[Gmsh] bug report & question

Christophe Geuzaine cag32 at case.edu
Thu Nov 17 19:41:47 CET 2005


Magdalena Stolarska wrote:
> Hi.  I've come across a fatal error in gmsh that results from a 
> segmentation violation.  The .gmsh-error file and the .geo file that I 
> used are attached to this email.  In order to compute the 3D mesh, I 
> used the isotropic algorithm.  

Strange, it works fine on my machine. According to your log file it 
seems to work fine the first time on your machine too, but then it 
crashes when you remesh a second time?


> The netgen algorithm was causing gmsh to 
> abort without any warning and without producing a .gmsh-errors file.  Is 
> there anything wrong with the geo file that would cause this to happen?  

Maybe: Netgen expects all volume boundaries to have outward-pointing 
normals. You should check if this is actually the case in your model.


> Any insight would be very helpful. Thanks in advance for your response.
> 
> Magda Stolarska
> 
> 
> ------------------------------------------------------------------------
> 
> h1 = 0.25;
> h2 = 0.4;
> Point(1) = {0.0,0.0,0.0,h1};
> Point(2) = {0.5,0.0,0.0,h1};
> Point(3) = {-0.5,0.0,0.0,h1};
> Point(4) = {0,0.5,0.0,h1};
> Point(5) = {0,-0.5,0.0,h1};
> Point(6) = {0,0,5,h2};
> Point(7) = {0.5,0,5,h2};
> Point(8) = {-0.5,0,5,h2};
> Point(9) = {0,0.5,5,h2};
> Point(10) = {0,-0.5,5,h2};
> Point(11) = {0,0,.2,h1};
> Point(12) = {0.2,0,0,h1};
> Point(13) = {-0.2,0,0,h1};
> Point(14) = {0,0.2,0,h1};
> Point(15) = {0,-0.2,0,h1};
> Circle(1) = {4,1,3};
> Circle(2) = {4,1,2};
> Circle(3) = {3,1,5};
> Circle(4) = {2,1,5};
> Circle(5) = {14,1,13};
> Circle(6) = {14,1,12};
> Circle(7) = {12,1,15};
> Circle(8) = {13,1,15};
> Circle(9) = {14,1,11};
> Circle(10) = {12,1,11};
> Circle(11) = {15,1,11};
> Circle(12) = {13,1,11};
> Circle(13) = {9,6,8};
> Circle(14) = {9,6,7};
> Circle(15) = {7,6,10};
> Circle(16) = {10,6,8};
> Line(17) = {7,2};
> Line(18) = {10,5};
> Line(19) = {8,3};
> Line(20) = {9,4};
> Line Loop(21) = {14,15,16,-13};
> Plane Surface(22) = {21};
> Line Loop(23) = {2,4,-3,-1};
> Line Loop(24) = {5,8,-7,-6};
> Plane Surface(25) = {23,24};
> Plane Surface(26) = {24};
> Line Loop(27) = {6,10,-9};
> Ruled Surface(28) = {27};
> Line Loop(29) = {5,12,-9};
> Ruled Surface(30) = {29};
> Line Loop(31) = {12,-11,-8};
> Ruled Surface(32) = {31};
> Line Loop(33) = {11,-10,7};
> Ruled Surface(34) = {33};
> Line Loop(35) = {17,4,-18,-15};
> Ruled Surface(36) = {35};
> Line Loop(37) = {17,-2,-20,14};
> Ruled Surface(38) = {37};
> Line Loop(39) = {13,19,-1,-20};
> Ruled Surface(40) = {39};
> Line Loop(41) = {16,19,3,-18};
> Ruled Surface(42) = {41};
> Surface Loop(43) = {26,-30,32,34,28};
> //Surface Loop(43) = {-26,30,-32,-34,-28};
> Volume(44) = {43};
> Surface Loop(45) = {22,-38,36,-25,-42,40,28,34,32,-30};
> //Surface Loop(45) = {-22,38,-36,25,42,-40,-28,-34,-32,30};
> Volume(46) = {45};
> Physical Surface(47) = {22};
> Physical Surface(48) = {38,36,40,42};
> Physical Surface(49) = {25,26};
> Physical Volume(50) = {44};
> Physical Volume(51) = {46};
> 
> 
> ------------------------------------------------------------------------
> 
> Info    : Plane Surface 22 (4 cross points)
> Info    : Plane Surface 25 (8 cross points)
> Info    : Plane Surface 26 (4 cross points)
> Info    : Mesh 1D...
