Fenicsx gmshio.model_to_mesh dies with SIGSEGV when converting mesh

BillS · January 19, 2023, 2:41pm

Hello everyone,
My GMSH meshing exercise seems to produce a good mesh, as seen in the GMSH GUI, but the model_to_mesh conversion process chokes, producing a segmentation fault.

[0]PETSC ERROR: ------------------------------------------------------------------------
[0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range
[0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
[0]PETSC ERROR: or see https://petsc.org/release/faq/#valgrind
[0]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS X to find memory corruption errors
[0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run 
[0]PETSC ERROR: to get more information on the crash.
[0]PETSC ERROR: Run with -malloc_debug to check if memory corruption is causing the crash.
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
with errorcode 59.

NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
--------------------------------------------------------------------------

The code I used is as follows:

import sys
import numpy as np
from scipy import optimize as opt
from mpi4py import MPI as nMPI
from petsc4py import PETSc
import gmsh
import meshio
import ufl
from dolfinx.mesh import locate_entities_boundary, meshtags
from dolfinx.io import gmshio
from dolfinx import fem

def Model(x):
   comm = nMPI.COMM_WORLD
   mpiRank = comm.rank
   modelRank = 0 # Where GMSH runs
   h = x[0] # cavity depth
   r = x[1] # cavity radius
   rgp = x[2] # Ground plane (and rad sphere) radius
   bl = x[3] # Bowtie length
   bt = x[4] # Metal thickness
   ba = x[5] # Bowtie width
   bx = x[6] # x offset of bowtie
   hd = x[7] # Dielectric thickness
   k0 = x[8] # Wavenumber
   eps = x[9] # Dk of dielectric
   lc = x[10] # Coax len
   rc = x[11] # coax shield rad
   rcc = x[12] # coax center cond rad
   rco = x[13] # coax center cond offset
   eta0 = 377.0
   mmin = 0.02
   mmax = 1.0
   err = 1.0e-3
   lm = 0.5
   ls = 0.025
   lq = 0.1

   if mpiRank == modelRank:
       print("Cavity height = {0:<f}, Cavity radius = {1:<f}, Rad shpere radius = {2:<f}".format(h, r, rgp))
       print("Bowtie Len = {0:<f}, Bowtie metal thickness = {1:<f}, Bowtie width = {2:<f}".format(bl, bt, ba))
       print("Bowtie x offset = {0:<f}, Diel thickness = {1:<f}, Wavenumber = {2:<f}, Dk = {3:<f}".format(bx, hd, k0, eps))

       gmsh.initialize()
       gmsh.option.setNumber('General.Terminal', 0)
       gmsh.model.add("BowtieAnt")
       gmsh.model.setCurrent("BowtieAnt")

       RadSphere = gmsh.model.occ.addSphere(0, 0, 0, rgp, 1)
       Box1 = gmsh.model.occ.addBox(0, -rgp, 0, rgp, 2*rgp, rgp, 2)
       PCB = gmsh.model.occ.addCylinder(0, 0, 0, 0, 0, hd, r, 7, angle=np.pi)
       Cavity = gmsh.model.occ.addCylinder(0, 0, -h, 0, 0, h, r, 8, angle=np.pi)
       CoaxShield = gmsh.model.occ.addCylinder(rco, 0, -h-lc, 0, 0, lc, rc, 9, angle=2*np.pi)
       CoaxCenter = gmsh.model.occ.addCylinder(rco, 0, -h-lc, 0, 0, h+lc+hd+bt/2, rcc, 10, angle=2*np.pi)
       gmsh.model.occ.rotate([(3,7),(3,8)], 0, 0, 0, 0, 0, 1, -np.pi/2)
       RadZone = gmsh.model.occ.intersect([(3,1)], [(3,2)], 3, removeObject=True, removeTool=True)
       print(RadZone)
       Bowtie1= gmsh.model.occ.addWedge(0, 0, hd, bl, ba, bt, 4, ltx=0)
       gmsh.model.occ.mirror([(3,4)], 0, 1, 0, 0)
       Bowtie2= gmsh.model.occ.addWedge(0, 0, hd, bl, ba, bt, 5, ltx=0)
       Bowtie = gmsh.model.occ.fuse([(3,4)], [(3,5)], 6, removeObject=True, removeTool=True)
       gmsh.model.occ.rotate([(3,6)], 0, 0, 0, 0, 0, 1, np.pi)
       gmsh.model.occ.translate([(3,6)], bl+bx, 0, 0) # Bowtie metal finished
       Metal = gmsh.model.occ.fuse([(3,6)], [(3,10)], 11, removeObject=True, removeTool=True)

