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fix the SSGPLVM with MPI

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This commit is contained in:
Zhenwen Dai 2014-06-25 13:57:25 +01:00
parent 08ed72b2f2
commit cf33808673
7 changed files with 28 additions and 30 deletions
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23
GPy/models/ss_gplvm.py
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@ -45,7 +45,6 @@ class SSGPLVM(SparseGP):
gamma[:] = 0.5 + 0.1 * np.random.randn(X.shape[0], input_dim)
gamma[gamma>1.-1e-9] = 1.-1e-9
gamma[gamma<1e-9] = 1e-9
gamma[:] = 0.5
if Z is None:
Z = np.random.permutation(X.copy())[:num_inducing]
@ -72,20 +71,19 @@ class SSGPLVM(SparseGP):
SparseGP.__init__(self, X, Y, Z, kernel, likelihood, inference_method, name, **kwargs)
self.add_parameter(self.X, index=0)
self.add_parameter(self.variational_prior)
if mpi_comm != None:
from ..util.mpi import divide_data
N_start, N_end, N_list = divide_data(Y.shape[0], mpi_comm)
self.N_range = (N_start, N_end)
self.N_list = np.array(N_list)
self.Y_local = self.Y[N_start:N_end]
print 'MPI RANK: '+str(self.mpi_comm.rank)+' with datasize: '+str(self.N_range)
mpi_comm.Bcast(self.param_array, root=0)
if self.group_spike:
[self.X.gamma[:,i].tie('tieGamma'+str(i)) for i in xrange(self.X.gamma.shape[1])] # Tie columns together
if mpi_comm != None:
from ..util.mpi import divide_data
Y_start, Y_end, Y_list = divide_data(Y.shape[0], mpi_comm)
self.Y_local = self.Y[Y_start:Y_end]
self.X_local = self.X[Y_start:Y_end]
self.Y_range = (Y_start, Y_end)
self.Y_list = np.array(Y_list)
print self.mpi_comm.rank, self.Y_range
mpi_comm.Bcast(self.param_array, root=0)
def set_X_gradients(self, X, X_grad):
"""Set the gradients of the posterior distribution of X in its specific form."""
X.mean.gradient, X.variance.gradient, X.binary_prob.gradient = X_grad
@ -124,9 +122,10 @@ class SSGPLVM(SparseGP):
dc = super(SSGPLVM, self).__getstate__()
dc['mpi_comm'] = None
if self.mpi_comm != None:
del dc['N_range']
del dc['N_list']
del dc['Y_local']
del dc['X_local']
del dc['Y_range']
return dc
def __setstate__(self, state):