Adaptive mesh refinement with MPI (UPDATED)

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1 year 6 months ago - 1 year 6 months ago #4556 by sigmunh
Im trying to convert the example for adaptive mesh refinement [1] to working with MPI, but im getting a segmentation fault when im calling the function

    mesh.Refine()

What is the correct way to do this? Do i need to 'collect' the mesh from the different cores, and run mesh.Refine() only on the rank=0 core (corresponding to that the mesh is distributed between the workers in the beginning)?

1: When run on two or more cores (mpirun -np 2 python3 adaptive.py), it creases with an segfault when the code reaches the line mesh.Refine().

[1] docu.ngsolve.org/v6.2.1808/whetting_the_appetite/adaptive.html

CODE
Code:
from ngsolve import * import ngsolve as ng from netgen.geom2d import SplineGeometry from ngsolve.krylovspace import CGSolver from mpi4py import MPI comm = MPI.COMM_WORLD #   point numbers 0, 1, ... 11 #   sub-domain numbers (1), (2), (3) #   # #             7-------------6 #             |             | #             |     (2)     | #             |             | #      3------4-------------5------2 #      |                           | #      |             11            | #      |           /   \           | #      |         10 (3) 9          | #      |           \   /     (1)   | #      |             8             | #      |                           | #      0---------------------------1 # def make_geometry():     geometry = SplineGeometry()          # point coordinates ...     pnts = [ (0,0), (1,0), (1,0.6), (0,0.6), \              (0.2,0.6), (0.8,0.6), (0.8,0.8), (0.2,0.8), \              (0.5,0.15), (0.65,0.3), (0.5,0.45), (0.35,0.3) ]     pnums = [geometry.AppendPoint(*p) for p in pnts]          # start-point, end-point, boundary-condition, domain on left side, domain on right side:     lines = [ (0,1,1,1,0), (1,2,2,1,0), (2,5,2,1,0), (5,4,2,1,2), (4,3,2,1,0), (3,0,2,1,0), \               (5,6,2,2,0), (6,7,2,2,0), (7,4,2,2,0), \               (8,9,2,3,1), (9,10,2,3,1), (10,11,2,3,1), (11,8,2,3,1) ]              for p1,p2,bc,left,right in lines:         geometry.Append( ["line", pnums[p1], pnums[p2]], bc=bc, leftdomain=left, rightdomain=right)     return geometry if comm.size > 1:     if comm.rank == 0:         mesh = make_geometry().GenerateMesh(maxh=0.2)         mesh = ng.Mesh(mesh.Distribute(comm))     else:         mesh = ng.Mesh(netgen.meshing.Mesh.Receive(comm)) else:     mesh = ng.Mesh(make_geometry().GenerateMesh(maxh=0.2)) vtk = ng.VTKOutput(     ma=mesh,     coefs=,     names=,     filename=f"mesh-rank-{comm.rank}",     subdivision=0) vtk.Do() fes = H1(mesh, order=3, dirichlet=[1]) u = fes.TrialFunction() v = fes.TestFunction() # one heat conductivity coefficient per sub-domain lam = CoefficientFunction([1, 1000, 10]) # a = BilinearForm(fes, symmetric=False) # a += SymbolicBFI(lam*grad(u)*grad(v)) a = BilinearForm(lam*grad(u)*grad(v) * dx) pre = ng.Preconditioner(a, "local") # a.Assemble() # heat-source in sub-domain 3 f = LinearForm(fes) f += SymbolicLFI(CoefficientFunction([0, 0, 1])*v) # c = Preconditioner(a, type="multigrid", inverse = "sparsecholesky") gfu = GridFunction(fes) # Draw(gfu) # finite element space and gridfunction to represent # the heatflux: space_flux = HDiv(mesh, order=2) gf_flux = GridFunction(space_flux, "flux") def SolveBVP(i):     fes.Update()     gfu.Update()     a.Assemble()     f.Assemble()     inv = CGSolver(a.mat, pre.mat, printrates=comm.rank == 0, maxiter=200, tol=1e-8)     gfu.vec.data = inv * f.vec     vtk = ng.VTKOutput(         ma=mesh,         coefs=[gfu],         names=["Temperature (K)"],         filename=f"results-{i}",         subdivision=0)     vtk.Do()     # Redraw(blocking=True) l = def CalcError():     space_flux.Update()     gf_flux.Update()     flux = lam * grad(gfu)     # interpolate finite element flux into H(div) space:     gf_flux.Set(flux)     # Gradient-recovery error estimator     err = 1/lam*(flux-gf_flux)*(flux-gf_flux)     elerr = Integrate (err, mesh, VOL, element_wise=True)     if len(elerr) == 0:         maxerr = 0     else:         maxerr = max(elerr)          maxerr = comm.allreduce(maxerr, MPI.MAX)     comm.Barrier()     l.append ( (fes.ndof, sqrt(sum(elerr)) ))     i = 0     i_nr = 0     for el in mesh.Elements():         i_nr += 1         if elerr[el.nr] > 0.25*maxerr:             i += 1         mesh.SetRefinementFlag(el, elerr[el.nr] > 0.25*maxerr)     print("# ", i, "number of elements refined. total=", i_nr) with TaskManager():     i = 0     while fes.ndof < 100000:           print(i)         i += 1         if i == 20:             break         SolveBVP(i)         CalcError()         print("before", comm.rank)         mesh.Refine()         print("after", comm.rank)         print()         print("# num elements after refinement =", len(list(mesh.Elements())))         vtk = ng.VTKOutput(             ma=mesh,             coefs=,             names=,             filename=f"mesh-{i}",             subdivision=0)         vtk.Do() import matplotlib.pyplot as plt plt.yscale('log') plt.xscale('log') plt.xlabel("ndof") plt.ylabel("H1 error-estimate") ndof,err = zip(*l) plt.plot(ndof,err, "-*") plt.ion() plt.savefig("hei.pdf")

 
Last edit: 1 year 6 months ago by sigmunh.
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