No convergence in test cases for Sundials 5.7.0 and Python 3.8 #118

Jaimenms · 2021-03-02T07:58:24Z

Hi,

I am testing the ODES using Sundials 5.7.0 and Python 3.8. Everything seems to be fine, except for some DeprecationWarning running nose. Nevertheless I cannot converge the tutorial cases or even the nose tests.

My packages:

(venv) ~/ pip freeze
nose==1.3.7
numpy==1.20.1
scikits.odes==2.6.1
scipy==1.6.1

Here it is a test case:

import numpy as np
from scikits.odes.dae import dae

SOLVER = 'ida'
tout = np.linspace(0, 1)
y_initial = np.array([0])
ydot_initial = np.array([0])
extra_options = {'old_api': False}

def right_hand_side(t, y, ydot, residue):
    """
    User's right hand side function
    """
    pass

dae_solver = dae(SOLVER, right_hand_side, **extra_options)
output = dae_solver.solve(tout, y_initial, ydot_initial)
print(output.values.y)

That outputs the following error:

[IDA ERROR]  IDASolve
  At t = 0 and h = 1.94627e-11, the corrector convergence failed repeatedly or with |h| = hmin.

[[0.]]

Here it is my nose tests output (all failed in Sundials calculations):

(venv) ~/ python -c "import scikits.odes as od; od.test()"
Running unit tests for scikits.odes
NumPy version 1.20.1
NumPy relaxed strides checking option: True
NumPy is installed in /Users/jaimenms/PycharmProjects/optimal-design/venv/lib/python3.8/site-packages/numpy
Python version 3.8.5 (v3.8.5:580fbb018f, Jul 20 2020, 12:11:27) [Clang 6.0 (clang-600.0.57)]
nose version 1.3.7
/Users/jaimenms/PycharmProjects/optimal-design/venv/lib/python3.8/site-packages/nose/suite.py:106: DeprecationWarning: Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated since Python 3.3, and in 3.9 it will stop working
  if isinstance(tests, collections.Callable) and not is_suite:
<__array_function__ internals>:5: DeprecationWarning: `np.alen` is deprecated, use `len` instead
../Users/jaimenms/PycharmProjects/optimal-design/venv/lib/python3.8/site-packages/scikits/odes/dae.py:389: DeprecationWarning: Old api is deprecated, move to new api
  return self._integrator.init_step(t0, y0, yp0, y_ic0_retn, yp_ic0_retn)
......ode.get_info() =
 {'NumSteps': 19, 'NumRhsEvals': 26, 'NumLinSolvSetups': 16, 'NumErrTestFails': 1, 'LastOrder': 2, 'CurrentOrder': 2, 'ActualInitStep': 0.0005000002493687262, 'LastStep': 5.632767015984214, 'CurrentStep': 11.121864790716213}
.True solution:
 [  1.   4.   9.  16.  25.  36.  49.  64.  81. 100.]
Integrated:
 [  1.           4.00000181   9.00000189  16.00000196  25.00000201
  36.00000205  49.00000213  64.00000218  81.00000222 100.00000225]
Difference:
 [0.00000000e+00 1.80709183e-06 1.88536923e-06 1.95964126e-06
 2.00559588e-06 2.05370031e-06 2.12527937e-06 2.18137136e-06
 2.22197630e-06 2.24709419e-06]
Relative:
 [0.00000000e+00 4.51772957e-07 2.09485470e-07 1.22477579e-07
 8.02238353e-08 5.70472309e-08 4.33730483e-08 3.40839275e-08
 2.74318062e-08 2.24709419e-08]
.ode.get_info() =
 {'NumSteps': 19, 'NumRhsEvals': 28, 'NumLinSolvSetups': 0, 'NumErrTestFails': 1, 'LastOrder': 2, 'CurrentOrder': 2, 'ActualInitStep': 0.0005000002493687262, 'LastStep': 5.632767015984214, 'CurrentStep': 11.121864790716213, 'NumPrecEvals': 0, 'NumPrecSolves': 0, 'NumJtimesEvals': 20, 'NumLinIters': 20, 'NumRhsEvalsJtimesFD': 20}
..............................
[CVLS ERROR]  cvLsSetup
  The Jacobian routine failed in an unrecoverable manner.


[CVODE ERROR]  CVode
  At t = 0, the setup routine failed in an unrecoverable manner.

