Example: Calling External Solvers

[finmod]

In the external solvers section,

sol =solve(prob::ODEProblem,tspan,Δt=Δt,alg=:ode45)
plot(sol,lab=["x" "y"])

LoadError: UndefVarError: ExplicitODE not defined
while loading In[4], in expression starting on line 1

in #solve#559(::Array{Any,1}, ::Function, ::DifferentialEquations.ODEProblem{Array{Float64,1},Float64}, ::Array{Int64,1}) at C:\Users\Denis.julia\v0.5\DifferentialEquations\src\ode\ode_solve.jl:256
in (::DifferentialEquations.#kw##solve)(::Array{Any,1}, ::DifferentialEquations.#solve, ::DifferentialEquations.ODEProblem{Array{Float64,1},Float64}, ::Array{Int64,1}) at .:0

then at

sol =solve(prob::ODEProblem,tspan,Δt=Δt,alg=:dopri5)
plot(sol,lab=["x" "y"])

[DifferentialEquations.jl] Initializing backend: ODEInterface
LoadError: Cannot find method(s) for dopri5! I've tried to loadODESolvers(), but it didn't work. Please check ODEInterface.help_solversupport() and call loadODESolvers and check also this output. For further information see also ODEInterface.help_install.

while loading In[5], in expression starting on line 1

in getAllMethodPtrs(::String) at C:\Users\Denis.julia\v0.5\ODEInterface\src.\DLSolvers.jl:229
in dopri5_impl(::Function, ::Float64, ::Float64, ::Array{Float64,1}, ::ODEInterface.OptionsODE, ::ODEInterface.DopriArguments{Int64}) at C:\Users\Denis.julia\v0.5\ODEInterface\src.\Dopri5.jl:128
in dopri5(::Function, ::Float64, ::Float64, ::Array{Float64,1}, ::ODEInterface.OptionsODE) at C:\Users\Denis.julia\v0.5\ODEInterface\src.\Dopri5.jl:102
in odecall(::ODEInterface.#dopri5, ::Function, ::Array{Float64,1}, ::Array{Float64,1}, ::ODEInterface.OptionsODE) at C:\Users\Denis.julia\v0.5\ODEInterface\src.\Call.jl:115
in #solve#559(::Array{Any,1}, ::Function, ::DifferentialEquations.ODEProblem{Array{Float64,1},Float64}, ::Array{Int64,1}) at C:\Users\Denis.julia\v0.5\DifferentialEquations\src\ode\ode_solve.jl:216
in (::DifferentialEquations.#kw##solve)(::Array{Any,1}, ::DifferentialEquations.#solve, ::DifferentialEquations.ODEProblem{Array{Float64,1},Float64}, ::Array{Int64,1}) at .:0

and again for the next two dopri5

Finally at

sol =solve(prob::ODEProblem,tspan,Δt=Δt,alg=:cvode_Adams)
plot(sol,lab=["x" "y"])

[DifferentialEquations.jl] Initializing backend: Sundials
LoadError: UndefVarError: cvode_fulloutput not defined
while loading In[8], in expression starting on line 1

in #solve#559(::Array{Any,1}, ::Function, ::DifferentialEquations.ODEProblem{Array{Float64,1},Float64}, ::Array{Int64,1}) at C:\Users\Denis.julia\v0.5\DifferentialEquations\src\ode\ode_solve.jl:317
in (::DifferentialEquations.#kw##solve)(::Array{Any,1}, ::DifferentialEquations.#solve, ::DifferentialEquations.ODEProblem{Array{Float64,1},Float64}, ::Array{Int64,1}) at .:0

[ChrisRackauckas]

Did you do the install from this page?

http://juliadiffeq.github.io/DifferentialEquations.jl/latest/man/conditional_dependencies.html

Most of the installs are not for the latest tag:

• Sundials needs to be on master until the next tag.
• ODE needs to use the JuliaODE branch (@pwl's iterator PR)
• ODEInterface should work just fine on its master.

Did ODEInterface build for you? Try `Pkg.build("ODEInterface").

I realized that the links in the README broke when we moved to JuliaDiffEq, so I just pushed up a fix for that (you might need to refresh).

[finmod]

The answer is no for some of them. Should I remove the existing packages and install from

http://juliadiffeq.github.io/DifferentialEquations.jl/latest/man/conditional_dependencies.html http://juliadiffeq.github.io/DifferentialEquations.jl/latest/man/conditional_dependencies.html

What is the right sequence of commands to return to this point.

From: Christopher Rackauckas [mailto:notifications@github.com]
Sent: Monday, September 12, 2016 9:54 PM
To: JuliaDiffEq/DifferentialEquations.jl DifferentialEquations.jl@noreply.github.com
Cc: finmod denis.richard@dr.com; Author author@noreply.github.com
Subject: Re: [JuliaDiffEq/DifferentialEquations.jl] Example: Calling External Solvers (#49)

Did you do the install from this page:?

http://juliadiffeq.github.io/DifferentialEquations.jl/latest/man/conditional_dependencies.html

Most of the installs are not for the latest tag:

• Sundials needs to be on master until the next tag.
• ODE needs to use the JuliaODE branch (@pwl https://github.com/pwl 's iterator PR)
• ODEInterface should work just fine on its master.

