No convergence in test cases for Sundials 5.7.0 and Python 3.8
Opened this issue · 3 comments
Jaimenms commented
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!
bmcage commented
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 commented
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 commented
@rstoddard24 latest release should fix this, see #131