def ToHypreParVec(vec):
import mfem.par as mfem
from mpi4py import MPI
if mfem.sizeof_HYPRE_Int() == 4:
dtype = 'int32'
else:
dtype = 'int64'
comm = MPI.COMM_WORLD
num_proc = MPI.COMM_WORLD.size
myid = MPI.COMM_WORLD.rank
vec = vec.flatten()
ml = vec.shape[0]
# collect col array to determin partitioning
m_array = comm.allgather(ml)
cols = [0] + list(np.cumsum(m_array))
glob_size = cols[-1]
col_starts = np.array([cols[myid], cols[myid + 1], glob_size], dtype=dtype)
vec = vec.astype('float', copy=False)
v = mfem.HypreParVector(MPI.COMM_WORLD, glob_size, [vec, col_starts])
return v
def schur(*names, **kwargs):
# schur("A1", "B1", scale=(1.0, 1e3))
prc = kwargs.pop('prc')
blockname = kwargs.pop('blockname')
r0 = prc.get_row_by_name(blockname)
c0 = prc.get_col_by_name(blockname)
scales = kwargs.pop('scale', [1] * len(names))
print_level = kwargs.pop('print_level', -1)
S = []
for name, scale in zip(names, scales):
r1 = prc.get_row_by_name(name)
c1 = prc.get_col_by_name(name)
B = prc.get_operator_block(r0, c1)
Bt = prc.get_operator_block(r1, c0)
B0 = prc.get_operator_block(r1, c1)
if use_parallel:
Bt = Bt.Transpose()
Bt = Bt.Transpose()
Md = mfem.HypreParVector(MPI.COMM_WORLD, B0.GetGlobalNumRows(),
B0.GetColStarts())
else:
Bt = Bt.Copy()
Md = mfem.Vector()
B0.GetDiag(Md)
Md *= scale
if use_parallel:
Bt.InvScaleRows(Md)
S.append(mfem.ParMult(B, Bt))
else:
S.append(mfem.Mult(B, Bt))
if use_parallel:
from mfem.common.parcsr_extra import ToHypreParCSR, ToScipyCoo
S2 = [ToScipyCoo(s) for s in S]
for s in S2[1:]:
S2[0] = S2[0] + s
S = ToHypreParCSR(S2[0].tocsr())
invA0 = mfem.HypreBoomerAMG(S)
else:
from mfem.common.sparse_utils import sparsemat_to_scipycsr
S2 = [sparsemat_to_scipycsr(s).tocoo() for s in S]
for s in S2[1:]:
S2[0] = S2[0] + s
S = mfem.SparseMatrix(S2.tocsr())
invA0 = mfem.DSmoother(S)
invA0.iterative_mode = False
invA0.SetPrintLevel(print_level)
invA0._S = S
return invA0
def ParMultVecComplex(A, v):
'''
A*v
'''
from mpi4py import MPI
comm = MPI.COMM_WORLD
num_proc = MPI.COMM_WORLD.size
myid = MPI.COMM_WORLD.rank
R_A, I_A = A
R_v, I_v = v
if I_A is None and I_v is None:
ans_r = mfem.HypreParVector(R_v)
R_A.Mult(R_v, ans_r)
return (ans_r, None)
ans_r = mfem.HypreParVector(R_v)
ans_i = mfem.HypreParVector(R_v)
if I_A is None:
R_A.Mult(R_v, ans_r)
R_A.Mult(I_v, ans_i)
elif I_v is None:
R_A.Mult(R_v, ans_r)
I_A.Mult(R_v, ans_i)
else:
ans_r2 = mfem.HypreParVector(R_v)
ans_i2 = mfem.HypreParVector(I_v)
R_A.Mult(R_v, ans_r)
I_A.Mult(I_v, ans_r2)
ans_r -= ans_r2
R_A.Mult(I_v, ans_i)
I_A.Mult(R_v, ans_i2)
ans_i += ans_i2
return (ans_r, ans_i)
x.Assign(0.0)
b.Assign(0.0)