.
[CVLS ERROR]  cvLsSetup
  The Jacobian routine failed in an unrecoverable manner.


[CVODE ERROR]  CVode
  At t = 0, the setup routine failed in an unrecoverable manner.

.
[CVODE ERROR]  CVode
  At t = 0 and h = 2.6974e-09, the corrector convergence test failed repeatedly or with |h| = hmin.

.
[CVODE ERROR]  CVode
  At t = 0 and h = 1.90735e-09, the corrector convergence test failed repeatedly or with |h| = hmin.

.
[CVLS ERROR]  cvLsSolve
  The Jacobian x vector routine failed in an unrecoverable manner.


[CVODE ERROR]  CVode
  At t = 0, the solve routine failed in an unrecoverable manner.

.
[CVLS ERROR]  cvLsSolve
  The Jacobian x vector routine failed in an unrecoverable manner.


[CVODE ERROR]  CVode
  At t = 0, the solve routine failed in an unrecoverable manner.

.
[CVODE ERROR]  CVode
  At t = 0.0314249, mxstep steps taken before reaching tout.

.
[CVODE ERROR]  CVode
  At t = 0.0222206, mxstep steps taken before reaching tout.

.......
[CVODE ERROR]  CVode
  At t = 0, the right-hand side routine failed in an unrecoverable manner.

.
[CVODE ERROR]  CVode
  At t = 0.458122, the right-hand side routine failed in an unrecoverable manner.

.
[CVODE ERROR]  CVode
  The right-hand side routine failed at the first call.

.
[CVODE WARNING]  CVode
  Internal t = 0.5 and h = 1.70033e-17 are such that t + h = t on the next step. The solver will continue anyway.


[CVODE WARNING]  CVode
  Internal t = 0.5 and h = 1.70033e-17 are such that t + h = t on the next step. The solver will continue anyway.


[CVODE WARNING]  CVode
  Internal t = 0.5 and h = 4.25083e-17 are such that t + h = t on the next step. The solver will continue anyway.


[CVODE WARNING]  CVode
  Internal t = 0.5 and h = 4.25083e-17 are such that t + h = t on the next step. The solver will continue anyway.


[CVODE WARNING]  CVode
  Internal t = 0.5 and h = 2.65677e-17 are such that t + h = t on the next step. The solver will continue anyway.


[CVODE WARNING]  CVode
  Internal t = 0.5 and h = 2.65677e-17 are such that t + h = t on the next step. The solver will continue anyway.


[CVODE WARNING]  CVode
  Internal t = 0.5 and h = 1.66048e-17 are such that t + h = t on the next step. The solver will continue anyway.


[CVODE WARNING]  CVode
  Internal t = 0.5 and h = 1.66048e-17 are such that t + h = t on the next step. The solver will continue anyway.


[CVODE WARNING]  CVode
  Internal t = 0.5 and h = 4.1512e-17 are such that t + h = t on the next step. The solver will continue anyway.


[CVODE WARNING]  CVode
  Internal t = 0.5 and h = 4.1512e-17 are such that t + h = t on the next step. The solver will continue anyway.


[CVODE WARNING]  CVode
  The above warning has been issued mxhnil times and will not be issued again for this problem.


[CVODE ERROR]  CVode
  At t = 0.5, mxstep steps taken before reaching tout.

..
[CVODE ERROR]  cvRcheck1
  At t = 0, the rootfinding routine failed in an unrecoverable manner.

.
[CVODE ERROR]  cvRcheck3
  At t = 0.458122, the rootfinding routine failed in an unrecoverable manner.

.
[CVODES WARNING]  CVode
  At the end of the first step, there are still some root functions identically 0. This warning will not be issued again.

...
[CVLS ERROR]  cvLsSetup
  The Jacobian routine failed in an unrecoverable manner.


[CVODE ERROR]  CVode
  At t = 0, the setup routine failed in an unrecoverable manner.

.
[CVLS ERROR]  cvLsSetup
  The Jacobian routine failed in an unrecoverable manner.


[CVODE ERROR]  CVode
  At t = 0, the setup routine failed in an unrecoverable manner.

.
[CVODE ERROR]  CVode
  At t = 0 and h = 2.6974e-09, the corrector convergence test failed repeatedly or with |h| = hmin.

.
[CVODE ERROR]  CVode
  At t = 0 and h = 1.90735e-09, the corrector convergence test failed repeatedly or with |h| = hmin.

