module 'scikits.odes' has no attribute 'test'
Opened this issue · 2 comments
Whitechapel-1888 commented
I assume there's an issue with pathing but I cannot seem to fix it.
Following the guide on https://scikits-odes.readthedocs.io/en/stable/installation.html, I installed sundials 5.1.0 using the command
cmake -DLAPACK_ENABLE=ON -DSUNDIALS_INDEX_SIZE=64 ..
inside a build directory that I created in the source folder (note that I do not specify an install path such that sundials is properly installed into /usr/local/lib and /usr/local/include).
Then, I install scikits.odes via pip. I also installed nose as is mentioned in the guide.
Running od.test() however outputs
---------------------------------------------------------------------------
AttributeError Traceback (most recent call last)
Cell In[2], line 1
----> 1 import scikits.odes as od; od.test()
AttributeError: module 'scikits.odes' has no attribute 'test'
Also, trying to use the solver returns an error:
import numpy as np
from scikits.odes import ode
tout = np.linspace(0, 1)
initial_values = np.array([1, 0])
omega = 6.0
def example1(t, y, ydot):
ydot[0] = x[1]
ydot[1] = - omega * x[0]
pass
solver = ode('cvode', example1, old_api=False)
solution = solver.solve([0.,1.,2.], initial_values)
Output:
libsundials_cvode.so.6: cannot open shared object file: No such file or directory
libsundials_cvode.so.6: cannot open shared object file: No such file or directory
---------------------------------------------------------------------------
ValueError Traceback (most recent call last)
Cell In[5], line 1
----> 1 solver = ode('cvode', example1, old_api=False)
2 solution = solver.solve([0.,1.,2.], initial_values)
File ~/source/miniconda3/envs/cyth/lib/python3.11/site-packages/scikits/odes/ode.py:273, in ode.__init__(self, integrator_name, eqsrhs, **options)
272 def __init__(self, integrator_name, eqsrhs, **options):
--> 273 integrator = find_ode_integrator(integrator_name)
274 if integrator is None:
275 raise ValueError('No integrator name match with %s or is not available.'\
276 %(repr(integrator_name)))
File ~/source/miniconda3/envs/cyth/lib/python3.11/site-packages/scikits/odes/ode.py:494, in find_ode_integrator(name)
492 elif hasattr(cl, name) and re.match(name, cl.name, re.I):
493 return cl
--> 494 raise ValueError('Integrator name %s does not exist' % name)
ValueError: Integrator name cvode does not exist
The libraries however do exist. What am I missing here?
Also, apparently the guide is out-of-date seeing that sundials 6 is supported as well. Will there be an update?
bmcage commented
You have the error
libsundials_cvode.so.6: cannot open shared object file: No such file or directory
So that must be fixed. Did the cmake not give an error? If so, to fix that. If not, to point to the correct location. See lower on that page
export LD_LIBRARY_PATH=/usr/local/lib:$LD_LIBRARY_PATH
Whitechapel-1888 commented
Did the cmake not give an error?
No, it ran without issues.
If not, to point to the correct location. See lower on that page
I did the lib location export, but the problem remains the same. And the files are definitely in the correct location:
└─ $ ls -la /usr/local/lib
total 15340
drwxr-xr-x 4 root root 12288 Feb 15 16:29 .
drwxr-xr-x 12 root root 4096 Feb 15 16:03 ..