# 10. Set up the 1x2 block Least Squares DPG operator, B = [B0 Bhat],
# the normal equation operator, A = B^t Sinv B, and
# the normal equation right-hand-size, b = B^t Sinv F.
B = mfem.BlockOperator(true_offsets_test, true_offsets)
B.SetBlock(0, 0, matB0)
B.SetBlock(0, 1, matBhat)
A = mfem.RAPOperator(B, matSinv, B)
trueF = F.ParallelAssemble()
SinvF = mfem.HypreParVector(test_space)
matSinv.Mult(trueF, SinvF)
B.MultTranspose(SinvF, b)
# 11. Set up a block-diagonal preconditioner for the 2x2 normal equation
#
# [ S0^{-1} 0 ]
# [ 0 Shat^{-1} ] Shat = (Bhat^T Sinv Bhat)
#
# corresponding to the primal (x0) and interfacial (xhat) unknowns.
# Since the Shat operator is equivalent to an H(div) matrix reduced to
# the interfacial skeleton, we approximate its inverse with one V-cycle
# of the ADS preconditioner from the hypre library (in 2D we use AMS for
# the rotated H(curl) problem).
S0inv = mfem.HypreBoomerAMG(matS0)
S0inv.SetPrintLevel(0)
bVarf.AddDomainIntegrator(mfem.VectorFEDivergenceIntegrator())
bVarf.Assemble()
bVarf.Finalize()
B = bVarf.ParallelAssemble()
B *= -1
BT = B.Transpose()
darcyOp = mfem.BlockOperator(block_trueOffsets)
darcyOp.SetBlock(0, 0, M)
darcyOp.SetBlock(0, 1, BT)
darcyOp.SetBlock(1, 0, B)
#M2 = M.Transpose()
#M3 = M2.Transpose()
MinvBt = B.Transpose()
Md = mfem.HypreParVector(MPI.COMM_WORLD, M.GetGlobalNumRows(),
M.GetRowStarts())
M.GetDiag(Md)
MinvBt.InvScaleRows(Md)
S = mfem.hypre.ParMult(B, MinvBt)
invM = mfem.HypreDiagScale(M)
invS = mfem.HypreBoomerAMG(S)
invM.iterative_mode = False
invS.iterative_mode = False
darcyPr = mfem.BlockDiagonalPreconditioner(block_trueOffsets)
darcyPr.SetDiagonalBlock(0, invM)
darcyPr.SetDiagonalBlock(1, invS)
maxIter = 500
rtol = 1e-6
def solve_parallel(self, A, b, x=None):
from mpi4py import MPI
myid = MPI.COMM_WORLD.rank
nproc = MPI.COMM_WORLD.size
from petram.helper.mpi_recipes import gather_vector
def get_block(Op, i, j):
try:
return Op._linked_op[(i, j)]
except KeyError:
return None
offset = A.RowOffsets()
rows = A.NumRowBlocks()
cols = A.NumColBlocks()
if self.gui.write_mat:
for i in range(cols):
for j in range(rows):
m = get_block(A, i, j)
if m is None: continue
m.Print('matrix_' + str(i) + '_' + str(j))
for i, bb in enumerate(b):
for j in range(rows):
v = bb.GetBlock(j)
v.Print('rhs_' + str(i) + '_' + str(j) + '.' + smyid)
if x is not None:
for j in range(rows):
xx = x.GetBlock(j)
xx.Print('x_' + str(i) + '_' + str(j) + '.' + smyid)
M = mfem.BlockDiagonalPreconditioner(offset)
prcs = dict(self.gui.preconditioners)
name = self.Aname
assert not self.gui.parent.is_complex(), "can not solve complex"
if self.gui.parent.is_converted_from_complex():
name = sum([[n, n] for n in name], [])
for k, n in enumerate(name):
prc = prcs[n][1]
if prc == "None": continue
name = "".join([tmp for tmp in prc if not tmp.isdigit()])
