Hi,
I am currently comparing a fenics based solver to some other open source
Navier-Stokes solvers and I just realized that I was using much more memory,
perhaps as much as a factor 3. I always thought it was the matrices, vectors
and Krylov solvers that were consuming memory, but on inspection I see that
memory is totally dominated by the boundary conditions (mesh connectivity?).
This was quite surprising to me, so I guess my question is - is this a well
known issue?
I have made a small test for memory use of a Poisson solver to illustrate.
Running it on one cpu returns the table showing the increment in RSS memory use
and total memory use for each new function down the script.
In [1]: run memorytest.py
RSS memory Increment Total
Starting weight of dolfin 75988 KB 75988 KB
Mesh 16760 KB 92748 KB
FunctionSpace 41600 KB 134348 KB
Matrix assembly 7792 KB 142140 KB
Function 304 KB 142444 KB
Solve 868 KB 143312 KB
Boundary condition 321428 KB 464740 KB
New solve 0 KB 464740 KB
Creating and applying the Dirichlet boundary condition calls mesh.init(D) and
mesh.init(D-1, D). I think this is were the extra memory comes in. The memory
cost is nearly 5 times more than for all the other stuff! Any comments?
Mikael
from dolfin import *
from commands import getoutput
from os import getpid
set_log_active(False)
def getRSSMemoryUsage():
mypid = getpid()
return eval(getoutput("ps -o rss %s" % mypid).split()[1])
class MemoryUsage:
def __init__(self, s):
self.memory = 0
info_blue(' '*21+'RSS memory Increment Total')
self(s)
def __call__(self, s):
self.prev = self.memory
self.memory = getRSSMemoryUsage()
#self.memory = memory_usage(False)[0]
info_blue('{0:26s} {1:10d} KB {2:10d} KB'.format(s,
self.memory-self.prev, self.memory))
memoryusage = MemoryUsage('Starting weight of dolfin')
mesh = UnitCubeMesh(40, 40, 40)
memoryusage("Mesh")
V = FunctionSpace(mesh, 'CG', 1)
memoryusage('FunctionSpace')
u, v = TrialFunction(V), TestFunction(V)
A = assemble(inner(grad(u), grad(v))*dx)
memoryusage("Matrix assembly")
b = assemble(Constant(6)*v*dx)
u = Function(V)
memoryusage("Function")
solve(A, u.vector(), b, 'gmres', 'hypre_amg')
memoryusage('Solve')
bc = DirichletBC(V, Constant(0), DomainBoundary())
bc.apply(A, b)
memoryusage('Boundary condition')
solve(A, u.vector(), b, 'gmres', 'hypre_amg')
memoryusage('New solve')
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