drwxr-xr-x 3 root root 4096 Feb 15 16:29 cmake
-rw-r--r-- 1 root root 1324408 Feb 15 16:28 libsundials_arkode.a
lrwxrwxrwx 1 root root 23 Feb 15 16:29 libsundials_arkode.so -> libsundials_arkode.so.5
lrwxrwxrwx 1 root root 27 Feb 15 16:03 libsundials_arkode.so.4 -> libsundials_arkode.so.4.1.0
-rw-r--r-- 1 root root 573040 Feb 15 16:02 libsundials_arkode.so.4.1.0
lrwxrwxrwx 1 root root 27 Feb 15 16:29 libsundials_arkode.so.5 -> libsundials_arkode.so.5.7.0
-rw-r--r-- 1 root root 939448 Feb 15 16:28 libsundials_arkode.so.5.7.0
-rw-r--r-- 1 root root 591164 Feb 15 16:28 libsundials_cvode.a
lrwxrwxrwx 1 root root 22 Feb 15 16:29 libsundials_cvode.so -> libsundials_cvode.so.6
lrwxrwxrwx 1 root root 26 Feb 15 16:03 libsundials_cvode.so.5 -> libsundials_cvode.so.5.1.0
-rw-r--r-- 1 root root 338944 Feb 15 16:02 libsundials_cvode.so.5.1.0
lrwxrwxrwx 1 root root 26 Feb 15 16:29 libsundials_cvode.so.6 -> libsundials_cvode.so.6.7.0
-rw-r--r-- 1 root root 446056 Feb 15 16:28 libsundials_cvode.so.6.7.0
-rw-r--r-- 1 root root 840318 Feb 15 16:28 libsundials_cvodes.a
lrwxrwxrwx 1 root root 23 Feb 15 16:29 libsundials_cvodes.so -> libsundials_cvodes.so.6
lrwxrwxrwx 1 root root 27 Feb 15 16:03 libsundials_cvodes.so.5 -> libsundials_cvodes.so.5.1.0
-rw-r--r-- 1 root root 491800 Feb 15 16:02 libsundials_cvodes.so.5.1.0
lrwxrwxrwx 1 root root 27 Feb 15 16:29 libsundials_cvodes.so.6 -> libsundials_cvodes.so.6.7.0
-rw-r--r-- 1 root root 608856 Feb 15 16:28 libsundials_cvodes.so.6.7.0
-rw-r--r-- 1 root root 127582 Feb 15 16:28 libsundials_generic.a
lrwxrwxrwx 1 root root 24 Feb 15 16:29 libsundials_generic.so -> libsundials_generic.so.6
lrwxrwxrwx 1 root root 28 Feb 15 16:29 libsundials_generic.so.6 -> libsundials_generic.so.6.7.0
-rw-r--r-- 1 root root 112640 Feb 15 16:28 libsundials_generic.so.6.7.0
-rw-r--r-- 1 root root 548156 Feb 15 16:28 libsundials_ida.a
lrwxrwxrwx 1 root root 20 Feb 15 16:29 libsundials_ida.so -> libsundials_ida.so.6
lrwxrwxrwx 1 root root 24 Feb 15 16:03 libsundials_ida.so.5 -> libsundials_ida.so.5.1.0
-rw-r--r-- 1 root root 325856 Feb 15 16:02 libsundials_ida.so.5.1.0
lrwxrwxrwx 1 root root 24 Feb 15 16:29 libsundials_ida.so.6 -> libsundials_ida.so.6.7.0
-rw-r--r-- 1 root root 414832 Feb 15 16:28 libsundials_ida.so.6.7.0
-rw-r--r-- 1 root root 783182 Feb 15 16:28 libsundials_idas.a
lrwxrwxrwx 1 root root 21 Feb 15 16:29 libsundials_idas.so -> libsundials_idas.so.5
lrwxrwxrwx 1 root root 25 Feb 15 16:03 libsundials_idas.so.4 -> libsundials_idas.so.4.1.0
-rw-r--r-- 1 root root 474432 Feb 15 16:02 libsundials_idas.so.4.1.0
lrwxrwxrwx 1 root root 25 Feb 15 16:29 libsundials_idas.so.5 -> libsundials_idas.so.5.7.0
-rw-r--r-- 1 root root 572928 Feb 15 16:28 libsundials_idas.so.5.7.0
-rw-r--r-- 1 root root 467570 Feb 15 16:28 libsundials_kinsol.a
lrwxrwxrwx 1 root root 23 Feb 15 16:29 libsundials_kinsol.so -> libsundials_kinsol.so.6
lrwxrwxrwx 1 root root 27 Feb 15 16:03 libsundials_kinsol.so.5 -> libsundials_kinsol.so.5.1.0