.
[CVLS ERROR]  cvLsSolve
  The Jacobian x vector routine failed in an unrecoverable manner.


[CVODE ERROR]  CVode
  At t = 0, the solve routine failed in an unrecoverable manner.

.
[CVLS ERROR]  cvLsSolve
  The Jacobian x vector routine failed in an unrecoverable manner.


[CVODE ERROR]  CVode
  At t = 0, the solve routine failed in an unrecoverable manner.

.
[CVODE ERROR]  CVode
  At t = 0.0314249, mxstep steps taken before reaching tout.

.
[CVODE ERROR]  CVode
  At t = 0.0222206, mxstep steps taken before reaching tout.

.......
[CVODE ERROR]  CVode
  At t = 0, the right-hand side routine failed in an unrecoverable manner.

.
[CVODE ERROR]  CVode
  At t = 0.458122, the right-hand side routine failed in an unrecoverable manner.

.
[CVODE ERROR]  CVode
  The right-hand side routine failed at the first call.

.
[CVODE WARNING]  CVode
  Internal t = 0.5 and h = 1.70033e-17 are such that t + h = t on the next step. The solver will continue anyway.


[CVODE WARNING]  CVode
  Internal t = 0.5 and h = 1.70033e-17 are such that t + h = t on the next step. The solver will continue anyway.


[CVODE WARNING]  CVode
  Internal t = 0.5 and h = 4.25083e-17 are such that t + h = t on the next step. The solver will continue anyway.


[CVODE WARNING]  CVode
  Internal t = 0.5 and h = 4.25083e-17 are such that t + h = t on the next step. The solver will continue anyway.


[CVODE WARNING]  CVode
  Internal t = 0.5 and h = 2.65677e-17 are such that t + h = t on the next step. The solver will continue anyway.


[CVODE WARNING]  CVode
  Internal t = 0.5 and h = 2.65677e-17 are such that t + h = t on the next step. The solver will continue anyway.


[CVODE WARNING]  CVode
  Internal t = 0.5 and h = 1.66048e-17 are such that t + h = t on the next step. The solver will continue anyway.


[CVODE WARNING]  CVode
  Internal t = 0.5 and h = 1.66048e-17 are such that t + h = t on the next step. The solver will continue anyway.


[CVODE WARNING]  CVode
  Internal t = 0.5 and h = 4.1512e-17 are such that t + h = t on the next step. The solver will continue anyway.


[CVODE WARNING]  CVode
  Internal t = 0.5 and h = 4.1512e-17 are such that t + h = t on the next step. The solver will continue anyway.


[CVODE WARNING]  CVode
  The above warning has been issued mxhnil times and will not be issued again for this problem.


[CVODE ERROR]  CVode
  At t = 0.5, mxstep steps taken before reaching tout.

..
[CVODE ERROR]  cvRcheck1
  At t = 0, the rootfinding routine failed in an unrecoverable manner.

.
[CVODE ERROR]  cvRcheck3
  At t = 0.458122, the rootfinding routine failed in an unrecoverable manner.

.
[CVODES WARNING]  CVode
  At the end of the first step, there are still some root functions identically 0. This warning will not be issued again.

...
[IDALS ERROR]  idaLsSetup
  The Jacobian routine failed in an unrecoverable manner.


[IDA ERROR]  IDASolve
  At t = 0, the linear solver setup failed unrecoverably.

.
[IDALS ERROR]  idaLsSetup
  The Jacobian routine failed in an unrecoverable manner.


[IDA ERROR]  IDASolve
  At t = 0, the linear solver setup failed unrecoverably.

.
[IDA ERROR]  IDASolve
  At t = 0 and h = 9.53674e-10, the corrector convergence failed repeatedly or with |h| = hmin.

.
[IDA ERROR]  IDASolve
  At t = 0 and h = 9.53674e-10, the corrector convergence failed repeatedly or with |h| = hmin.

.....
[IDA ERROR]  IDASolve
  At t = 0, the residual function failed unrecoverably.

.
[IDA ERROR]  IDASolve
  At t = 0.287979, the residual function failed unrecoverably.

.
[IDA ERROR]  IDASolve
  At t = 0, repeated recoverable residual errors.

.
[IDA ERROR]  IDASolve
  At t = 0.5, , mxstep steps taken before reaching tout.

