owl-ode-sundials 0.5.0 · OCaml Package

README

Tutorial
Supported Solvers
JavaScript and Mirage backends
Citing
Notes
Further comments
Contributing

Tutorial

Please refer to the relevant owl projects page for more details.

The library is published on the opam repository and can be installed with opam:

opam install owl-ode

The bindings for SUNDIALS and ODEPACK can be installed separately in the same fashion: opam install owl-ode-sundials and opam install owl-ode-odepack respectively.

You can run the current examples as follows

# owl-ode
dune exec examples/damped.exe
dune exec examples/custom_rk45.exe

# owl-ode-sundials
dune exec examples/van_der_pol_sundials.exe

# owl-ode-odepack
dune exec examples/van_der_pol_odepack.exe

provided that you have installed the relevant libraries and their external dependencies (e.g. openblas, sundials).
In most cases, you can leverage opam itself to install the necessary external dependencies by running opam depext owl-ode owl-ode-odepack owl-ode-sundials before attempting the installation of the ocaml libraries.

In case of linking issues, please refer to owl's README (especially if you are running a variant of ubuntu): https://github.com/owlbarn/owl/blob/master/README.md#troubleshooting

See also the SUNDIALS section of this README if you need sundials on macosx, and to https://github.com/inria-parkas/sundialsml for more general issues with sundials.

The documentation for the library is accessible at ocaml.xyz/owl_ode/owl-ode.

Overview

Consider the problem of integrating a linear dymaical system that evolves according to

dx/dt = f(x,t) = Ax      x(t0) = x0,

where x is the state of the system, dx/dt is the time derivative of the state, and t is time.
Our system A is the matrix [[1,-1; 2,-3]] and the system's initial state x0 is at [[-1]; [1]].
We want to integrate for 2 seconds with a step size of 1 millisecond. Here is how you would solve this
problem using OwlDE:

(* f(x,t) *)
let f x t = 
   let a = [|[|1.; -1.|];
             [|2.; -3.|]|]
           |> Owl.Mat.of_arrays in
   Owl.Mat.(a *@ x)

(* temporal specification:
   construct a record using the constructor T1 and 
   includes information of start time, duration, 
   and step size.*)
let tspec = Owl_ode.Types.(T1 {t0 = 0.; duration = 2.; dt=1E-3})

(* initial state of the system *)
let x0 = Mat.of_array [|-1.; 1.|] 2 1

(* putting everything together *)
let ts, xs = Owl_ode.Ode.odeint (module Owl_ode.Native.D.RK4) f x0 tspec () 

(* or equivalently *)
let ts, xs = Owl_ode.Ode.odeint Owl_ode.Native.D.rk4 f x0 tspec ()

The results of odeint in this example are two matrices xs and ts, which contain the value of the state x at each time t. More specifically, column 0 of the matrix xs contains x(t0), while column 2000 contains x(t0 +. duration).

Here, we integrated the dynamical system with Native.D.RK4, a fixed-step, double-precision Runge-Kutta solver.

In Owl Ode, We support a number of natively-implemented double-precision solvers in Native.D and single-precision ones in Native.S.

The simple example above illustrates the basic components of defining and solving an ode problem using Owl Ode.
The main function Owl_ode.odeint takes as its arguments:

a solver module of type Solver,
a function f that evolves the state,
an initial state x0, and
temporal spsecification tspec.

The solver module constrains the the type of x0 and that of function f . For example, the solvers in Owl_ode.Native, assume that the states are matrices (i.e. x:mat is a matrix) and f:mat->float->mat returns the time derivative of x at time t.

We have provided a number of single and double-precision symplectic solvers in Owl_ode.Symplectic.
For symplectic ode problems, the state of the system is a tuple (x,p):mat * mat, where x and p are the position and momentum coordinates of the system and f:(mat,mat)->float->mat is a forcing function defined with at state (x,p) and time t. For a detailed example on how to call symplectic solvers, see example/damped.ml.

Sundials Cvode

We have implemented a thin wrapper over Sundials Cvode (via sundialsml wrapper). To use Cvode, one can use

Owl_ode_sundials.Owl_Cvode or
Owl_ode_sundials.Owl_Cvode_Stiff.

Currently, we only support double-precision Sundials solvers. To use Sundials in Owl Ode, one needs to install Sundials and sundialsml (see sundialsml for instructions).

Note that the sundials formula on osx installs a too recent version of sundials. You can use the custom formula https://gist.github.com/mseri/60d26461b764e77b45d82ad7f0b0d7de to install the correct one.

ODEPACK Lsoda

We have implemented a thin wrapper over ODEPACK (via the odepack OCaml library).
Currently only Owl_ode_odepack.lsoda is provided, with configurable absolute and relative tolerances.

Automatic inference of state dimensionality

All the provided solvers automatically infer the dimensionality of the state from the initial state.
Consider Native solvers, for which the state of the system is a matrix. The initial state can be a row vector, a column vector, or a matrix, so long as it is consistent with that of f.
If the initial state x0 is a row vector with dimensions 1xN and we integrate the system for T time steps, the time and states will be stacked vertically in the output (i.e. ts will have dimensions Tx1 and and xs will have dimensions TxN). On the contrary, if the initial state x0 is a column vector with dimensions, the results will be stacked horizontally (i.e. ts will have dimensions 1xT and xs will have dimensions NxT).

We also support temporal integration of matrices. That is, cases in which the state x is a matrix of dimensions of dimensions NxM. By default, in the output, we flatten and stack the states vertically (i.e., ts has dimensions Tx1 and xs has dimensions TxNM. We have a helper function Native.D.to_state_array which can be used to "unflatten" xs into an array of matrices.