       RadZoneFinal = gmsh.model.occ.cut([(3,3)], [(3,11)], 12, removeObject=True, removeTool=False)
       PCBFinal = gmsh.model.occ.cut([(3,7)],[(3,11)], 13, removeObject=True, removeTool=False)
       CavityAndCoax = gmsh.model.occ.fuse([(3,8)], [(3,9)], 14, removeObject=True, removeTool=True)
       CavityAndCoaxFinal = gmsh.model.occ.cut([(3,14)], [(3,11)], 15, removeObject=True, removeTool=True)
       gmsh.model.occ.fragment([(3,12),(3,13),(3,15)], [], -1)

       gmsh.model.occ.synchronize()
       gmsh.option.setNumber('Mesh.MeshSizeMin', mmin)
       gmsh.option.setNumber('Mesh.MeshSizeMax', mmax)
       gmsh.option.setNumber('Mesh.Algorithm', 6) #1=Mesh Adapt, 2=Auto, 3=Initial mesh only, 5=Delaunay, 6=Frontal-Delaunay
       gmsh.option.setNumber('Mesh.MshFileVersion', 2.2)
       gmsh.option.setNumber('Mesh.Format', 1)
       #gmsh.option.setNumber('Mesh.Smoothing', 100)
       gmsh.option.setNumber('Mesh.MinimumCirclePoints', 36)
       gmsh.option.setNumber('Mesh.CharacteristicLengthFromCurvature', 1)

#Set max mesh size
       pt = gmsh.model.getEntities(0)
       gmsh.model.mesh.setSize(pt, lm)
       print(pt)
# Set denser mesh along bowtie metal edges
       pt = gmsh.model.getEntitiesInBoundingBox(bx-err, -ba-err, hd-err, bl+bx+err, ba+err, hd+bt+err)
       print(pt, ls)
       gmsh.model.mesh.setSize(pt,ls)
# Set mesh density along coax
       pt = gmsh.model.getEntitiesInBoundingBox(rco-rcc-err, -rcc-err, hd-err, rcc+rco+err, rcc+err, hd+err)
       print(pt, lq)
       gmsh.model.mesh.setSize(pt,lq)
       pt = gmsh.model.getEntitiesInBoundingBox(rco-rc-err, -rc-err, -lc-h-err, rc+rco+err, rc+err, err)
       print(pt, lq)
       gmsh.model.mesh.setSize(pt,lq)
       gmsh.model.addPhysicalGroup(3, [12], 1)
       gmsh.model.addPhysicalGroup(3, [13], 2)
       gmsh.model.addPhysicalGroup(3, [15], 3)
       gmsh.model.setPhysicalName(3, 1, "RadZone")
       gmsh.model.setPhysicalName(3, 2, "PCB")
       gmsh.model.setPhysicalName(3, 3, "Cavity")


# set mesh density along dielectric
       gmsh.model.mesh.setTransfiniteCurve(13, 200, meshType="Progression", coef=1.0)
       gmsh.model.mesh.setTransfiniteCurve(15, 200, meshType="Progression", coef=1.0)
       
# Reduce mesh density on bowtie surface
       P1 = gmsh.model.occ.addPoint(bx+bl/3, 0, hd, lm, tag=100)
       P2 = gmsh.model.occ.addPoint(bx+bl/3, 0, hd+bt, lm, tag=101)
       P3 = gmsh.model.occ.addPoint(bx+2*bl/3, -ba/3, hd, lm, tag=102)
       P4 = gmsh.model.occ.addPoint(bx+2*bl/3, ba/3, hd, lm, tag=103)
       P5 = gmsh.model.occ.addPoint(bx+2*bl/3, -ba/3, hd+bt, lm, tag=104)
       P6 = gmsh.model.occ.addPoint(bx+2*bl/3, ba/3, hd+bt, lm, tag=105)
       gmsh.model.occ.synchronize()
       gmsh.model.mesh.embed(0, [P2,P5,P6], 2, 10)
       gmsh.model.mesh.embed(0, [P1,P3,P4], 2, 14)