> Info    : Meshing curve 1
> Info    : Meshing curve 2
> Info    : Meshing curve 3
> Info    : Meshing curve 4
> Info    : Meshing curve 5
> Info    : Meshing curve 6
> Info    : Meshing curve 7
> Info    : Meshing curve 8
> Info    : Meshing curve 9
> Info    : Meshing curve 10
> Info    : Meshing curve 11
> Info    : Meshing curve 12
> Info    : Meshing curve 13
> Info    : Meshing curve 14
> Info    : Meshing curve 15
> Info    : Meshing curve 16
> Info    : Meshing curve 17
> Info    : Meshing curve 18
> Info    : Meshing curve 19
> Info    : Meshing curve 20
> Info    : Mesh 1D complete (0.002999 s)
> Info    : Mesh 2D...
> Info    : Meshing surface 22
> Info    : Meshing surface 25
> Info    : Meshing surface 26
> Info    : Meshing surface 28
> Info    : Meshing surface 30
> Info    : Meshing surface 32
> Info    : Meshing surface 34
> Info    : Meshing surface 36
> Info    : Meshing surface 38
> Info    : Meshing surface 40
> Info    : Meshing surface 42
> Info    : Mesh 2D complete (0.085987 s)
> Info    : Mesh 3D...
> Info    : Mesh 3D... (initial)
> Info    : Nod=35/713 Elm=160
> Info    : Vol=13.72 (33 1 1)
> Info    : Nod=70/713 Elm=357
> Info    : Vol=13.72 (59 10 1)
> Info    : Nod=105/713 Elm=570
> Info    : Vol=13.72 (82 22 1)
> Info    : Nod=140/713 Elm=799
> Info    : Vol=13.72 (108 31 1)
> Info    : Nod=175/713 Elm=1061
> Info    : Vol=13.72 (122 52 1)
> Info    : Nod=210/713 Elm=1301
> Info    : Vol=13.72 (146 63 1)
> Info    : Nod=245/713 Elm=1540
> Info    : Vol=13.72 (164 80 1)
> Info    : Nod=280/713 Elm=1797
> Info    : Vol=13.72 (187 92 1)
> Info    : Nod=315/713 Elm=2027
> Info    : Vol=13.72 (215 99 1)
> Info    : Nod=350/713 Elm=2281
> Info    : Vol=13.72 (250 99 1)
> Info    : Nod=385/713 Elm=2564
> Info    : Vol=13.72 (284 100 1)
> Info    : Nod=420/713 Elm=2764
> Info    : Vol=13.72 (306 113 1)
> Info    : Nod=455/713 Elm=3078
> Info    : Vol=13.72 (330 124 1)
> Info    : Nod=490/713 Elm=3319
> Info    : Vol=13.72 (350 139 1)
> Info    : Nod=525/713 Elm=3620
> Info    : Vol=13.72 (374 150 1)
> Info    : Nod=560/713 Elm=3863
> Info    : Vol=13.72 (394 165 1)
> Info    : Nod=595/713 Elm=4159
> Info    : Vol=13.72 (416 178 1)
> Info    : Nod=630/713 Elm=4465
> Info    : Vol=13.72 (441 188 1)
> Info    : Nod=665/713 Elm=4792
> Info    : Vol=13.72 (466 198 1)
> Info    : Nod=700/713 Elm=5048
> Info    : Vol=13.72 (499 200 1)
> Info    : Boundary edges recovery
> Info    : Boundary faces recovery
> Info    : Volume recovery
> Info    : Surface 22
> Info    : Surface 25
> Info    : Surface 26
> Info    : Surface 36
> Info    : Surface 38
> Info    : Surface 40
> Info    : Surface 42
> Info    : Surface 22
> Info    : Surface 25
> Info    : Surface 28
> Info    : Surface 30
> Info    : Surface 32
> Info    : Surface 34
> Info    : Surface 36
> Info    : Surface 38
> Info    : Surface 40
> Info    : Surface 42
> Info    : Surface 26
> Info    : Surface 28
> Info    : Surface 30
> Info    : Surface 32
> Info    : Surface 34
