Hi Joe, > On 1 Aug 2019, at 18:48, Joe Schickler <[email protected]> wrote: > > Prof. Geuzaine, > > Wow! That seems super useful, thank you! Please let me know what you find > and I will also keep looking into it. > > (gdb) r -merge model3dbin.msh modelpart.geo -part_no_topo > Starting program: /home/joe/bigdrive/gmsh -merge model3dbin.msh modelpart.geo > -part_no_topo > Info : Running '/home/joe/bigdrive/gmsh -merge model3dbin.msh > modelpart.geo -part_no_topo' [Gmsh 4.4.1, 1 node, max. 1 thread] > Info : Started on Thu Aug 1 16:33:15 2019 > Info : Reading 'model3dbin.msh'... > Info : 166593827 nodes > Info : 1030066524 elements > Info : Done reading 'model3dbin.msh' > Info : Reading 'modelpart.geo'... > Info : Partitioning mesh... > > Program received signal SIGSEGV, Segmentation fault. > 0x0000555555c52ff1 in Graph::eind (this=0x7fffffff9d50, eind=<optimized out>, > i=2147483648) > at /home/joe/bigdrive/gmsh-4.4.1-source/Mesh/meshPartition.cpp:212 > 212 void eind(unsigned int i, unsigned int eind) { _eind[i] = eind; }; > (gdb) bt > #0 0x0000555555c52ff1 in Graph::eind (this=0x7fffffff9d50, > eind=<optimized out>, i=2147483648) > at /home/joe/bigdrive/gmsh-4.4.1-source/Mesh/meshPartition.cpp:212
OK so we have an entity index i = 2147483648, which is the next one just above the max value of an int - we probably get over the max for edges or faces in the graph. The partitioning code has not yet been ported to support 64 bit indices/tags, so this is "normal". Porting to 64 bits would be nice: any help is clearly welcome! Could you open an issue in our gitlab so we keep track of the issue? Thanks, Christophe > #1 fillElementsToNodesMap<__gnu_cxx::__normal_iterator<MTetrahedron* const*, > std::vector<MTetrahedron*> > > (entity=0x55555ac1acb0, it_end=..., > it_beg=..., > numVertex=<synthetic pointer>: 137366842, > eindIndex=<synthetic pointer>: -2147483648, > eptrIndex=<synthetic pointer>: <optimized out>, graph=...) > at /home/joe/bigdrive/gmsh-4.4.1-source/Mesh/meshPartition.cpp:476 > #2 MakeGraph (model=model@entry=0x555556813b50, graph=..., > selectDim=selectDim@entry=-1) > at /home/joe/bigdrive/gmsh-4.4.1-source/Mesh/meshPartition.cpp:589 > #3 0x0000555555c63ab0 in PartitionMesh (model=0x555556813b50) > at /home/joe/bigdrive/gmsh-4.4.1-source/Mesh/meshPartition.cpp:2336 > #4 0x0000555555dd8013 in gmsh_yyparse () at Gmsh.y:3399 > #5 0x0000555555853f8d in ParseFile (fileName="modelpart.geo", > close=close@entry=true, warnIfMissing=warnIfMissing@entry=false) > at /home/joe/bigdrive/gmsh-4.4.1-source/Common/OpenFile.cpp:209 > #6 0x00005555559cefcd in GModel::readGEO (name="modelpart.geo") > at /home/joe/bigdrive/gmsh-4.4.1-source/Geo/GModel.cpp:2928 > #7 0x0000555555853e17 in MergeFile (fileName="modelpart.geo", > warnIfMissing=warnIfMissing@entry=false, > setBoundingBox=setBoundingBox@entry=true, > importPhysicalsInOnelab=importPhysicalsInOnelab@entry=true, > partitionToRead=partitionToRead@entry=-1) > at /home/joe/bigdrive/gmsh-4.4.1-source/Common/OpenFile.cpp:520 > #8 0x000055555580bc7b in GmshBatch () > at /home/joe/bigdrive/gmsh-4.4.1-source/Common/GmshGlobal.cpp:299 > #9 0x000055555580c175 in GmshMainBatch (argc=5, argv=0x7fffffffe518) > at /home/joe/bigdrive/gmsh-4.4.1-source/Common/GmshGlobal.cpp:467 > #10 0x00007ffff70c6b97 in __libc_start_main ( > main=0x555555800480 <main(int, char**)>, argc=5, argv=0x7fffffffe518, > init=<optimized out>, fini=<optimized out>, rtld_fini=<optimized out>, > stack_end=0x7fffffffe508) at ../csu/libc-start.c:310 > #11 0x000055555580ad7a in _start () > > > Regards, > > Joe Schickler > J&J Technologies LLC > > > On Thu, Aug 1, 2019 at 8:21 AM Christophe Geuzaine <[email protected]> > wrote: > If you don't want to send the full core (which I might not be able to > use...), you can also just do e.g. > > gdb ./gmsh > > r -merge model3dbin.msh modelpart.geo -part_no_topo > > (crash) > > bt > > Christophe > > > On 