bmcage / odes

The ODES scikit for ordinary differential and algebraic equations, an extension to scipy

ODES is a scikit for Python 3.7+ offering extra ode/dae solvers, as an extension to what is available in scipy. The documentation is available at Read The Docs, and API docs can be found at https://bmcage.github.io/odes.

Available solvers:

ODES provides interfaces to the following solvers:

• BDF linear multistep method for stiff problems (CVODE and IDA from SUNDIALS)
• Adams-Moulton linear multistep method for nonstiff problems (CVODE and IDA from SUNDIALS)
• Explicit Runge-Kutta method of order (4)5 with stepsize control ( dopri5 from scipy.integrate)
• Explicit Runge-Kutta method of order 8(5,3) with stepsize control ( dop853 from scipy.integrate)
• Historical solvers: lsodi and ddaspk are available for comparison reasons. Use IDA instead! Note that lsodi fails on architecture aarch64.

Usage

A simple example solving the Van der Pol oscillator is as follows:

import matplotlib.pyplot as plt
import numpy as np
from scikits.odes import ode

t0, y0 = 1, np.array([0.5, 0.5])  # initial condition
def van_der_pol(t, y, ydot):
    """ we create rhs equations for the problem"""
    ydot[0] = y[1]
    ydot[1] = 1000*(1.0-y[0]**2)*y[1]-y[0]

solution = ode('cvode', van_der_pol, old_api=False).solve(np.linspace(t0,500,200), y0)
plt.plot(solution.values.t, solution.values.y[:,0], label='Van der Pol oscillator')
plt.show()

For simplicity there is also a convenience function odeint wrapping the ode solver class. See the User Guide for a simple example for odeint, as well as simple examples for object orientated interfaces and further examples using ODES solvers.

Projects that use odes

You can learn by example from following code that uses ODES:

• Centrifuge simulation, a wrapper around the ida solver: see centrifuge-1d

You have a project using odes? Do a pull request to add your project.

Citing ODES

If you use ODES as part of your research, can you please cite the ODES JOSS paper. Additionally, if you use one of the SUNDIALS solvers, we strongly encourage you to cite the SUNDIALS papers.

odes's Issues

Installation issues Mac

Hello. I am trying to install scikits.odes on Mac OS 10.14. I am using Python 3.6 and 3.7 and SUNDIALS 3.1.1.

Both when using pip install and python setup.py install after cloning, I run into

/usr/local/bin/gfortran [... lots of linking] -lgfortran -o build/lib.macosx-10.9-x86_64-3.7/scikits/odes/ddaspk.cpython-37m-darwin.so
  Undefined symbols for architecture x86_64:
    "_PyArg_ParseTupleAndKeywords", referenced from:
        _f2py_rout_ddaspk_ddaspk in ddaspkmodule.o
    [... more stuff like this]
    "__Py_NoneStruct", referenced from:
        _f2py_rout_ddaspk_ddaspk in ddaspkmodule.o
        _cb_res_in_ddaspk__user__routines in ddaspkmodule.o
        _create_cb_arglist in ddaspkmodule.o
        _cb_jac_in_ddaspk__user__routines in ddaspkmodule.o
        _fortran_getattr in fortranobject.o
        _fortran_setattr in fortranobject.o
        _array_from_pyobj in fortranobject.o
        ...
    "_main", referenced from:
       implicit entry/start for main executable
  ld: symbol(s) not found for architecture x86_64

and then

error: Command "/usr/local/bin/gfortran [... lots of linking] -lgfortran -o build/lib.macosx-10.9-x86_64-3.7/scikits/odes/ddaspk.cpython-37m-darwin.so" failed with exit status 1

Could you please guide me how to resolve this problem?

scikits.odes installed successfully through pip3 / git version but failed at od.test()

Hi,

What I did:

sudo apt update
sudo apt upgrade
sudo apt install build-essential python3-gdbm cmake
sudo apt install python3-dev gfortran libblas-dev libopenblas-dev liblapack-dev libatlas-base-dev

curl -o sundials-2.7.0.tar.gz https://computation.llnl.gov/projects/sundials/download/sundials-2.7.0.tar.gz
tar -xzf sundials-2.7.0.tar.gz
mkdir build-sundials-2.7.0
cd build-sundials-2.7.0/
cmake -DLAPACK_ENABLE=ON -DCMAKE_INSTALL_PREFIX=/usr/lib/sundials-2.7.0/ /home/ubuntu/sundials-2.7.0

After running above, Return: 
-- The C compiler identification is GNU 5.4.0
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Looking for _POSIX_TIMERS
-- Looking for _POSIX_TIMERS - found
-- The Fortran compiler identification is GNU 5.4.0
-- Searching for a Fortran compiler... /usr/bin/gfortran
-- Trying to compile and link a simple Fortran program... OK
-- Determining Fortran name-mangling scheme... OK
-- Looking for Fortran dgemm
-- Looking for Fortran dgemm - found
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Looking for pthread_create
-- Looking for pthread_create - not found
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE
-- A library with BLAS API found.
-- Looking for Fortran cheev
-- Looking for Fortran cheev - found
-- A library with LAPACK API found.
-- Looking for LAPACK libraries... OK
-- Checking if Lapack works... OK
-- Added NVECTOR_SERIAL module
-- Added ARKODE module
-- Added CVODE module
-- Added CVODES module
-- Added IDA module
-- Added IDAS module
-- Added KINSOL module
-- Found PythonInterp: /usr/bin/python (found version "2.7.12")
-- Configuring done
-- Generating done
-- Build files have been written to: /home/ubuntu/build-sundials-2.7.0

(And I have changed python to python3.6 in CMakeCache.txt as below:

//Path to a program.
PYTHON_EXECUTABLE:FILEPATH=/usr/bin/python3.6
//Details about finding PythonInterp
FIND_PACKAGE_MESSAGE_DETAILS_PythonInterp:INTERNAL=[/usr/bin/python3.6][]

And rerun cmake -DLAPACK_ENABLE=ON -DCMAKE_INSTALL_PREFIX=/usr/lib/sundials-2.7.0/ /home/ubuntu/sundials-2.7.0;

Result:

-- The Fortran compiler identification is GNU 5.4.0
-- Searching for a Fortran compiler... /usr/bin/gfortran
-- Trying to compile and link a simple Fortran program... OK
-- Determining Fortran name-mangling scheme... OK
-- Looking for LAPACK libraries... OK
-- Checking if Lapack works... OK
-- Added NVECTOR_SERIAL module
-- Added ARKODE module
-- Added CVODE module
-- Added CVODES module
-- Added IDA module
-- Added IDAS module
-- Added KINSOL module
-- Found PythonInterp: /usr/bin/python3.6 (found version "3.6.4")
-- Configuring done
-- Generating done
-- Build files have been written to: /home/ubuntu/build-sundials-2.7.0
)

sudo make install;

Result of installation seems no problem at all.

I have changed .bashrc $SUNDIALS_INST as
export SUNDIALS_INST=/usr/lib/sundials-2.7.0/

install scikits.odes through pip3 (I have installed Cython through pip3 as well)

sudo pip3 install scikits.odes;

Result:

Collecting scikits.odes
Requirement already satisfied: scipy in /usr/local/lib/python3.6/dist-packages (from scikits.odes)
Requirement already satisfied: numpy>=1.8.2 in /usr/local/lib/python3.6/dist-packages (from scipy->scikits.odes)
Installing collected packages: scikits.odes
Successfully installed scikits.odes-2.3.2

However, when i try to run test code as below:

ubuntu:~/ctrnn_ann$ ipython

Python 3.6.4 (default, Jan 28 2018, 17:52:01)
Type 'copyright', 'credits' or 'license' for more information
IPython 6.1.0 -- An enhanced Interactive Python. Type '?' for help.

In [1]: import scikits.odes as od;

In [2]: od.test()
Running unit tests for scikits.odes
NumPy version 1.13.3
NumPy relaxed strides checking option: True
NumPy is installed in /usr/local/lib/python3.6/dist-packages/numpy
Python version 3.6.4 (default, Jan 28 2018, 17:52:01) [GCC 5.4.0 20160609]
nose version 1.3.7
/usr/lib/python3.6/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
  return f(*args, **kwds)
libsundials_ida.so.2: cannot open shared object file: No such file or directory
libsundials_cvode.so.2: cannot open shared object file: No such file or directory
EEException ignored in: <bound method dae.__del__ of <scikits.odes.dae.dae object at 0x7fca5fbb3be0>>
Traceback (most recent call last):
  File "/usr/local/lib/python3.6/dist-packages/scikits/odes/dae.py", line 445, in __del__
    del self._integrator
AttributeError: _integrator
EException ignored in: <bound method dae.__del__ of <scikits.odes.dae.dae object at 0x7fca5fbb3e10>>
Traceback (most recent call last):
  File "/usr/local/lib/python3.6/dist-packages/scikits/odes/dae.py", line 445, in __del__
    del self._integrator
AttributeError: _integrator
E.EEEEEE.EE.EEEE
======================================================================
ERROR: Check the ddaspk solver
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/local/lib/python3.6/dist-packages/scikits/odes/tests/test_dae.py", line 52, in test_ddaspk
    problem = problem_cls()
  File "/usr/local/lib/python3.6/dist-packages/scikits/odes/tests/test_dae.py", line 211, in __init__
    old_api=False,
  File "/usr/local/lib/python3.6/dist-packages/scikits/odes/ode.py", line 273, in __init__
    integrator = find_ode_integrator(integrator_name)
  File "/usr/local/lib/python3.6/dist-packages/scikits/odes/ode.py", line 486, in find_ode_integrator
    raise ValueError('Integrator name %s does not exist' % name)
ValueError: Integrator name cvode does not exist

======================================================================
ERROR: Check the ida solver
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/local/lib/python3.6/dist-packages/scikits/odes/tests/test_dae.py", line 71, in test_ida
    self._do_problem(problem, 'ida', old_api=False, **problem.ida_pars)
  File "/usr/local/lib/python3.6/dist-packages/scikits/odes/tests/test_dae.py", line 27, in _do_problem
    ig = dae(integrator, res, jacfn=jac, old_api=old_api)
  File "/usr/local/lib/python3.6/dist-packages/scikits/odes/dae.py", line 280, in __init__
    integrator = find_dae_integrator(integrator_name)
  File "/usr/local/lib/python3.6/dist-packages/scikits/odes/dae.py", line 481, in find_dae_integrator
    raise ValueError('Integrator name %s does not exsist' % name)
ValueError: Integrator name ida does not exsist

======================================================================
ERROR: Check the ida solver
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/local/lib/python3.6/dist-packages/scikits/odes/tests/test_dae.py", line 65, in test_ida_old_api
    self._do_problem(problem, 'ida', old_api=True, **problem.ida_pars)
  File "/usr/local/lib/python3.6/dist-packages/scikits/odes/tests/test_dae.py", line 27, in _do_problem
    ig = dae(integrator, res, jacfn=jac, old_api=old_api)
  File "/usr/local/lib/python3.6/dist-packages/scikits/odes/dae.py", line 280, in __init__
    integrator = find_dae_integrator(integrator_name)
  File "/usr/local/lib/python3.6/dist-packages/scikits/odes/dae.py", line 481, in find_dae_integrator
    raise ValueError('Integrator name %s does not exsist' % name)
ValueError: Integrator name ida does not exsist

======================================================================
ERROR: Check the lsodi solver
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/local/lib/python3.6/dist-packages/scikits/odes/tests/test_dae.py", line 58, in test_lsodi
    problem = problem_cls()
  File "/usr/local/lib/python3.6/dist-packages/scikits/odes/tests/test_dae.py", line 211, in __init__
    old_api=False,
  File "/usr/local/lib/python3.6/dist-packages/scikits/odes/ode.py", line 273, in __init__
    integrator = find_ode_integrator(integrator_name)
  File "/usr/local/lib/python3.6/dist-packages/scikits/odes/ode.py", line 486, in find_ode_integrator
    raise ValueError('Integrator name %s does not exist' % name)
ValueError: Integrator name cvode does not exist

======================================================================
ERROR: test_get_info_is_exposed_on_ode (scikits.odes.tests.test_get_info.GetInfoTest)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/local/lib/python3.6/dist-packages/scikits/odes/tests/test_get_info.py", line 23, in setUp
    self.ode = ode('cvode', rhs, old_api=False)
  File "/usr/local/lib/python3.6/dist-packages/scikits/odes/ode.py", line 273, in __init__
    integrator = find_ode_integrator(integrator_name)
  File "/usr/local/lib/python3.6/dist-packages/scikits/odes/ode.py", line 486, in find_ode_integrator
    raise ValueError('Integrator name %s does not exist' % name)
ValueError: Integrator name cvode does not exist

======================================================================
ERROR: test_get_info_returns_dict (scikits.odes.tests.test_get_info.GetInfoTest)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/local/lib/python3.6/dist-packages/scikits/odes/tests/test_get_info.py", line 23, in setUp
    self.ode = ode('cvode', rhs, old_api=False)
  File "/usr/local/lib/python3.6/dist-packages/scikits/odes/ode.py", line 273, in __init__
    integrator = find_ode_integrator(integrator_name)
  File "/usr/local/lib/python3.6/dist-packages/scikits/odes/ode.py", line 486, in find_ode_integrator
    raise ValueError('Integrator name %s does not exist' % name)
ValueError: Integrator name cvode does not exist

======================================================================
ERROR: test_ode_exposes_num_rhs_evals (scikits.odes.tests.test_get_info.GetInfoTest)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/local/lib/python3.6/dist-packages/scikits/odes/tests/test_get_info.py", line 23, in setUp
    self.ode = ode('cvode', rhs, old_api=False)
  File "/usr/local/lib/python3.6/dist-packages/scikits/odes/ode.py", line 273, in __init__
    integrator = find_ode_integrator(integrator_name)
  File "/usr/local/lib/python3.6/dist-packages/scikits/odes/ode.py", line 486, in find_ode_integrator
    raise ValueError('Integrator name %s does not exist' % name)
ValueError: Integrator name cvode does not exist

======================================================================
ERROR: test_we_integrated_correctly (scikits.odes.tests.test_get_info.GetInfoTest)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/local/lib/python3.6/dist-packages/scikits/odes/tests/test_get_info.py", line 23, in setUp
    self.ode = ode('cvode', rhs, old_api=False)
  File "/usr/local/lib/python3.6/dist-packages/scikits/odes/ode.py", line 273, in __init__
    integrator = find_ode_integrator(integrator_name)
  File "/usr/local/lib/python3.6/dist-packages/scikits/odes/ode.py", line 486, in find_ode_integrator
    raise ValueError('Integrator name %s does not exist' % name)
ValueError: Integrator name cvode does not exist

