def run_test():
comm = MPI.COMM_WORLD
size = comm.Get_size()
rank = comm.Get_rank()
if size!=3:
if rank==0: print "###Error: the number of processors should be 3. Please use: mpiexec -n 3 python p_arpack.py"
sys.exit(1)
if rank == 0: a = np.array([[1,2,0]], dtype='float');
if rank == 1: a = np.array([[2,0,3]], dtype='float');
if rank == 2: a = np.array([[0,3,0]], dtype='float');
slice_thread=slice(rank,rank+1)
params= _ParallelSymmetricArpackParams(comm, a, 1)
while not params.converged:
params.iterate()
vals, vecs = params.extract(return_eigenvectors=True)
if rank == 0:
print 'parallel arpack'
print vecs, '\n'
A = np.array([[1,2,0],[2,0,3],[0,3,0]], dtype='float')
vals, vecs = eigsh(A, k=1)
if rank==0:
print 'serial arpack'
print vecs
def _layout_positions(g, g_extended=None):
'''Return a dictionary that maps pedigree nodes to graph layout positions (x,y). Uses
a layered spring model. Capable of handling both normal and extended pedigree graphs.'''
g_extended = g_extended if g_extended else g
# x-positions: spring model
L = laplacian(g_extended, dtype=np.float)
[_, v] = eigsh(L, 2, which='SM')
x = v[:, 1]
# Compute depths based on -original- graph
y = pt.node_depth(g)
for node in g_extended.nodes_iter():
# Marriage node: 0.5 above child depth. Note that marriage nodes must have children
if node < 0:
y[node] = y[g_extended.successors_iter(node).next()] - 0.5
ymax = max(d for d in y.itervalues())
# Reverse the y-axis (generation 0 on top)
return dict(zip(g_extended.nodes_iter(), zip(x, ((ymax - y[node]) for node in g_extended.nodes_iter()))))
def _layout_positions(g, g_extended=None):
'''Return a dictionary that maps pedigree nodes to graph layout positions (x,y). Uses
a layered spring model. Capable of handling both normal and extended pedigree graphs.'''
g_extended = g_extended if g_extended else g
# x-positions: spring model
L = laplacian(g_extended, dtype=np.float)
[_, v] = eigsh(L, 2, which='SM')
x = v[:, 1]
# Compute depths based on -original- graph
y = pt.node_depth(g)
for node in g_extended.nodes_iter():
# Marriage node: 0.5 above child depth. Note that marriage nodes must have children
if node < 0:
y[node] = y[g_extended.successors_iter(node).next()] - 0.5
ymax = max(d for d in y.itervalues())
# Reverse the y-axis (generation 0 on top)
return dict(
zip(g_extended.nodes_iter(),
zip(x, ((ymax - y[node]) for node in g_extended.nodes_iter()))))
def smallest_ev_arpack(R,U,rows,cols,tolerance=1e-4): X = build_sparse(R, U, rows, cols) (eis,_)=eigsh(X, k=1, sigma=-3, which='LM',tol=tolerance,maxiter=1000) ei = eis[0] return ei
def is_psd_arpack(R,U,rows,cols,tolerance=1e-4): X = build_sparse(R, U, rows, cols) (eis,_)=eigsh(X, k=1, sigma=-1, which='LM') ei = eis[0] return ei>tolerance