Did ODEInterface build for you? Try `Pkg.build("ODEInterface").

I realized that the links in the README broke when we moved to JuliaDiffEq, so I just pushed up a fix for that (you might need to refresh).

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[ChrisRackauckas]

To get to the right branch for Sundials, you just need to do

Pkg.checkout("Sundials")

If you followed the previous instructions for using it pre-JuliaDiffEq/Sundials.jl#67, you will need to

Pkg.rm("Sundials")
Pkg.add("Sundials")
Pkg.checkout("Sundials")
Pkg.build("Sundials") #Maybe? It might build for you automatically

After SciML/Sundials.jl#75, Sundials will get a new minor tag and this will no longer be necessary.

For ODE.jl, you need to make sure you're on pwl's repo:

Pkg.rm("ODE")
Pkg.clone("https://github.com/JuliaODE/ODE.jl")

Notice that the command here is clone since Pkg.add will get the version from JuliaDiffEq which is not the work-in-progress branch that DifferentialEquations.jl is compatible with (this work-in-progress branch is set to replace the current ODE.jl sometime "soon")

ODEInterface should just work, though it might have building issues. If you run

using ODEInterface
loadODESolvers()

Do you get errors?

[finmod]

Sundials is now fine. Let get through the rest.

From: Christopher Rackauckas [mailto:notifications@github.com]
Sent: Monday, September 12, 2016 10:26 PM
To: JuliaDiffEq/DifferentialEquations.jl DifferentialEquations.jl@noreply.github.com
Cc: finmod denis.richard@dr.com; Author author@noreply.github.com
Subject: Re: [JuliaDiffEq/DifferentialEquations.jl] Example: Calling External Solvers (#49)

To get to the right branch for Sundials, you just need to do

Pkg.checkout("Sundials")

If you followed the previous instructions for using it pre-JuliaDiffEq/Sundials.jl#67, you will need to

Pkg.rm("Sundials")
Pkg.add("Sundials")
Pkg.checkout("Sundials")
Pkg.build("Sundials") #Maybe? It might build for you automatically

After SciML/Sundials.jl#75 SciML/Sundials.jl#75 , Sundials will get a new minor tag and this will no longer be necessary.

For ODE.jl, you need to make sure you're on pwl's repo:

Pkg.rm("ODE")
Pkg.clone("https://github.com/JuliaODE/ODE.jl")

Notice that the command here is clone since Pkg.add will get the version from JuliaDiffEq which is not the work-in-progress branch that DifferentialEquations.jl is compatible with (this work-in-progress branch is set to replace the current ODE.jl sometime "soon")

ODEInterface should just work, though it might have building issues. If you run

using ODEInterface
loadODESolvers()

Do you get errors?

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Reply to this email directly, view it on GitHub #49 (comment) , or mute the thread https://github.com/notifications/unsubscribe-auth/AMHyIqKaN1qwugmB_D-PFM1xJFwPnkr8ks5qpcNLgaJpZM4J7A8c . https://github.com/notifications/beacon/AMHyIgrzruaimtGIz38IlXXk8fWo6zN_ks5qpcNLgaJpZM4J7A8c.gif

[finmod]

For ODE, it says that the package already exists.

This is after: Pkg.rm(“ODE”)

For ODEInterface, nothing doing.

From: Christopher Rackauckas [mailto:notifications@github.com]
Sent: Monday, September 12, 2016 10:26 PM
To: JuliaDiffEq/DifferentialEquations.jl DifferentialEquations.jl@noreply.github.com
Cc: finmod denis.richard@dr.com; Author author@noreply.github.com
Subject: Re: [JuliaDiffEq/DifferentialEquations.jl] Example: Calling External Solvers (#49)

To get to the right branch for Sundials, you just need to do

Pkg.checkout("Sundials")

If you followed the previous instructions for using it pre-JuliaDiffEq/Sundials.jl#67, you will need to

Pkg.rm("Sundials")
Pkg.add("Sundials")
Pkg.checkout("Sundials")
Pkg.build("Sundials") #Maybe? It might build for you automatically

After SciML/Sundials.jl#75 SciML/Sundials.jl#75 , Sundials will get a new minor tag and this will no longer be necessary.

For ODE.jl, you need to make sure you're on pwl's repo:

Pkg.rm("ODE")
Pkg.clone("https://github.com/JuliaODE/ODE.jl")

Notice that the command here is clone since Pkg.add will get the version from JuliaDiffEq which is not the work-in-progress branch that DifferentialEquations.jl is compatible with (this work-in-progress branch is set to replace the current ODE.jl sometime "soon")

ODEInterface should just work, though it might have building issues. If you run

using ODEInterface
loadODESolvers()

Do you get errors?

