Hi Andre,
Can you try recompiling? I have updated the version of Netgen used in Gmsh to
the latest SVN.
Thanks,
Christophe
On 16 Dec 2011, at 11:33, Andre Nicolle wrote:
> Hi all,
>
> I have been using Gmsh for many years and found it to be a great program. We
> are now expanding our calculations and now require bigger meshes but have
> started to find this to be a problem when meshing (using netgen) larger than
> 100 million elements. Our system has adequate RAM (256Gb) but gmsh exits with
> a segmentation fault, as shown below. At present we are using Ubuntu 10.04
> 64Bit AMD 6100. The problem can be found with 2.42, 2.5 and svn revision
> 10744 versions of the code. Interestingly for some reason the latest version
> of Gmsh crashes considerably sooner than the older versions.
>
> Gmsh 2.50 and repository version were compiled using gcc version 4.4.3, Atlas
> Blas with the following command:
> cmake ../CMakeLists.txt -DENABLE_FLTK=0
>
> 2.42 was from ubuntu repository
>
> The meshing command is:
>
> gmsh box3d.geo -3 -bin -algo front3d -optimize_netgen -smooth 5 -clscale 1.0
> -rand 1.e-8 -o box_c_new.msh
>
> The box3d.geo file is very simple box with resolutions (0.002) set on the
> points as can be seen below .
>
> To help find the problem I have tried to recompile Gmsh with debugging on.
> I'm not sure which flags got set.
>
> cmake ../CMakeLists.txt -DENABLE_FLTK=0 -DCMAKE_BUILD_TYPE=Debug
>
> and rerun Gmsh using gdb, output below:
>
> The error seems to be generated in Netgen moveablemem.cpp which has
> disappeared in the latest version of Netgen 4.9 anyway. Given that Gmsh is
> still using Netgen 4.5, is it possible to link to the later version of netgen
> library installed locally instead of the built-in version to see if this
> helps.
>
> Thanks
>
> Andre
>
> ///////////////////////////////////////////////////////////////////////////////////////////////////////////////
>
> RES = 0.002;
> Point(1) = {0, 0, 0, RES};
> Point(2) = {1, 0, 0, RES};
> Point(3) = {1, 0, 1, RES};
> Point(4) = {0, 0, 1, RES};
> Point(5) = {0, 1, 0, RES};
> Point(6) = {1, 1, 0, RES};
> Point(7) = {1, 1, 1, RES};
> Point(8) = {0, 1, 1, RES};
> Line (1) = {1, 2};
> Line (2) = {2, 3};
> Line (3) = {3, 4};
> Line (4) = {4, 1};
> Line (5) = {1, 5};
> Line (6) = {5, 6};
> Line (7) = {6, 2};
> Line (8) = {5, 8};
> Line (9) = {8, 4};
> Line (10) = {8, 7};
> Line (11) = {7, 6};
> Line (12) = {7, 3};
> Line Loop (15) = {1, 2, 3, 4};
> Plane Surface (16) = {15};
> Line Loop (17) = {12, -2, -7, -11};
> Plane Surface (18) = {17};
> Line Loop (19) = {3, -9, 10, 12};
> Plane Surface (20) = {19};
> Line Loop (21) = {10, 11, -6, 8};
> Plane Surface (22) = {21};
> Line Loop (23) = {8, 9, 4, 5};
> Plane Surface (24) = {23};
> Line Loop (25) = {6, 7, -1, 5};
> Plane Surface (26) = {25};
> Surface Loop(27) = {20, 16, 26, 22, 18, 24};
> Volume(28) = {27};
>
> //////////////////////////////////////////////////////////////////////////////////////////////////////////////////
>
> Info : Started on Thu Dec 15 20:45:53 2011
> Info : Reading 'box3d.geo'...
> Info : Done reading 'box3d.geo'
> Info : Meshing 1D...
> Info : Meshing curve 1 (Line)
> Info : Meshing curve 2 (Line)
> Info : Meshing curve 3 (Line)
> Info : Meshing curve 4 (Line)
> Info : Meshing curve 5 (Line)
> Info : Meshing curve 6 (Line)
> Info : Meshing curve 7 (Line)
> Info : Meshing curve 8 (Line)
> Info : Meshing curve 9 (Line)
> Info : Meshing curve 10 (Line)
> Info : Meshing curve 11 (Line)
> Info : Meshing curve 12 (Line)
> Info : Done meshing 1D (0.01 s)
> Info : Meshing 2D...
> Info : Meshing surface 16 (Plane, Delaunay)
> Info : Meshing surface 18 (Plane, Delaunay)
> Info : Meshing surface 20 (Plane, Delaunay)
> Info : Meshing surface 22 (Plane, Delaunay)
> Info : Meshing surface 24 (Plane, Delaunay)
> Info : Meshing surface 26 (Plane, Delaunay)
> Info : Done meshing 2D (603.87 s)
> Info : Meshing 3D...
> Info : Meshing volume 28 (Frontal)
> Info : Region 28 Face 20, 0 intersect
> Info : Region 28 Face 16, 1 intersect
> Info : Region 28 Face 26, 1 intersect
> Info : Region 28 Face 22, 1 intersect
> Info : Region 28 Face 18, 1 intersect
> Info : Region 28 Face 24, 1 intersect
> Info : CalcLocalH: 1984450 Points 0 Elements 3968896 Surface Elements
> Info : Check subdomain 1 / 1
> Info : 3968896 open elements
> Info : Meshing subdomain 1 of 1
> Info : 3968896 open elements
> Info : Use internal rules
> Info : 3968896 open elements
> Info : Delaunay meshing
> Info : number of points: 1984450
> Info : blockfill local h
> Info : number of points: 44035686
>
> Program received signal SIGSEGV, Segmentation fault.
