Re: [Libmesh-users] mass lumping in FEMsystem

[Matteo S. <mat...@un...>]

On 05/06/2013 16:56, Roy Stogner wrote:
>
> On Wed, 5 Jun 2013, Matteo Semplice wrote:
>
>> matteo@montebianco:~/ufficio/Ricerca/popolazioni$ ./planctonstd-opt
> ...
>> [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation,
> ...
>
> If you're seeing a segfault, the first thing you should do is switch
> from opt to debug mode.  Then typically you'll fail an informative
> assertion before you ever get to the segfault point, and even in the
> worst case at least you can start things up in a debugger and have
> more context to step through.
> ---
> Roy
>
Hi, I am afraid I don't seem to hit any assertion failure... The 
backtrace at the bottom of my email was obtained with the program 
compiled in debug mode. Anyway, here it is again. But perhaps I should 
change my question to "what is the proper way to change the quadrature 
rule in a FEMSystem?"

Matteo

matteo@montebianco:~/ufficio/Ricerca/popolazioni$ gdb ./planctonstd-dbg
GNU gdb (GDB) 7.0.1-debian
Copyright (C) 2009 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later 
<http://gnu.org/licenses/gpl.html>
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.  Type "show copying"
and "show warranty" for details.
This GDB was configured as "i486-linux-gnu".
For bug reporting instructions, please see:
<http://www.gnu.org/software/gdb/bugs/>...
Reading symbols from 
/home/matteo/ufficio/Ricerca/popolazioni/planctonstd-dbg...done.
(gdb) run
Starting program: /home/matteo/ufficio/Ricerca/popolazioni/planctonstd-dbg
[Thread debugging using libthread_db enabled]
Running /home/matteo/ufficio/Ricerca/popolazioni/planctonstd-dbg

Refined initial mesh 8 times

Side Boundary conditions:
-------------------------
   (ID, number of sides)
   (0, 1)
   (1, 1)
hmax is 0.00390625
hmed is 0.00390625
hmin is 0.00390625
Homogeneous coexistence equilibrium is (5.47143, 10.1429, 5.29082)
eq_sys initialized
time_solver initialized
set options of diff_solver
  EquationSystems
   n_systems()=1
    System #0, "Plancton"
     Type "Implicit"
     Variables="p1" "p2" "p3"
     Finite Element Types="LAGRANGE" "LAGRANGE" "LAGRANGE"
     Approximation Orders="FIRST" "FIRST" "FIRST"
     n_dofs()=771
     n_local_dofs()=771
     n_constrained_dofs()=0
     n_vectors()=2
     DofMap Sparsity
       Average  On-Processor Bandwidth <= 8.97665
       Average Off-Processor Bandwidth <= 0
       Maximum  On-Processor Bandwidth <= 9
       Maximum Off-Processor Bandwidth <= 0
     DofMap Constraints
       Number of DoF Constraints = 0

*** Warning, This code is untested, experimental, or likely to see 
future API changes: 
/home/matteo/libmesh-0.7.2/libmesh/include/mesh/vtk_io.h, line 153, 
compiled Jun  6 2013 at 16:57:15 ***
######## Solving time step 0, time= 0

Program received signal SIGSEGV, Segmentation fault.
0x08129372 in ?? ()
(gdb) bt
#0  0x08129372 in ?? ()
#1  0xb7bada8b in libMesh::FEMContext::elem_fe_reinit (this=0x8129ba8) 
at src/systems/fem_context.C:575
#2  0xb7bb4146 in operator() (this=0xbfffec3c, range=...) at 
src/systems/fem_system.C:75
#3  0xb7bba2db in 
parallel_for<libMesh::StoredRange<libMesh::MeshBase::const_element_iterator, 
const libMesh::Elem*>, <unnamed>::AssemblyContributions> (range=..., 
body=...) at 
/home/matteo/libmesh-0.7.2/libmesh/include/parallel/threads.h:278
#4  0xb7bb65f3 in libMesh::FEMSystem::assembly (this=0x81546c8, 
get_residual=true, get_jacobian=true) at src/systems/fem_system.C:594
#5  0xb7b6b046 in libMesh::NewtonSolver::solve (this=0x81612f8) at 
src/solvers/newton_solver.C:301
#6  0xb7b7ffb6 in libMesh::UnsteadySolver::solve (this=0x8161170) at 
src/solvers/unsteady_solver.C:76
#7  0xb7b92e7d in libMesh::DifferentiableSystem::solve (this=0x81546c8) 
at src/systems/diff_system.C:118
#8  0xb7bb69c7 in libMesh::FEMSystem::solve (this=0x81546c8) at 
src/systems/fem_system.C:637
#9  0x0806f495 in main (argc=1, argv=0xbffff3b4) at plancton.cpp:203







-- 
Matteo Semplice			Dip. di Matematica
Phone: 011-6702831		Università degli Studi di Torino
Skype: matteosemplice		Via Carlo Alberto, 10 - Torino