..
[IDA ERROR]  IDARcheck1
  At t = 0, , the rootfinding routine failed in an unrecoverable manner.

.
[IDA ERROR]  IDARcheck3
  At t = 0.287979, , the rootfinding routine failed in an unrecoverable manner.

.
[IDA WARNING]  IDASolve
  At the end of the first step, there are still some root functions identically 0. This warning will not be issued again.

...
[IDALS ERROR]  idaLsSetup
  The Jacobian routine failed in an unrecoverable manner.


[IDA ERROR]  IDASolve
  At t = 0, the linear solver setup failed unrecoverably.

.
[IDALS ERROR]  idaLsSetup
  The Jacobian routine failed in an unrecoverable manner.


[IDA ERROR]  IDASolve
  At t = 0, the linear solver setup failed unrecoverably.

.
[IDA ERROR]  IDASolve
  At t = 0 and h = 9.53674e-10, the corrector convergence failed repeatedly or with |h| = hmin.

.
[IDA ERROR]  IDASolve
  At t = 0 and h = 9.53674e-10, the corrector convergence failed repeatedly or with |h| = hmin.

.....
[IDA ERROR]  IDASolve
  At t = 0, the residual function failed unrecoverably.

.
[IDA ERROR]  IDASolve
  At t = 0.287979, the residual function failed unrecoverably.

.
[IDA ERROR]  IDASolve
  At t = 0, repeated recoverable residual errors.

.
[IDA ERROR]  IDASolve
  At t = 0.5, , mxstep steps taken before reaching tout.

..
[IDA ERROR]  IDARcheck1
  At t = 0, , the rootfinding routine failed in an unrecoverable manner.

.
[IDA ERROR]  IDARcheck3
  At t = 0.287979, , the rootfinding routine failed in an unrecoverable manner.

.
[IDA WARNING]  IDASolve
  At the end of the first step, there are still some root functions identically 0. This warning will not be issued again.

...
----------------------------------------------------------------------
Ran 124 tests in 0.748s

OK

I would like to know if it is a incompatibility with my Sundials version. If so, what is the most recent version that can be wrapped by ODES?

Thanks!

The text was updated successfully, but these errors were encountered:

bmcage · 2021-12-11T12:59:38Z

Current ODES is for Sundials 5.1.0
as written here: https://scikits-odes.readthedocs.io/en/stable/installation.html#requirements-before-install
Quite some of the tests are working I see, the failing ones could be due to wrong sundials versions, so test that first.

About your testcase, as the doc writes: assuming you have implemented the ODE right_hand_side mentioned above
https://scikits-odes.readthedocs.io/en/stable/guide.html#object-oriented-interface-ode-and-dae
You do pass in it as in the doc, instead give a function, eg as in
https://github.com/bmcage/odes/blob/master/ipython_examples/Simple%20Oscillator.ipynb

rstoddard24 · 2022-01-05T22:46:45Z

I cannot get scikits.odes to work with python 3.8. Upon install I get the following error:

 File "/private/var/folders/qz/4s8vn6v90nv8_r7_472q7g1c0000gn/T/pip-build-env-lfjzcav3/overlay/lib/python3.8/site-packages/numpy/distutils/command/build_ext.py", line 380, in build_extension
      extra_cflags = ext.extra_c_compile_args or []
  AttributeError: 'Extension' object has no attribute 'extra_c_compile_args'
  ----------------------------------------
  ERROR: Failed building wheel for scikits.odes

When I use python 3.6 everything works.

I am using macOS, Sundials 5.1.0, all other depenedencies installed, and everything is working with Python 3.6, but would like to get 3.8 working

bmcage · 2022-01-09T17:02:49Z

@rstoddard24 latest release should fix this, see #131

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No convergence in test cases for Sundials 5.7.0 and Python 3.8 #118

No convergence in test cases for Sundials 5.7.0 and Python 3.8 #118

Jaimenms commented Mar 2, 2021

bmcage commented Dec 11, 2021

rstoddard24 commented Jan 5, 2022

bmcage commented Jan 9, 2022

No convergence in test cases for Sundials 5.7.0 and Python 3.8 #118

No convergence in test cases for Sundials 5.7.0 and Python 3.8 #118

Comments

Jaimenms commented Mar 2, 2021

bmcage commented Dec 11, 2021

rstoddard24 commented Jan 5, 2022

bmcage commented Jan 9, 2022