======================================================================
ERROR: test_ode_exposes_num_njtimes_evals (scikits.odes.tests.test_get_info.GetInfoTestSpils)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/local/lib/python3.6/dist-packages/scikits/odes/tests/test_get_info.py", line 50, in setUp
    self.ode = ode('cvode', rhs, linsolver="spgmr", old_api=False)
  File "/usr/local/lib/python3.6/dist-packages/scikits/odes/ode.py", line 273, in __init__
    integrator = find_ode_integrator(integrator_name)
  File "/usr/local/lib/python3.6/dist-packages/scikits/odes/ode.py", line 486, in find_ode_integrator
    raise ValueError('Integrator name %s does not exist' % name)
ValueError: Integrator name cvode does not exist

======================================================================
ERROR: test_odeint (scikits.odes.tests.test_odeint.TestOdeint)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/local/lib/python3.6/dist-packages/scikits/odes/tests/test_odeint.py", line 47, in test_odeint
    self._do_problem(problem)
  File "/usr/local/lib/python3.6/dist-packages/scikits/odes/tests/test_odeint.py", line 33, in _do_problem
    sol = odeint(problem.f, t, problem.z0, method=method)
  File "/usr/local/lib/python3.6/dist-packages/scikits/odes/odeint.py", line 215, in odeint
    solver = ode(int_name, rhsfun, **options)
  File "/usr/local/lib/python3.6/dist-packages/scikits/odes/ode.py", line 273, in __init__
    integrator = find_ode_integrator(integrator_name)
  File "/usr/local/lib/python3.6/dist-packages/scikits/odes/ode.py", line 486, in find_ode_integrator
    raise ValueError('Integrator name %s does not exist' % name)
ValueError: Integrator name cvode does not exist

======================================================================
ERROR: scikits.odes.tests.test_odeint.test_odeint_banded_jacobian
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/local/lib/python3.6/dist-packages/nose/case.py", line 198, in runTest
    self.test(*self.arg)
  File "/usr/local/lib/python3.6/dist-packages/scikits/odes/tests/test_odeint.py", line 292, in test_odeint_banded_jacobian
    jacfn=jac)
  File "/usr/local/lib/python3.6/dist-packages/scikits/odes/odeint.py", line 215, in odeint
    solver = ode(int_name, rhsfun, **options)
  File "/usr/local/lib/python3.6/dist-packages/scikits/odes/ode.py", line 273, in __init__
    integrator = find_ode_integrator(integrator_name)
  File "/usr/local/lib/python3.6/dist-packages/scikits/odes/ode.py", line 486, in find_ode_integrator
    raise ValueError('Integrator name %s does not exist' % name)
ValueError: Integrator name cvode does not exist

======================================================================
ERROR: scikits.odes.tests.test_odeint.test_odeint_errors
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/local/lib/python3.6/dist-packages/nose/case.py", line 198, in runTest
    self.test(*self.arg)
  File "/usr/local/lib/python3.6/dist-packages/scikits/odes/tests/test_odeint.py", line 403, in test_odeint_errors
    assert_raises(ZeroDivisionError, odeint, bad1, [0, 1], [1.0])
  File "/usr/local/lib/python3.6/dist-packages/numpy/testing/utils.py", line 1190, in assert_raises
    return nose.tools.assert_raises(*args,**kwargs)
  File "/usr/lib/python3.6/unittest/case.py", line 733, in assertRaises
    return context.handle('assertRaises', args, kwargs)
  File "/usr/lib/python3.6/unittest/case.py", line 178, in handle
    callable_obj(*args, **kwargs)
  File "/usr/local/lib/python3.6/dist-packages/scikits/odes/odeint.py", line 215, in odeint
    solver = ode(int_name, rhsfun, **options)
  File "/usr/local/lib/python3.6/dist-packages/scikits/odes/ode.py", line 273, in __init__
    integrator = find_ode_integrator(integrator_name)
  File "/usr/local/lib/python3.6/dist-packages/scikits/odes/ode.py", line 486, in find_ode_integrator
    raise ValueError('Integrator name %s does not exist' % name)
ValueError: Integrator name cvode does not exist

======================================================================
ERROR: Failure: ImportError (libsundials_cvode.so.2: cannot open shared object file: No such file or directory)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/local/lib/python3.6/dist-packages/nose/failure.py", line 39, in runTest
    raise self.exc_val.with_traceback(self.tb)
  File "/usr/local/lib/python3.6/dist-packages/nose/loader.py", line 418, in loadTestsFromName
    addr.filename, addr.module)
  File "/usr/local/lib/python3.6/dist-packages/nose/importer.py", line 47, in importFromPath
    return self.importFromDir(dir_path, fqname)
  File "/usr/local/lib/python3.6/dist-packages/nose/importer.py", line 94, in importFromDir
    mod = load_module(part_fqname, fh, filename, desc)
  File "/usr/lib/python3.6/imp.py", line 235, in load_module
    return load_source(name, filename, file)
  File "/usr/lib/python3.6/imp.py", line 172, in load_source
    module = _load(spec)
  File "<frozen importlib._bootstrap>", line 684, in _load
  File "<frozen importlib._bootstrap>", line 665, in _load_unlocked
  File "<frozen importlib._bootstrap_external>", line 678, in exec_module
  File "<frozen importlib._bootstrap>", line 219, in _call_with_frames_removed
  File "/usr/local/lib/python3.6/dist-packages/scikits/odes/tests/test_on_funcs.py", line 16, in <module>
    from scikits.odes.sundials.cvode import StatusEnum
ImportError: libsundials_cvode.so.2: cannot open shared object file: No such file or directory

======================================================================
ERROR: Failure: ImportError (libsundials_ida.so.2: cannot open shared object file: No such file or directory)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/local/lib/python3.6/dist-packages/nose/failure.py", line 39, in runTest
    raise self.exc_val.with_traceback(self.tb)
  File "/usr/local/lib/python3.6/dist-packages/nose/loader.py", line 418, in loadTestsFromName
    addr.filename, addr.module)
  File "/usr/local/lib/python3.6/dist-packages/nose/importer.py", line 47, in importFromPath
    return self.importFromDir(dir_path, fqname)
  File "/usr/local/lib/python3.6/dist-packages/nose/importer.py", line 94, in importFromDir
    mod = load_module(part_fqname, fh, filename, desc)
  File "/usr/lib/python3.6/imp.py", line 235, in load_module
    return load_source(name, filename, file)
  File "/usr/lib/python3.6/imp.py", line 172, in load_source
    module = _load(spec)
  File "<frozen importlib._bootstrap>", line 684, in _load
  File "<frozen importlib._bootstrap>", line 665, in _load_unlocked
  File "<frozen importlib._bootstrap_external>", line 678, in exec_module
  File "<frozen importlib._bootstrap>", line 219, in _call_with_frames_removed
  File "/usr/local/lib/python3.6/dist-packages/scikits/odes/tests/test_on_funcs_ida.py", line 16, in <module>
    from scikits.odes.sundials.ida import StatusEnumIDA
ImportError: libsundials_ida.so.2: cannot open shared object file: No such file or directory

======================================================================
ERROR: Failure: ImportError (libsundials_cvode.so.2: cannot open shared object file: No such file or directory)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/local/lib/python3.6/dist-packages/nose/failure.py", line 39, in runTest
    raise self.exc_val.with_traceback(self.tb)
  File "/usr/local/lib/python3.6/dist-packages/nose/loader.py", line 418, in loadTestsFromName
    addr.filename, addr.module)
  File "/usr/local/lib/python3.6/dist-packages/nose/importer.py", line 47, in importFromPath
    return self.importFromDir(dir_path, fqname)
  File "/usr/local/lib/python3.6/dist-packages/nose/importer.py", line 94, in importFromDir
    mod = load_module(part_fqname, fh, filename, desc)
  File "/usr/lib/python3.6/imp.py", line 235, in load_module
    return load_source(name, filename, file)
  File "/usr/lib/python3.6/imp.py", line 172, in load_source
    module = _load(spec)
  File "<frozen importlib._bootstrap>", line 684, in _load
  File "<frozen importlib._bootstrap>", line 665, in _load_unlocked
  File "<frozen importlib._bootstrap_external>", line 678, in exec_module
  File "<frozen importlib._bootstrap>", line 219, in _call_with_frames_removed
  File "/usr/local/lib/python3.6/dist-packages/scikits/odes/tests/test_user_return_vals_cvode.py", line 5, in <module>
    from ..sundials.cvode import StatusEnum
ImportError: libsundials_cvode.so.2: cannot open shared object file: No such file or directory

======================================================================
ERROR: Failure: ImportError (libsundials_ida.so.2: cannot open shared object file: No such file or directory)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/local/lib/python3.6/dist-packages/nose/failure.py", line 39, in runTest
    raise self.exc_val.with_traceback(self.tb)
  File "/usr/local/lib/python3.6/dist-packages/nose/loader.py", line 418, in loadTestsFromName
    addr.filename, addr.module)
  File "/usr/local/lib/python3.6/dist-packages/nose/importer.py", line 47, in importFromPath
    return self.importFromDir(dir_path, fqname)
  File "/usr/local/lib/python3.6/dist-packages/nose/importer.py", line 94, in importFromDir
    mod = load_module(part_fqname, fh, filename, desc)
  File "/usr/lib/python3.6/imp.py", line 235, in load_module
    return load_source(name, filename, file)
  File "/usr/lib/python3.6/imp.py", line 172, in load_source
    module = _load(spec)
  File "<frozen importlib._bootstrap>", line 684, in _load
  File "<frozen importlib._bootstrap>", line 665, in _load_unlocked
  File "<frozen importlib._bootstrap_external>", line 678, in exec_module
  File "<frozen importlib._bootstrap>", line 219, in _call_with_frames_removed
  File "/usr/local/lib/python3.6/dist-packages/scikits/odes/tests/test_user_return_vals_ida.py", line 5, in <module>
    from ..sundials.ida import StatusEnumIDA
ImportError: libsundials_ida.so.2: cannot open shared object file: No such file or directory

----------------------------------------------------------------------
Ran 19 tests in 0.013s

FAILED (errors=16)
Out[2]: <nose.result.TextTestResult run=19 errors=16 failures=0>

May I know what is the reason for the errors? I have been trying out many different ways and tried to check online if anything similar but to no avail. Does anyone have any idea?

pip install fails on my Arch box

Been using odes for a year or so but suddenly won't work. I'm on python 3.7.0, Arch linux. Sundials 3.1.2 is installed. I try reinstalling with pip install scikits.odes and get many errors as below. Thanks for any help!
odes_errors.txt

Example that uses atol to adjust absolute tolerances for CVODE

I'm using scikits because it's listed on the CVODE webpage. I'm building a biochemical simulator. Since populations of molecules must be non-negative, I'm following the advice in Hindmarsh, Serban and Reynolds, User Documentation for cvode v5.0.0, 2019, which recommends that tighter absolute tolerances be used to reduce the magnitude of negative values. However, I find that changing atol does not change the solver behavior. I'm passing atol like this:

from scikits.odes import ode
options = {'atol': 1e-11}
CVODE_SOLVER = 'cvode'
solver = ode(CVODE_SOLVER, right_hand_side, old_api=False, **options)

Is this correct? Do you have an example that uses atol to adjust absolute tolerances for CVODE?

Thanks, Arthur

How to stop `cvode` when a root is found?

From the freefall.py example, I see how to find roots, and, I infer that the nr_rootfns=1 keyword argument is used to save them in the object returned when old_api=False is given (though I can't find any documentation of this).

Is there a way to stop the integrator when it has found a root to some tolerance? Or do I just have to keep extending my solution until I find a root, then manually prune the excess trajectory using the information in result.roots?

Performance of different integrators

Hi, I have a question regarding the performance graph in the documentation.

I tried cvode and rk5 on a small 3d finite difference discretization (11x11x11), cvode turned out to be much slower than rk5:

RK5: 22 ms
CVODE: 1.57 s

I think the performance graph in the docs is for a relatively small system (<100 equations), and as the number of equations increase, explicit integrators tend to outperform implicit ones, even though they use a much larger number of time steps (to maintain stability). What do you think?

Unable to install scikits.odes using conda

I am going to install scikit.odes on Ubuntu
I do the following steps from an earlier post

conda create -n odes numpy cython
conda install -n odes -c conda-forge sundials=2.7.0
export SUNDIALS_INST="${HOME}/anaconda3/pkgs/sundials-2.7.0-blas_openblash0edd121_6"

source activate odes
pip install scikits.odes

but I get an error log.txt

from scikits.odes.sundials.cvode cimport CV_RhsFunction does not work

Following up with issue #107, when I am using the command

from scikits.odes.sundials.cvode cimport CV_RhsFunction

and cythonize, I get the following error

Error compiling Cython file:

...
print("Hello")
import numpy as np
from cpython cimport bool
cimport numpy as np
from scikits.odes.sundials.cvode cimport CV_RhsFunction
^

hello.pyx:5:0: 'scikits/odes/sundials/cvode.pxd' not found

Error compiling Cython file:

...
print("Hello")
import numpy as np
from cpython cimport bool
cimport numpy as np
from scikits.odes.sundials.cvode cimport CV_RhsFunction
^

hello.pyx:5:0: 'scikits/odes/sundials/cvode/CV_RhsFunction.pxd' not found
Traceback (most recent call last):
File "setup.py", line 5, in
ext_modules=cythonize("hello.pyx"))
File "/gscratch/pfaendtner/Chowdhury/codes/Anaconda/envs/odes/lib/python3.6/site-packages/Cython/Build/Dependencies.py", line 1096, in cythonize
cythonize_one(*args)
File "/gscratch/pfaendtner/Chowdhury/codes/Anaconda/envs/odes/lib/python3.6/site-packages/Cython/Build/Dependencies.py", line 1219, in cythonize_one
raise CompileError(None, pyx_file)
Cython.Compiler.Errors.CompileError: hello.pyx

I get the same error too when I try to use cython magic in Jupiter notebook. I think I managed to install both the sundials and scikits.odes successfully as I can run other non-cython examples and nosetests. I also have set SUNDIALS_INST and LD_LIBRARY_PATH.

Any idea why this is not working?

