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"""distributedmatrix.py -- classes for distributed matrices
This file contains the python classes to use with the wrapper.
"""
import numpy as np
from functools import wraps
from .wrapper import Elpa
class ProcessorLayout:
"""Create rectangular processor layout for use with distributed matrices"""
def __init__(self, comm):
"""Initialize processor layout.
Args:
comm: MPI communicator from mpi4py
"""
nprocs = comm.Get_size()
rank = comm.Get_rank()
for np_cols in range(int(np.sqrt(nprocs)), 0, -1):
if nprocs % np_cols == 0:
break
#if nprocs == 1:
# np_cols = 1
np_rows = nprocs//np_cols
# column major distribution of processors
my_pcol = rank // np_rows
my_prow = rank % np_rows
self.np_cols, self.np_rows = np_cols, np_rows
self.my_pcol, self.my_prow = my_pcol, my_prow
self.comm = comm
self.comm_f = comm.py2f()
class DistributedMatrix:
"""Class for generating a distributed block-cyclic matrix
The data attribute contains the array in the correct size for the local
processor.
"""
def __init__(self, processor_layout, na, nev, nblk, dtype=np.float64):
"""Initialize distributed matrix for a given processor layout.
Args:
processor_layout (ProcessorLayout): has to be created from MPI
communicator
na (int): dimension of matrix
nev (int): number of eigenvectors/eigenvalues to be computed
nblk (int): block size of distributed matrix
dtype: data type of matrix
"""
self.na = na
self.nev = nev
self.nblk = nblk
self.processor_layout = processor_layout
# get local size
self.na_rows = self.numroc(na, nblk, processor_layout.my_prow, 0,
processor_layout.np_rows)
self.na_cols = self.numroc(na, nblk, processor_layout.my_pcol, 0,
processor_layout.np_cols)
# create array
self.data = np.empty((self.na_rows, self.na_cols),
dtype=dtype, order='F')
self.elpa = None
@classmethod
def from_communicator(cls, comm, na, nev, nblk, dtype=np.float64):
"""Initialize distributed matrix from a MPI communicator.
Args:
comm: MPI communicator from mpi4py
na (int): dimension of matrix
nev (int): number of eigenvectors/eigenvalues to be computed
nblk (int): block size of distributed matrix
dtype: data type of matrix
"""
processor_layout = ProcessorLayout(comm)
return cls(processor_layout, na, nev, nblk, dtype)
@classmethod
def from_comm_world(cls, na, nev, nblk, dtype=np.float64):
"""Initialize distributed matrix from the MPI_COMM_WORLD communicator.
Args:
na (int): dimension of matrix
nev (int): number of eigenvectors/eigenvalues to be computed
nblk (int): block size of distributed matrix
dtype: data type of matrix
"""
from mpi4py import MPI
comm = MPI.COMM_WORLD
processor_layout = ProcessorLayout(comm)
return cls(processor_layout, na, nev, nblk, dtype)
@classmethod
def like(cls, matrix):
"""Get a DistributedMatrix with the same parameters as matrix"""
return cls(matrix.processor_layout, matrix.na, matrix.nev, matrix.nblk,
matrix.data.dtype)
def get_local_index(self, global_row, global_col):
"""compute local row and column indices from global ones
Returns a tuple of the local row and column indices
"""
local_row = self.indxg2l(global_row, self.nblk,
self.processor_layout.my_prow, 0,
self.processor_layout.np_rows)
local_col = self.indxg2l(global_col, self.nblk,
self.processor_layout.my_pcol, 0,
self.processor_layout.np_cols)
return local_row, local_col
def get_global_index(self, local_row, local_col):
"""compute global row and column indices from local ones
Returns a tuple of the global row and column indices
"""
global_row = self.indxl2g(local_row, self.nblk,
self.processor_layout.my_prow, 0,
self.processor_layout.np_rows)
global_col = self.indxl2g(local_col, self.nblk,
self.processor_layout.my_pcol, 0,
self.processor_layout.np_cols)
return global_row, global_col
def is_local_index(self, global_row, global_col):
"""check if global index is stored on current processor"""
return self.is_local_row(global_row) and self.is_local_col(global_col)
def is_local_row(self, global_row):
"""check if global row is stored on this processor"""
process_row = self.indxg2p(global_row, self.nblk,
self.processor_layout.my_prow, 0,
self.processor_layout.np_rows)
return process_row == self.processor_layout.my_prow
def is_local_col(self, global_col):
