Double Free on Writing to File

Try to create a simpler example if you want us to debug.

To begin with, there seems to be a call to new in

  xy = new Array<double>(dim, geometry.x(vertex->index()));

which is never freed.

--
Anders

On Tue, Jun 29, 2010 at 02:53:57PM -0000, Pietro Maximoff wrote:
> New question #116136 on DOLFIN:
> https://answers.launchpad.net/dolfin/+question/116136
>
> Hi
>
> I have the following snippet of code which I'm trying to use to colour a mesh:
>
> double inner_radius = 20;
> double outer_radius = 35;
>
> for (VertexIterator vertex(mesh); !vertex.end(); ++vertex) {
> xy = new Array<double>(dim, geometry.x(vertex->index()));
> x0 = (*xy)[0]; x1 = (*xy)[1]; x2 = 0; //(*xy)[2];
>
> if (sqrt(x0*x0 + x1*x1) < inner_radius + 0.3*(outer_radius-inner_radius))
> new cell_A;
> else
> new cell_B;
> }
>
> Vector temp(mesh.num_vertices());
> double block[mesh.num_vertices()];
> dolfin::uint rows[mesh.num_vertices()];
>
> // Indices of the row of the vector to set
> for (unsigned int i = 0; i < mesh.num_vertices(); ++i)
> rows[i] = i;
>
> // Output file in VTK format
> File file("out.pvd");
>
>
> int i = 0;
> for (std::vector<Cells*>::iterator p = Cell::instances_.begin(); p != Cell::instances_.end(); ++p) {
> if((*p)->celltype == Cell_A) {
> block[i] = 20;
> }
> else
> block[i] = -86;
>
> ++i;
> }
>
> temp.set(block, mesh.num_vertices(), rows);
> Function u(V, temp);
>
> file << u;
>
> plot(u);
>
> I get the following error(s) when I run it [ There's no error if I remove file << u and plot(u) ]:
>
> *** glibc detected *** ./colour_mesh: double free or corruption (out): 0x00000000128961e0 ***
> ======= Backtrace: =========
> /lib/libc.so.6(+0x775b6)[0x7f751b8f55b6]
> /lib/libc.so.6(cfree+0x73)[0x7f751b8fbe53]
> /home/pietro/FEniCS/lib/libdolfin.so.0(_ZN6dolfin7UFCCellD1Ev+0x51)[0x7f7523c6fdc1]
> /home/pietro/FEniCS/lib/libdolfin.so.0(_ZNK6dolfin8Function21compute_vertex_valuesERNS_5ArrayIdEERKNS_4MeshE+0x6c8)[0x7f7523cb8d08]
> /home/pietro/FEniCS/lib/libdolfin.so.0(_ZNK6dolfin7VTKFile16write_point_dataERKNS_15GenericFunctionERKNS_4MeshESs+0x123)[0x7f7523cd43d3]
> /home/pietro/FEniCS/lib/libdolfin.so.0(_ZNK6dolfin7VTKFile13results_writeERKNS_8FunctionESs+0xdc)[0x7f7523cd594c]
> /home/pietro/FEniCS/lib/libdolfin.so.0(_ZN6dolfin7VTKFilelsERKNS_8FunctionE+0x87)[0x7f7523cd7347]
> ./colour_mesh(main+0x805)[0x417fa5]
> /lib/libc.so.6(__libc_start_main+0xfd)[0x7f751b89cc4d]
> ./colour_mesh[0x40fd19]
> ======= Memory map: ========
> 00400000-00438000 r-xp 00000000 08:01 16450481 /home/pietro/workspace/colour_mesh
> 00637000-00638000 r--p 00037000 08:01 16450481 /home/pietro/workspace/colour_mesh
> 00638000-00639000 rw-p 00038000 08:01 16450481 /home/pietro/workspace/colour_mesh
> 01975000-129bb000 rw-p 00000000 00:00 0 [heap]
> 7f7510000000-7f7510021000 rw-p 00000000 00:00 0
> 7f7510021000-7f7514000000 ---p 00000000 00:00 0
> 7f75144cc000-7f75144d8000 r-xp 00000000 08:01 43846511 /usr/local/lib/openmpi/mca_osc_rdma.so