> Info    : Mesh 3D... (final)
> Info    : Nod=735 Elm=1963
> Info    : Vol(3.82351) Conv(2.12209->0.8)
> Info    : Nod=759 Elm=2140
> Info    : Vol(3.82351) Conv(1.844->0.8)
> Info    : Nod=783 Elm=2318
> Info    : Vol(3.82351) Conv(1.6142->0.8)
> Info    : Nod=807 Elm=2498
> Info    : Vol(3.82351) Conv(1.52943->0.8)
> Info    : Nod=831 Elm=2683
> Info    : Vol(3.82351) Conv(1.43614->0.8)
> Info    : Nod=855 Elm=2844
> Info    : Vol(3.82351) Conv(1.36667->0.8)
> Info    : Nod=879 Elm=3028
> Info    : Vol(3.82351) Conv(1.32745->0.8)
> Info    : Nod=903 Elm=3193
> Info    : Vol(3.82351) Conv(1.29444->0.8)
> Info    : Nod=927 Elm=3371
> Info    : Vol(3.82351) Conv(1.25236->0.8)
> Info    : Nod=951 Elm=3539
> Info    : Vol(3.82351) Conv(1.19972->0.8)
> Info    : Nod=975 Elm=3715
> Info    : Vol(3.82351) Conv(1.17294->0.8)
> Info    : Nod=999 Elm=3883
> Info    : Vol(3.82351) Conv(1.1521->0.8)
> Info    : Nod=1023 Elm=4049
> Info    : Vol(3.82351) Conv(1.12663->0.8)
> Info    : Nod=1047 Elm=4189
> Info    : Vol(3.82351) Conv(1.10436->0.8)
> Info    : Nod=1071 Elm=4357
> Info    : Vol(3.82351) Conv(1.08356->0.8)
> Info    : Nod=1095 Elm=4503
> Info    : Vol(3.82351) Conv(1.069->0.8)
> Info    : Nod=1119 Elm=4637
> Info    : Vol(3.82351) Conv(1.05405->0.8)
> Info    : Nod=1143 Elm=4782
> Info    : Vol(3.82351) Conv(1.03843->0.8)
> Info    : Nod=1167 Elm=4929
> Info    : Vol(3.82351) Conv(1.02492->0.8)
> Info    : Nod=1191 Elm=5096
> Info    : Vol(3.82351) Conv(1.00304->0.8)
> Info    : Nod=1215 Elm=5246
> Info    : Vol(3.82351) Conv(0.987187->0.8)
> Info    : Nod=1239 Elm=5404
> Info    : Vol(3.82351) Conv(0.975215->0.8)
> Info    : Nod=1263 Elm=5553
> Info    : Vol(3.82351) Conv(0.962466->0.8)
> Info    : Nod=1287 Elm=5720
> Info    : Vol(3.82351) Conv(0.952105->0.8)
> Info    : Nod=1311 Elm=5872
> Info    : Vol(3.82351) Conv(0.942153->0.8)
> Info    : Nod=1335 Elm=6017
> Info    : Vol(3.82351) Conv(0.932487->0.8)
> Info    : Nod=1359 Elm=6160
> Info    : Vol(3.82351) Conv(0.92357->0.8)
> Info    : Nod=1383 Elm=6314
> Info    : Vol(3.82351) Conv(0.909862->0.8)
> Info    : Nod=1407 Elm=6482
> Info    : Vol(3.82351) Conv(0.903469->0.8)
> Info    : Nod=1431 Elm=6632
> Info    : Vol(3.82351) Conv(0.897597->0.8)
> Info    : Nod=1455 Elm=6771
> Info    : Vol(3.82351) Conv(0.891553->0.8)
> Info    : Nod=1478 Elm=6928
> Info    : Vol(3.82351) Conv(0.885092->0.8)
> Info    : Nod=1502 Elm=7091
> Info    : Vol(3.82351) Conv(0.878992->0.8)
> Info    : Nod=1526 Elm=7241
> Info    : Vol(3.82351) Conv(0.873392->0.8)
> Info    : Nod=1550 Elm=7414
> Info    : Vol(3.82351) Conv(0.868922->0.8)
> Info    : Nod=1573 Elm=7551
> Info    : Vol(3.82351) Conv(0.863861->0.8)
> Info    : Nod=1597 Elm=7705
> Info    : Vol(3.82351) Conv(0.857172->0.8)
> Info    : Nod=1621 Elm=7848
> Info    : Vol(3.82351) Conv(0.851277->0.8)
> Info    : Nod=1642 Elm=7991
> Info    : Vol(3.82351) Conv(0.845036->0.8)
> Info    : Nod=1664 Elm=8131
> Info    : Vol(3.82351) Conv(0.839822->0.8)
> Info    : Nod=1688 Elm=8267