No module named 'scikits'

I have successfully installed scikits.odes using the following commands:

cmake -DLAPACK_ENABLE=ON -DCMAKE_INSTALL_PREFIX=/usr/local/lib/sundials-3.1.1/ -DEXAMPLES_INSTALL_PATH=/home/xenhua/Downloads/cantera-related/sundials-3.1.1/examples-3.1.1 ../sundials-3.1.1/
make
sudo make install

export SUNDIALS_INST=/usr/local/lib/sundials-3.1.1/

pip3 install scikits.odes

I can then verify the correct installation by using the "pip3 freeze" command: For example,

pip3 freeze | grep scikits
scikits.bootstrap==0.3.3
scikits.odes==2.4.0

and

pip freeze | grep scikit
scikit-learn==0.21.2

But then when I try to run the tests by importing scikits.odes as od, I get the following "ModuleNotFoundError:

import scikits.odes as od
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
ModuleNotFoundError: No module named 'scikits'

Trouble finding sundials during the test stage of installing odes

I installed odes, but the tests using the command
import scikits.odes as od; od.test()

fail. I get the following output:

Running unit tests for scikits.odes
NumPy version 1.14.3
NumPy relaxed strides checking option: True
NumPy is installed in /usr/lib64/python2.7/site-packages/numpy
Python version 2.7.15 (default, May 16 2018, 17:50:09) [GCC 8.1.1 20180502 (Red Hat 8.1.1-1)]
nose version 1.3.7
libsundials_ida.so.2: cannot open shared object file: No such file or directory
libsundials_cvode.so.2: cannot open shared object file: No such file or directory
EEException AttributeError: "'dae' object has no attribute '_integrator'" in <bound method dae.__del__ of <scikits.odes.dae.dae object at 0x7f4a48da2c50>> ignored
EException AttributeError: "'dae' object has no attribute '_integrator'" in <bound method dae.__del__ of <scikits.odes.dae.dae object at 0x7f4a488eb410>> ignored
E.EEEEEE.EE.EEEE
======================================================================
ERROR: Check the ddaspk solver
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/dhalpern/.local/lib/python2.7/site-packages/scikits/odes/tests/test_dae.py", line 52, in test_ddaspk
    problem = problem_cls()
  File "/home/dhalpern/.local/lib/python2.7/site-packages/scikits/odes/tests/test_dae.py", line 211, in __init__
    old_api=False,
  File "/home/dhalpern/.local/lib/python2.7/site-packages/scikits/odes/ode.py", line 273, in __init__
    integrator = find_ode_integrator(integrator_name)
  File "/home/dhalpern/.local/lib/python2.7/site-packages/scikits/odes/ode.py", line 486, in find_ode_integrator
    raise ValueError('Integrator name %s does not exist' % name)
ValueError: Integrator name cvode does not exist

======================================================================
ERROR: Check the ida solver
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/dhalpern/.local/lib/python2.7/site-packages/scikits/odes/tests/test_dae.py", line 71, in test_ida
    self._do_problem(problem, 'ida', old_api=False, **problem.ida_pars)
  File "/home/dhalpern/.local/lib/python2.7/site-packages/scikits/odes/tests/test_dae.py", line 27, in _do_problem
    ig = dae(integrator, res, jacfn=jac, old_api=old_api)
  File "/home/dhalpern/.local/lib/python2.7/site-packages/scikits/odes/dae.py", line 280, in __init__
    integrator = find_dae_integrator(integrator_name)
  File "/home/dhalpern/.local/lib/python2.7/site-packages/scikits/odes/dae.py", line 481, in find_dae_integrator
    raise ValueError('Integrator name %s does not exsist' % name)
ValueError: Integrator name ida does not exsist

======================================================================
ERROR: Check the ida solver
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/dhalpern/.local/lib/python2.7/site-packages/scikits/odes/tests/test_dae.py", line 65, in test_ida_old_api
    self._do_problem(problem, 'ida', old_api=True, **problem.ida_pars)
  File "/home/dhalpern/.local/lib/python2.7/site-packages/scikits/odes/tests/test_dae.py", line 27, in _do_problem
    ig = dae(integrator, res, jacfn=jac, old_api=old_api)
  File "/home/dhalpern/.local/lib/python2.7/site-packages/scikits/odes/dae.py", line 280, in __init__
    integrator = find_dae_integrator(integrator_name)
  File "/home/dhalpern/.local/lib/python2.7/site-packages/scikits/odes/dae.py", line 481, in find_dae_integrator
    raise ValueError('Integrator name %s does not exsist' % name)
ValueError: Integrator name ida does not exsist

======================================================================
ERROR: Check the lsodi solver
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/dhalpern/.local/lib/python2.7/site-packages/scikits/odes/tests/test_dae.py", line 58, in test_lsodi
    problem = problem_cls()
  File "/home/dhalpern/.local/lib/python2.7/site-packages/scikits/odes/tests/test_dae.py", line 211, in __init__
    old_api=False,
  File "/home/dhalpern/.local/lib/python2.7/site-packages/scikits/odes/ode.py", line 273, in __init__
    integrator = find_ode_integrator(integrator_name)
  File "/home/dhalpern/.local/lib/python2.7/site-packages/scikits/odes/ode.py", line 486, in find_ode_integrator
    raise ValueError('Integrator name %s does not exist' % name)
ValueError: Integrator name cvode does not exist

======================================================================
ERROR: test_get_info_is_exposed_on_ode (scikits.odes.tests.test_get_info.GetInfoTest)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/dhalpern/.local/lib/python2.7/site-packages/scikits/odes/tests/test_get_info.py", line 23, in setUp
    self.ode = ode('cvode', rhs, old_api=False)
  File "/home/dhalpern/.local/lib/python2.7/site-packages/scikits/odes/ode.py", line 273, in __init__
    integrator = find_ode_integrator(integrator_name)
  File "/home/dhalpern/.local/lib/python2.7/site-packages/scikits/odes/ode.py", line 486, in find_ode_integrator
    raise ValueError('Integrator name %s does not exist' % name)
ValueError: Integrator name cvode does not exist

======================================================================
ERROR: test_get_info_returns_dict (scikits.odes.tests.test_get_info.GetInfoTest)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/dhalpern/.local/lib/python2.7/site-packages/scikits/odes/tests/test_get_info.py", line 23, in setUp
    self.ode = ode('cvode', rhs, old_api=False)
  File "/home/dhalpern/.local/lib/python2.7/site-packages/scikits/odes/ode.py", line 273, in __init__
    integrator = find_ode_integrator(integrator_name)
  File "/home/dhalpern/.local/lib/python2.7/site-packages/scikits/odes/ode.py", line 486, in find_ode_integrator
    raise ValueError('Integrator name %s does not exist' % name)
ValueError: Integrator name cvode does not exist

======================================================================
ERROR: test_ode_exposes_num_rhs_evals (scikits.odes.tests.test_get_info.GetInfoTest)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/dhalpern/.local/lib/python2.7/site-packages/scikits/odes/tests/test_get_info.py", line 23, in setUp
    self.ode = ode('cvode', rhs, old_api=False)
  File "/home/dhalpern/.local/lib/python2.7/site-packages/scikits/odes/ode.py", line 273, in __init__
    integrator = find_ode_integrator(integrator_name)
  File "/home/dhalpern/.local/lib/python2.7/site-packages/scikits/odes/ode.py", line 486, in find_ode_integrator
    raise ValueError('Integrator name %s does not exist' % name)
ValueError: Integrator name cvode does not exist

======================================================================
ERROR: test_we_integrated_correctly (scikits.odes.tests.test_get_info.GetInfoTest)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/dhalpern/.local/lib/python2.7/site-packages/scikits/odes/tests/test_get_info.py", line 23, in setUp
    self.ode = ode('cvode', rhs, old_api=False)
  File "/home/dhalpern/.local/lib/python2.7/site-packages/scikits/odes/ode.py", line 273, in __init__
    integrator = find_ode_integrator(integrator_name)
  File "/home/dhalpern/.local/lib/python2.7/site-packages/scikits/odes/ode.py", line 486, in find_ode_integrator
    raise ValueError('Integrator name %s does not exist' % name)
ValueError: Integrator name cvode does not exist

======================================================================
ERROR: test_ode_exposes_num_njtimes_evals (scikits.odes.tests.test_get_info.GetInfoTestSpils)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/dhalpern/.local/lib/python2.7/site-packages/scikits/odes/tests/test_get_info.py", line 50, in setUp
    self.ode = ode('cvode', rhs, linsolver="spgmr", old_api=False)
  File "/home/dhalpern/.local/lib/python2.7/site-packages/scikits/odes/ode.py", line 273, in __init__
    integrator = find_ode_integrator(integrator_name)
  File "/home/dhalpern/.local/lib/python2.7/site-packages/scikits/odes/ode.py", line 486, in find_ode_integrator
    raise ValueError('Integrator name %s does not exist' % name)
ValueError: Integrator name cvode does not exist

======================================================================
ERROR: test_odeint (scikits.odes.tests.test_odeint.TestOdeint)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/dhalpern/.local/lib/python2.7/site-packages/scikits/odes/tests/test_odeint.py", line 47, in test_odeint
    self._do_problem(problem)
  File "/home/dhalpern/.local/lib/python2.7/site-packages/scikits/odes/tests/test_odeint.py", line 33, in _do_problem
    sol = odeint(problem.f, t, problem.z0, method=method)
  File "/home/dhalpern/.local/lib/python2.7/site-packages/scikits/odes/odeint.py", line 215, in odeint
    solver = ode(int_name, rhsfun, **options)
  File "/home/dhalpern/.local/lib/python2.7/site-packages/scikits/odes/ode.py", line 273, in __init__
    integrator = find_ode_integrator(integrator_name)
  File "/home/dhalpern/.local/lib/python2.7/site-packages/scikits/odes/ode.py", line 486, in find_ode_integrator
    raise ValueError('Integrator name %s does not exist' % name)
ValueError: Integrator name cvode does not exist

======================================================================
ERROR: scikits.odes.tests.test_odeint.test_odeint_banded_jacobian
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/lib/python2.7/site-packages/nose/case.py", line 197, in runTest
    self.test(*self.arg)
  File "/home/dhalpern/.local/lib/python2.7/site-packages/scikits/odes/tests/test_odeint.py", line 292, in test_odeint_banded_jacobian
    jacfn=jac)
  File "/home/dhalpern/.local/lib/python2.7/site-packages/scikits/odes/odeint.py", line 215, in odeint
    solver = ode(int_name, rhsfun, **options)
  File "/home/dhalpern/.local/lib/python2.7/site-packages/scikits/odes/ode.py", line 273, in __init__
    integrator = find_ode_integrator(integrator_name)
  File "/home/dhalpern/.local/lib/python2.7/site-packages/scikits/odes/ode.py", line 486, in find_ode_integrator
    raise ValueError('Integrator name %s does not exist' % name)
ValueError: Integrator name cvode does not exist

======================================================================
ERROR: scikits.odes.tests.test_odeint.test_odeint_errors
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/lib/python2.7/site-packages/nose/case.py", line 197, in runTest
    self.test(*self.arg)
  File "/home/dhalpern/.local/lib/python2.7/site-packages/scikits/odes/tests/test_odeint.py", line 403, in test_odeint_errors
    assert_raises(ZeroDivisionError, odeint, bad1, [0, 1], [1.0])
  File "/usr/lib64/python2.7/site-packages/numpy/testing/nose_tools/utils.py", line 1191, in assert_raises
    return nose.tools.assert_raises(*args,**kwargs)
  File "/usr/lib64/python2.7/unittest/case.py", line 511, in assertRaises
    callableObj(*args, **kwargs)
  File "/home/dhalpern/.local/lib/python2.7/site-packages/scikits/odes/odeint.py", line 215, in odeint
    solver = ode(int_name, rhsfun, **options)
  File "/home/dhalpern/.local/lib/python2.7/site-packages/scikits/odes/ode.py", line 273, in __init__
    integrator = find_ode_integrator(integrator_name)
  File "/home/dhalpern/.local/lib/python2.7/site-packages/scikits/odes/ode.py", line 486, in find_ode_integrator
    raise ValueError('Integrator name %s does not exist' % name)
ValueError: Integrator name cvode does not exist

======================================================================
ERROR: Failure: ImportError (libsundials_cvode.so.2: cannot open shared object file: No such file or directory)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/lib/python2.7/site-packages/nose/loader.py", line 418, in loadTestsFromName
    addr.filename, addr.module)
  File "/usr/lib/python2.7/site-packages/nose/importer.py", line 47, in importFromPath
    return self.importFromDir(dir_path, fqname)
  File "/usr/lib/python2.7/site-packages/nose/importer.py", line 94, in importFromDir
    mod = load_module(part_fqname, fh, filename, desc)
  File "/home/dhalpern/.local/lib/python2.7/site-packages/scikits/odes/tests/test_on_funcs.py", line 16, in <module>
    from scikits.odes.sundials.cvode import StatusEnum
ImportError: libsundials_cvode.so.2: cannot open shared object file: No such file or directory

======================================================================
ERROR: Failure: ImportError (libsundials_ida.so.2: cannot open shared object file: No such file or directory)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/lib/python2.7/site-packages/nose/loader.py", line 418, in loadTestsFromName
    addr.filename, addr.module)
  File "/usr/lib/python2.7/site-packages/nose/importer.py", line 47, in importFromPath
    return self.importFromDir(dir_path, fqname)
  File "/usr/lib/python2.7/site-packages/nose/importer.py", line 94, in importFromDir
    mod = load_module(part_fqname, fh, filename, desc)
  File "/home/dhalpern/.local/lib/python2.7/site-packages/scikits/odes/tests/test_on_funcs_ida.py", line 16, in <module>
    from scikits.odes.sundials.ida import StatusEnumIDA
ImportError: libsundials_ida.so.2: cannot open shared object file: No such file or directory

======================================================================
ERROR: Failure: ImportError (libsundials_cvode.so.2: cannot open shared object file: No such file or directory)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/lib/python2.7/site-packages/nose/loader.py", line 418, in loadTestsFromName
    addr.filename, addr.module)
  File "/usr/lib/python2.7/site-packages/nose/importer.py", line 47, in importFromPath
    return self.importFromDir(dir_path, fqname)
  File "/usr/lib/python2.7/site-packages/nose/importer.py", line 94, in importFromDir
    mod = load_module(part_fqname, fh, filename, desc)
  File "/home/dhalpern/.local/lib/python2.7/site-packages/scikits/odes/tests/test_user_return_vals_cvode.py", line 5, in <module>
    from ..sundials.cvode import StatusEnum
ImportError: libsundials_cvode.so.2: cannot open shared object file: No such file or directory

======================================================================
ERROR: Failure: ImportError (libsundials_ida.so.2: cannot open shared object file: No such file or directory)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/lib/python2.7/site-packages/nose/loader.py", line 418, in loadTestsFromName
    addr.filename, addr.module)
  File "/usr/lib/python2.7/site-packages/nose/importer.py", line 47, in importFromPath
    return self.importFromDir(dir_path, fqname)
  File "/usr/lib/python2.7/site-packages/nose/importer.py", line 94, in importFromDir
    mod = load_module(part_fqname, fh, filename, desc)
  File "/home/dhalpern/.local/lib/python2.7/site-packages/scikits/odes/tests/test_user_return_vals_ida.py", line 5, in <module>
    from ..sundials.ida import StatusEnumIDA
ImportError: libsundials_ida.so.2: cannot open shared object file: No such file or directory

----------------------------------------------------------------------
Ran 19 tests in 0.009s

FAILED (errors=16)
<nose.result.TextTestResult run=19 errors=16 failures=0>
>>> 

FYI, I have sundials installed in /usr/local/sundials27

I tried to modify scikits/odes/sundials/setup.py but this didn't work.