       gmsh.model.occ.synchronize()
       bb = gmsh.model.getEntities(dim=3)
       pt = gmsh.model.getBoundary(bb, combined=True, oriented=False, recursive=False)
       print(pt)
       inportA = []
       radA = []
       pecA =[]
       for bnd in pt:
          CoM = gmsh.model.occ.getCenterOfMass(bnd[0], bnd[1])
          print(CoM)
          if np.allclose(CoM, [rco, 0, -h-lc]): # Coax input port
              inportA.append(bnd[1])
          elif (np.abs(CoM[0]) < err) or (CoM[2] < hd + bt + err):
              pecA.append(bnd[1])
          else:
              radA.append(bnd[1])
       print(inportA, pecA, radA)
       gmsh.model.addPhysicalGroup(2, pecA, 1)
       gmsh.model.setPhysicalName(2, 1, "PEC")
       gmsh.model.addPhysicalGroup(2, inportA, 2)
       gmsh.model.setPhysicalName(2, 2, "Inlet")
       gmsh.model.addPhysicalGroup(2, radA, 3)
       gmsh.model.setPhysicalName(2, 3, "Radiation")
       gmsh.model.occ.synchronize()



       gmsh.model.mesh.generate(3)
       gmsh.model.mesh.optimize("Gmsh")
       gmsh.fltk.run()
#XXXXX Program dies here XXXXXX
   mesh, ct, fm = gmshio.model_to_mesh(gmsh.model, comm, modelRank, gdim=3)
#XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

   if mpiRank == modelRank:
       gmsh.finalize()

   mesh.topology.create_connectivity(mesh.topology.dim-1, mesh.topology.dim)

   return 0

xin = np.array([1.5, 4.0, 8.0, 3.0, 0.05, 1.0, 0.20, 0.25, 1.25, 3.6, 1.0, 0.23, 0.1, 0.6])
res = Model(xin)

sys.exit(0)

Does anyone have an idea where this fault may lie?

Bill

dokken · January 19, 2023, 4:42pm

BillS:

       gmsh.model.addPhysicalGroup(2, pecA, 1)
       gmsh.model.setPhysicalName(2, 1, "PEC")
       gmsh.model.addPhysicalGroup(2, inportA, 2)
       gmsh.model.setPhysicalName(2, 2, "Inlet")
       gmsh.model.addPhysicalGroup(2, radA, 3)
       gmsh.model.setPhysicalName(2, 3, "Radiation")
       gmsh.model.occ.synchronize()

My guess here is to remove the syncronize() at the end of your code. This usually removes the physical groups.

BillS · January 19, 2023, 5:20pm

That did not work.

Created physical groups after all synchronizing in the following code and same error pops up.

import sys
import numpy as np
from scipy import optimize as opt
from mpi4py import MPI as nMPI
from petsc4py import PETSc
import gmsh
import meshio
import ufl
from dolfinx.mesh import locate_entities_boundary, meshtags
from dolfinx.io import gmshio
from dolfinx import fem

def Model(x):
   comm = nMPI.COMM_WORLD
   mpiRank = comm.rank
   modelRank = 0 # Where GMSH runs
   h = x[0] # cavity depth
   r = x[1] # cavity radius
   rgp = x[2] # Ground plane (and rad sphere) radius
   bl = x[3] # Bowtie length
   bt = x[4] # Metal thickness
   ba = x[5] # Bowtie width
   bx = x[6] # x offset of bowtie
   hd = x[7] # Dielectric thickness
   k0 = x[8] # Wavenumber
   eps = x[9] # Dk of dielectric
   lc = x[10] # Coax len
   rc = x[11] # coax shield rad
   rcc = x[12] # coax center cond rad
   rco = x[13] # coax center cond offset
   eta0 = 377.0
   mmin = 0.02
   mmax = 1.0
   err = 1.0e-3
   lm = 0.5
   ls = 0.025
   lq = 0.1

   if mpiRank == modelRank:
       print("Cavity height = {0:<f}, Cavity radius = {1:<f}, Rad shpere radius = {2:<f}".format(h, r, rgp))
       print("Bowtie Len = {0:<f}, Bowtie metal thickness = {1:<f}, Bowtie width = {2:<f}".format(bl, bt, ba))
       print("Bowtie x offset = {0:<f}, Diel thickness = {1:<f}, Wavenumber = {2:<f}, Dk = {3:<f}".format(bx, hd, k0, eps))

       gmsh.initialize()
       gmsh.option.setNumber('General.Terminal', 0)
       gmsh.model.add("BowtieAnt")
       gmsh.model.setCurrent("BowtieAnt")