-rw-r--r-- 1 root root 271440 Feb 15 16:02 libsundials_kinsol.so.5.1.0
lrwxrwxrwx 1 root root 27 Feb 15 16:29 libsundials_kinsol.so.6 -> libsundials_kinsol.so.6.7.0
-rw-r--r-- 1 root root 355768 Feb 15 16:28 libsundials_kinsol.so.6.7.0
-rw-r--r-- 1 root root 155866 Feb 15 16:28 libsundials_nvecmanyvector.a
lrwxrwxrwx 1 root root 31 Feb 15 16:29 libsundials_nvecmanyvector.so -> libsundials_nvecmanyvector.so.6
lrwxrwxrwx 1 root root 35 Feb 15 16:03 libsundials_nvecmanyvector.so.5 -> libsundials_nvecmanyvector.so.5.1.0
-rw-r--r-- 1 root root 50144 Feb 15 16:02 libsundials_nvecmanyvector.so.5.1.0
lrwxrwxrwx 1 root root 35 Feb 15 16:29 libsundials_nvecmanyvector.so.6 -> libsundials_nvecmanyvector.so.6.7.0
-rw-r--r-- 1 root root 136424 Feb 15 16:28 libsundials_nvecmanyvector.so.6.7.0
-rw-r--r-- 1 root root 166988 Feb 15 16:28 libsundials_nvecserial.a
lrwxrwxrwx 1 root root 27 Feb 15 16:29 libsundials_nvecserial.so -> libsundials_nvecserial.so.6
lrwxrwxrwx 1 root root 31 Feb 15 16:03 libsundials_nvecserial.so.5 -> libsundials_nvecserial.so.5.1.0
-rw-r--r-- 1 root root 63184 Feb 15 16:02 libsundials_nvecserial.so.5.1.0
lrwxrwxrwx 1 root root 31 Feb 15 16:29 libsundials_nvecserial.so.6 -> libsundials_nvecserial.so.6.7.0
-rw-r--r-- 1 root root 145032 Feb 15 16:28 libsundials_nvecserial.so.6.7.0
-rw-r--r-- 1 root root 133450 Feb 15 16:28 libsundials_sunlinsolband.a
lrwxrwxrwx 1 root root 30 Feb 15 16:29 libsundials_sunlinsolband.so -> libsundials_sunlinsolband.so.4
lrwxrwxrwx 1 root root 34 Feb 15 16:03 libsundials_sunlinsolband.so.3 -> libsundials_sunlinsolband.so.3.1.0
-rw-r--r-- 1 root root 26424 Feb 15 16:02 libsundials_sunlinsolband.so.3.1.0
lrwxrwxrwx 1 root root 34 Feb 15 16:29 libsundials_sunlinsolband.so.4 -> libsundials_sunlinsolband.so.4.7.0
-rw-r--r-- 1 root root 117568 Feb 15 16:28 libsundials_sunlinsolband.so.4.7.0
-rw-r--r-- 1 root root 133010 Feb 15 16:28 libsundials_sunlinsoldense.a
lrwxrwxrwx 1 root root 31 Feb 15 16:29 libsundials_sunlinsoldense.so -> libsundials_sunlinsoldense.so.4
lrwxrwxrwx 1 root root 35 Feb 15 16:03 libsundials_sunlinsoldense.so.3 -> libsundials_sunlinsoldense.so.3.1.0
-rw-r--r-- 1 root root 30720 Feb 15 16:02 libsundials_sunlinsoldense.so.3.1.0
lrwxrwxrwx 1 root root 35 Feb 15 16:29 libsundials_sunlinsoldense.so.4 -> libsundials_sunlinsoldense.so.4.7.0
-rw-r--r-- 1 root root 117392 Feb 15 16:28 libsundials_sunlinsoldense.so.4.7.0
-rw-r--r-- 1 root root 133502 Feb 15 16:28 libsundials_sunlinsollapackband.a
lrwxrwxrwx 1 root root 36 Feb 15 16:29 libsundials_sunlinsollapackband.so -> libsundials_sunlinsollapackband.so.4
lrwxrwxrwx 1 root root 40 Feb 15 16:29 libsundials_sunlinsollapackband.so.4 -> libsundials_sunlinsollapackband.so.4.7.0
-rw-r--r-- 1 root root 117696 Feb 15 16:28 libsundials_sunlinsollapackband.so.4.7.0
-rw-r--r-- 1 root root 133126 Feb 15 16:28 libsundials_sunlinsollapackdense.a
lrwxrwxrwx 1 root root 37 Feb 15 16:29 libsundials_sunlinsollapackdense.so -> libsundials_sunlinsollapackdense.so.4