—
You are receiving this because you authored the thread.
Reply to this email directly, view it on GitHub #49 (comment) , or mute the thread https://github.com/notifications/unsubscribe-auth/AMHyIqKaN1qwugmB_D-PFM1xJFwPnkr8ks5qpcNLgaJpZM4J7A8c . https://github.com/notifications/beacon/AMHyIgrzruaimtGIz38IlXXk8fWo6zN_ks5qpcNLgaJpZM4J7A8c.gif

[ChrisRackauckas]

You may want to use the web interface when showing code / error messages. If you tried to put them there, they didn't show up.

It might be a little messy to install pwl's branch for ODE.jl. You may need to mess with your local METADATA. Personally, when I switched back and forth I just wiped the METADATA, though that's a nuclear option which requires you re-install your packages (good for testing, bad thing to tell users). You may be able to remove the ODE folder from METADAT (METADATA/ODE), and remove the compile cache ODE.ji, and then run Pkg.clone("https://github.com/JuliaODE/ODE.jl"). However, note that this will make your METADATA dirty, so it may not Pkg.update() anymore.

Maybe @mauro3 or @pwl knows of a better way to switch ODE between the different repos more seamlessly?

[ChrisRackauckas]

For ODEInterface, restart from the beginning. It should be:

Pkg.rm("ODEInterface")
Pkg.add("ODEInterface")
Pkg.build("ODEInterface")
loadODESolvers()

If nothing errors there, then it should be working.

[finmod]

At Pkg.build(“ODEInterface”), it says that currently only gfrtran is supported.

Does not build.

From: Christopher Rackauckas [mailto:notifications@github.com]
Sent: Monday, September 12, 2016 11:16 PM
To: JuliaDiffEq/DifferentialEquations.jl DifferentialEquations.jl@noreply.github.com
Cc: finmod denis.richard@dr.com; Author author@noreply.github.com
Subject: Re: [JuliaDiffEq/DifferentialEquations.jl] Example: Calling External Solvers (#49)

For ODEInterface, restart from the beginning. It should be:

Pkg.rm("ODEInterface")
Pkg.add("ODEInterface")
Pkg.build("ODEInterface")
loadODESolvers()

If nothing errors there, then it should be working.

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[ChrisRackauckas]

Ahh, and you said you're on Windows? You might have the same path issue I had when I first tried it: luchr/ODEInterface.jl#2

If you are using Juno and added Julia to the path to do so, that can cause this issue.

[finmod]

So a fast resolution is to remove Juno with Pkg.rm(“Juno”) and then the series on ODEInterface again?

From: Christopher Rackauckas [mailto:notifications@github.com]
Sent: Monday, September 12, 2016 11:25 PM
To: JuliaDiffEq/DifferentialEquations.jl DifferentialEquations.jl@noreply.github.com
Cc: finmod denis.richard@dr.com; Author author@noreply.github.com
Subject: Re: [JuliaDiffEq/DifferentialEquations.jl] Example: Calling External Solvers (#49)

Ahh, and you said you're on Windows? You might have the same path issue I had when I first tried it: luchr/ODEInterface.jl#2 luchr/ODEInterface.jl#2

If you are using Juno and added Julia to the path to do so, that can cause this issue.

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[ChrisRackauckas]

No. You need to explicitly give Juno the path, like:

Then you need to make sure Julia is not in your path, install mingw-64 from here, and add it to your path like here:

(the third path on the far right is where the mingw path is)

Then ODEInterface should build correctly on Windows if you're using Juno (this is one of the reasons why I am making native Julia versions of all of those, because this can be a nightmare to get right!)

[mauro3]

The reason Pkg.rm("ODE") does not remove ODE is because other packages depend on it, see.

The way I switch is add a remote and checkout that. I don't think this can be done from the Julia REPL. In the shell cd to the directory of ODE.jl, (~/.julia/v0.5/ODE on my system):

git remote add JuliaODE https://github.com/JuliaODE/ODE.jl.git
git checkout JuliaODE/master

it will say something about a detached head, don't worry. To go back to the original:

git checkout origin/master

(I think) Edited according to Chris' comment

[ChrisRackauckas]

Yeah, I feared there wasn't a pure Julia way to do it. What you're saying should work, though maybe it might need to be git checkout origin/master, and since master is used in both, if someone uses Github Desktop it will bug if you try to change between the two. So it's a little bit of a mess, but it'll fix itself when the PR is done and goes through.

[mauro3]

I guess you could open a feature request issue:

Pkg.checkout(pkg, [branch="master"]; merge=true, pull=true, remote=origin)

But probably it's fine to just leave that. For trickier git-stuff it's easier to just git-it.

[ChrisRackauckas]

Yeah, I don't know if it's necessary since at the point where you want to specify the remote, you will have had to add the remote with Git anyways, so you probably know git (or are just following someone's instructions line by line which could just be terminal commands)