Any suggestions would be greatly appreciated.

Documentation for cvode interface is sparse.

I'm working from the the freefall.py example. I see how to find roots, and, I infer that the nr_rootfns=1 keyword argument is used to save them in the object returned when old_api=False is given (though I can't find any documentation of this).

Is there any better documentation for the keyword arguments available when using cvode? I see

options :  additional options of the solver
    See set_options method of the `integrator_name` you selected for
    details.
    Set option `old_api=False` to use the new API. In the future, this
    will become the default!

In the docstring for scikits.odes.ode, but the docstring for my cvode solver's set_options method is just

Set specific options for the solver.
See the solver documentation for details.

Calling set_options a second time, is only possible for options that
can change during runtime.

This is true whether or not I create the solver with old_api=False.

Re-importing scikits.odes seems to break it

I use Spyder IDE with its embedded IPython console to write/run Python code. If you run the code snippet in #127 more than once (in the same IPython console), the package seems to break and no longer returns correct values (actually, most of the time it diverges, it only runs correctly the first time). So, every time I have to restart Spyder's IPython console for it to work. I don't exactly know what's causing the issue, but it seems to occur when re-importing the already imported scikits.odes library.

Build problems on Python >= 3.8

I have build problems on my Mac (Big Sur) for python versions larger than 3.7. I try to compile the git-version of odes with sundials version 5.8 (since 6.0 changed the API).

It works for Python 3.7 but not for 3.8 and 3.9 and there is something in the build system I think. The error is AttributeError: 'Extension' object has no attribute 'extra_c_compile_args' and I unfortunately don't know how to solve the problem.

Below is the traceback reporting the error.

Best,
Erik

Traceback (most recent call last):
  File "setup.py", line 45, in <module>
    setup(
  File "/Users/erifr93/tmp/odes_build/env/lib/python3.8/site-packages/numpy/distutils/core.py", line 169, in setup
    return old_setup(**new_attr)
  File "/Users/erifr93/tmp/odes_build/env/lib/python3.8/site-packages/setuptools/__init__.py", line 155, in setup
    return distutils.core.setup(**attrs)
  File "/Users/erifr93/tmp/odes_build/env/lib/python3.8/site-packages/setuptools/_distutils/core.py", line 148, in setup
    return run_commands(dist)
  File "/Users/erifr93/tmp/odes_build/env/lib/python3.8/site-packages/setuptools/_distutils/core.py", line 163, in run_commands
    dist.run_commands()
  File "/Users/erifr93/tmp/odes_build/env/lib/python3.8/site-packages/setuptools/_distutils/dist.py", line 967, in run_commands
    self.run_command(cmd)
  File "/Users/erifr93/tmp/odes_build/env/lib/python3.8/site-packages/setuptools/_distutils/dist.py", line 986, in run_command
    cmd_obj.run()
  File "/Users/erifr93/tmp/odes_build/env/lib/python3.8/site-packages/wheel/bdist_wheel.py", line 299, in run
    self.run_command('build')
  File "/Users/erifr93/tmp/odes_build/env/lib/python3.8/site-packages/setuptools/_distutils/cmd.py", line 313, in run_command
    self.distribution.run_command(command)
  File "/Users/erifr93/tmp/odes_build/env/lib/python3.8/site-packages/setuptools/_distutils/dist.py", line 986, in run_command
    cmd_obj.run()
  File "/Users/erifr93/tmp/odes_build/env/lib/python3.8/site-packages/numpy/distutils/command/build.py", line 61, in run
    old_build.run(self)
  File "/Users/erifr93/tmp/odes_build/env/lib/python3.8/site-packages/setuptools/_distutils/command/build.py", line 135, in run
    self.run_command(cmd_name)
  File "/Users/erifr93/tmp/odes_build/env/lib/python3.8/site-packages/setuptools/_distutils/cmd.py", line 313, in run_command
    self.distribution.run_command(command)
  File "/Users/erifr93/tmp/odes_build/env/lib/python3.8/site-packages/setuptools/_distutils/dist.py", line 986, in run_command
    cmd_obj.run()
  File "/Users/erifr93/tmp/odes_build/odes/setup_build.py", line 338, in run
    _build_ext.run(self) # actually do the build
  File "/Users/erifr93/tmp/odes_build/env/lib/python3.8/site-packages/numpy/distutils/command/build_ext.py", line 316, in run
    self.build_extensions()
  File "/Users/erifr93/tmp/odes_build/env/lib/python3.8/site-packages/setuptools/_distutils/command/build_ext.py", line 448, in build_extensions
    self._build_extensions_serial()
  File "/Users/erifr93/tmp/odes_build/env/lib/python3.8/site-packages/setuptools/_distutils/command/build_ext.py", line 473, in _build_extensions_serial
    self.build_extension(ext)
  File "/Users/erifr93/tmp/odes_build/env/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'

installation of scikits.odes and sundials - error

I want to use scikits.odes and Sundials for the solution of differential algebraic equations in Python and therefore I am trying to install it on Ubuntu.

For the installation of Sundials, I followed the installation instructions and for my understanding it worked well.

cmake -DLAPACK_ENABLE=ON -DCMAKE_INSTALL_PREFIX=/usr/local/lib/sundials-4.0.2/ -DEXAMPLES_INSTALL_PATH=/home/myname/opt/sundials/examples-4.0.2 /home/myname/opt/sundials/sundials-4.0.2
make
sudo make install

Then I tried to install scikits.odes with the command pip3 install scikits.odes, but I get the following error message (the last rows of the terminal output).

    In file included from /home/veit/.local/lib/python3.6/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822:0,
                     from /home/veit/.local/lib/python3.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
                     from /home/veit/.local/lib/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h:4,
                     from scikits/odes/sundials/common_defs.c:639:
    /home/veit/.local/lib/python3.6/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
     #warning "Using deprecated NumPy API, disable it with " \
      ^~~~~~~
    scikits/odes/sundials/common_defs.c:641:10: fatal error: sundials/sundials_types.h: Datei oder Verzeichnis nicht gefunden
     #include "sundials/sundials_types.h"
              ^~~~~~~~~~~~~~~~~~~~~~~~~~~
    compilation terminated.
    error: Command "x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/home/veit/.local/lib/python3.6/site-packages/numpy/core/include -I/usr/include/python3.6m -c scikits/odes/sundials/common_defs.c -o build/temp.linux-x86_64-3.6/scikits/odes/sundials/common_defs.o -MMD -MF build/temp.linux-x86_64-3.6/scikits/odes/sundials/common_defs.o.d" failed with exit status 1
    
    ----------------------------------------
Command "/usr/bin/python3 -u -c "import setuptools, tokenize;__file__='/tmp/pip-build-z5r81sw1/scikits.odes/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /tmp/pip-gbpyrsno-record/install-record.txt --single-version-externally-managed --compile --user --prefix=" failed with error code 1 in /tmp/pip-build-z5r81sw1/scikits.odes/

What is wrong and how can I fix it? Any help would be appreciated!

<sundials/sundials_pcg.h> not found

Hi,

Thanks for bringing together this very nice work! I tried to compile it on macOS Catalina with Sundials 5.0.0. It says #include <sundials/sundials_pcg.h> file not found.

I downgraded to sundials=4.1.0 and it compiles. There is no particular reason for me to use a higher version though. I'm posting the issue here for reference.

I will look into it later.

Latest release v2.2.1 does not match JOSS submission version v2.3.0

sparse jacobians and iterative solvers in IDA

Hi!

Nice work with odes! But, of course, i have a question. Is this possible to use sparse jacobians in IDA? And another one: can i use iterative preconditioned solvers with custom preconditioner? Unfortunately my problems are quite large and dense jacobians is not an option for me so i'm looking for possible solutions...

Best regards,
Marek

test_lsodi fails on aarch64

While packaging scikits-odes for nixpkgs, I noticed TestDae.test_lsodi fails on aarch64-linux

============================= test session starts ==============================
platform linux -- Python 3.7.4, pytest-4.6.3, py-1.7.0, pluggy-0.12.0
rootdir: /nix/store/avziwbawg0ibqccizgxfmhjcnjbbg7nd-python3.7-scikits.odes-2.4.0/lib/python3.7/site-packages/scikits/odes/tests
collected 81 items
test_dae.py ...F                                                         [  4%]
test_dop.py .                                                            [  6%]
test_get_info.py .....                                                   [ 12%]
test_odeint.py .....                                                     [ 18%]
test_on_funcs.py ............                                            [ 33%]
test_on_funcs_ida.py ............                                        [ 48%]
test_user_return_vals_cvode.py ........................                  [ 77%]
test_user_return_vals_ida.py ..................                          [100%]

=================================== FAILURES ===================================
______________________________ TestDae.test_lsodi ______________________________
self = <odes.tests.test_dae.TestDae testMethod=test_lsodi>
    def test_lsodi(self):
        """Check the lsodi solver"""
        for problem_cls in PROBLEMS_LSODI:
            problem = problem_cls()
>           self._do_problem(problem, 'lsodi', **problem.lsodi_pars)
test_dae.py:59:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
test_dae.py:34: in _do_problem
    soln = ig.step(time, z[i], zprime[i])
../dae.py:439: in step
    return self._integrator.step(t, y_retn, yp_retn)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <scikits.odes.lsodiint.lsodi object at 0xffff7ae2b310>, t = 400.0
y_retn = array([4.70187465e-01, 3.48124556e-06, 5.29809054e-01])
yp_retn = array([4.50537891e-01, 3.22315111e-06, 5.49458886e-01])
    def step(self, t, y_retn, yp_retn = None):
        """ See dae.DaeBase
        """
        if not self.initialized:
            raise ValueError('Method ''init_step'' has to be called prior to the'
                    'first call of ''step'' method, or after changing options')
        if t > 0.0:
            if self.tstop is None:
                itask = 1
                self.call_args[3] = 1
            else:
                itask = self.call_args[3]
                self.call_args[3] = 4
            self.y, self.yp, self.t = self.__run(self.y, self.yp, self.t, t)
            self.call_args[3] = itask
        else:
            itask = self.call_args[3]
            if self.tstop is None:
                self.call_args[3] = 2
            else:
                self.call_args[3] = 5
            self.y, self.yp, self.t  = self.__run(self.y, self.yp, self.t, -t)
            self.call_args[3] = itask
        y_retn[:] = self.y[:]
        if yp_retn is not None:
>           yp_retn[:] = self.yp[:]
E           TypeError: 'NoneType' object is not subscriptable
../lsodiint.py:376: TypeError
----------------------------- Captured stdout call -----------------------------
lsodi: excess work done on this call (check all inputs).
lsodi: present residual is [-1.17961196e-15  5.42101086e-20 -6.17733149e-12]
=============================== warnings summary ===============================
test_dae.py::TestDae::test_ida_old_api
test_dae.py::TestDae::test_ida_old_api
test_dae.py::TestDae::test_ida_old_api
  /nix/store/avziwbawg0ibqccizgxfmhjcnjbbg7nd-python3.7-scikits.odes-2.4.0/lib/python3.7/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)
-- Docs: https://docs.pytest.org/en/latest/warnings.html
=============== 1 failed, 80 passed, 3 warnings in 1.94 seconds ================
builder for '/nix/store/p3r9d2bn6dl34ghgpq7fv3v0i4p9ql5l-python3.7-scikits.odes-2.4.0.drv' failed with exit code 1

It's only that one test, and it runs on both x86_64-linux and x86_64-darwin just fine. Anybody knows what's going on here?

Do a new release

I should do a new release, but with all doc changes an pypi changes, I'm not sure about all steps. It used to be:

For a Release:

1. set in common.py version string and DEV=False, commit this.
2. In github, draft a new release by clicking the appropriate button. Give correct version number, and hit release. This will upload the release for a DOI to Zenado as draft
3. Go to uploads in Zenado, edit the uploaded new release, save and hit the publish button. This will generate a DOI.
4. update to pypi repo: python setup.py sdist --formats=gztar register upload
5. update version string to a higher number in common.py, and DEV=True, next copy the DOI badge of Zenado in the README.md, commit these two files.

Nothing changed to these instructions? I'd like to add these instructions to a dorelease.md in the project, so as to easily retrieve them later.

For the release number 2.3.2 or 2.4.0 ? I'd take 2.3.2 as changes mostly doc related, not API.

Or do you have something in the pipeline you would want in the next release?

CVODE default multistep method?

Hey, guys, really nice work!

I checked in cvode.pyx and apparently CVODE's default multistep (lmm_type in defaults dictionary) method is BDF, is that right? Just wanted a confirmation. Maybe I didn't see it, but I couldn't find it on the documentation.