> 7f75144d8000-7f75146d7000 ---p 0000c000 08:01 43846511 /usr/local/lib/openmpi/mca_osc_rdma.so
> 7f75146d7000-7f75146d8000 r--p 0000b000 08:01 43846511 /usr/local/lib/openmpi/mca_osc_rdma.so
> 7f75146d8000-7f75146d9000 rw-p 0000c000 08:01 43846511 /usr/local/lib/openmpi/mca_osc_rdma.so
> 7f75146d9000-7f75146e3000 r-xp 00000000 08:01 43846509 /usr/local/lib/openmpi/mca_osc_pt2pt.so
> 7f75146e3000-7f75148e2000 ---p 0000a000 08:01 43846509 /usr/local/lib/openmpi/mca_osc_pt2pt.so
> 7f75148e2000-7f75148e3000 r--p 00009000 08:01 43846509 /usr/local/lib/openmpi/mca_osc_pt2pt.so
> 7f75148e3000-7f75148e4000 rw-p 0000a000 08:01 43846509 /usr/local/lib/openmpi/mca_osc_pt2pt.so
> 7f75148e4000-7f75148fc000 r-xp 00000000 08:01 43846497 /usr/local/lib/openmpi/mca_coll_tuned.so
> 7f75148fc000-7f7514afb000 ---p 00018000 08:01 43846497 /usr/local/lib/openmpi/mca_coll_tuned.so
> 7f7514afb000-7f7514afc000 r--p 00017000 08:01 43846497 /usr/local/lib/openmpi/mca_coll_tuned.so
> 7f7514afc000-7f7514afd000 rw-p 00018000 08:01 43846497 /usr/local/lib/openmpi/mca_coll_tuned.so
> 7f7514afd000-7f7514b00000 r-xp 00000000 08:01 43846495 /usr/local/lib/openmpi/mca_coll_sync.so
> 7f7514b00000-7f7514cff000 ---p 00003000 08:01 43846495 /usr/local/lib/openmpi/mca_coll_sync.so
> 7f7514cff000-7f7514d00000 r--p 00002000 08:01 43846495 /usr/local/lib/openmpi/mca_coll_sync.so
> 7f7514d00000-7f7514d01000 rw-p 00003000 08:01 43846495 /usr/local/lib/openmpi/mca_coll_sync.so
> 7f7514f07000-7f7514f09000 r-xp 00000000 08:01 43846491 /usr/local/lib/openmpi/mca_coll_self.so
> 7f7514f09000-7f7515108000 ---p 00002000 08:01 43846491 /usr/local/lib/openmpi/mca_coll_self.so
> 7f7515108000-7f7515109000 r--p 00001000 08:01 43846491 /usr/local/lib/openmpi/mca_coll_self.so
> 7f7515109000-7f751510a000 rw-p 00002000 08:01 43846491 /usr/local/lib/openmpi/mca_coll_self.so
> 7f751510a000-7f751510d000 r-xp 00000000 08:01 43846489 /usr/local/lib/openmpi/mca_coll_inter.so
> 7f751510d000-7f751530c000 ---p 00003000 08:01 43846489 /usr/local/lib/openmpi/mca_coll_inter.so
> 7f751530c000-7f751530d000 r--p 00002000 08:01 43846489 /usr/local/lib/openmpi/mca_coll_inter.so
> 7f751530d000-7f751530e000 rw-p 00003000 08:01 43846489 /usr/local/lib/openmpi/mca_coll_inter.so
> 7f751530e000-7f7515312000 r-xp 00000000 08:01 43846487 /usr/local/lib/openmpi/mca_coll_hierarch.so
> 7f7515312000-7f7515512000 ---p 00004000 08:01 43846487 /usr/local/lib/openmpi/mca_coll_hierarch.so
> 7f7515512000-7f7515513000 r--p 00004000 08:01 43846487 /usr/local/lib/openmpi/mca_coll_hierarch.so
> 7f7515513000-7f7515514000 rw-p 00005000 08:01 43846487 /usr/local/lib/openmpi/mca_coll_hierarch.so
> 7f7515514000-7f751551c000 r-xp 00000000 08:01 43846485 /usr/local/lib/openmpi/mca_coll_basic.so
> 7f751551c000-7f751571b000 ---p 00008000 08:01 43846485 /usr/local/lib/openmpi/mca_coll_basic.so
> 7f751571b000-7f751571c000 r--p 00007000 08:01 43846485 /usr/local/lib/openmpi/mca_coll_basic.so
> 7f751571c000-7f751571d000 rw-p 00008000 08:01 43846485 /usr/local/lib/openmpi/mca_coll_basic.so