       RadSphere = gmsh.model.occ.addSphere(0, 0, 0, rgp, 1)
       Box1 = gmsh.model.occ.addBox(0, -rgp, 0, rgp, 2*rgp, rgp, 2)
       PCB = gmsh.model.occ.addCylinder(0, 0, 0, 0, 0, hd, r, 7, angle=np.pi)
       Cavity = gmsh.model.occ.addCylinder(0, 0, -h, 0, 0, h, r, 8, angle=np.pi)
       CoaxShield = gmsh.model.occ.addCylinder(rco, 0, -h-lc, 0, 0, lc, rc, 9, angle=2*np.pi)
       CoaxCenter = gmsh.model.occ.addCylinder(rco, 0, -h-lc, 0, 0, h+lc+hd+bt/2, rcc, 10, angle=2*np.pi)
       gmsh.model.occ.rotate([(3,7),(3,8)], 0, 0, 0, 0, 0, 1, -np.pi/2)
       RadZone = gmsh.model.occ.intersect([(3,1)], [(3,2)], 3, removeObject=True, removeTool=True)
       print(RadZone)
       Bowtie1= gmsh.model.occ.addWedge(0, 0, hd, bl, ba, bt, 4, ltx=0)
       gmsh.model.occ.mirror([(3,4)], 0, 1, 0, 0)
       Bowtie2= gmsh.model.occ.addWedge(0, 0, hd, bl, ba, bt, 5, ltx=0)
       Bowtie = gmsh.model.occ.fuse([(3,4)], [(3,5)], 6, removeObject=True, removeTool=True)
       gmsh.model.occ.rotate([(3,6)], 0, 0, 0, 0, 0, 1, np.pi)
       gmsh.model.occ.translate([(3,6)], bl+bx, 0, 0) # Bowtie metal finished
       Metal = gmsh.model.occ.fuse([(3,6)], [(3,10)], 11, removeObject=True, removeTool=True)

       RadZoneFinal = gmsh.model.occ.cut([(3,3)], [(3,11)], 12, removeObject=True, removeTool=False)
       PCBFinal = gmsh.model.occ.cut([(3,7)],[(3,11)], 13, removeObject=True, removeTool=False)
       CavityAndCoax = gmsh.model.occ.fuse([(3,8)], [(3,9)], 14, removeObject=True, removeTool=True)
       CavityAndCoaxFinal = gmsh.model.occ.cut([(3,14)], [(3,11)], 15, removeObject=True, removeTool=True)
       gmsh.model.occ.fragment([(3,12),(3,13),(3,15)], [], -1)

       gmsh.model.occ.synchronize()
       gmsh.option.setNumber('Mesh.MeshSizeMin', mmin)
       gmsh.option.setNumber('Mesh.MeshSizeMax', mmax)
       gmsh.option.setNumber('Mesh.Algorithm', 6) #1=Mesh Adapt, 2=Auto, 3=Initial mesh only, 5=Delaunay, 6=Frontal-Delaunay
       gmsh.option.setNumber('Mesh.MshFileVersion', 2.2)
       gmsh.option.setNumber('Mesh.Format', 1)
       #gmsh.option.setNumber('Mesh.Smoothing', 100)
       gmsh.option.setNumber('Mesh.MinimumCirclePoints', 36)
       gmsh.option.setNumber('Mesh.CharacteristicLengthFromCurvature', 1)

#Set max mesh size
       pt = gmsh.model.getEntities(0)
       gmsh.model.mesh.setSize(pt, lm)
       print(pt)
# Set denser mesh along bowtie metal edges
       pt = gmsh.model.getEntitiesInBoundingBox(bx-err, -ba-err, hd-err, bl+bx+err, ba+err, hd+bt+err)
       print(pt, ls)
       gmsh.model.mesh.setSize(pt,ls)
# Set mesh density along coax
       pt = gmsh.model.getEntitiesInBoundingBox(rco-rcc-err, -rcc-err, hd-err, rcc+rco+err, rcc+err, hd+err)
       print(pt, lq)
       gmsh.model.mesh.setSize(pt,lq)
       pt = gmsh.model.getEntitiesInBoundingBox(rco-rc-err, -rc-err, -lc-h-err, rc+rco+err, rc+err, err)
       print(pt, lq)
       gmsh.model.mesh.setSize(pt,lq)