The release version for JOSS needs a DOI

See this github page for a good guide to get a DOI via Zenodo. The badge can also be added to the read-me if desired

Lapack falsely accused

I believe I have built sundials with lapack:

cmake -DLAPACK_ENABLE=ON -DSUNDIALS_INDEX_TYPE=int32_t -DCMAKE_INSTALL_PREFIX=/Users/dominic.steinitz/MySundials/instdir -DEXAMPLES_INSTALL_PATH=/Users/dominic.steinitz/MySundials/instdir/examples /Users/dominic.steinitz/sundials-3.1.1
-- The Fortran compiler identification is GNU 9.1.0
-- Searching for a Fortran compiler... /usr/local/bin/gfortran
-- Checking whether Fortran compiler has -isysroot
-- Checking whether Fortran compiler has -isysroot - yes
-- Checking whether Fortran compiler supports OSX deployment target flag
-- Checking whether Fortran compiler supports OSX deployment target flag - yes
-- Trying to compile and link a simple Fortran program... OK
-- Determining Fortran name-mangling scheme... OK
-- Looking for LAPACK libraries... OK
-- Checking if LAPACK works... OK
-- Added NVECTOR_SERIAL module
-- Added SUNMATRIX_DENSE module
-- Added SUNMATRIX_BAND module
-- Added SUNMATRIX_SPARSE module
-- Added SUNLINSOL_BAND module
-- Added SUNLINSOL_DENSE module
-- Added SUNLINSOL_LAPACKBAND module
-- Added SUNLINSOL_LAPACKDENSE module
-- Added SUNLINSOL_SPGMR module
-- Added SUNLINSOL_SPFGMR module
-- Added SUNLINSOL_SPBCGS module
-- Added SUNLINSOL_SPTFQMR module
-- Added SUNLINSOL_PCG module
-- Added ARKODE module
-- Added CVODE module
-- Added CVODES module
-- Added IDA module
-- Added IDAS module
-- Added KINSOL module
-- Configuring done
CMake Warning (dev):
  Policy CMP0042 is not set: MACOSX_RPATH is enabled by default.  Run "cmake
  --help-policy CMP0042" for policy details.  Use the cmake_policy command to
  set the policy and suppress this warning.

  MACOSX_RPATH is not specified for the following targets:

   sundials_arkode_shared
   sundials_cvode_shared
   sundials_cvodes_shared
   sundials_ida_shared
   sundials_idas_shared
   sundials_kinsol_shared
   sundials_nvecserial_shared
   sundials_sunlinsolband_shared
   sundials_sunlinsoldense_shared
   sundials_sunlinsollapackband_shared
   sundials_sunlinsollapackdense_shared
   sundials_sunlinsolpcg_shared
   sundials_sunlinsolspbcgs_shared
   sundials_sunlinsolspfgmr_shared
   sundials_sunlinsolspgmr_shared
   sundials_sunlinsolsptfqmr_shared
   sundials_sunmatrixband_shared
   sundials_sunmatrixdense_shared
   sundials_sunmatrixsparse_shared

This warning is for project developers.  Use -Wno-dev to suppress it.

-- Generating done

But if I run the tests I get this error

python3
Python 3.7.0 (default, Oct  2 2018, 09:20:07) 
[Clang 10.0.0 (clang-1000.11.45.2)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import scikits.odes as od; od.test()
import scikits.odes as od; od.test()
Running unit tests for scikits.odes
NumPy version 1.16.4
NumPy relaxed strides checking option: True
NumPy is installed in /usr/local/lib/python3.7/site-packages/numpy
Python version 3.7.0 (default, Oct  2 2018, 09:20:07) [Clang 10.0.0 (clang-1000.11.45.2)]
nose version 1.3.7
/usr/local/lib/python3.7/site-packages/nose/suite.py:106: DeprecationWarning: Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated, and in 3.8 it will stop working
  if isinstance(tests, collections.Callable) and not is_suite:
../usr/local/lib/python3.7/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': 27, '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 1.95964127e-06
 2.00559588e-06 2.05370031e-06 2.12527937e-06 2.18137134e-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 3.40839272e-08
 2.74318062e-08 2.24709419e-08]
.ode.get_info() =
 {'NumSteps': 19, 'NumRhsEvals': 29, '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}
..............................
[CVDLS ERROR]  cvDlsSetup
  The Jacobian routine failed in an unrecoverable manner.


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

.
[CVDLS ERROR]  cvDlsSetup
  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.

.
[CVSPILS ERROR]  cvSpilsSolve
  The Jacobian x vector routine failed in an unrecoverable manner.


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

.
[CVSPILS ERROR]  cvSpilsSolve
  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.

...
[IDADLS ERROR]  idaDlsSetup
  The Jacobian routine failed in an unrecoverable manner.


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

.
[IDADLS ERROR]  idaDlsSetup
  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 81 tests in 0.599s

OK
<nose.result.TextTestResult run=81 errors=0 failures=0>

No convergence in test cases for Sundials 5.7.0 and Python 3.8

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!

gcc error with cpython

Hi, I am trying to use Performance tests.ipynb with Cython to check the speedup.
However, I encountered CompileError, I think that is due to Cython/gcc.
Any idea about this? Thanks.

---

CompileError                              Traceback (most recent call last)
<ipython-input-15-12eebe5eed09> in <module>()
----> 1 get_ipython().run_cell_magic(u'cython', u'-I /home/yangh/odes-master/odes/scikits/odes/sundials/ -I /home/yangh/anaconda2/lib/python2.7/site-packages/scikits/odes/sundials/', u"## update include flag -I to point to odes/sundials directory!\nimport numpy as np\nfrom cpython cimport bool\ncimport numpy as np\nfrom scikits.odes.sundials.cvode cimport CV_RhsFunction\n\n#scikits.odes allows cython functions only if derived from correct class\n\ncdef class egfngf_cython_model(CV_RhsFunction):\n    cdef public ts, k, y0, userdata\n    cdef public object name\n    cdef public CV_RhsFunction f_odes\n    cdef public bool has_userdata, has_userdata_odes\n    \n    def __cinit__(self):\n        self.name = 'egfngf_cython'\n        self.ts = np.linspace(0, 120, 121, dtype=float)\n        self.has_userdata = True\n        self.has_userdata_odes = True\n        self.k = np.array([\n                    2.18503E-5,\n                    0.0121008,\n                    1.38209E-7,\n                    0.00723811,\n                    694.731,\n                    6086070.0,\n                    389.428,\n                    2112.66,\n                    1611.97,\n                    896896.0,\n                    32.344,\n                    35954.3,\n                    1509.36,\n                    1432410.0,\n                    0.884096,\n                    62464.6,\n                    185.759,\n                    4768350.0,\n                    125.089,\n                    157948.0,\n                    2.83243,\n                    518753.0,\n                    9.85367,\n                    1007340.0,\n                    8.8912,\n                    3496490.0,\n                    0.0213697,\n                    763523.0,\n                    10.6737,\n                    184912.0,\n                    0.0771067,\n                    272056.0,\n                    0.0566279,\n                    653951.0,\n                    15.1212,\n                    119355.0,\n                    146.912,\n                    12876.2,\n                    1.40145,\n                    10965.6,\n                    27.265,\n                    295990.0,\n                    2.20995,\n                    1025460.0,\n                    0.126329,\n                    1061.71,\n                    441.287,\n                    1.08795E7\n                ], float)\n        \n        self.userdata = self.k\n\n        self.y0 = np.array([\n                    1000,\n                    4560,\n                    80000.0,\n                    0.0,\n                    10000.0,\n                    0.0,\n                    120000.0,\n                    0.0,\n                    120000.0,\n                    0.0,\n                    120000.0,\n                    0.0,\n                    120000.0,\n                    0.0,\n                    120000.0,\n                    0.0,\n                    600000.0,\n                    0.0,\n                    600000.0,\n                    0.0,\n                    120000.0,\n                    0.0,\n                    120000.0,\n                    0.0,\n                    120000.0,\n                    0.0,\n                    120000.0,\n                    0.0,\n                    120000.0,\n                    120000.0,\n                    120000.0,\n                    120000.0\n                ], float)\n\n    cpdef np.ndarray[double, ndim=1] f(self, double t, np.ndarray[double, ndim=1] y, \n                                       np.ndarray[double, ndim=1] k):\n        return np.array([\n            ((-1.0 * k[0] * y[0] * y[2])) + (1.0 * k[1] * y[3]),\n            ((-1.0 * k[2] * y[1] * y[4])) + (1.0 * k[3] * y[5]),\n            ((-1.0 * k[0] * y[0] * y[2])) + (1.0 * k[1] * y[3]),\n            ((1.0 * k[0] * y[0] * y[2]) + (-1.0 * k[1] * y[3])),\n            ((-1.0 * k[2] * y[1] * y[4]) + (1.0 * k[3] * y[5])),\n            ((1.0 * k[2] * y[1] * y[4]) + (-1.0 * k[3] * y[5])),\n            ((-1.0 * k[4] * y[3] * y[6] / (y[6] + k[5])) + (-1.0 * k[6] * y[5] * y[6] / (y[6] + k[7])) + (\n                1.0 * k[8] * y[9] * y[7] / (y[7] + k[9]))),\n            ((1.0 * k[4] * y[3] * y[6] / (y[6] + k[5])) + (1.0 * k[6] * y[5] * y[6] / (y[6] + k[7])) + (\n                -1.0 * k[8] * y[9] * y[7] / (y[7] + k[9]))),\n            ((-1.0 * k[26] * y[19] * y[8] / (y[8] + k[27]))),\n            ((1.0 * k[26] * y[19] * y[8] / (y[8] + k[27]))),\n            ((-1.0 * k[10] * y[7] * y[10] / (y[10] + k[11])) + (1.0 * k[12] * y[28] * y[11] / (y[11] + k[13]))),\n            ((1.0 * k[10] * y[7] * y[10] / (y[10] + k[11])) + (-1.0 * k[12] * y[28] * y[11] / (y[11] + k[13]))),\n            ((-1.0 * k[14] * y[11] * y[12] / (y[12] + k[15])) + (1.0 * k[44] * y[31] * y[13] / (y[13] + k[45])) + (\n                1.0 * k[34] * y[23] * y[13] / (y[13] + k[35]))),\n            ((1.0 * k[14] * y[11] * y[12] / (y[12] + k[15])) + (-1.0 * k[44] * y[31] * y[13] / (y[13] + k[45])) + (\n                -1.0 * k[34] * y[23] * y[13] / (y[13] + k[35]))),\n            ((-1.0 * k[42] * y[27] * y[14] / (y[14] + k[43])) + (1.0 * k[46] * y[31] * y[15] / (y[15] + k[47]))),\n            ((1.0 * k[42] * y[27] * y[14] / (y[14] + k[43])) + (-1.0 * k[46] * y[31] * y[15] / (y[15] + k[47]))),\n            ((-1.0 * k[16] * y[13] * y[16] / (y[16] + k[17])) + (-1.0 * k[18] * y[15] * y[16] / (y[16] + k[19])) + (\n                1.0 * k[20] * y[30] * y[17] / (y[17] + k[21]))),\n            ((1.0 * k[16] * y[13] * y[16] / (y[16] + k[17])) + (1.0 * k[18] * y[15] * y[16] / (y[16] + k[19])) + (\n                -1.0 * k[20] * y[30] * y[17] / (y[17] + k[21]))),\n            ((-1.0 * k[22] * y[17] * y[18] / (y[18] + k[23])) + (1.0 * k[24] * y[30] * y[19] / (y[19] + k[25]))),\n            ((1.0 * k[22] * y[17] * y[18] / (y[18] + k[23])) + (-1.0 * k[24] * y[30] * y[19] / (y[19] + k[25]))),\n            ((-1.0 * k[28] * y[3] * y[20] / (y[20] + k[29])) + (-1.0 * k[30] * y[11] * y[20] / (y[20] + k[31]))),\n            ((1.0 * k[28] * y[3] * y[20] / (y[20] + k[29])) + (1.0 * k[30] * y[11] * y[20] / (y[20] + k[31]))),\n            ((-1.0 * k[32] * y[21] * y[22] / (y[22] + k[33]))),\n            ((1.0 * k[32] * y[21] * y[22] / (y[22] + k[33]))),\n            ((-1.0 * k[36] * y[5] * y[24] / (y[24] + k[37]))),\n            ((1.0 * k[36] * y[5] * y[24] / (y[24] + k[37]))),\n            ((-1.0 * k[38] * y[25] * y[26] / (y[26] + k[39])) + (1.0 * k[40] * y[29] * y[27] / (y[27] + k[41]))),\n            ((1.0 * k[38] * y[25] * y[26] / (y[26] + k[39])) + (-1.0 * k[40] * y[29] * y[27] / (y[27] + k[41]))),\n            0,\n            0,\n            0,\n            0], float)\n\n    \n    cpdef int evaluate(self, double t,\n                       np.ndarray[double, ndim=1] y,\n                       np.ndarray[double, ndim=1] yout,\n                       object userdata = None) except? -1:\n        #cdef np.ndarray[double, ndim=1] k = self.k  # avoid self.k gives quite some speedup!\n        cdef np.ndarray[double, ndim=1] k = userdata\n        # avoiding creation of temporary arrays gives quite some speedup!\n        yout[0] = ((-1.0 * k[0] * y[0] * y[2])) + (1.0 * k[1] * y[3])\n        yout[1] = ((-1.0 * k[2] * y[1] * y[4])) + (1.0 * k[3] * y[5])\n        yout[2] = ((-1.0 * k[0] * y[0] * y[2])) + (1.0 * k[1] * y[3])\n        yout[3] = ((1.0 * k[0] * y[0] * y[2]) + (-1.0 * k[1] * y[3]))\n        yout[4] = ((-1.0 * k[2] * y[1] * y[4]) + (1.0 * k[3] * y[5]))\n        yout[5] = ((1.0 * k[2] * y[1] * y[4]) + (-1.0 * k[3] * y[5]))\n        yout[6] = ((-1.0 * k[4] * y[3] * y[6] / (y[6] + k[5])) + (-1.0 * k[6] * y[5] * y[6] / (y[6] + k[7])) + (\n                1.0 * k[8] * y[9] * y[7] / (y[7] + k[9])))\n        yout[7] = ((1.0 * k[4] * y[3] * y[6] / (y[6] + k[5])) + (1.0 * k[6] * y[5] * y[6] / (y[6] + k[7])) + (\n                -1.0 * k[8] * y[9] * y[7] / (y[7] + k[9])))\n        yout[8] = ((-1.0 * k[26] * y[19] * y[8] / (y[8] + k[27])))\n        yout[9] = ((1.0 * k[26] * y[19] * y[8] / (y[8] + k[27])))\n        yout[10] = ((-1.0 * k[10] * y[7] * y[10] / (y[10] + k[11])) + (1.0 * k[12] * y[28] * y[11] / (y[11] + k[13])))\n        yout[11] = ((1.0 * k[10] * y[7] * y[10] / (y[10] + k[11])) + (-1.0 * k[12] * y[28] * y[11] / (y[11] + k[13])))\n        yout[12] = ((-1.0 * k[14] * y[11] * y[12] / (y[12] + k[15])) + (1.0 * k[44] * y[31] * y[13] / (y[13] + k[45])) + (\n                1.0 * k[34] * y[23] * y[13] / (y[13] + k[35])))\n        yout[13] = ((1.0 * k[14] * y[11] * y[12] / (y[12] + k[15])) + (-1.0 * k[44] * y[31] * y[13] / (y[13] + k[45])) + (\n                -1.0 * k[34] * y[23] * y[13] / (y[13] + k[35])))\n        yout[14] = ((-1.0 * k[42] * y[27] * y[14] / (y[14] + k[43])) + (1.0 * k[46] * y[31] * y[15] / (y[15] + k[47])))\n        yout[15] = ((1.0 * k[42] * y[27] * y[14] / (y[14] + k[43])) + (-1.0 * k[46] * y[31] * y[15] / (y[15] + k[47])))\n        yout[16] = ((-1.0 * k[16] * y[13] * y[16] / (y[16] + k[17])) + (-1.0 * k[18] * y[15] * y[16] / (y[16] + k[19])) + (\n                1.0 * k[20] * y[30] * y[17] / (y[17] + k[21])))\n        yout[17] = ((1.0 * k[16] * y[13] * y[16] / (y[16] + k[17])) + (1.0 * k[18] * y[15] * y[16] / (y[16] + k[19])) + (\n                -1.0 * k[20] * y[30] * y[17] / (y[17] + k[21])))\n        yout[18] = ((-1.0 * k[22] * y[17] * y[18] / (y[18] + k[23])) + (1.0 * k[24] * y[30] * y[19] / (y[19] + k[25])))\n        yout[19] = ((1.0 * k[22] * y[17] * y[18] / (y[18] + k[23])) + (-1.0 * k[24] * y[30] * y[19] / (y[19] + k[25])))\n        yout[20] = ((-1.0 * k[28] * y[3] * y[20] / (y[20] + k[29])) + (-1.0 * k[30] * y[11] * y[20] / (y[20] + k[31])))\n        yout[21] = ((1.0 * k[28] * y[3] * y[20] / (y[20] + k[29])) + (1.0 * k[30] * y[11] * y[20] / (y[20] + k[31])))\n        yout[22] = ((-1.0 * k[32] * y[21] * y[22] / (y[22] + k[33])))\n        yout[23] = ((1.0 * k[32] * y[21] * y[22] / (y[22] + k[33])))\n        yout[24] = ((-1.0 * k[36] * y[5] * y[24] / (y[24] + k[37])))\n        yout[25] = ((1.0 * k[36] * y[5] * y[24] / (y[24] + k[37])))\n        yout[26] = ((-1.0 * k[38] * y[25] * y[26] / (y[26] + k[39])) + (1.0 * k[40] * y[29] * y[27] / (y[27] + k[41])))\n        yout[27] = ((1.0 * k[38] * y[25] * y[26] / (y[26] + k[39])) + (-1.0 * k[40] * y[29] * y[27] / (y[27] + k[41])))\n        yout[28] = 0\n        yout[29] = 0\n        yout[30] = 0\n        yout[31] = 0\n        return 0\n    ")

