basnijholt / mumpy

Python bindings for the MUMPS package MUMPS: a parallel sparse direct solver

mumpy

Python bindings for the MUMPS package MUMPS: a parallel sparse direct solver

Installation

On Linux

Either install mumps with:

sudo apt-get instal libmumps-scotch-dev

Both on Linux and OSX

or use the conda package on conda-forge

conda config --add channels conda-forge
conda install cython mumps numpy scipy libgfortran
pip install [email protected]:basnijholt/mumpy.git

and use the following build.conf (if on Linux, not needed for OSX)

[mumps]
include_dirs = $CONDA_PREFIX/include
library_dirs = $CONDA_PREFIX/lib
libraries = zmumps mumps_common pord metis esmumps scotch scotcherr mpiseq gfortran
extra_link_args = -Wl,-rpath=$CONDA_PREFIX/lib

Usage

import scipy.sparse.linalg as sla
from scipy.sparse import identity
import mumpy.mumps as mumps


def sparse_diag(matrix, k, sigma, **kwargs):
    """Call sla.eigsh with mumps support.

    Please see scipy.sparse.linalg.eigsh for documentation.
    
    Notes
    -----
    mumpy only works with complex numbers at the moment.
    """
    class LuInv(sla.LinearOperator):
        def __init__(self, A):
            inst = mumps.MUMPSContext()
            inst.analyze(A, ordering='pord')
            inst.factor(A)
            self.solve = inst.solve
            sla.LinearOperator.__init__(self, A.dtype, A.shape)

        def _matvec(self, x):
            return self.solve(x.astype(self.dtype))

    opinv = LuInv(matrix - sigma * identity(matrix.shape[0]))
    return sla.eigsh(matrix, k, sigma=sigma, OPinv=opinv, **kwargs)

mumpy's Issues

error when importing mumpy

In [1]: import mumpy.mumps as mumps

ImportError Traceback (most recent call last)
in ()
Hello,

I get an error when I import mumpy. Do you know what could be the origin of the issue?

Thanks!

Alexandre

============================

----> 1 import mumpy.mumps as mumps

~/anaconda/lib/python3.5/site-packages/mumpy/mumps.py in ()
16 import scipy.sparse
17 import warnings
---> 18 from . import _mumps
19 from .fortran_helpers import prepare_for_fortran
20

ImportError: dlopen(/Users/myuser/anaconda/lib/python3.5/site-packages/mumpy/_mumps.cpython-35m-darwin.so, 2): Symbol not found: _zmumps_c
Referenced from: /Users/myuser/anaconda/lib/python3.5/site-packages/mumpy/_mumps.cpython-35m-darwin.so
Expected in: flat namespace
in /Users/myuser/anaconda/lib/python3.5/site-packages/mumpy/_mumps.cpython-35m-darwin.so