Solved: SUNSPGMR undefined scikits.odes on python 3.10?
Closed this issue · 1 comments
I'm on Arch linux, installed Sundials 5.1.0, scikits.odes version 2.6.3. But I get:
ImportError: /usr/lib/python3.10/site-packages/scikits/odes/sundials/ida.cpython-310-x86_64-linux-gnu.so: undefined symbol: SUNSPGMR when I try to create a solver with the name 'ida'. Also if I do
import scikits.odes.sundials.ida as ida
I get the same error.
I ran
make test
and 100% passed.
I also did:
import scikits.odes as od
od.test()
And I get:
Running unit tests for scikits.odes
NumPy version 1.22.3
NumPy relaxed strides checking option: True
NumPy is installed in /usr/lib/python3.10/site-packages/numpy
Python version 3.10.4 (main, Mar 23 2022, 23:05:40) [GCC 11.2.0]
nose version 1.3.7
/usr/lib/python3.10/site-packages/numpy/distutils/ccompiler.py:8: DeprecationWarning: The distutils package is deprecated and slated for removal in Python 3.12. Use setuptools or check PEP 632 for potential alternatives
from distutils import ccompiler
/usr/lib/python3.10/site-packages/numpy/distutils/ccompiler.py:17: DeprecationWarning: The distutils.sysconfig module is deprecated, use sysconfig instead
from distutils.sysconfig import customize_compiler
Traceback (most recent call last):
File "", line 1, in
File "/usr/lib/python3.10/site-packages/numpy/testing/_private/nosetester.py", line 461, in test
t = NumpyTestProgram(argv=argv, exit=False, plugins=plugins)
File "/home/paul/.local/lib/python3.10/site-packages/nose/core.py", line 118, in init
unittest.TestProgram.init(
File "/usr/lib/python3.10/unittest/main.py", line 100, in init
self.parseArgs(argv)
File "/home/paul/.local/lib/python3.10/site-packages/nose/core.py", line 179, in parseArgs
self.createTests()
File "/home/paul/.local/lib/python3.10/site-packages/nose/core.py", line 193, in createTests
self.test = self.testLoader.loadTestsFromNames(self.testNames)
File "/home/paul/.local/lib/python3.10/site-packages/nose/loader.py", line 481, in loadTestsFromNames
return unittest.TestLoader.loadTestsFromNames(self, names, module)
File "/usr/lib/python3.10/unittest/loader.py", line 220, in loadTestsFromNames
suites = [self.loadTestsFromName(name, module) for name in names]
File "/usr/lib/python3.10/unittest/loader.py", line 220, in
suites = [self.loadTestsFromName(name, module) for name in names]
File "/home/paul/.local/lib/python3.10/site-packages/nose/loader.py", line 431, in loadTestsFromName
return self.loadTestsFromModule(
File "/home/paul/.local/lib/python3.10/site-packages/nose/loader.py", line 354, in loadTestsFromModule
tests.extend(self.loadTestsFromDir(module_path))
File "/home/paul/.local/lib/python3.10/site-packages/nose/loader.py", line 191, in loadTestsFromDir
yield self.loadTestsFromName(
File "/home/paul/.local/lib/python3.10/site-packages/nose/loader.py", line 431, in loadTestsFromName
return self.loadTestsFromModule(
File "/home/paul/.local/lib/python3.10/site-packages/nose/loader.py", line 359, in loadTestsFromModule
return self.suiteClass(ContextList(tests, context=module))
File "/home/paul/.local/lib/python3.10/site-packages/nose/suite.py", line 428, in call
return self.makeSuite(tests, context, **kw)
File "/home/paul/.local/lib/python3.10/site-packages/nose/suite.py", line 475, in makeSuite
suite = self.suiteClass(
File "/home/paul/.local/lib/python3.10/site-packages/nose/suite.py", line 159, in init
super(ContextSuite, self).init(tests)
File "/home/paul/.local/lib/python3.10/site-packages/nose/suite.py", line 53, in init
super(LazySuite, self).init()
File "/usr/lib/python3.10/unittest/suite.py", line 22, in init
self._tests = []
File "/home/paul/.local/lib/python3.10/site-packages/nose/suite.py", line 106, in _set_tests
if isinstance(tests, collections.Callable) and not is_suite:
AttributeError: module 'collections' has no attribute 'Callable'
solved: due to an installation of octave I had a more recent version of sundials installed. had to do:
sudo pip uninstall scikits.odes
sudo python -m pip cache purge
export SUNDIALS_INST=/usr/local
sudo -E pip install scikits.odes