# set mesh density along dielectric
       gmsh.model.mesh.setTransfiniteCurve(13, 200, meshType="Progression", coef=1.0)
       gmsh.model.mesh.setTransfiniteCurve(15, 200, meshType="Progression", coef=1.0)
       
# Reduce mesh density on bowtie surface
       P1 = gmsh.model.occ.addPoint(bx+bl/3, 0, hd, lm, tag=100)
       P2 = gmsh.model.occ.addPoint(bx+bl/3, 0, hd+bt, lm, tag=101)
       P3 = gmsh.model.occ.addPoint(bx+2*bl/3, -ba/3, hd, lm, tag=102)
       P4 = gmsh.model.occ.addPoint(bx+2*bl/3, ba/3, hd, lm, tag=103)
       P5 = gmsh.model.occ.addPoint(bx+2*bl/3, -ba/3, hd+bt, lm, tag=104)
       P6 = gmsh.model.occ.addPoint(bx+2*bl/3, ba/3, hd+bt, lm, tag=105)
       gmsh.model.occ.synchronize()
       gmsh.model.mesh.embed(0, [P2,P5,P6], 2, 10)
       gmsh.model.mesh.embed(0, [P1,P3,P4], 2, 14)
       gmsh.model.occ.synchronize()

       bb = gmsh.model.getEntities(dim=3)
       pt = gmsh.model.getBoundary(bb, combined=True, oriented=False, recursive=False)
       print(pt)
       inportA = []
       radA = []
       pecA =[]
       for bnd in pt:
          CoM = gmsh.model.occ.getCenterOfMass(bnd[0], bnd[1])
          print(CoM)
          if np.allclose(CoM, [rco, 0, -h-lc]): # Coax input port
              inportA.append(bnd[1])
          elif (np.abs(CoM[0]) < err) or (CoM[2] < hd + bt + err):
              pecA.append(bnd[1])
          else:
              radA.append(bnd[1])
       print(inportA, pecA, radA)
       gmsh.model.addPhysicalGroup(2, pecA, 1)
       gmsh.model.setPhysicalName(2, 1, "PEC")
       gmsh.model.addPhysicalGroup(2, inportA, 2)
       gmsh.model.setPhysicalName(2, 2, "Inlet")
       gmsh.model.addPhysicalGroup(2, radA, 3)
       gmsh.model.setPhysicalName(2, 3, "Radiation")
       gmsh.model.addPhysicalGroup(3, [12], 1)
       gmsh.model.addPhysicalGroup(3, [13], 2)
       gmsh.model.addPhysicalGroup(3, [15], 3)
       gmsh.model.setPhysicalName(3, 1, "RadZone")
       gmsh.model.setPhysicalName(3, 2, "PCB")
       gmsh.model.setPhysicalName(3, 3, "Cavity")




       gmsh.model.mesh.generate(3)
       gmsh.model.mesh.optimize("Gmsh")
       gmsh.fltk.run()
#XXXXX Program dies here XXXXXX
   mesh, ct, fm = gmshio.model_to_mesh(gmsh.model, comm, modelRank, gdim=3)
#XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

   if mpiRank == modelRank:
       gmsh.finalize()

   mesh.topology.create_connectivity(mesh.topology.dim-1, mesh.topology.dim)

   return 0

xin = np.array([1.5, 4.0, 8.0, 3.0, 0.05, 1.0, 0.20, 0.25, 1.25, 3.6, 1.0, 0.23, 0.1, 0.6])
res = Model(xin)

sys.exit(0)

BillS · January 19, 2023, 5:31pm

I found the error. You were right that it was a problem with the physical group definition. I needed to use the correct entity tags in the Physical Group definitions. Once I fixed that, it worked.

Cheers!

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Fenicsx gmshio.model_to_mesh dies with SIGSEGV when converting mesh

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