Custom Solvers

We can define new solver module by creating a module of type Solver. For example, to create a custom Cvode solver that has a relative tolerance of 1E-7 as opposed to the default 1E-4, we can define and use custom_cvode as follows:

let custom_cvode = Owl_ode_sundials.cvode ~stiff:false ~relative_tol:1E-7 ~abs_tol:1E-4 
(* usage *)
let ts, xs = Owl_ode.Ode.odeint custom_cvode f x0 tspec ()

Here, we use the cvode function construct a solver module Custom_Owl_Cvode. This function is conveniently defined in src/sundials/owl_ode_sundials.ml. It takes the parameters (stiff, relative_tol, and abs_tol) and returns a solver module of type

val custom_cvode : (module Solver with 
                     type state = Mat.mat
                     and type f = Mat.mat -> float -> Mat.mat
                     and type step_output = Mat.mat * float
                     and type solve_output = Mat.mat * Mat.mat)

Similar helper functions like cvode have been also defined for native and symplectic solvers.

Supported Solvers

Native

Euler
Midpoint
RK4
RK23
RK45

example usage: Owl_ode.Native.D.Euler (or Owl_ode.Native.D.euler), Owl_ode.Native.S.Euler (or Owl_ode.Native.S.euler)

Symplectic

Symplectic_Euler
PseudoLeapFrog
LeapFrog
Ruth3
Ruth4

example usage: Owl_ode.Native.D.Symplectic_Euler, Owl_ode.Symplectic.S.Symplectic_Euler

Sundials

Owl_Cvode (Adams)
Owl_Cvode_Stiff (BDF)

example usage: Owl_ode_sundials.Owl_Cvode

We only support double-precisions Sundials solvers.

ODEPACK

LSODA (automatic switching to stiff/non-stiff algorithms)

We only support double-precision Odepack solvers.

JavaScript and Mirage backends

The owl-ode-base contains implementations that are purely written in OCaml.
As such, they are compatible for use in Mirage OS or in conjunction with js_of_ocaml, where C library linking is not supported.

You can see an example of this here: http://www.mseri.me/owlde-demo-icfp2019/ (source code: https://github.com/mseri/owlde-demo-icfp2019)

Citing

If you have used this package for research that resulted in a publication, please be kind enough to cite the software paper associated with DynamicalBilliards. The DOI is https://doi.org/10.21105/joss.01812 and you can cite as:

or if you use BibTeX:

@article{Seri2019,
  doi = {10.21105/joss.01812},
  url = {https://doi.org/10.21105/joss.01812},
  year = {2019},
  publisher = {The Open Journal},
  volume = {4},
  number = {44},
  pages = {1812},
  author = {Marcello Seri and Ta-Chu Kao},
  title = {OwlDE: making ODEs first-class `Owl` citizens},
  journal = {Journal of Open Source Software}
}

Notes

The main idea is develop a uniform interface to integrate ODE solvers (and in the future finite element methods) into Owl.
Currently there are three options available, providing incompatible underlying representations:

sundialsml, providing a wrapper over Sundials
ocaml-odepack, providing bindings for ODEPACK (same solvers used by scipy's old interface scipy.integrate.odeint)
gsl-ocaml, providing bindings for GSL, in particular the ODE integrator bindings are here mmottl/gsl-ocaml/src/odeiv.mli

Of course such an interface could provide additional purely OCaml functionalities, like robust native implementations of

[x] standard fixed-step ode solvers, like Euler, Midpoint, Runge-Kutta 4
[x] standard adaptive solvers, say rk2(3), and rk4(5) or Tsit5 (in progress, missing Tsit5)
[x] symplectic ode solvers, like Störmer-Verlet, Forest-Ruth or Yoshida
[x] sundialsml interface (already partially implemented)
[x] odepack interface (already partially implemented, currently not fully configurable/controllable) and
[ ] implementations leveraging Owl's specific capabilities, e.g. for a Taylor integrator built upon Algodiff.
Albeit relatively old and standard, a good starting point could be the two references from TaylorSeries.jl, namely:
- W. Tucker, Validated numerics: A short introduction to rigorous computations, Princeton University Press (2011).
- A. Haro, Automatic differentiation methods in computational dynamical systems: Invariant manifolds and normal forms of vector fields at fixed points, preprint.

Some important points to address for this are:

[X] provide a uniform type safe interface, capable of accepting pluggable new engines and dealing with the different sets of configuration options of each of them (maybe extensible types or GADTs can help in this regard more than Functors?)
[X] full Owl types interoperability
[X] ease of use (compared to JuliaDiffEq and Scipy)
[ ] make the native implementations more robust (right now they are naive OCaml implementations)
...

OwlDE can be used to implement the Neural ODE idea in Owl: see https://github.com/tachukao/adjoint_ode/ and https://github.com/mseri/owlde-demo-icfp2019

Further comments

We currently cannot have implicit methods for the lack of vector-valued root finding functions. We should add implementations for those, and then introduce some implicit methods (e.g. the implicit Störmer-Verlet is much more robust and works nicely for non-separable Hamiltonians). At least we can use Sundials for now :-)

It would also be nice to provide a function that takes the pair (t, y) and returns the interpolated function.

We should make the integrators more robust and with better failure modes, we could take inspiration from the very readable scipy implementation [https://github.com/scipy/scipy/blob/v1.2.0/scipy/integrate/_ivp/rk.py#L15].

Contributing

We use ocamlformat to format out code. Our preferred ocamlformat setup is specified in .ocamlformat.
With dune, it is super simple to reformat the entire code base. Once you have ocamlformat installed,
all you have to do in the project directory is do

dune build @fmt
dune promote

owl-ode-sundials

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