DOLFIN

Large Matrices Error

Asked by Oluwaseun Sharomi

When I try to write a stiffness matrix for large mesh to file, I get the following error

"
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/home/osharomi/Work/FEniCS/lib/python2.7/site-packages/dolfin/cpp.py", line 2980, in array
    A = zeros((m_range[1] - m_range[0], self.size(1)))
MemoryError
"
I get the error specifically at A=A.array(). My guess is that numpy cannot create an array that large because of memory requirement.

Is there any easy way to go around this error for large matrices. My code is below.

from dolfin import *
import numpy
import scipy.io
# Create mesh and define function space
mesh=BoxMesh(0, 0, 0, 2, 0.7, 0.3, 400, 140, 60);
V = FunctionSpace(mesh, 'CG', 1)

u = TrialFunction(V)
v = TestFunction(V)

a1 = u*v*dx
a2 = -inner(nabla_grad(v),nabla_grad(u))*dx

A = assemble(a1)
B = assemble(a2)

A = A.array()
B = B.array()

scipy.io.savemat("abc.mat", {"A": A, "B": B})

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Oluwaseun Sharomi
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Revision history for this message
Oluwaseun Sharomi (oluwaseun-sharomi) said : 		#1

I fixed it using a different backend.

Revision history for this message
Mandrake (felix-linder) said : 		#2

I've got the same problem, can you tell me which backend works?

Revision history for this message
Oluwaseun Sharomi (oluwaseun-sharomi) said : 		#3

I used this

parameters["linear_algebra_backend"] = "uBLAS"
parameters.reorder_dofs_serial = False

then I created the function

def dump_matrix(filename, AA):
    row_ptr, col_ind, val = AA.data()
    Acsr = csr_matrix((val, col_ind, row_ptr))
    Acsr.eliminate_zeros()
    mmio.mmwrite(filename, Acsr )

so that the matrices can be saved into a Matrix Market file with the following

a1 = u*v*dx
A = assemble(a1)
dump_matrix("A",A)

needed imports

from scipy.io import mmio
from scipy.sparse import csr_matrix

Revision history for this message
Oluwaseun Sharomi (oluwaseun-sharomi) said : 		#4

I used this
parameters["linear_algebra_backend"] = "uBLAS"
parameters.reorder_dofs_serial = False
then I created the function
def dump_matrix(filename, AA):
    row_ptr, col_ind, val = AA.data()
    Acsr = csr_matrix((val, col_ind, row_ptr))
    Acsr.eliminate_zeros()
    mmio.mmwrite(filename, Acsr )
so that the matrices can be saved into a Matrix Market file with the following
a1 = u*v*dx
A = assemble(a1)
dump_matrix("A",A)
needed imports
from scipy.io import mmio
from scipy.sparse import csr_matrix

-------------------------------------------------
Oluwaseun Sharomi, PhD
PIMS Post-doctoral Research Fellow,
Department of Computer Science
University of Saskatchewan
Saskatoon, SK, S7N 5C9,
Phone: (306) 966-1498
Fax:     (306) 966-4884

Email: <email address hidden>

________________________________
 From: Mandrake <email address hidden>
To: <email address hidden>
Sent: Wednesday, July 31, 2013 12:16:11 PM
Subject: Re: [Question #221970]: Large Matrices Error

Your question #221970 on DOLFIN changed:
https://answers.launchpad.net/dolfin/+question/221970

Mandrake posted a new comment:
I've got the same problem, can you tell me which backend works?

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You received this question notification because you asked the question.

Revision history for this message
Mandrake (felix-linder) said : 		#5

Thank you, this gave me some useful hints, but finally i wrote my own dump-routine as uBLAS doesn't support distributed vectors.

Revision history for this message
Oluwaseun Sharomi (oluwaseun-sharomi) said : 		#6

All glory to the Almighty God. I am pleased that it helped.

Sent from Windows Mail

From: Mandrake
Sent: ‎Saturday‎, ‎August‎ ‎03‎, ‎2013 ‎9‎:‎21‎ ‎AM
To: <email address hidden>

Your question #221970 on DOLFIN changed:
https://answers.launchpad.net/dolfin/+question/221970

Mandrake posted a new comment:
Thank you, this gave me some useful hints, but finally i wrote my own
dump-routine as uBLAS doesn't support distributed vectors.

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You received this question notification because you asked the question.