Re: [Getfem-users] Python interface memory use ...

[Yves Renard]

Dear Magnus,

This memory used is not because of mf.basic_dof_nodes() but of the enumeration 
of dof it
calls (the enumeration of dof is done only once after the definition of a 
mesh_fem
object or when it changes itself or its linked mesh changes).

This enumeration of dof has been recently adpated to be more robust for 
situtations where
some elements share some nodes with the same location but assumed to be 
different
(in order to represent cracks betweens some elements for instance).

The consequence of this modification is that some information is stored locally 
on each
element during the enumeration of dof, which is more costly than before in term 
of memory.
However, the memory used during the enumeration of dof is released after the 
enumeration is
completed but, since there is no garbage collector in C++,
the resulting memory may be fragmented and not released to python. So, this 
memory is not
lost because it will be used by Getfem in the sequel but it may be not usable 
in python.

I commited a small fix which limitates a bit the necessary memory during 
enumeration of dof.
May be, I will think for the modification of the algorithm in order to reduce 
even more the
necessary memory. 


Best regards,

Yves.



----- Original Message -----
From: "Magnus Paulsson" <address@hidden>
To: "getfem-users" <address@hidden>
Sent: Friday, May 6, 2016 3:31:01 PM
Subject: [Getfem-users] Python interface memory use ...

It seems that mf.basic_dof_nodes() takes huge amount of memory and is running 
very slowly. 
In the example below the size of the DOF array should be ~ 3MB which is 
returned but it 
takes considerable time uses up approx. 1 GB. 

To make things more complicated I do not get consistent results. I.e., 
getfem-5.0 on one 
machine it’s not too bad … while getfem-5321 (new svn) on with slightly 
different numpy etc 
uses 1 GB. 

I’m sorry I have not been able to nail it down better. 

-Magnus 

import getfem as GF 
import numpy as N 
import resource, gc 

NN=50 

print "Mem use before mesh generation %i 
kb"%(resource.getrusage(resource.RUSAGE_SELF).ru_maxrss) 

mesh = GF.Mesh('regular simplices', N.arange(NN), 
N.arange(NN),N.arange(NN)) 
mf = GF.MeshFem(mesh,1) 
mf.set_fem(GF.Fem('FEM_PK(3,1)')) 
print "Mem use after mesh generation %i 
kb"%(resource.getrusage(resource.RUSAGE_SELF).ru_maxrss) 
dof=mf.basic_dof_nodes() 
print "DOF size %i kb"%(dof.size*8.0/1024.0) 
print "Mem use after DOF %i 
kb"%(resource.getrusage(resource.RUSAGE_SELF).ru_maxrss) 
del mesh, mf, dof 
gc.collect() 
print "Mem use after deleting objects %i 
kb"%(resource.getrusage(resource.RUSAGE_SELF).ru_maxrss) 






----------------------------------------------- 
Magnus Paulsson 
Associate Professor 
Dept. of Physics and Electrical Engineering 
Linnaeus University 
Phone: +46-480-446308 
Mobile: +46-70-6942987 


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