[Gmsh] Large Mesh Partitioning Segmentation Fault

[Joe Schickler]

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 at cmsmeshing2:~/bigdrive$ ulimit -s unlimited
joe at cmsmeshing2:~/bigdrive$ ulimit -c unlimited
joe at cmsmeshing2:~/bigdrive$ sudo sysctl -w
kernel.core_pattern=/tmp/core-%e.%p.%h.%t
kernel.core_pattern = /tmp/core-%e.%p.%h.%t
joe at 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 at cmsmeshing2:~/bigdrive$ ulimit -s unlimited
joe at cmsmeshing2:~/bigdrive$ ulimit -c unlimited
joe at cmsmeshing2:~/bigdrive$ sudo sysctl -w
kernel.core_pattern=/tmp/core-%e.%p.%h.%t
kernel.core_pattern = /tmp/core-%e.%p.%h.%t
joe at 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 <cgeuzaine at uliege.be>
wrote:

>
>
> > On 31 Jul 2019, at 16:37, Joe Schickler <joeschickler.jjtech at gmail.com>
> 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: JoeSchickler.JJTech at gmail.com
> >
> > <modelpart.geo>_______________________________________________
> > gmsh mailing list
> > gmsh at onelab.info
> > http://onelab.info/mailman/listinfo/gmsh
>
> —
> Prof. Christophe Geuzaine
> University of Liege, Electrical Engineering and Computer Science
> http://www.montefiore.ulg.ac.be/~geuzaine
>
>
>
>
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