> 7f751571d000-7f7515728000 r-xp 00000000 08:01 43846483 /usr/local/lib/openmpi/mca_btl_tcp.so
> 7f7515728000-7f7515927000 ---p 0000b000 08:01 43846483 /usr/local/lib/openmpi/mca_btl_tcp.so
> 7f7515927000-7f7515928000 r--p 0000a000 08:01 43846483 /usr/local/lib/openmpi/mca_btl_tcp.so
> 7f7515928000-7f7515929000 rw-p 0000b000 08:01 43846483 /usr/local/lib/openmpi/mca_btl_tcp.so
> 7f7515929000-7f75159a9000 rw-p 00000000 00:00 0
> 7f75159a9000-7f75159af000 r-xp 00000000 08:01 43846477 /usr/local/lib/openmpi/mca_btl_sm.so
> 7f75159af000-7f7515bae000 ---p 00006000 08:01 43846477 /usr/local/lib/openmpi/mca_btl_sm.so
> 7f7515bae000-7f7515baf000 r--p 00005000 08:01 43846477 /usr/local/lib/openmpi/mca_btl_sm.so
> 7f7515baf000-7f7515bb0000 rw-p 00006000 08:01 43846477 /usr/local/lib/openmpi/mca_btl_sm.so
> 7f7515bb0000-7f7515bb3000 r-xp 00000000 08:01 43846475 /usr/local/lib/openmpi/mca_btl_self.so
> 7f7515bb3000-7f7515db2000 ---p 00003000 08:01 43846475 /usr/local/lib/openmpi/mca_btl_self.so
> 7f7515db2000-7f7515db3000 r--p 00002000 08:01 43846475 /usr/local/lib/openmpi/mca_btl_self.so
> 7f7515db3000-7f7515db4000 rw-p 00003000 08:01 43846475 /usr/local/lib/openmpi/mca_btl_self.so
> 7f75163fc000-7f7516400000 r-xp 00000000 08:01 43846473 /usr/local/lib/openmpi/mca_bml_r2.so
> 7f7516400000-7f75165ff000 ---p 00004000 08:01 43846473 /usr/local/lib/openmpi/mca_bml_r2.so
> 7f75165ff000-7f7516600000 r--p 00003000 08:01 43846473 /usr/local/lib/openmpi/mca_bml_r2.so[wm:17807] *** Process received signal ***
> [wm:17807] Signal: Aborted (6)
> [wm:17807] Signal code: (-6)
> [wm:17807] [ 0] /lib/libpthread.so.0(+0xf8f0) [0x7f751bc0f8f0]
> [wm:17807] [ 1] /lib/libc.so.6(gsignal+0x35) [0x7f751b8b1a75]
> [wm:17807] [ 2] /lib/libc.so.6(abort+0x180) [0x7f751b8b55c0]
> [wm:17807] [ 3] /lib/libc.so.6(+0x6d4fb) [0x7f751b8eb4fb]
> [wm:17807] [ 4] /lib/libc.so.6(+0x775b6) [0x7f751b8f55b6]
> [wm:17807] [ 5] /lib/libc.so.6(cfree+0x73) [0x7f751b8fbe53]
> [wm:17807] [ 6] /home/pietro/FEniCS/lib/libdolfin.so.0(_ZN6dolfin7UFCCellD1Ev+0x51) [0x7f7523c6fdc1]
> [wm:17807] [ 7] /home/pietro/FEniCS/lib/libdolfin.so.0(_ZNK6dolfin8Function21compute_vertex_valuesERNS_5ArrayIdEERKNS_4MeshE+0x6c8) [0x7f7523cb8d08]
> [wm:17807] [ 8] /home/pietro/FEniCS/lib/libdolfin.so.0(_ZNK6dolfin7VTKFile16write_point_dataERKNS_15GenericFunctionERKNS_4MeshESs+0x123) [0x7f7523cd43d3]
> [wm:17807] [ 9] /home/pietro/FEniCS/lib/libdolfin.so.0(_ZNK6dolfin7VTKFile13results_writeERKNS_8FunctionESs+0xdc) [0x7f7523cd594c]
> [wm:17807] [10] /home/pietro/FEniCS/lib/libdolfin.so.0(_ZN6dolfin7VTKFilelsERKNS_8FunctionE+0x87) [0x7f7523cd7347]
> [wm:17807] [11] ./colour_mesh(main+0x805) [0x417fa5]
> [wm:17807] [12] /lib/libc.so.6(__libc_start_main+0xfd) [0x7f751b89cc4d]
> [wm:17807] [13] ./colour_mesh() [0x40fd19]
> [wm:17807] *** End of error message ***
>
> ===
>
> It seems the error has to do with : file << u
>
> How can I resolve this?
>
> Thanks
>
> Pietro
>
>
>

