While all package of python3 are installed, I still get the error of ‘scipy.sparse.linalg.eigsh’ not found.
Please help.
You need to supply more information for this question to be informative.
- what version of fenics have you installed?
- how Did you install fenics on wls?
- what commands are you calling to get this error?
- provide the full errormessagw with the full trace.
Hi Dokken,
I have used the following commands in WSL(Windows Subsystem for Linux) to install Fenics
add-apt-repository ppa:fenics-packages/fenics
apt update
apt install fenicsx
But when I run the ‘test.py’ using python3 test.py in the shell I get the following error:
Traceback (most recent call last):
File “/mnt/d/Research/Fenics/annulus_flow.py”, line 6, in
from scipy.sparse.linalg.eigen.arpack import eigsh
ModuleNotFoundError: No module named ‘scipy.sparse.linalg.eigen.arpack’; ‘scipy.sparse.linalg.eigen’ is not a package
The ‘test.py’ has the following code:
from dolfin import *
from mshr import *
import numpy as np
import matplotlib.pyplot as plt
from numpy import linalg as LA
from scipy.sparse.linalg.eigen.arpack import eigsh
from scipy import sparse, io
import time
import pdb
Time info and viscosity coefficents
t_init = 0.0
t_final = 10.0
t_num = 1000
dt = (t_final - t_init)/t_num
eps_be = dt
t = t_init
Viscosity coefficient.
nu = 0.001
Generate the mesh.
circle_outx = 0.0
circle_outy = 0.0
circle_outr = 1.0
circle_inx = 0.5
circle_iny = 0.0
circle_inr = 0.1
domain = Circle(Point(circle_outx,circle_outy),circle_outr) - Circle(Point(circle_inx,circle_iny),circle_inr)
mesh = generate_mesh ( domain, 30 )
Declare Finite Element Spaces
P2 = VectorElement(“P”,triangle,2)
P1 = FiniteElement(“P”,triangle,1)
TH = P2 * P1
V = VectorFunctionSpace(mesh, “P”, 2)
Q = FunctionSpace(mesh, “P”, 1)
W = FunctionSpace(mesh,TH)
Declare Finite Element Functions
(u, p) = TrialFunctions(W)
(v, q) = TestFunctions(W)
w = Function(W)
u0 = Function(V)
p0 = Function(Q)
Macros needed for weak formulation.
def contract(u,v):
return inner(nabla_grad(u),nabla_grad(v))
def b(u,v,w):
return 0.5*(inner(dot(u,nabla_grad(v)),w)-inner(dot(u,nabla_grad(w)),v))
Declare Boundary Conditions.
def u0_boundary(x, on_boundary):
return on_boundary
noslip = Constant((0.0, 0.0))
class OriginPoint(SubDomain):
def inside(self, x, on_boundary):
return (near(x[0], 0.0) and near(x[1], 1.0))
originpoint = OriginPoint()
def lower_boundary_fixed_point(x,on_boundary):
tol=1E-15
return (abs(x[1]) < tol) and (abs(x[0]-0.5)<tol)
bc0 = DirichletBC(W.sub(0),noslip,u0_boundary)
bc_test = DirichletBC(W.sub(1), Constant(0.0), lower_boundary_fixed_point, method = ‘pointwise’)
bcs = [bc0,bc_test]
Generate Initial Conditions
Right Handside
f_stokes = Expression((“-14x[1](1 - x[0]x[0] - x[1]x[1])","4x[0](1 - x[0]x[0] - x[1]x[1])“),pi=np.pi, degree = 4)
f = Expression((”-14x[1](1 - x[0]x[0] - x[1]x[1])","4x[0](1 - x[0]*x[0] - x[1]*x[1])”),pi=np.pi, degree = 4)
Set up Stokes problem for IC
Functions for Stokes Equation
(us, ps) = TrialFunctions(W)
(vs, qs) = TestFunctions(W)
r = Function(W)
LStokes = inner(f_stokes, vs)*dx
Stokes = (inner(grad(us), grad(vs)) - div(vs)ps + qsdiv(us))*dx
solve(Stokes == LStokes, r, bcs,solver_parameters=dict(linear_solver=“lu”))
assign(u0,r.sub(0))
assign(p0,r.sub(1))
weak form NSE
NSE = (1./dt)*inner(u,v)*dx + b(u0,u,v)dx + nucontract(u,v)dx - div(v)pdx + qdiv(u)*dx
LNSE = inner(f,v)*dx + (1./dt)*inner(u0,v)*dx
####File for Plotting in Paraview##############################################
velocity_paraview_file = File(“para_plotting/velocity_solution.pvd”)
pressure_paraview_file = File(“para_plotting/pressure_solution.pvd”)
for jj in range(0,t_num):
t = t + dt
print('Numerical Time Level: t = '+ str(t))
A, b = assemble_system(NSE, LNSE, bcs)
solve(A,w.vector(),b)
assign(u0,w.sub(0))
assign(p0,w.sub(1))
#Save Solutions to Paraview File
velocity_paraview_file << (u0,t)
pressure_paraview_file << (p0,t)
The scipy package is installed in python3 because when I import in the shell in python3 shell it works.
Please help!
Thanks
First of all, you are installing fenicsx, not FEniCS (legacy). FEniCSx is the code available at: GitHub - FEniCS/dolfinx: Next generation FEniCS problem solving environment.
Secondly,
you are expecting scipy to be installed, but scipy is not a core dependency of dolfinx, thus you woudl have to install it yourself, for instnace by calling apt-get install python3-scipy
Thanks dokken,
Yes, I am installing FeniCSx. Scipy is already installed in python3 because simply doing ‘import scipy’ works. I think there is issue with some function is scipy such as eigsh.
Why are you installing FEniCSx when your source code is using legacy dolfin?
As for the scipy issue, this is unrelated to dolfin, and up to the version of scipy you are using. See for instance
and Sparse eigenvalue problems with ARPACK — SciPy v1.10.0 Manual
Thanks.
Got it, so I should be using dolfinx. Also, would you please guide me on creating mesh for FEniCSx? I can create mesh in gmsh but I don’t know how to make it work for FEniCSx. There are many posts on internet about meshing but I am unable to differentiate between FEniCSx or Legacy code.
I have made a tutorial for DOLFINx at:
https://jsdokken.com/dolfinx-tutorial/
which goes through how to use Gmsh:
- through the Python API: Implementation — FEniCSx tutorial
- using Meshio to read and convert msh files: Defining subdomains for different materials — FEniCSx tutorial
1 Like
Thanks for your help.
Just one more question, does FEniCSx work in Windows Anaconda ?
No, see GitHub - FEniCS/dolfinx: Next generation FEniCS problem solving environment
Note Windows packages are not available. This is due to some DOLFINx dependencies not supporting Windows
Thanks for your continued help. I am unable to write a vtk file in dolfinx. It does not recognize VTKWriter. Here is the traceback
Traceback (most recent call last):
File “/mnt/d/Research/Fenics/fundamentals_code.py”, line 334, in
with io.VTXWriter(domain.comm, “output.bp”, [uh]) as vtx:
AttributeError: module ‘dolfinx.io’ has no attribute ‘VTXWriter’
For usage of FidesWriter and VTXWriter, you need to have adios2 installed on your system at the time you install dolfinx: dolfinx/utils.py at main · FEniCS/dolfinx · GitHub