process_col = self.indxg2p(global_col, self.nblk,
self.processor_layout.my_pcol, 0,
self.processor_layout.np_cols)
return process_col == self.processor_layout.my_pcol
@staticmethod
def indxg2l(indxglob, nb, iproc, isrcproc, nprocs):
"""compute local index from global index indxglob
original netlib scalapack source:
.. code-block:: fortran
INDXG2L = NB*((INDXGLOB-1)/(NB*NPROCS))+MOD(INDXGLOB-1,NB)+1
"""
# adapt to python 0-based indexing
return nb*(indxglob//(nb*nprocs)) + indxglob%nb
@staticmethod
def indxl2g(indxloc, nb, iproc, isrcproc, nprocs):
"""compute global index from local index indxloc
original netlib scalapack source:
.. code-block:: fortran
INDXL2G = NPROCS*NB*((INDXLOC-1)/NB) + MOD(INDXLOC-1,NB) +
MOD(NPROCS+IPROC-ISRCPROC, NPROCS)*NB + 1
"""
# adapt to python 0-based indexing
return nprocs*nb*(indxloc//nb) + indxloc%nb + \
((nprocs+iproc-isrcproc)%nprocs)*nb
@staticmethod
def indxg2p(indxglob, nb, iproc, isrcproc, nprocs):
"""compute process coordinate for global index
original netlib scalapack source:
.. code-block:: fortran
INDXG2P = MOD( ISRCPROC + (INDXGLOB - 1) / NB, NPROCS )
"""
# adapt to python 0-based indexing
return (isrcproc + indxglob // nb) % nprocs
@staticmethod
def numroc(n, nb, iproc, isrcproc, nprocs):
"""Get local dimensions of distributed block-cyclic matrix.
Programmed after scalapack source (tools/numroc.f on netlib).
"""
mydist = (nprocs + iproc - isrcproc) % nprocs
nblocks = n // nb
result = (nblocks // nprocs) * nb
extrablks = nblocks % nprocs
if mydist < extrablks:
result += nb
elif mydist == extrablks:
result += n % nb
return int(result)
def _initialized_elpa(function):
# wrapper to ensure one-time initialization of Elpa object
@wraps(function)
def wrapped_function(self):
if self.elpa is None:
self.elpa = Elpa.from_distributed_matrix(self)
return function(self)
return wrapped_function
@_initialized_elpa
def compute_eigenvectors(self):
"""Compute eigenvalues and eigenvectors
The eigenvectors are stored in columns.
This function returns a dictionary with entries 'eigenvalues' and
'eigenvectors'.
After computing the eigenvectors, the original content of the matrix is
lost.
"""
eigenvectors = DistributedMatrix.like(self)
eigenvalues = np.zeros(self.na, dtype=np.float64)
# call ELPA
self.elpa.eigenvectors(self.data, eigenvalues, eigenvectors.data)
return {'eigenvalues': eigenvalues, 'eigenvectors': eigenvectors}
@_initialized_elpa
def compute_eigenvalues(self):
"""Compute only the eigenvalues.
This function returns the eigenvalues as an array.
After computing the eigenvalues, the original content of the matrix is
lost.
"""
eigenvalues = np.zeros(self.na, dtype=np.float64)
# call ELPA
self.elpa.eigenvalues(self.data, eigenvalues)
return eigenvalues
def set_data_from_global_matrix(self, matrix):
"""Set local part of the global matrix"""
for local_row in range(self.na_rows):
for local_col in range(self.na_cols):
global_row, global_col = self.get_global_index(local_row,
local_col)
self.data[local_row, local_col] = matrix[global_row,
global_col]
def dot(self, vector):
"""Compute dot product of matrix with vector.
This blocked implementation is much faster than the naive
implementation.
"""
if len(vector.shape) > 1 or vector.shape[0] != self.na:
raise ValueError("Error: shape of vector {} incompatible to "
"matrix of size {:d}x{:d}.".format(
vector.shape, self.na, self.na))
from mpi4py import MPI
summation = np.zeros_like(vector)
# loop only over blocks here
for local_row in range(0, self.na_rows, self.nblk):
for local_col in range(0, self.na_cols, self.nblk):
# do not go beyond the end of the matrix
row_block_size = min(local_row + self.nblk,
self.na_rows) - local_row
col_block_size = min(local_col + self.nblk,
self.na_cols) - local_col
global_row, global_col = self.get_global_index(local_row,
local_col)
# use numpy for faster dot product of local block
summation[global_row:global_row+row_block_size] += \
np.dot(self.data[local_row:local_row + row_block_size,
local_col:local_col + col_block_size],
vector[global_col:global_col+col_block_size])
result = np.zeros_like(vector)
self.processor_layout.comm.Allreduce(summation, result, op=MPI.SUM)
return result
def _dot_naive(self, vector):
"""Compute naive dot product of matrix with vector.