1 Aug 2019, at 13:47, Joe Schickler <[email protected]> > > wrote: > > > > Thanks for getting back to me. Gmsh partitions fine with metis or the > > plugin with smaller mesh sample. I ran gmsh with the -part_no_topo option > > and it still seg faulted. I am running on a cloud machine with over 400GB > > of RAM. I even tried over 3TB of RAM and still seg faults. Also tried > > ulimit -s unlimited > > > > OUTPUT FOR METIS > > joe@cmsmeshing2:~/bigdrive$ ulimit -s unlimited > > joe@cmsmeshing2:~/bigdrive$ ulimit -c unlimited > > joe@cmsmeshing2:~/bigdrive$ sudo sysctl -w > > kernel.core_pattern=/tmp/core-%e.%p.%h.%t > > kernel.core_pattern = /tmp/core-%e.%p.%h.%t > > joe@cmsmeshing2:~/bigdrive$ ./gmsh -merge model3dbin.msh modelpart.geo > > -part_no_topo > > Info : Running './gmsh -merge model3dbin.msh modelpart.geo > > -part_no_topo' [Gmsh 4.4.1, 1 node, max. 1 thread] > > Info : Started on Thu Aug 1 06:42:54 2019 > > Info : Reading 'model3dbin.msh'... > > Info : 166593827 nodes > > Info : 1030066524 elements > > Info : Done reading 'model3dbin.msh' > > Info : Reading 'modelpart.geo'... > > Info : Partitioning mesh... > > Segmentation fault (core dumped) > > > > OUTPUT FOR PLUGIN SIMPLEPARTITION > > joe@cmsmeshing2:~/bigdrive$ ulimit -s unlimited > > joe@cmsmeshing2:~/bigdrive$ ulimit -c unlimited > > joe@cmsmeshing2:~/bigdrive$ sudo sysctl -w > > kernel.core_pattern=/tmp/core-%e.%p.%h.%t > > kernel.core_pattern = /tmp/core-%e.%p.%h.%t > > joe@cmsmeshing2:~/bigdrive$ ./gmsh -merge model3dbin.msh -part_no_topo > > modelpart2.geo > > Info : Running './gmsh -merge model3dbin.msh -part_no_topo > > modelpart2.geo' [Gmsh 4.4.1, 1 node, max. 1 thread] > > Info : Started on Thu Aug 1 07:04:30 2019 > > Info : Reading 'model3dbin.msh'... > > Info : 166593827 nodes > > Info : 1030066524 elements > > Info : Done reading 'model3dbin.msh' > > Info : Reading 'modelpart2.geo'... > > Info : Running Plugin(SimplePartition)... > > Segmentation fault (core dumped) > > > > core dumps are large files and I am uploading them now to attach to next > > email. I don't have too much confidence that I did the core dump > > correctly, hopefully it is correct and helpful. > > > > Regards, > > Joe Schickler > > > > > > > > On Thu, Aug 1, 2019 at 2:07 AM Christophe Geuzaine <[email protected]> > > wrote: > > > > > > > On 31 Jul 2019, at 16:37, Joe Schickler <[email protected]> > > > wrote: > > > > > > Hello all, > > > > > > I am getting segmentation faults in gmsh 4.4.1 (and other versions) when > > > I try to partition a mesh with > > > Info : 166593827 nodes > > > Info : 1030066524 elements > > > > > > The seg fault happens when I use metis and when I use the Plugin > > > SimplePartition > > > > > > Attached is copy of geo file. Command I use at terminal is > > > ./gmsh -merge model3dbin.msh modelpart.geo -bin -save > > > > > > > Does it happen on smaller meshes? Does it happen if you specify > > "-part_no_topo"? Can you run Gmsh inside a debugger and send us the > > backtrace? > > > > Christophe > > > > > Regards, > > > Joe Schickler > > > J&J Technologies LLC > > > Stratford, NJ 08084 > > > Tel: (856) 437-0401 > > > Email: [email protected] > > > > > > <modelpart.geo>_______________________________________________ > > > gmsh mailing list > > > [email protected] > > > http://onelab.info/mailman/listinfo/gmsh > > > > — > > Prof. Christophe Geuzaine > > University of Liege, Electrical Engineering and Computer Science > > http://www.montefiore.ulg.ac.be/~geuzaine > > > > > > > > — > Prof. Christophe Geuzaine > University of Liege, Electrical Engineering and Computer Science > http://www.montefiore.ulg.ac.be/~geuzaine > > > — Prof. Christophe Geuzaine University of Liege, Electrical Engineering and Computer Science http://www.montefiore.ulg.ac.be/~geuzaine _______________________________________________ gmsh mailing list [email protected] http://onelab.info/mailman/listinfo/gmsh
