Re: [FEniCS] Memory consumption of mesh

Chris Richardson Wed, 08 Jan 2014 06:57:26 -0800

On 08/01/2014 14:43, Garth N. Wells wrote:

On 2014-01-08 14:29, Chris Richardson wrote:

I patched MeshTopology.cpp to print out more information.
Looks like most of the memory is being using in MeshConnectivity 3--3.
I'm not sure what that means...


I recall some discussions on this before. d--d connectivity doesn't
make sense because what constitutes a connection is undefined. For the
d--d case, DOLFIN (in TopologyComputation.cpp) is assuming a shared
vertex constitutes a connection, which in 3D and for d=3 gives a lot
of connections.


Seems like it was explicitly wanted for some reason:-

TopologyComputation.cpp line 84

  // Compute connectivity dim - dim if not already computed

compute_connectivity(mesh, mesh.topology().dim(),mesh.topology().dim());



Chris

Garth


--- a/dolfin/mesh/MeshTopology.cpp
+++ b/dolfin/mesh/MeshTopology.cpp
@@ -16,7 +16,7 @@
 // along with DOLFIN. If not, see <http://www.gnu.org/licenses/>.
 //
 // First added:  2006-05-08
-// Last changed: 2013-02-03
+// Last changed: 2014-01-08

 #include <numeric>
 #include <sstream>
@@ -236,8 +236,22 @@ std::string MeshTopology::str(bool verbose) const
     }
   }
   else
-    s << "<MeshTopology of dimension " << _dim << ">";
-
+  {
+    s << "<MeshTopology of dimension " << _dim << ">\n";
+    s << "num_entities.size() = " << num_entities.size() << "\n";

+ s << "global_num_entities.size() = " <<global_num_entities.size() << "\n";+ s << "_global_indices.size() = " << _global_indices.size() <<"\n";+ s << "_shared_entities.size() = " << _shared_entities.size() <<"\n";

+    for(unsigned int i = 0; i < connectivity.size(); ++i)
+    {

+ s << "connectivity [" << i << "].size() = " <<connectivity[i].size();

+      for (unsigned int j = 0; j<connectivity[i].size(); ++j)
+      {
+        s << connectivity[i][j].str(false) << "\n";
+      }
+    }
+  }
+
   return s.str();
 }

//-----------------------------------------------------------------------------




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')

mesh.init(2)
print 'nfacets = ', mesh.num_facets()
print 'ncells = ', mesh.num_cells()

print mesh.topology().str(False)

memoryusage('mesh.init(2)')

mesh.init(2, 3)

memoryusage('mesh.init(2, 3)')

bc = DirichletBC(V, Constant(0), DomainBoundary())
bc.apply(A, b)

memoryusage('Boundary condition')

solve(A, u.vector(), b, 'gmres', 'hypre_amg')

memoryusage('New solve')




                     RSS memory Increment       Total
Starting weight of dolfin       120684 KB     120684 KB
Mesh                             16648 KB     137332 KB
FunctionSpace                    35908 KB     173240 KB
Matrix assembly                  14920 KB     188160 KB
Function                           376 KB     188536 KB
Solve                            21360 KB     209896 KB
nfacets =  777600
ncells =  384000
<MeshTopology of dimension 3>
num_entities.size() = 4
global_num_entities.size() = 4
_global_indices.size() = 4
_shared_entities.size() = 1
connectivity [0].size() = 4<MeshConnectivity 0 -- 0 of size 0>
<MeshConnectivity 0 -- 1 of size 0>
<MeshConnectivity 0 -- 2 of size 0>
<MeshConnectivity 0 -- 3 of size 1536000>
connectivity [1].size() = 4<MeshConnectivity 1 -- 0 of size 0>
<MeshConnectivity 1 -- 1 of size 0>
<MeshConnectivity 1 -- 2 of size 0>
<MeshConnectivity 1 -- 3 of size 0>
connectivity [2].size() = 4<MeshConnectivity 2 -- 0 of size 2332800>
<MeshConnectivity 2 -- 1 of size 0>
<MeshConnectivity 2 -- 2 of size 0>
<MeshConnectivity 2 -- 3 of size 0>
connectivity [3].size() = 4<MeshConnectivity 3 -- 0 of size 1536000>
<MeshConnectivity 3 -- 1 of size 0>
<MeshConnectivity 3 -- 2 of size 1536000>
<MeshConnectivity 3 -- 3 of size 25707504>

mesh.init(2)                    302072 KB     511968 KB
mesh.init(2, 3)                      0 KB     511968 KB
Boundary condition                 216 KB     512184 KB
New solve                            4 KB     512188 KB



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--
Chris Richardson
BP Institute
Madingley Road
Cambridge CB3 0EZ
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Re: [FEniCS] Memory consumption of mesh

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