Still in here as an example and for testing purposes.
"""
from mpi4py import MPI
summation = np.zeros_like(vector)
for local_row in range(self.na_rows):
for local_col in range(self.na_cols):
global_row, global_col = self.get_global_index(local_row,
local_col)
summation[global_row] += self.data[local_row, local_col] *\
vector[global_col]
result = np.zeros_like(vector)
self.processor_layout.comm.Allreduce(summation, result, op=MPI.SUM)
return result
def get_column(self, global_col):
"""Return global column"""
from mpi4py import MPI
column = np.zeros(self.na, dtype=self.data.dtype)
temporary = np.zeros_like(column)
if self.is_local_col(global_col):
for global_row in range(self.na):
if not self.is_local_row(global_row):
continue
local_row, local_col = self.get_local_index(global_row,
global_col)
temporary[global_row] = self.data[local_row, local_col]
# this could be done more efficiently with a gather
self.processor_layout.comm.Allreduce(temporary, column, op=MPI.SUM)
return column
def get_row(self, global_row):
"""Return global row"""
from mpi4py import MPI
row = np.zeros(self.na, dtype=self.data.dtype)
temporary = np.zeros_like(row)
if self.is_local_row(global_row):
for global_col in range(self.na):
if not self.is_local_col(global_col):
continue
local_row, local_col = self.get_local_index(global_row,
global_col)
temporary[global_col] = self.data[local_row, local_col]
# this could be done more efficiently with a gather
self.processor_layout.comm.Allreduce(temporary, row, op=MPI.SUM)
return row
def global_indices(self):
"""Return iterator over global indices of matrix.
Use together with set_data_global_index and get_data_global_index.
"""
for local_row in range(self.na_rows):
for local_col in range(self.na_cols):
yield self.get_global_index(local_row, local_col)
def set_data_for_global_index(self, global_row, global_col, value):
"""Set value of matrix at global coordinates"""
if self.is_local_index(global_row, global_col):
local_row, local_col = self.get_local_index(global_row, global_col)
self.data[local_row, local_col] = value
def get_data_for_global_index(self, global_row, global_col):
"""Get value of matrix at global coordinates"""
if self.is_local_index(global_row, global_col):
local_row, local_col = self.get_local_index(global_row, global_col)
return self.data[local_row, local_col]
else:
raise ValueError('Index out of bounds: global row {:d}, '
'global col {:d}'.format(global_row, global_col))
def global_block_indices(self):
"""Return iterator over global indices of matrix blocks.
Use together with set_block_global_index and get_block_global_index
for more efficient loops.
"""
for local_row in range(0, self.na_rows, self.nblk):
for local_col in range(0, self.na_cols, self.nblk):
# do not go beyond the end of the matrix
row_block_size = min(local_row + self.nblk,
self.na_rows) - local_row
col_block_size = min(local_col + self.nblk,
self.na_cols) - local_col
global_row, global_col = self.get_global_index(local_row,
local_col)
yield global_row, global_col, row_block_size, col_block_size
def set_block_for_global_index(self, global_row, global_col,
row_block_size, col_block_size, value):
"""Set value of block of matrix at global coordinates"""
if self.is_local_index(global_row, global_col):
local_row, local_col = self.get_local_index(global_row, global_col)
if value.shape != (row_block_size, col_block_size):
raise ValueError("value has the wrong shape. "
"Expected: {}, found: {}."
.format((row_block_size, col_block_size),
value.shape)
)
self.data[local_row:local_row+row_block_size,
local_col:local_col+col_block_size] = value
def get_block_for_global_index(self, global_row, global_col,
row_block_size, col_block_size):
"""Get value of block of matrix at global coordinates"""
if self.is_local_index(global_row, global_col):
local_row, local_col = self.get_local_index(global_row, global_col)
if local_row+row_block_size > self.na_rows or \
local_col+col_block_size > self.na_cols:
raise ValueError("Block size wrong: exceeds dimensions of"
" matrix.")
return self.data[local_row:local_row+row_block_size,
local_col:local_col+col_block_size]
else:
raise ValueError('Index out of bounds: global row {:d}, '
'global col {:d}'.format(global_row, global_col))
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