> Info    : Vol(3.82351) Conv(0.835383->0.8)
> Info    : Nod=1712 Elm=8417
> Info    : Vol(3.82351) Conv(0.830876->0.8)
> Info    : Nod=1736 Elm=8571
> Info    : Vol(3.82351) Conv(0.823484->0.8)
> Info    : Nod=1759 Elm=8725
> Info    : Vol(3.82351) Conv(0.819886->0.8)
> Info    : Nod=1781 Elm=8866
> Info    : Vol(3.82351) Conv(0.81363->0.8)
> Info    : Nod=1802 Elm=9004
> Info    : Vol(3.82351) Conv(0.808183->0.8)
> Info    : Nod=1825 Elm=9148
> Info    : Vol(3.82351) Conv(0.802846->0.8)
> Info    : Nod=1847 Elm=9287
> Info    : Vol(3.82351) Conv(0.800283->0.8)
> Info    : Mesh 3D complete (1.60576 s)
> Info    : Optimize volume mesh...
> Info    : Optimizing volume 44
> Info    : Optimizing volume 46
> Info    : Optimize volume mesh complete (6.36703 s)
> Info    : Plane Surface 22 (4 cross points)
> Info    : Plane Surface 25 (8 cross points)
> Info    : Plane Surface 26 (4 cross points)
> Info    : Mesh 1D...
> Info    : Meshing curve 1
> Info    : Meshing curve 2
> Info    : Meshing curve 3
> Info    : Meshing curve 4
> Info    : Meshing curve 5
> Info    : Meshing curve 6
> Info    : Meshing curve 7
> Info    : Meshing curve 8
> Info    : Meshing curve 9
> Info    : Meshing curve 10
> Info    : Meshing curve 11
> Info    : Meshing curve 12
> Info    : Meshing curve 13
> Info    : Meshing curve 14
> Info    : Meshing curve 15
> Info    : Meshing curve 16
> Info    : Meshing curve 17
> Info    : Meshing curve 18
> Info    : Meshing curve 19
> Info    : Meshing curve 20
> Info    : Mesh 1D complete (0.002 s)
> Info    : Mesh 2D...
> Info    : Meshing surface 22
> Info    : Meshing surface 25
> Info    : Meshing surface 26
> Info    : Meshing surface 28
> Info    : Meshing surface 30
> Info    : Meshing surface 32
> Info    : Meshing surface 34
> Info    : Meshing surface 36
> Info    : Meshing surface 38
> Info    : Meshing surface 40
> Info    : Meshing surface 42
> Info    : Mesh 2D complete (0.020997 s)
> Info    : Mesh 3D...
> Info    : Mesh 3D... (initial)
> Info    : Nod=7/158 Elm=32
> Info    : Vol=13.72 (6 0 1)
> Info    : Nod=14/158 Elm=60
> Info    : Vol=13.72 (13 0 1)
> Info    : Nod=21/158 Elm=99
> Info    : Vol=13.72 (19 1 1)
> Info    : Nod=28/158 Elm=131
> Info    : Vol=13.72 (26 1 1)
> Info    : Nod=35/158 Elm=169
> Info    : Vol=13.72 (30 4 1)
> Info    : Nod=42/158 Elm=211
> Info    : Vol=13.72 (34 7 1)
> Info    : Nod=49/158 Elm=255
> Info    : Vol=13.72 (39 9 1)
> Info    : Nod=56/158 Elm=303
> Info    : Vol=13.72 (46 9 1)
> Info    : Nod=63/158 Elm=341
> Info    : Vol=13.72 (53 9 1)
> Info    : Nod=70/158 Elm=393
> Info    : Vol=13.72 (60 9 1)
> Info    : Nod=77/158 Elm=433
> Info    : Vol=13.72 (66 10 1)
> Info    : Nod=84/158 Elm=475
> Info    : Vol=13.72 (73 10 1)
> Info    : Nod=91/158 Elm=522
> Info    : Vol=13.72 (80 10 1)
> Info    : Nod=98/158 Elm=568
> Info    : Vol=13.72 (87 10 1)
> Info    : Nod=105/158 Elm=626
> Info    : Vol=13.72 (93 11 1)
> Info    : Nod=112/158 Elm=671
> Info    : Vol=13.72 (100 11 1)