lrwxrwxrwx 1 root root 41 Feb 15 16:29 libsundials_sunlinsollapackdense.so.4 -> libsundials_sunlinsollapackdense.so.4.7.0
-rw-r--r-- 1 root root 117536 Feb 15 16:28 libsundials_sunlinsollapackdense.so.4.7.0
-rw-r--r-- 1 root root 141330 Feb 15 16:28 libsundials_sunlinsolpcg.a
lrwxrwxrwx 1 root root 29 Feb 15 16:29 libsundials_sunlinsolpcg.so -> libsundials_sunlinsolpcg.so.4
lrwxrwxrwx 1 root root 33 Feb 15 16:03 libsundials_sunlinsolpcg.so.3 -> libsundials_sunlinsolpcg.so.3.1.0
-rw-r--r-- 1 root root 44976 Feb 15 16:02 libsundials_sunlinsolpcg.so.3.1.0
lrwxrwxrwx 1 root root 33 Feb 15 16:29 libsundials_sunlinsolpcg.so.4 -> libsundials_sunlinsolpcg.so.4.7.0
-rw-r--r-- 1 root root 122088 Feb 15 16:28 libsundials_sunlinsolpcg.so.4.7.0
-rw-r--r-- 1 root root 144826 Feb 15 16:28 libsundials_sunlinsolspbcgs.a
lrwxrwxrwx 1 root root 32 Feb 15 16:29 libsundials_sunlinsolspbcgs.so -> libsundials_sunlinsolspbcgs.so.4
lrwxrwxrwx 1 root root 36 Feb 15 16:03 libsundials_sunlinsolspbcgs.so.3 -> libsundials_sunlinsolspbcgs.so.3.1.0
-rw-r--r-- 1 root root 49144 Feb 15 16:02 libsundials_sunlinsolspbcgs.so.3.1.0
lrwxrwxrwx 1 root root 36 Feb 15 16:29 libsundials_sunlinsolspbcgs.so.4 -> libsundials_sunlinsolspbcgs.so.4.7.0
-rw-r--r-- 1 root root 126248 Feb 15 16:28 libsundials_sunlinsolspbcgs.so.4.7.0
-rw-r--r-- 1 root root 145774 Feb 15 16:28 libsundials_sunlinsolspfgmr.a
lrwxrwxrwx 1 root root 32 Feb 15 16:29 libsundials_sunlinsolspfgmr.so -> libsundials_sunlinsolspfgmr.so.4
lrwxrwxrwx 1 root root 36 Feb 15 16:03 libsundials_sunlinsolspfgmr.so.3 -> libsundials_sunlinsolspfgmr.so.3.1.0
-rw-r--r-- 1 root root 49304 Feb 15 16:02 libsundials_sunlinsolspfgmr.so.3.1.0
lrwxrwxrwx 1 root root 36 Feb 15 16:29 libsundials_sunlinsolspfgmr.so.4 -> libsundials_sunlinsolspfgmr.so.4.7.0
-rw-r--r-- 1 root root 126312 Feb 15 16:28 libsundials_sunlinsolspfgmr.so.4.7.0
-rw-r--r-- 1 root root 146568 Feb 15 16:28 libsundials_sunlinsolspgmr.a
lrwxrwxrwx 1 root root 31 Feb 15 16:29 libsundials_sunlinsolspgmr.so -> libsundials_sunlinsolspgmr.so.4
lrwxrwxrwx 1 root root 35 Feb 15 16:03 libsundials_sunlinsolspgmr.so.3 -> libsundials_sunlinsolspgmr.so.3.1.0
-rw-r--r-- 1 root root 49280 Feb 15 16:02 libsundials_sunlinsolspgmr.so.3.1.0
lrwxrwxrwx 1 root root 35 Feb 15 16:29 libsundials_sunlinsolspgmr.so.4 -> libsundials_sunlinsolspgmr.so.4.7.0
-rw-r--r-- 1 root root 126288 Feb 15 16:28 libsundials_sunlinsolspgmr.so.4.7.0
-rw-r--r-- 1 root root 149590 Feb 15 16:28 libsundials_sunlinsolsptfqmr.a
lrwxrwxrwx 1 root root 33 Feb 15 16:29 libsundials_sunlinsolsptfqmr.so -> libsundials_sunlinsolsptfqmr.so.4
lrwxrwxrwx 1 root root 37 Feb 15 16:03 libsundials_sunlinsolsptfqmr.so.3 -> libsundials_sunlinsolsptfqmr.so.3.1.0
-rw-r--r-- 1 root root 53280 Feb 15 16:02 libsundials_sunlinsolsptfqmr.so.3.1.0
lrwxrwxrwx 1 root root 37 Feb 15 16:29 libsundials_sunlinsolsptfqmr.so.4 -> libsundials_sunlinsolsptfqmr.so.4.7.0
