize_string(p) for p in obj["parameters"]]
params = [parse(p) for p in obj["parameters"]]
println("Params: ", params)

# Make sure these are always floats
tspan = (Float64(obj["timeSpan"][1]),Float64(obj["timeSpan"][2]))
println("tspan: ", tspan)
u0 = [parse(Float64, u) for u in obj["initialConditions"]]
println("u0: ", u0)
# Also need sanitization here!
sanitize_string(obj["vars"])
vars = eval(parse(obj["vars"]))
println("vars: ", vars, " type: ", typeof(vars))
algstr = obj["solver"] #Get this from the reqest in the future!
f = ode_def_opts(name, opts, ex, params...)

if haskey(obj,"noiseText")
noise_name = Symbol(strObj*"noise")
exstr = string("begin\n", obj["noiseText"], "\nend")
sanitize_string(exstr)
noise_ex = parse(exstr)
println("Noise equ: ", noise_ex)
[sanitize_string(p) for p in obj["noiseParameters"]]
noise_params = [parse(p) for p in obj["noiseParameters"]]
g = ode_def_opts(noise_name, opts, noise_ex, noise_params...)
prob = QuickSDEProblem{Vector{Float64},Float64,true,:Diagonal,typeof(randn)}(f,g,u0,tspan,DiffEqBase.WHITE_NOISE)
else
prob = QuickODEProblem{Vector{Float64},Float64,true}(f,u0,tspan)
end
alg = algs[parse(algstr)]
end
println("Setup time: $setup_time")

length(f.syms) != length(u0) && error("Initial conditions inconsistent with the differential equation. Make sure there is an initial value for every variable.")
(maximum(isinf.(u0)) || maximum(isnan.(u0))) && error("Initial conditions must be finite values")

maxiters = 1e4

solve_time = @elapsed sol = solve(prob,alg,Vector{Vector{Float64}}(),Vector{Float64}(),[],Val{false},maxiters=maxiters)
println("Solve time: $solve_time")

length(sol)>= .9*maxiters && error("Max iterations reached. The equation may be stiff, blow up to infinity, or you choose too long of a timespan. Try the stiff solver (Rosenbrock23 for ODEs) or make sure that the equation has a valid solution. If you need more computing power/time try DifferentialEquations.jl!")

plot_time = @elapsed p = plot(sol,vars=vars)
println("Plot time: $plot_time")

layout = Plots.plotly_layout_json(p)
series = Plots.plotly_series_json(p)

res = Dict("layout" =>layout, "series"=>series, "title" => title)
end
println("Setup time: $setup_time")

length(f.syms) != length(u0) && error("Initial conditions inconsistent with the differential equation. Make sure there is an initial value for every variable.")
(maximum(isinf.(u0)) || maximum(isnan.(u0))) && error("Initial conditions must be finite values")

maxiters = 1e4

solve_time = @elapsed sol = solve(prob,alg,Vector{Vector{Float64}}(),Vector{Float64}(),[],Val{false},maxiters=maxiters)
println("Solve time: $solve_time")

length(sol)>= .9*maxiters && error("Max iterations reached. The equation may be stiff, blow up to infinity, or you choose too long of a timespan. Try the stiff solver (Rosenbrock23 for ODEs) or make sure that the equation has a valid solution. If you need more computing power/time try DifferentialEquations.jl!")

plot_time = @elapsed p = plot(sol,vars=vars)
println("Plot time: $plot_time")

layout = Plots.plotly_layout_json(p)
series = Plots.plotly_series_json(p)

res = Dict("layout" =>layout, "series"=>series, "title" => title)
println("Done, took this long: ", toq())
println("Done, took this long: ", time)
return JSON.json(Dict("data" => res, "error" => false))
end

Expand Down