module 'scikits.odes' has no attribute 'test'

[Whitechapel-1888]

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]

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]

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