Dear Fipy developers and users,
The official parallel running way works for me, however, I would like to
try an different way shown in the attached script. When running by $time
mpiexec -n 4 python My_Fipy_Parallel.py, it gets stuck at time step 179
without any error message pop out, four cores are full but enough memory
left. The bigger the mesh is, the sooner it will get stuck. Does any
know why and how to solve this problem? Thanks.
Regards
Ronghai
import fipy as fp
# from fipy.solvers.scipy import LinearGMRESSolver, LinearCGSSolver, LinearPCGSolver, LinearLUSolver, LinearBicgstabSolver
# from fipy.solvers.pyAMG import LinearGMRESSolver, LinearCGSSolver, LinearPCGSolver, LinearLUSolver
from fipy.solvers.trilinos import LinearGMRESSolver, LinearCGSSolver, LinearPCGSolver, LinearLUSolver, LinearBicgstabSolver
import numpy as np
from mpi4py import MPI
class Test:
def __init__(self):
self.nx = 300
self.ny = self.nx
self.dx = 1.
self.dy = 1.
self.nt = 100
self.dt = 10.
self.mesh = fp.PeriodicGrid2D(nx=self.nx, ny=self.ny, dx=self.dx, dy=self.dy)
self.x = self.mesh.cellCenters[0]
self.y = self.mesh.cellCenters[1]
self.sigma = 0.1*self.nx*self.dx
self.x0 = 0.5*self.nx*self.dx
self.y0 = 0.5*self.ny*self.dy
self.A = 100./(self.sigma*np.sqrt(2.*np.pi))
self.gauss = self.A*np.exp( -( (self.x-self.x0)**2/(2.*self.sigma**2) + (self.y-self.y0)**2/(2.*self.sigma**2) ) )
self.phi1_global =self.gauss
self.phi2_global =self.gauss
self.phi3_global =self.gauss
self.phi4_global =self.gauss
self.solver = LinearBicgstabSolver
def equation1(self, (phi1_global, phi2_global, phi3_global, phi4_global)):
phi1 = fp.CellVariable(mesh=self.mesh, value=phi1_global, hasOld=1)
eq1 = fp.TransientTerm(var=phi1, coeff=1.) == fp.DiffusionTerm(var=phi1, coeff=1.)
res = 1.e4
while res > 1.e-1:
eq1.cacheMatrix()
eq1.cacheRHSvector()
res = eq1.sweep(dt=1, solver=self.solver())
mat = eq1.matrix
vec = eq1.RHSvector
phi1.updateOld()
print 'mat shape = ', np.shape(mat.matrix)
print 'phi1 shape = ', np.shape(phi1.value)
return phi1.value
def equation2(self, (phi1_global, phi2_global, phi3_global, phi4_global)):
phi2 = fp.CellVariable(mesh=self.mesh, value=phi2_global, hasOld=1)
eq2 = fp.TransientTerm(var=phi2, coeff=1.) == fp.DiffusionTerm(var=phi2, coeff=1.)
res = 1.e4
while res > 1.e-1:
res = eq2.sweep(dt=1, solver=self.solver())
phi2.updateOld()
return phi2.value
def equation3(self, (phi1_global, phi2_global, phi3_global, phi4_global)):
phi3 = fp.CellVariable(mesh=self.mesh, value=phi3_global, hasOld=1)
eq3 = fp.TransientTerm(var=phi3, coeff=1.) == fp.DiffusionTerm(var=phi3, coeff=1.)
res = 1.e4
while res > 1.e-3:
res = eq3.sweep(dt=1, solver=self.solver())
phi3.updateOld()
return phi3.value
def equation4(self, (phi1_global, phi2_global, phi3_global, phi4_global)):
phi4 = fp.CellVariable(mesh=self.mesh, value=phi4_global, hasOld=1)
eq4 = fp.TransientTerm(var=phi4, coeff=1.) == fp.DiffusionTerm(var=phi4, coeff=1.)
res = 1.e4
while res > 1.e-3:
res = eq4.sweep(dt=1, solver=self.solver())
phi4.updateOld()
return phi4.value
def run(self):
for time_step in range(self.nt):
print 'time step is:', time_step
comm = MPI.COMM_WORLD
rank = comm.Get_rank()
if rank == 0:
phi1_value = self.equation1((self.phi1_global, self.phi2_global, self.phi3_global, self.phi4_global))
self.phi1_global = phi1_value
if rank == 1:
phi2_value = self.equation2((self.phi1_global, self.phi2_global, self.phi3_global, self.phi4_global))
self.phi2_global = phi2_value
if rank == 2:
phi3_value = self.equation3((self.phi1_global, self.phi2_global, self.phi3_global, self.phi4_global))
self.phi3_global = phi3_value
if rank == 3:
phi4_value = self.equation4((self.phi1_global, self.phi2_global, self.phi3_global, self.phi4_global))
self.phi4_global = phi4_value
comm.bcast(self.phi1_global, root=0)
comm.bcast(self.phi2_global, root=1)
comm.bcast(self.phi3_global, root=2)
comm.bcast(self.phi4_global, root=3)
if __name__ == '__main__':
myclass = Test()
myclass.run()
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