A0 = get_block(A, k, k)
if A0 is None and not name.startswith('schur'): continue
if hasattr(mfem.HypreSmoother, prc):
invA0 = mfem.HypreSmoother(A0)
invA0.SetType(getattr(mfem.HypreSmoother, prc))
elif prc == 'ams':
depvar = self.engine.r_dep_vars[k]
dprint1("setting up AMS for ", depvar)
prec_fespace = self.engine.fespaces[depvar]
invA0 = mfem.HypreAMS(A0, prec_fespace)
invA0.SetSingularProblem()
elif name == 'MUMPS':
cls = SparseSmootherCls[name][0]
invA0 = cls(A0, gui=self.gui[prc], engine=self.engine)
elif name.startswith('schur'):
args = name.split("(")[-1].split(")")[0].split(",")
dprint1("setting up schur for ", args)
if len(args) > 1:
assert False, "not yet supported"
for arg in args:
r1 = self.engine.dep_var_offset(arg.strip())
c1 = self.engine.r_dep_var_offset(arg.strip())
B = get_block(A, k, c1)
Bt = get_block(A, r1, k).Transpose()
Bt = Bt.Transpose()
B0 = get_block(A, r1, c1)
Md = mfem.HypreParVector(MPI.COMM_WORLD,
B0.GetGlobalNumRows(),
B0.GetColStarts())
B0.GetDiag(Md)
Bt.InvScaleRows(Md)
S = mfem.ParMult(B, Bt)
invA0 = mfem.HypreBoomerAMG(S)
invA0.iterative_mode = False
else:
cls = SparseSmootherCls[name][0]
invA0 = cls(A0, gui=self.gui[prc])
invA0.iterative_mode = False
M.SetDiagonalBlock(k, invA0)
'''
We should support Shur complement type preconditioner
if offset.Size() > 2:
B = get_block(A, 1, 0)
MinvBt = get_block(A, 0, 1)
#Md = mfem.HypreParVector(MPI.COMM_WORLD,
# A0.GetGlobalNumRows(),
# A0.GetRowStarts())
Md = mfem.Vector()
A0.GetDiag(Md)
MinvBt.InvScaleRows(Md)
S = mfem.ParMult(B, MinvBt)
invS = mfem.HypreBoomerAMG(S)
invS.iterative_mode = False
M.SetDiagonalBlock(1, invS)
'''
maxiter = int(self.maxiter)
atol = self.abstol
rtol = self.reltol
kdim = int(self.kdim)
printit = 1
sol = []
solver = mfem.GMRESSolver(MPI.COMM_WORLD)
solver.SetKDim(kdim)
#solver = mfem.MINRESSolver(MPI.COMM_WORLD)
#solver.SetOperator(A)
#solver = mfem.CGSolver(MPI.COMM_WORLD)
solver.SetOperator(A)
solver.SetAbsTol(atol)
solver.SetRelTol(rtol)
solver.SetMaxIter(maxiter)
solver.SetPreconditioner(M)
solver.SetPrintLevel(1)
# solve the problem and gather solution to head node...
# may not be the best approach
for bb in b:
rows = MPI.COMM_WORLD.allgather(np.int32(bb.Size()))
rowstarts = np.hstack((0, np.cumsum(rows)))
dprint1("rowstarts/offser", rowstarts, offset.ToList())
if x is None:
xx = mfem.BlockVector(offset)
xx.Assign(0.0)
else:
xx = x
#for j in range(cols):
# dprint1(x.GetBlock(j).Size())
# dprint1(x.GetBlock(j).GetDataArray())
#assert False, "must implement this"
solver.Mult(bb, xx)
s = []
for i in range(offset.Size() - 1):
v = xx.GetBlock(i).GetDataArray()
vv = gather_vector(v)
if myid == 0:
s.append(vv)
else:
pass
if myid == 0:
sol.append(np.hstack(s))
if myid == 0:
sol = np.transpose(np.vstack(sol))
return sol
else:
return None