-rw-r--r-- 1 root root 130368 Feb 15 16:28 libsundials_sunlinsolsptfqmr.so.4.7.0
-rw-r--r-- 1 root root 139142 Feb 15 16:28 libsundials_sunmatrixband.a
lrwxrwxrwx 1 root root 30 Feb 15 16:29 libsundials_sunmatrixband.so -> libsundials_sunmatrixband.so.4
lrwxrwxrwx 1 root root 34 Feb 15 16:03 libsundials_sunmatrixband.so.3 -> libsundials_sunmatrixband.so.3.1.0
-rw-r--r-- 1 root root 40800 Feb 15 16:02 libsundials_sunmatrixband.so.3.1.0
lrwxrwxrwx 1 root root 34 Feb 15 16:29 libsundials_sunmatrixband.so.4 -> libsundials_sunmatrixband.so.4.7.0
-rw-r--r-- 1 root root 122128 Feb 15 16:28 libsundials_sunmatrixband.so.4.7.0
-rw-r--r-- 1 root root 135638 Feb 15 16:28 libsundials_sunmatrixdense.a
lrwxrwxrwx 1 root root 31 Feb 15 16:29 libsundials_sunmatrixdense.so -> libsundials_sunmatrixdense.so.4
lrwxrwxrwx 1 root root 35 Feb 15 16:03 libsundials_sunmatrixdense.so.3 -> libsundials_sunmatrixdense.so.3.1.0
-rw-r--r-- 1 root root 40512 Feb 15 16:02 libsundials_sunmatrixdense.so.3.1.0
lrwxrwxrwx 1 root root 35 Feb 15 16:29 libsundials_sunmatrixdense.so.4 -> libsundials_sunmatrixdense.so.4.7.0
-rw-r--r-- 1 root root 121808 Feb 15 16:28 libsundials_sunmatrixdense.so.4.7.0
-rw-r--r-- 1 root root 150930 Feb 15 16:28 libsundials_sunmatrixsparse.a
lrwxrwxrwx 1 root root 32 Feb 15 16:29 libsundials_sunmatrixsparse.so -> libsundials_sunmatrixsparse.so.4
lrwxrwxrwx 1 root root 36 Feb 15 16:03 libsundials_sunmatrixsparse.so.3 -> libsundials_sunmatrixsparse.so.3.1.0
-rw-r--r-- 1 root root 49248 Feb 15 16:02 libsundials_sunmatrixsparse.so.3.1.0
lrwxrwxrwx 1 root root 36 Feb 15 16:29 libsundials_sunmatrixsparse.so.4 -> libsundials_sunmatrixsparse.so.4.7.0
-rw-r--r-- 1 root root 134688 Feb 15 16:28 libsundials_sunmatrixsparse.so.4.7.0
-rw-r--r-- 1 root root 146522 Feb 15 16:28 libsundials_sunnonlinsolfixedpoint.a
lrwxrwxrwx 1 root root 39 Feb 15 16:29 libsundials_sunnonlinsolfixedpoint.so -> libsundials_sunnonlinsolfixedpoint.so.3
lrwxrwxrwx 1 root root 43 Feb 15 16:03 libsundials_sunnonlinsolfixedpoint.so.2 -> libsundials_sunnonlinsolfixedpoint.so.2.1.0
-rw-r--r-- 1 root root 54392 Feb 15 16:02 libsundials_sunnonlinsolfixedpoint.so.2.1.0
lrwxrwxrwx 1 root root 43 Feb 15 16:29 libsundials_sunnonlinsolfixedpoint.so.3 -> libsundials_sunnonlinsolfixedpoint.so.3.7.0
-rw-r--r-- 1 root root 126312 Feb 15 16:28 libsundials_sunnonlinsolfixedpoint.so.3.7.0
-rw-r--r-- 1 root root 138098 Feb 15 16:28 libsundials_sunnonlinsolnewton.a
lrwxrwxrwx 1 root root 35 Feb 15 16:29 libsundials_sunnonlinsolnewton.so -> libsundials_sunnonlinsolnewton.so.3
lrwxrwxrwx 1 root root 39 Feb 15 16:03 libsundials_sunnonlinsolnewton.so.2 -> libsundials_sunnonlinsolnewton.so.2.1.0
-rw-r--r-- 1 root root 50096 Feb 15 16:02 libsundials_sunnonlinsolnewton.so.2.1.0
lrwxrwxrwx 1 root root 39 Feb 15 16:29 libsundials_sunnonlinsolnewton.so.3 -> libsundials_sunnonlinsolnewton.so.3.7.0
-rw-r--r-- 1 root root 122072 Feb 15 16:28 libsundials_sunnonlinsolnewton.so.3.7.0