> Info    : Nod=119/158 Elm=712
> Info    : Vol=13.72 (104 14 1)
> Info    : Nod=126/158 Elm=762
> Info    : Vol=13.72 (109 16 1)
> Info    : Nod=133/158 Elm=818
> Info    : Vol=13.72 (114 18 1)
> Info    : Nod=140/158 Elm=874
> Info    : Vol=13.72 (121 18 1)
> Info    : Nod=147/158 Elm=918
> Info    : Vol=13.72 (128 18 1)
> Info    : Nod=154/158 Elm=968
> Info    : Vol=13.72 (135 18 1)
> Info    : Boundary edges recovery
> Info    : Boundary faces recovery
> Info    : Volume recovery
> Info    : Surface 22
> Info    : Surface 25
> Info    : Surface 26
> Info    : Surface 36
> Info    : Surface 38
> Info    : Surface 40
> Info    : Surface 42
> Info    : Surface 26
> Info    : Surface 28
> Info    : Surface 30
> Info    : Surface 32
> Info    : Surface 34
> Info    : Surface 22
> Info    : Surface 25
> Info    : Surface 28
> Info    : Surface 30
> Info    : Surface 32
> Info    : Surface 34
> Info    : Surface 36
> Info    : Surface 38
> Info    : Surface 40
> Info    : Surface 42
> Info    : Mesh 3D... (final)
> Info    : Nod=162 Elm=423
> Info    : Vol(3.57464) Conv(1.52652->0.8)
> Info    : Nod=168 Elm=435
> Info    : Vol(3.57464) Conv(1.187->0.8)
> Info    : Nod=174 Elm=485
> Info    : Vol(3.57464) Conv(1.11365->0.8)
> Info    : Nod=180 Elm=540
> Info    : Vol(3.57464) Conv(1.03598->0.8)
> Info    : Nod=186 Elm=578
> Info    : Vol(3.57464) Conv(1.00313->0.8)
> Info    : Nod=192 Elm=622
> Info    : Vol(3.57464) Conv(0.968589->0.8)
> Info    : Nod=198 Elm=665
> Info    : Vol(3.57464) Conv(0.95392->0.8)
> Info    : Nod=204 Elm=707
> Info    : Vol(3.57464) Conv(0.937352->0.8)
> Info    : Nod=210 Elm=734
> Info    : Vol(3.57464) Conv(0.923661->0.8)
> Info    : Nod=216 Elm=783
> Info    : Vol(3.57464) Conv(0.91226->0.8)
> Info    : Nod=222 Elm=813
> Info    : Vol(3.57464) Conv(0.887802->0.8)
> Info    : Nod=228 Elm=842
> Info    : Vol(3.57464) Conv(0.870903->0.8)
> Info    : Nod=234 Elm=877
> Info    : Vol(3.57464) Conv(0.851815->0.8)
> Info    : Nod=240 Elm=908
> Info    : Vol(3.57464) Conv(0.843642->0.8)
> Info    : Nod=246 Elm=938
> Info    : Vol(3.57464) Conv(0.828406->0.8)
> Info    : Nod=252 Elm=974
> Info    : Vol(3.57464) Conv(0.819225->0.8)
> Info    : Nod=254 Elm=986
> Info    : Vol(3.57464) Conv(0.806347->0.8)
> Info    : Mesh 3D complete (0.201969 s)
> Info    : Optimize volume mesh...
> Info    : Optimizing volume 44
> Fatal   : Segmentation violation (invalid memory reference)
>         : ------------------------------------------------------
>         : You have discovered a bug in Gmsh! You may report it
>         : by e-mail (together with any helpful data permitting to
>         : reproduce it) to <gmsh at geuz.org>
> 
> 
> ------------------------------------------------------------------------
> 
> _______________________________________________
> gmsh mailing list
> gmsh at geuz.org
> http://www.geuz.org/mailman/listinfo/gmsh


-- 
Christophe Geuzaine
Assistant Professor, Case University, Mathematics
http://www.case.edu/artsci/math/geuzaine