/home/yangh/anaconda2/lib/python2.7/site-packages/IPython/core/interactiveshell.pyc in run_cell_magic(self, magic_name, line, cell)
   2113             magic_arg_s = self.var_expand(line, stack_depth)
   2114             with self.builtin_trap:
-> 2115                 result = fn(magic_arg_s, cell)
   2116             return result
   2117 

<decorator-gen-124> in cython(self, line, cell)

/home/yangh/anaconda2/lib/python2.7/site-packages/IPython/core/magic.pyc in <lambda>(f, *a, **k)
    186     # but it's overkill for just that one bit of state.
    187     def magic_deco(arg):
--> 188         call = lambda f, *a, **k: f(*a, **k)
    189 
    190         if callable(arg):

/home/yangh/anaconda2/lib/python2.7/site-packages/Cython/Build/IpythonMagic.pyc in cython(self, line, cell)
    289             build_extension.build_temp = os.path.dirname(pyx_file)
    290             build_extension.build_lib  = lib_dir
--> 291             build_extension.run()
    292             self._code_cache[key] = module_name
    293 

/home/yangh/anaconda2/lib/python2.7/distutils/command/build_ext.pyc in run(self)
    338 
    339         # Now actually compile and link everything.
--> 340         self.build_extensions()
    341 
    342     def check_extensions_list(self, extensions):

/home/yangh/anaconda2/lib/python2.7/distutils/command/build_ext.pyc in build_extensions(self)
    447 
    448         for ext in self.extensions:
--> 449             self.build_extension(ext)
    450 
    451     def build_extension(self, ext):

/home/yangh/anaconda2/lib/python2.7/distutils/command/build_ext.pyc in build_extension(self, ext)
    497                                          debug=self.debug,
    498                                          extra_postargs=extra_args,
--> 499                                          depends=ext.depends)
    500 
    501         # XXX -- this is a Vile HACK!

/home/yangh/anaconda2/lib/python2.7/distutils/ccompiler.pyc in compile(self, sources, output_dir, macros, include_dirs, debug, extra_preargs, extra_postargs, depends)
    572             except KeyError:
    573                 continue
--> 574             self._compile(obj, src, ext, cc_args, extra_postargs, pp_opts)
    575 
    576         # Return *all* object filenames, not just the ones we just built.

/home/yangh/anaconda2/lib/python2.7/distutils/unixccompiler.pyc in _compile(self, obj, src, ext, cc_args, extra_postargs, pp_opts)
    122                        extra_postargs)
    123         except DistutilsExecError, msg:
--> 124             raise CompileError, msg
    125 
    126     def create_static_lib(self, objects, output_libname,

CompileError: command 'gcc' failed with exit status 1

problem with pip install, can't import common

I'm trying to install odes on an ubuntu 18.04 system. I've installed the dependencies and sundials as per the instructions here: https://scikits-odes.readthedocs.io/en/latest/installation.html#requirements-before-install

when I try to install odes with the command:

SUNDIALS_INST=/home/mrobins/sundials-3.1.1/install pip install scikits.odes

It falls over with the error shown below.

Collecting scikits.odes
  Using cached https://files.pythonhosted.org/packages/91/65/ab7ebd1a9a921f96bfb3d4e38db3c203e0f7e0781d73e35139277ea04baa/scikits.odes-2.4.0.tar.gz
  Installing build dependencies ... done
  Getting requirements to build wheel ... error
  Complete output from command /home/mrobins/tmp/test/bin/python3 /home/mrobins/tmp/test/lib/python3.6/site-packages/pip/_vendor/pep517/_in_process.py get_requires_for_build_wheel /tmp/tmp4httixax:
  Traceback (most recent call last):
    File "/home/mrobins/tmp/test/lib/python3.6/site-packages/pip/_vendor/pep517/_in_process.py", line 207, in <module>
      main()
    File "/home/mrobins/tmp/test/lib/python3.6/site-packages/pip/_vendor/pep517/_in_process.py", line 197, in main
      json_out['return_val'] = hook(**hook_input['kwargs'])
    File "/home/mrobins/tmp/test/lib/python3.6/site-packages/pip/_vendor/pep517/_in_process.py", line 54, in get_requires_for_build_wheel
      return hook(config_settings)
    File "/tmp/pip-build-env-163crzl0/overlay/lib/python3.6/site-packages/setuptools/build_meta.py", line 115, in get_requires_for_build_wheel
      return _get_build_requires(config_settings, requirements=['wheel'])
    File "/tmp/pip-build-env-163crzl0/overlay/lib/python3.6/site-packages/setuptools/build_meta.py", line 101, in _get_build_requires
      _run_setup()
    File "/tmp/pip-build-env-163crzl0/overlay/lib/python3.6/site-packages/setuptools/build_meta.py", line 85, in _run_setup
      exec(compile(code, __file__, 'exec'), locals())
    File "setup.py", line 15, in <module>
      from common import *
  ModuleNotFoundError: No module named 'common'

  ----------------------------------------
Command "/home/mrobins/tmp/test/bin/python3 /home/mrobins/tmp/test/lib/python3.6/site-packages/pip/_vendor/pep517/_in_process.py get_requires_for_build_wheel /tmp/tmp4httixax" failed with error code 1 in /tmp/pip-install-nja1jf80/scikits.odes

It looks like it can't see the common.py in the root directory of your repo, but I can't see why not.

Make scikits.odes citable

One of my officemates was trying to cite scikits.odes (in https://arxiv.org/abs/1612.09383), but there's currently no citable object (e.g. paper, doi). We should add to http://joss.theoj.org/ (and maybe http://ascl.net/), so that scikits.odes can be cited.

Issue with correctness of the results

I was trying to integrate the heat equation on a 100x100x100 grid, and scikits.odes's rk5 gives incorrect results (compared to scipy's solve_ivp). The values I get from scipy are always bounded between 0 and 1 (which they should be since I use 0 and 1 as Dirichlet boundary conditions), but those I get from scikits.odes blow up to ~10^10. Here's how to reproduce it:

# %% Import libraries
import matplotlib.pyplot as plt
import numpy as np
from scipy.integrate import solve_ivp
from scikits.odes.odeint import odeint
from time import time

# %% Define du/dt
def func(t, v, du, params):
    h, k, Nx, Ny, Nz = params
    is3d = True if Nz > 1 else False
    u = v.reshape((Nx, Ny, Nz))
    idx = np.arange(1, Nx-1)
    idy = np.arange(1, Ny-1)
    idz = np.arange(1, Nz-1) if is3d else np.array([0])
    u_xx = (u[np.ix_(idx-1, idy, idz)] - 2*u[np.ix_(idx, idy, idz)] + u[np.ix_(idx+1, idy, idz)]) / h**2
    u_yy = (u[np.ix_(idx, idy-1, idz)] - 2*u[np.ix_(idx, idy, idz)] + u[np.ix_(idx, idy+1, idz)]) / h**2
    if is3d:
        u_zz = (u[np.ix_(idx, idy, idz-1)] - 2*u[np.ix_(idx, idy, idz)] + u[np.ix_(idx, idy, idz+1)]) / h**2
    else:
        u_zz = 0.0
    idx1d = np.ravel_multi_index(np.ix_(idx, idy, idz), (Nx, Ny, Nz)).flatten()
    du[idx1d] = k * (u_xx + u_yy + u_zz).flatten()
    return du

# %% Define model parameters
Nx, Ny, Nz = 100, 100, 100
Lx = 1.0
Ly = Lx * (Ny-1)/(Nx-1)
Lz = Lx * (Nz-1)/(Nx-1)
h = Lx/(Nx-1)
D = 5e-3
params = (h, D, Nx, Ny, Nz)

# Safety checks
assert Nx >= 3
assert Ny >= 3
if Nz != 1:
    assert Nz >= 3

# %% Scikits.Odes
def func_odes(t, u, du):
    func(t, u, du, params)

tspan = (0.0, 5.0)
tout = np.linspace(tspan[0], tspan[1], 10)
u0 = np.zeros((Nx, Ny, Nz))     # IC @ t = 0 ; u = 0.0
u0[0, ...] = 1.0                # BC @ x = 0 ; u = 1.0
u0[-1, ...] = 1.0               # BC @ x = L ; u = 1.0
u0[:, 0, :] = 1.0               # BC @ y = 0 ; u = 1.0
u0[:, -1, :] = 1.0              # BC @ y = L ; u = 1.0

t0 = time()
out = odeint(func_odes, tout, u0.flatten(), method="rk5",
             rtol=1e-3, atol=1e-3)
print(f"Scikits.Odes runtime (rk5): {time()-t0:.2f} s")

# t0 = time()
# out = odeint(func_odes, tout, u0.flatten(), method="cvode", rtol=1e-3, atol=1e-3)
# print(f"Scikits.Odes runtime (cvode): {time()-t0:.2f} s")

u3d_odes = out.values.y.reshape((tout.size, Nx, Ny, Nz))

fig, ax = plt.subplots()
f = ax.imshow(u3d_odes[-1, ..., Nz//2], vmin=0, vmax=u3d_odes.max())
ax.set_title("Scikits.Odes")
plt.colorbar(f)

# %% Scipy
du = np.zeros(u0.size)
def func_scipy(t, u):
    return func(t, u, du, params)

t0 = time()
sol = solve_ivp(func_scipy, tspan, u0.flatten(), method="RK45",
                t_eval=tout, rtol=1e-3, atol=1e-3)
print(f"Scipy runtime (rk45): {time()-t0:.2f} s")

u3d_scipy = sol.y.reshape(Nx, Ny, Nz, sol.t.size)

fig, ax = plt.subplots()
f = ax.imshow(u3d_scipy[..., Nz//2, -1], vmin=0, vmax=u3d_scipy.max())
ax.set_title("Scipy")
plt.colorbar(f)
plt.show()

Can't install on Ubuntu (Docker)

Using ubuntu:16.04 image.

apt-get install python python-dev python-virtualenv virtualenvwrapper cmake cmake-curses-gui libopenblas-* libatlas-* liblapack-*

I compiled sundials with LAPACK interface as for documentation

mkvirtualenv pysundials
pip install numpy
pip install scikits.odes

tid@ab44bef2e9ee:~$ SUNDIALS_INST=/opt/sundials pip install scikits.odes
Collecting scikits.odes
  Using cached scikits.odes-2.3.1.tar.gz
    Complete output from command python setup.py egg_info:
    =============================================
    parent package is scikits
    top path is /tmp/pip-build-qar7lr/scikits.odes
    =============================================
    pkgconfig module not found, using preset paths
    SUNDIALS installation path set to `/opt/sundials` via $SUNDIALS_INST.
    lapack_opt_info:
    lapack_mkl_info:
    customize UnixCCompiler
      libraries mkl_rt not found in ['/home/tid/.virtualenvs/pysundials/lib', '/usr/local/lib', '/usr/lib', '/usr/lib/x86_64-linux-gnu']
      NOT AVAILABLE

    openblas_lapack_info:
    customize UnixCCompiler
    customize UnixCCompiler
    customize UnixCCompiler
    C compiler: x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC

    creating /tmp/tmpYg2j4J/tmp
    creating /tmp/tmpYg2j4J/tmp/tmpYg2j4J
    compile options: '-c'
    x86_64-linux-gnu-gcc: /tmp/tmpYg2j4J/source.c
    /tmp/tmpYg2j4J/source.c:1:1: warning: function declaration isn't a prototype [-Wstrict-prototypes]
     void zungqr();
     ^
    /tmp/tmpYg2j4J/source.c: In function 'main':
    /tmp/tmpYg2j4J/source.c:4:13: warning: implicit declaration of function 'zungqr_' [-Wimplicit-function-declaration]
                 zungqr_();
                 ^
    x86_64-linux-gnu-gcc -pthread /tmp/tmpYg2j4J/tmp/tmpYg2j4J/source.o -lopenblas -o /tmp/tmpYg2j4J/a.out
    customize UnixCCompiler
      FOUND:
        libraries = ['openblas', 'openblas']
        library_dirs = ['/usr/lib']
        language = c
        define_macros = [('HAVE_CBLAS', None)]