> 0x00007ffff577b1c3 in ?? () from /lib/libc.so.6
> (gdb) where
> #0 0x00007ffff577b1c3 in ?? () from /lib/libc.so.6
> #1 0x00007ffff577ee83 in free () from /lib/libc.so.6
> #2 0x0000000000f9c2cf in netgen::BaseMoveableMem::ReAlloc (
> this=0x7fffffffb3b8, s=12612)
> at
> /home/andre/gmsh/svn/gmsh/contrib/Netgen/libsrc/general/moveablemem.cpp:159
> #3 0x0000000000f950e7 in netgen::MoveableMem<netgen::INDEX_3>::ReAlloc (
> this=0x7fffffffb3b8, s=1051)
> at
> /home/andre/gmsh/svn/gmsh/contrib/Netgen/libsrc/include/../general/moveablemem.hpp:63
> #4 0x0000000000f94f2f in netgen::MoveableArray<netgen::INDEX_3, 0>::SetSize (
> this=0x7fffffffb3b0, nsize=1051)
> at
> /home/andre/gmsh/svn/gmsh/contrib/Netgen/libsrc/include/../general/array.hpp:447
> #5 0x0000000000f945c2 in netgen::BASE_INDEX_3_CLOSED_HASHTABLE::BaseSetSize (
> this=0x7fffffffb3b0, size=1051)
> at /home/andre/gmsh/svn/gmsh/contrib/Netgen/libsrc/general/hashtabl.cpp:294
> #6 0x000000000105a6ba in netgen::INDEX_3_CLOSED_HASHTABLE<int>::SetSize (
> this=0x7fffffffb3b0, size=1051)
> at
> /home/andre/gmsh/svn/gmsh/contrib/Netgen/libsrc/include/../general/hashtabl.hpp:870
> #7 0x000000000105a4ae in netgen::MeshNB::ResetFaceHT (this=0x7fffffffb3b0,
> size=1051)
> at /home/andre/gmsh/svn/gmsh/contrib/Netgen/libsrc/meshing/delaunay.cpp:144
> #8 0x0000000001053a54 in netgen::AddDelaunayPoint (newpi=..., newp=...,
> tempels=..., mesh=..., tettree=..., meshnb=..., centers=..., radi2=...,
> connected=..., treesearch=..., freelist=..., list=..., insphere=...,
> closesphere=...)
> at /home/andre/gmsh/svn/gmsh/contrib/Netgen/libsrc/meshing/delaunay.cpp:496
> #9 0x0000000001055625 in netgen::Delaunay1 (mesh=..., mp=...,
> adfront=0x205a4d90, tempels=..., oldnp=1984450, startel=..., pmin=...,
> pmax=...)
> at /home/andre/gmsh/svn/gmsh/contrib/Netgen/libsrc/meshing/delaunay.cpp:765
> #10 0x0000000001055d9f in netgen::Meshing3::Delaunay (this=0x7fffffffd3f0,
> mesh=..., domainnr=1, mp=...)
> at /home/andre/gmsh/svn/gmsh/contrib/Netgen/libsrc/meshing/delaunay.cpp:816
> #11 0x000000000106555b in netgen::MeshVolume (mp=..., mesh3d=...)
> at /home/andre/gmsh/svn/gmsh/contrib/Netgen/libsrc/meshing/meshfunc.cpp:192
> #12 0x0000000000f92263 in nglib::NgAddOn_GenerateVolumeMesh (mesh=0x2078cdc0,
> maxh=1e+22) at /home/andre/gmsh/svn/gmsh/contrib/Netgen/nglib_addon.cpp:80
> #13 0x0000000000b2a33e in meshGRegion::operator() (this=0x7fffffffe240,
> gr=0x1844820) at /home/andre/gmsh/svn/gmsh/Mesh/meshGRegion.cpp:883
> #14 0x0000000000a79d90 in
> std::for_each<std::_Rb_tree_const_iterator<GRegion*>,
> at /usr/include/c++/4.4/bits/stl_algo.h:4200
> #15 0x0000000000a7768c in Mesh3D (m=0x1833a20)
> at /home/andre/gmsh/svn/gmsh/Mesh/Generator.cpp:533
> #16 0x0000000000a77c0d in GenerateMesh (m=0x1833a20, ask=3)
> at /home/andre/gmsh/svn/gmsh/Mesh/Generator.cpp:636
> #17 0x000000000093e1b4 in GModel::mesh (this=0x1833a20, dimension=3)
> at /home/andre/gmsh/svn/gmsh/Geo/GModel.cpp:510
> #18 0x00000000007c4c75 in GmshBatch ()
> at /home/andre/gmsh/svn/gmsh/Common/Gmsh.cpp:170
> #19 0x00000000007c42e3 in main (argc=15, argv=0x7fffffffe5d8)
> at /home/andre/gmsh/svn/gmsh/Common/Main.cpp:27
>
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--
Prof. Christophe Geuzaine
University of Liege, Electrical Engineering and Computer Science
http://www.montefiore.ulg.ac.be/~geuzaine
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