FunctionSpace error for large RectangleMesh

Question

Hi!

I'm trying to make a huge rectangle mesh, but the I cannot create a FunctionSpace for it. Anyone know why? Here is the code:

from fenics import *
mesh = RectangleMesh(-638000.0, -3349500.0, 864700.0, -657600.0, 10018, 17946)
Q    = FunctionSpace(mesh, "CG", 1)

and the error:

/home/pf4d/Work/FEniCS/lib/python2.7/site-packages/dolfin/functions/functionspace.pyc in __init__(self, mesh, family, degree, form_degree, constrained_domain, restriction)
    466
    467         # Initialize base class
--> 468         FunctionSpaceBase.__init__(self, mesh, element, constrained_domain)
    469
    470         self.___degree = degree

/home/pf4d/Work/FEniCS/lib/python2.7/site-packages/dolfin/functions/functionspace.pyc in __init__(self, mesh, element, constrained_domain)
    166                 mesh = mesh.mesh()
    167             else:
--> 168                 dolfin_dofmap  = cpp.DofMap(ufc_dofmap, mesh)
    169
    170         # Initialize the cpp_FunctionSpace

/home/pf4d/Work/FEniCS/lib/python2.7/site-packages/dolfin/cpp/fem.pyc in __init__(self, *args)
    640
    641         """
--> 642         _fem.DofMap_swiginit(self,_fem.new_DofMap(*args))
    643     __swig_destroy__ = _fem.delete_DofMap
    644     def is_restricted(self):

StandardError: vector::reserve

I just ran into this problem as well. The machine I am running on has 5TB of RAM so I do not believe I am running out of physical memory.

My mesh has about 30m elements and I want to use MINI elements. The mesh is based on real world data (ct-scan of a complex structure) - generating a smaller mesh is not really an option. In fact, I want to run a much larger problem than this. Given that dolfin can run on ~10k processors this is an unfortunate bottleneck.

The trace back from master is:
File "/apps/dolfin/1.4.0/lib/python2.7/site-packages/dolfin/functions/functionspace.py", line 195, in add
return EnrichedFunctionSpace((self, other))
File "/apps/dolfin/1.4.0/lib/python2.7/site-packages/dolfin/functions/functionspace.py", line 524, in init
FunctionSpaceBase.init(self, mesh, element, constrained_domain=constrained_domain)
File "/apps/dolfin/1.4.0/lib/python2.7/site-packages/dolfin/functions/functionspace.py", line 168, in init
dolfin_dofmap = cpp.DofMap(ufc_dofmap, mesh)
File "/apps/dolfin/1.4.0/lib/python2.7/site-packages/dolfin/cpp/fem.py", line 555, in init
_fem.DofMap_swiginit(self,_fem.new_DofMap(*args))
StandardError: vector::reserve — ggorman, Dec 18, 2014

martinal · Answer 1 · Oct 23, 2014

Your mesh has about 360 million cells, try a smaller mesh to fit in memory.

answered Oct 23, 2014 by martinal FEniCS User (2,800 points)

Negative, not out of physical memory.

commented Oct 23, 2014 by pf4d FEniCS User (2,970 points)

FunctionSpace error for large RectangleMesh

1 Answer