      FOUND:
        libraries = ['openblas', 'openblas']
        library_dirs = ['/usr/lib']
        language = c
        define_macros = [('HAVE_CBLAS', None)]

    Found LAPACK paths via lapack_opt ...
    =============================================
    parent package is scikits.odes
    top path is /tmp/pip-build-qar7lr/scikits.odes
    =============================================
    cython -2 -o /tmp/pip-build-qar7lr/scikits.odes/scikits/odes/sundials/common_defs.c.new /tmp/pip-build-qar7lr/scikits.odes/scikits/odes/sundials/common_defs.pyx
    Traceback (most recent call last):
      File "<string>", line 1, in <module>
      File "/tmp/pip-build-qar7lr/scikits.odes/setup.py", line 62, in <module>
        setup_package()
      File "/tmp/pip-build-qar7lr/scikits.odes/setup.py", line 56, in setup_package
        '': ['*.pxd'],
      File "/home/tid/.virtualenvs/pysundials/local/lib/python2.7/site-packages/numpy/distutils/core.py", line 135, in setup
        config = configuration()
      File "/tmp/pip-build-qar7lr/scikits.odes/setup.py", line 36, in configuration
        config.add_subpackage(DISTNAME)
      File "/home/tid/.virtualenvs/pysundials/local/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 1024, in add_subpackage
        caller_level = 2)
      File "/home/tid/.virtualenvs/pysundials/local/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 993, in get_subpackage
        caller_level = caller_level + 1)
      File "/home/tid/.virtualenvs/pysundials/local/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 930, in _get_configuration_from_setup_py
        config = setup_module.configuration(*args)
      File "scikits/odes/setup.py", line 26, in configuration
        config.add_subpackage('sundials')
      File "/home/tid/.virtualenvs/pysundials/local/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 1024, in add_subpackage
        caller_level = 2)
      File "/home/tid/.virtualenvs/pysundials/local/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 993, in get_subpackage
        caller_level = caller_level + 1)
      File "/home/tid/.virtualenvs/pysundials/local/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 930, in _get_configuration_from_setup_py
        config = setup_module.configuration(*args)
      File "scikits/odes/sundials/setup.py", line 114, in configuration
        include_dirs=[])
      File "/tmp/pip-build-qar7lr/scikits.odes/scikits/odes/_build.py", line 85, in cython
        status = subprocess.call(['cython', '-2', '-o', c_file_new, pyxfile])
      File "/usr/lib/python2.7/subprocess.py", line 523, in call
        return Popen(*popenargs, **kwargs).wait()
      File "/usr/lib/python2.7/subprocess.py", line 711, in __init__
        errread, errwrite)
      File "/usr/lib/python2.7/subprocess.py", line 1343, in _execute_child
        raise child_exception
    OSError: [Errno 2] No such file or directory

    ----------------------------------------
Command "python setup.py egg_info" failed with error code 1 in /tmp/pip-build-qar7lr/scikits.odes/
(pysundials) tid@ab44bef2e9ee:~$ ls /opt/sundials/
LICENSE  examples  include  lib

What am I missing?

doesn't build with sundials 5.1.0

I tried pointing scikits-odes to sundials 5.1.0, but it fails to compile:

Python 2.7

/nix/store/fdgwwak9g61j6jyilqpiswih02llm81l-gfortran-wrapper-9.2.0/bin/gfortran -Wall -g -Wall -g -shared build/temp.linux-x86_64-2.7/build/src.linux-x86_64-2.7/scikits/odes/lsodimodule.o build/temp.linux-x86_64-2.7/build/src.linux-x86_64-2.7/build/src.linux-x86_64-2.7/scikits/odes/fortranobject.o build/temp.linux-x86_64-2.7/scikits/odes/daepack/xerrwv.o build/temp.linux-x86_64-2.7/scikits/odes/daepack/vnorm.o build/temp.linux-x86_64-2.7/scikits/odes/daepack/stodi.o build/temp.linux-x86_64-2.7/scikits/odes/daepack/solsy.o build/temp.linux-x86_64-2.7/scikits/odes/daepack/prepji.o build/temp.linux-x86_64-2.7/scikits/odes/daepack/lsodi.o build/temp.linux-x86_64-2.7/scikits/odes/daepack/intdy.o build/temp.linux-x86_64-2.7/scikits/odes/daepack/ewset.o build/temp.linux-x86_64-2.7/scikits/odes/daepack/dlinpk.o build/temp.linux-x86_64-2.7/scikits/odes/daepack/ddaspk.o build/temp.linux-x86_64-2.7/scikits/odes/daepack/daux.o build/temp.linux-x86_64-2.7/scikits/odes/daepack/cfode.o build/temp.linux-x86_64-2.7/scikits/odes/daepack/ainvg.o -L/nix/store/m62n6i62f7vkman907blw7znjlkvla2b-gfortran-9.2.0-lib/lib -L/nix/store/m62n6i62f7vkman907blw7znjlkvla2b-gfortran-9.2.0-lib/lib -L/nix/store/bh447min7f6vqdw3x1iywr1vxyx4ix8y-python-2.7.17/lib -lpython2.7 -lgfortran -o build/lib.linux-x86_64-2.7/scikits/odes/lsodi.so
building 'scikits.odes.sundials.common_defs' extension
compiling C sources
C compiler: gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC

creating build/temp.linux-x86_64-2.7/scikits/odes/sundials
compile options: '-I/nix/store/q1sxwhf9zysd4vhkxqzzh4l1sd28spaz-python2.7-numpy-1.16.5/lib/python2.7/site-packages/numpy/core/include -I/nix/store/bh447min7f6vqdw3x1iywr1vxyx4ix8y-python-2.7.17/include/python2.7 -c'
gcc: scikits/odes/sundials/common_defs.c
In file included from /nix/store/q1sxwhf9zysd4vhkxqzzh4l1sd28spaz-python2.7-numpy-1.16.5/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822,
                 from /nix/store/q1sxwhf9zysd4vhkxqzzh4l1sd28spaz-python2.7-numpy-1.16.5/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
                 from /nix/store/q1sxwhf9zysd4vhkxqzzh4l1sd28spaz-python2.7-numpy-1.16.5/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4,
                 from scikits/odes/sundials/common_defs.c:631:
/nix/store/q1sxwhf9zysd4vhkxqzzh4l1sd28spaz-python2.7-numpy-1.16.5/lib/python2.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
   17 | #warning "Using deprecated NumPy API, disable it with " \
      |  ^~~~~~~
scikits/odes/sundials/common_defs.c:641:10: fatal error: sundials/sundials_pcg.h: No such file or directory
  641 | #include "sundials/sundials_pcg.h"
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~
compilation terminated.
error: Command "gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/nix/store/q1sxwhf9zysd4vhkxqzzh4l1sd28spaz-python2.7-numpy-1.16.5/lib/python2.7/site-packages/numpy/core/include -I/nix/store/bh447min7f6vqdw3x1iywr1vxyx4ix8y-python-2.7.17/include/python2.7 -c scikits/odes/sundials/common_defs.c -o build/temp.linux-x86_64-2.7/scikits/odes/sundials/common_defs.o -MMD -MF build/temp.linux-x86_64-2.7/scikits/odes/sundials/common_defs.o.d" failed with exit status 1
builder for '/nix/store/n8hmyyvyjhvlhxmjpb95j612kwgdyp92-python2.7-scikits.odes-2.4.0-9-g93075ae.drv' failed with exit code 1
error: build of '/nix/store/n8hmyyvyjhvlhxmjpb95j612kwgdyp92-python2.7-scikits.odes-2.4.0-9-g93075ae.drv' failed

Python 3.7

/nix/store/fdgwwak9g61j6jyilqpiswih02llm81l-gfortran-wrapper-9.2.0/bin/gfortran -Wall -g -Wall -g -shared build/temp.linux-x86_64-3.7/build/src.linux-x86_64-3.7/scikits/odes/lsodimodule.o build/temp.linux-x86_64-3.7/build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/scikits/odes/fortranobject.o build/temp.linux-x86_64-3.7/scikits/odes/daepack/xerrwv.o build/temp.linux-x86_64-3.7/scikits/odes/daepack/vnorm.o build/temp.linux-x86_64-3.7/scikits/odes/daepack/stodi.o build/temp.linux-x86_64-3.7/scikits/odes/daepack/solsy.o build/temp.linux-x86_64-3.7/scikits/odes/daepack/prepji.o build/temp.linux-x86_64-3.7/scikits/odes/daepack/lsodi.o build/temp.linux-x86_64-3.7/scikits/odes/daepack/intdy.o build/temp.linux-x86_64-3.7/scikits/odes/daepack/ewset.o build/temp.linux-x86_64-3.7/scikits/odes/daepack/dlinpk.o build/temp.linux-x86_64-3.7/scikits/odes/daepack/ddaspk.o build/temp.linux-x86_64-3.7/scikits/odes/daepack/daux.o build/temp.linux-x86_64-3.7/scikits/odes/daepack/cfode.o build/temp.linux-x86_64-3.7/scikits/odes/daepack/ainvg.o -L/nix/store/m62n6i62f7vkman907blw7znjlkvla2b-gfortran-9.2.0-lib/lib -L/nix/store/m62n6i62f7vkman907blw7znjlkvla2b-gfortran-9.2.0-lib/lib -L/nix/store/ja04f3cmapzb3f2mvjrb883bfqclsirq-python3-3.7.6/lib -lpython3.7m -lgfortran -o build/lib.linux-x86_64-3.7/scikits/odes/lsodi.cpython-37m-x86_64-linux-gnu.so
building 'scikits.odes.sundials.common_defs' extension
compiling C sources
C compiler: gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC

creating build/temp.linux-x86_64-3.7/scikits/odes/sundials
compile options: '-I/nix/store/hzh4nqhzr0a86mh1dd8r806cq5sn95pn-python3.7-numpy-1.18.1/lib/python3.7/site-packages/numpy/core/include -I/nix/store/ja04f3cmapzb3f2mvjrb883bfqclsirq-python3-3.7.6/include/python3.7m -c'
gcc: scikits/odes/sundials/common_defs.c
In file included from /nix/store/hzh4nqhzr0a86mh1dd8r806cq5sn95pn-python3.7-numpy-1.18.1/lib/python3.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1832,
                 from /nix/store/hzh4nqhzr0a86mh1dd8r806cq5sn95pn-python3.7-numpy-1.18.1/lib/python3.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
                 from /nix/store/hzh4nqhzr0a86mh1dd8r806cq5sn95pn-python3.7-numpy-1.18.1/lib/python3.7/site-packages/numpy/core/include/numpy/arrayobject.h:4,
                 from scikits/odes/sundials/common_defs.c:631:
/nix/store/hzh4nqhzr0a86mh1dd8r806cq5sn95pn-python3.7-numpy-1.18.1/lib/python3.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
   17 | #warning "Using deprecated NumPy API, disable it with " \
      |  ^~~~~~~
scikits/odes/sundials/common_defs.c:641:10: fatal error: sundials/sundials_pcg.h: No such file or directory
  641 | #include "sundials/sundials_pcg.h"
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~
compilation terminated.
error: Command "gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/nix/store/hzh4nqhzr0a86mh1dd8r806cq5sn95pn-python3.7-numpy-1.18.1/lib/python3.7/site-packages/numpy/core/include -I/nix/store/ja04f3cmapzb3f2mvjrb883bfqclsirq-python3-3.7.6/include/python3.7m -c scikits/odes/sundials/common_defs.c -o build/temp.linux-x86_64-3.7/scikits/odes/sundials/common_defs.o -MMD -MF build/temp.linux-x86_64-3.7/scikits/odes/sundials/common_defs.o.d" failed with exit status 1
builder for '/nix/store/8721l6n8czwy6nmf10gyghkcnixifgqa-python3.7-scikits.odes-2.4.0-9-g93075ae.drv' failed with exit code 1
error: build of '/nix/store/8721l6n8czwy6nmf10gyghkcnixifgqa-python3.7-scikits.odes-2.4.0-9-g93075ae.drv' failed

cc @idontgetoutmuch

Move away from numpy.distutils

numpy.distutils is going to go away sometime in the near future (the timeline is unclear, likely due to it being driven by the CPython core devs). scipy seems to be switching to meson, so once they do a release with meson, I'll look at what's needed to convert this over.

