bmcage/odes

Install successfully, but fail to test

Cyclohexane1998 opened this issue · 0 comments

I have installed scikits.odes successfully, but fail to test.

first i install the sundials 5.1.0, which is located in /usr/local/lib
root@R7000-2020:/usr/local/lib# ls libsundials_arkode.a libsundials_arkode.so libsundials_arkode.so.4 libsundials_arkode.so.4.1.0 libsundials_cvode.a libsundials_cvodes.a libsundials_cvode.so libsundials_cvode.so.5
...
and then
pip install scikits.odes

finnally, i test odes.with
import scikits.odes as od od.test()

it doesn't work, and raises error as the follows:

/usr/local/lib/python3.9/dist-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 3.10 it will stop working
if isinstance(tests, collections.Callable) and not is_suite:
E.EEEEEEEEEE

ERROR: Failure: ImportError (libsundials_nvecserial.so.5: cannot open shared object file: No such file or directory)

Traceback (most recent call last):
File "/usr/local/lib/python3.9/dist-packages/nose/failure.py", line 39, in runTest
raise self.exc_val.with_traceback(self.tb)
File "/usr/local/lib/python3.9/dist-packages/nose/loader.py", line 417, in loadTestsFromName
module = self.importer.importFromPath(
File "/usr/local/lib/python3.9/dist-packages/nose/importer.py", line 47, in importFromPath
return self.importFromDir(dir_path, fqname)
File "/usr/local/lib/python3.9/dist-packages/nose/importer.py", line 94, in importFromDir
mod = load_module(part_fqname, fh, filename, desc)
File "/usr/lib/python3.9/imp.py", line 234, in load_module
return load_source(name, filename, file)
File "/usr/lib/python3.9/imp.py", line 171, in load_source
module = _load(spec)
File "", line 711, in _load
File "", line 680, in _load_unlocked
File "", line 850, in exec_module
File "", line 228, in _call_with_frames_removed
File "/usr/local/lib/python3.9/dist-packages/scikits/odes/tests/test_dae.py", line 18, in
from scikits.odes.sundials.common_defs import DTYPE
File "/snap/pycharm-professional/278/plugins/python/helpers/pydev/_pydev_bundle/pydev_import_hook.py", line 21, in do_import
module = self._system_import(name, *args, **kwargs)
ImportError: libsundials_nvecserial.so.5: cannot open shared object file: No such file or directory

ERROR: test_get_info_is_exposed_on_ode (odes.tests.test_get_info.GetInfoTest)

Traceback (most recent call last):
File "/usr/local/lib/python3.9/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/python3.9/dist-packages/scikits/odes/ode.py", line 273, in init
integrator = find_ode_integrator(integrator_name)
File "/usr/local/lib/python3.9/dist-packages/scikits/odes/ode.py", line 494, 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 (odes.tests.test_get_info.GetInfoTest)

Traceback (most recent call last):
File "/usr/local/lib/python3.9/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/python3.9/dist-packages/scikits/odes/ode.py", line 273, in init
integrator = find_ode_integrator(integrator_name)
File "/usr/local/lib/python3.9/dist-packages/scikits/odes/ode.py", line 494, 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 (odes.tests.test_get_info.GetInfoTest)

Traceback (most recent call last):
File "/usr/local/lib/python3.9/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/python3.9/dist-packages/scikits/odes/ode.py", line 273, in init
integrator = find_ode_integrator(integrator_name)
File "/usr/local/lib/python3.9/dist-packages/scikits/odes/ode.py", line 494, 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 (odes.tests.test_get_info.GetInfoTest)

Traceback (most recent call last):
File "/usr/local/lib/python3.9/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/python3.9/dist-packages/scikits/odes/ode.py", line 273, in init
integrator = find_ode_integrator(integrator_name)
File "/usr/local/lib/python3.9/dist-packages/scikits/odes/ode.py", line 494, 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 (odes.tests.test_get_info.GetInfoTestSpils)

Traceback (most recent call last):
File "/usr/local/lib/python3.9/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/python3.9/dist-packages/scikits/odes/ode.py", line 273, in init
integrator = find_ode_integrator(integrator_name)
File "/usr/local/lib/python3.9/dist-packages/scikits/odes/ode.py", line 494, in find_ode_integrator
raise ValueError('Integrator name %s does not exist' % name)
ValueError: Integrator name cvode does not exist

ERROR: Failure: ImportError (libsundials_nvecserial.so.5: cannot open shared object file: No such file or directory)

ERROR: Failure: ImportError (libsundials_ida.so.5: cannot open shared object file: No such file or directory)

Ran 12 tests in 0.005s
FAILED (errors=11)
libsundials_cvode.so.5: cannot open shared object file: No such file or directory
libsundials_cvode.so.5: cannot open shared object file: No such file or directory

the above error is similar to> #71
i try to edit ./bashrc with
export LD_LIBRARY_PATH=/usr/local/lib:$LD_LIBRARY_PATH

but it cannot solve my problem.
Can you do me a favor? thank you in advance.