I assumed/assume the call to 'new' in
         xy = new Array<double>(dim, geometry.x(vertex->index()));
would be freed as the Array class has a destructor.

But the main problem seems to be writing to the output to VTK file

                 *** glibc detected *** ./colour_mesh: double free or corruption (out):

Also, if I create a MATLAB output file, instead of a VTK output file, it works fine, i.e.,

File file("out.m");
file << u.vector();

What I've essentially tried to do in the code is:

Load a 2D mesh (shape of a doughnut).
For every vertex in the mesh, if it's within a certain distance, the solution at that vertex is output as 20 otherwise as -86.

I've used a vector to gather the individual entries and then converted it to a function for output. Please let me know If there's a more efficient way.

Thanks.

Pietro

===========

Vector temp(mesh.num_vertices());
double block[mesh.num_vertices()];
dolfin::uint rows[mesh.num_vertices()];

int i = 0;
 for (VertexIterator vertex(mesh); !vertex.end(); ++vertex) {
  xy = new Array<double>(dim, geometry.x(vertex->index()));
  x0 = (*xy)[0];
  x1 = (*xy)[1];

  if (sqrt(x0*x0 + x1*x1) < 21.5)
     block[i] = 20;;
  else
    block[i] = -86;

 ++i;
 }

 // Indices of the row of the vector to set --- ALL indices
 for (unsigned int i = 0; i < mesh.num_vertices(); ++i)
            rows[i] = i;

 // Output file in VTK format
 File file("out.pvd");

 temp.set(block, mesh.num_vertices(), rows);
 Function u(V, temp);

 file << u;

 plot(u);

On Tue, Jun 29, 2010 at 04:34:04PM -0000, Pietro Maximoff wrote:
> Question #116136 on DOLFIN changed:
> https://answers.launchpad.net/dolfin/+question/116136
>
> Status: Answered => Open
>
> Pietro Maximoff is still having a problem:
> I assumed/assume the call to 'new' in
> xy = new Array<double>(dim, geometry.x(vertex->index()));
> would be freed as the Array class has a destructor.

No it won't since there's no object that goes out of scope and calls
the destructor.

> But the main problem seems to be writing to the output to VTK file
>
> *** glibc detected *** ./colour_mesh: double free or
> corruption (out):
>
> Also, if I create a MATLAB output file, instead of a VTK output file,
> it works fine, i.e.,
>
> File file("out.m");
> file << u.vector();
>
>
> What I've essentially tried to do in the code is:
>
> Load a 2D mesh (shape of a doughnut).
> For every vertex in the mesh, if it's within a certain distance, the solution at that vertex is output as 20 otherwise as -86.
>
> I've used a vector to gather the individual entries and then converted
> it to a function for output. Please let me know If there's a more
> efficient way.

Unfortunately I don't have time to think about what the best solution
to your problem is right now, but if you send me a stripped down and
simple test program that segfaults because of a bug in DOLFIN, I will
fix the bug.

--
Anders

Hi

My sincere apologies. I just checked the UFL form. I forgot to change the element from tetrahedron to triangle.

That fixed the problem.

Thanks Anders.

Isn't it strange though, that I still got output in matlab format?

Pietro

On Tue, Jun 29, 2010 at 04:59:17PM -0000, Pietro Maximoff wrote:
> Question #116136 on DOLFIN changed:
> https://answers.launchpad.net/dolfin/+question/116136
>
> Status: Answered => Solved
>
> Pietro Maximoff confirmed that the question is solved:
> Hi
>
> My sincere apologies. I just checked the UFL form. I forgot to change
> the element from tetrahedron to triangle.
>
> That fixed the problem.
>
> Thanks Anders.
>
> Isn't it strange though, that I still got output in matlab format?
>
> Pietro

It might do things in different ways.

--
Anders