Tests Fail

I appear to have installed scikit-odes successfully

bash-3.2$ CC=gcc-9 pip3 install scikits.odes
CC=gcc-9 pip3 install scikits.odes
Collecting scikits.odes
  Using cached https://files.pythonhosted.org/packages/91/65/ab7ebd1a9a921f96bfb3d4e38db3c203e0f7e0781d73e35139277ea04baa/scikits.odes-2.4.0.tar.gz
  Installing build dependencies ... done
Requirement already satisfied: scipy in /usr/local/lib/python3.7/site-packages (from scikits.odes) (1.3.0)
Requirement already satisfied: numpy>=1.13.3 in /usr/local/lib/python3.7/site-packages (from scipy->scikits.odes) (1.16.0)
Building wheels for collected packages: scikits.odes
  Running setup.py bdist_wheel for scikits.odes ... done
  Stored in directory: /Users/dominic.steinitz/Library/Caches/pip/wheels/5f/6e/6e/e0623cfb3bc8e90514e6b4c66e9587ecd83922304912fc9bed
Successfully built scikits.odes
Installing collected packages: scikits.odes
Successfully installed scikits.odes-2.4.0
bash-3.2$ python3
python3
Python 3.7.0 (default, Oct  2 2018, 09:20:07) 
[Clang 10.0.0 (clang-1000.11.45.2)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import pkg_resources
import pkg_resources
>>> pkg_resources.get_distribution("scikits.odes").version
pkg_resources.get_distribution("scikits.odes").version
'2.4.0'
>>> quit()
quit()

But the tests fail

bash-3.2$ python3
python3
Python 3.7.0 (default, Oct  2 2018, 09:20:07) 
[Clang 10.0.0 (clang-1000.11.45.2)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import scikits.odes as od; od.test()
import scikits.odes as od; od.test()
Running unit tests for scikits.odes
NumPy version 1.16.0
NumPy relaxed strides checking option: True
NumPy is installed in /usr/local/lib/python3.7/site-packages/numpy
Python version 3.7.0 (default, Oct  2 2018, 09:20:07) [Clang 10.0.0 (clang-1000.11.45.2)]
nose version 1.3.7
/usr/local/lib/python3.7/site-packages/nose/suite.py:106: DeprecationWarning: Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated, and in 3.8 it will stop working
  if isinstance(tests, collections.Callable) and not is_suite:
../usr/local/lib/python3.7/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': 27, '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 1.95964127e-06
 2.00559588e-06 2.05370031e-06 2.12527937e-06 2.18137134e-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 3.40839272e-08
 2.74318062e-08 2.24709419e-08]
.ode.get_info() =
 {'NumSteps': 19, 'NumRhsEvals': 29, '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}
...E..........................
[CVDLS ERROR]  cvDlsSetup
  The Jacobian routine failed in an unrecoverable manner.


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

.
[CVDLS ERROR]  cvDlsSetup
  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.

.
[CVSPILS ERROR]  cvSpilsSolve
  The Jacobian x vector routine failed in an unrecoverable manner.


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

.
[CVSPILS ERROR]  cvSpilsSolve
  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.

...
[IDADLS ERROR]  idaDlsSetup
  The Jacobian routine failed in an unrecoverable manner.


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

.
[IDADLS ERROR]  idaDlsSetup
  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.

...
======================================================================
ERROR: odes.tests.test_odeint.test_odeint_banded_jacobian
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/local/lib/python3.7/site-packages/nose/case.py", line 198, in runTest
    self.test(*self.arg)
  File "/usr/local/lib/python3.7/site-packages/scikits/odes/tests/test_odeint.py", line 330, in test_odeint_banded_jacobian
    linsolver='lapackdense')
  File "/usr/local/lib/python3.7/site-packages/scikits/odes/odeint.py", line 216, in odeint
    return solver.solve(t, y0)
  File "/usr/local/lib/python3.7/site-packages/scikits/odes/ode.py", line 333, in solve
    return self._integrator.solve(tspan, y0)
  File "scikits/odes/sundials/cvode.pyx", line 1724, in scikits.odes.sundials.cvode.CVODE.solve
  File "scikits/odes/sundials/cvode.pyx", line 1762, in scikits.odes.sundials.cvode.CVODE._solve
  File "scikits/odes/sundials/cvode.pyx", line 1577, in scikits.odes.sundials.cvode.CVODE._init_step
ValueError: LinSolver: Unknown solver type: lapackdense

----------------------------------------------------------------------
Ran 81 tests in 0.519s

FAILED (errors=1)
<nose.result.TextTestResult run=81 errors=1 failures=0>
>>> quit()
quit()

Specifying the compiler for ODES build on Mac OS X

I'm attempting to build ODES on a MacBook Pro running Mac OS X El Capitan (10.11.6). The problem I'm having is with the build ODES Scikits step of the procedure (see attached file).

One issue I've observed is that the script uses the gfortran compiler instead of the Absoft 2016 Pro Fortran compiler used in building the sundials procedure.

Please advise.
build_log_odes.txt

define another parameter in eqsrhs when using CVODE?

Hello Folks

Is it possible to pass a python reference to scikits.odes.ode.ode() and then have the solver pass the reference back to eqsrhs()? It appears from

                Values: function of class CV_RhsFunction or a python function
                    with signature (t, y, yp) or (t, y, yp, userdata)

in odes/scikits/odes/sundials/cvode.pyx that this might be possible, but I'm not confident that I understand it.

The reference would be handy, but not essential. Otherwise I can hack a class variable that eqsrhs() can use to obtain the necessary data.

Thanks
Arthur

pip install scikits.odes not working

I am trying to install and use scikits.odes through pip on a Windows machine, but it is not working. The final error I get in the command prompt is:

Command "c:\users\miles\anaconda2\python.exe -u -c "import setuptools, tokenize;file='c:\users\miles\appdata\local\temp\pip-build-sekgu8\scikits.odes\setup.py';f=getattr(tokenize, 'open', open)(file);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, file, 'exec'))" install --record c:\users\miles\appdata\local\temp\pip-sr8fq6-record\install-record.txt --single-version-externally-managed --compile" failed with error code 1 in c:\users\miles\appdata\local\temp\pip-build-sekgu8\scikits.odes\

I also got this error:

Failed building wheel for scikits.odes

Any ideas what the problem could be? I got assimulo up and running fine. I am running into a problem where my model is very slow, and I wanted to see if scikits.odes has any potential to improve the simulation speed.

Miles

Issue using scikits.odes with Python 3.5 and 3.7 but not with 3.6

We're using scikits.odes in a battery modelling project PyBaMM. We've run into the following difficulty getting it working as expected with our continuous integration: everything works fine with Python 3.6, but not with Python 3.5 and 3.7.

Example failure on 3.5
Example success on 3.6
Example failure on 3.7

In each of the failures the errors are reported as

ValueError: Integrator name <ida or cvode> does not exsist

With these specific failures I have tried using your Sundials installation scripts, and can't see any obvious reason that there would be any difference between python versions.

Have you seen this before? Any ideas what the problem might be? Thanks for your help!

IDA option algebraic_vars_idx documentation is wrong

in the file ida.pyx there is a description of the option 'algebraic_vars_idx' that says "... These are denoted by the position (index) in the residual vector..." This is wrong. It should be "... These are denoted by the position (index) in the state vector y..."

This may seem like a small thing, but it caused me some grief. This change also aligns the documentation with the way Octave documents its implementation of IDA.

Thanks!

image not found error while running scikits.odes

Hi,

I am trying to use scikits.odes and managed to successfully install and run at Linux-based Hyak mox supercomputing cluster in University of Washington. Following the same protocol, I installed scikits.odes in my iMac (deleted the relevant words as found in #105). I got confirmation that it got installed properly (Successfully installed scikits.odes-2.4.1.dev0 scipy-1.3.1). However, when I try to run the simple piece of code for solving theVan der Pol oscillator, I get the following error

dlopen(/Users/chowdhury/anaconda2/envs/odes/lib/python3.6/site-packages/scikits/odes/sundials/cvode.cpython-36m-darwin.so, 2): Library not loaded: libsundials_cvode.3.dylib
Referenced from: /Users/chowdhury/anaconda2/envs/odes/lib/python3.6/site-packages/scikits/odes/sundials/cvode.cpython-36m-darwin.so
Reason: image not found
Traceback (most recent call last):
File "test.py", line 11, in
solution = ode('cvode', van_der_pol, old_api=False).solve(np.linspace(t0,500,200), y0)
File "/Users/chowdhury/anaconda2/envs/odes/lib/python3.6/site-packages/scikits/odes/ode.py", line 273, in init
integrator = find_ode_integrator(integrator_name)
File "/Users/chowdhury/anaconda2/envs/odes/lib/python3.6/site-packages/scikits/odes/ode.py", line 486, in find_ode_integrator
raise ValueError('Integrator name %s does not exist' % name)

I was wondering if you have any suggestion regarding this issue. Thanks a lot.

is it possible to get the result of CVodeGetNumRhsEvals with python code?

I'm trying to find out how many evaluations of the RHS the integrator needed to reach a certain time. Is it possible to get the result of CVodeGetNumRhsEvals? Haven't found anything besides the definition while digging through the code base.

If I haven't overlooked it, I'd be happy to implement this. Any preferences for the API? I'm imagining adding it to the CVODE class in scikits/odes/sundials/cvode.pyx.

Performance test has user data as object

In https://github.com/bmcage/odes/blob/master/docs/ipython/Performance%20tests.ipynb
the userdata k is passed as an object.
Is that the reason for little speedup for cvode in cythonized version?

Make Install Process Easier

I spent several hours installing this morning :( I'm still not convinced everything is correct #95 but I can solve a simple ode now).

Even installing sundials wasn't entirely trivial. It would better to use homebrew or nixpkgs to ensure the required version (in fact nix or something similar is really the way to go packages that rely on other packages outside the the python ecosystem IMHO).

cd MyWorkingSundials/
cmake -DCMAKE_INSTALL_PREFIX=/Users/myname/MySundials/instdir -DEXAMPLES_INSTALL_PATH=/Users/myname/MySundials/instdir/examples /Users/myname/sundials-3.1.1

export SUNDIALS_INST=/Users/myname/MySundials/instdir

CC=gcc-9 pip3 install scikits.odes

export DYLD_LIBRARY_PATH=/Users/myname/MySundials/instdir/lib

I may have missed some steps.

Community guidelines must be added to address JOSS requirements

There should be clear guidelines for third-parties wishing to:
-Contribute to the software
-Report issues or problems with the software
-Seek support

See for example this Contributing.md

Linker issue during fedora installation: missing -L$ SUNDIALS_INST/lib64 compiler flag

Fedora 31 x86_64, Python 3.7, openblas from fedora repo, scikits.odes ver. 2.6.1
Sundials 5.1.0 (as recomended) installed to $HOME/opt/sundials/:

cmake -DLAPACK_ENABLE=ON -DSUNDIALS_INDEX_SIZE=64 -DCMAKE_INSTALL_PREFIX=$HOME/opt/sundials/ ../sundials-5.1.0/
make install

For my setup, snippet above installs libraries to lib64 subdirectory not lib/

After that pip fails due to ld cannot locate sundials libraries:

export  SUNDIALS_INST=$HOME/opt/sundials
pip3 install scikits.odes
<...>
 gcc -pthread -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -g build/temp.linux-x86_64-3.7/scikits/odes/sundials/common_defs.o -L/home/my_user/opt/sundials/lib -L/usr/lib64 -L/usr/lib64 -lsundials_nvecserial -lsundials_sunlinsollapackband -lsundials_sunlinsollapackdense -lsundials_sunlinsolband -lsundials_sunlinsoldense -lsundials_sunlinsolpcg -lsundials_sunlinsolspbcgs -lsundials_sunlinsolspfgmr -lsundials_sunlinsolspgmr -lsundials_sunlinsolsptfqmr -lsundials_sunmatrixband -lsundials_sunmatrixdense -lsundials_sunmatrixsparse -lopenblas -lopenblas -lpython3.7m -o build/lib.linux-x86_64-3.7/scikits/odes/sundials/common_defs.cpython-37m-x86_64-linux-gnu.so
  /usr/bin/ld: cannot find -lsundials_nvecserial
  /usr/bin/ld: cannot find -lsundials_sunlinsollapackband
  /usr/bin/ld: cannot find -lsundials_sunlinsollapackdense
<...>

So we can see there's only -L/home/my_user/opt/sundials/lib library path and no lib64 one.

Exporting LD_LIBRARY_PATH didn't help.
But when I created link ln -s $SUNDIALS_INST/lib64/ $SUNDIALS_INST/lib , installation worked well.

Exception handling from #27 does not function as expected

Was digging to why I was getting errors like SystemError: x returned a result with an error set (x is a placeholder) from inside odes, it appears except -1/except? -1 doesn't behave like we expected (or at least how I expect it): it appears what it does is propagate the exception upwards when -1 is returned (rather than returning -1 on an exception). This means if you do raise an exception inside user code, you get weird SystemErrors which occur at the next "python" frame (which may be inside cython-compiled code). I think the solution is to remove the except tags and use try-except with Exception (or BaseException), and return the error code manually in the except statement. I guess we should ask about this on the one of the cython mailing lists?

@florian98765 Did you have an example of where the exception handling works? I currently have a short test which I'll provide as a PR which breaks for me, but if you have an working example it may help understand what's going on...

Set extra parameters for right-hand-side function

Hi All,
I wondered whether we set parameters for rhs function in scikits.odes.ode, something similar to sicpy: scipy.integrate.ode.set_f_params.
I have tried to set parameters as global ones which works indeed. However, I still want to know whether I can set parameters more explicitly because that will probably make easier in some cases e.g when multiple cores are used for different sets of parameter values. Thanks.
Regards,
Huan

Upgrade to the latest sundials 4.1.0

I know this is a pain as I've had to do it for the Haskell bindings to sundials but it would be good if it happened :)

Can't install with pip (in conda)

I've been struggling with the instalation of scikits.odes through pip. I am currently working with Anaconda so I installed sundials using conda install -c conda-forge sundials. Then, I read the conda documentation and said that for non-conda packages (like scikits.odes), one can use pip.

So I did sudo pip install scikits.odes and surprisingly, an error occurred while executing setup.py, specifically: ImportError: No module named 'numpy'.

I don't know why numpy is not found during the installation. Any ideas on how to fix this problem?

Python version: 2.7
conda version: 4.3.29
pip version: 9.0.1
scikits.odes version: 2.3.1
OS: Linux Mint 18

Thanks.

sensitivity equation

Hi all, I wonder whether odes offers sensitivity equations from the Cvodes. Do we have some example for that? Thanks. Huan

Installation on Windows 10 with Anaconda3 (64 bits)

Dear fellows,

I have tried to install scikits.odes on a Windows 10 OS with Anaconda 3, but I had some issues.

Packages Installed successfully:
SUNDIALS (conda install -c conda-forge sundials)
c-complier (conda install -c conda-forge c-compiler)
fortran-compiles (conda install -c conda-forge fortran-compiler)
lapack (conda install -c conda-forge lapack)
blas (conda install -c conda-forge blas)

However, I had the following problems in order to install scikits.odes (pip install scikits.odes)
error_scikits_odes.txt

Even with pip install -v scikits.odes i had problems

ERROR: Failed building wheel for scikits.odes
ERROR: Could not build wheels for scikits.odes which use PEP 517 and cannot be installed directly

Could you help me ?

Thanks in advance.

Deprecation warning: `np.alen`

np.alen is deprecated in 1.18. It can be replaced with len.

move to sundials 3.1.1

We should move to latest sundials.
Much to do as solvers have been abstracted away.

start of a working branch: https://github.com/bmcage/odes/tree/sundials_3_1