[petsc-users] How to compile PETSC4py correctly with MPI ?

[Jan Grießer]

Hey,
i started again trying to solve an eigenvalue problem with petsc4py and
slepc4py. I followed the instruction on the website and installed petsc and
petsc4py via pip3. MPI4PY and the corresponding MPI version is already
compiled on our cluster.
Unfortunately when i start the following script by using:
mpirun -n 2 python3 test3.py

import time
import numpy as np
import sys, petsc4py
petsc4py.init(sys.argv)
from petsc4py import PETSc

from mpi4py import MPI
print(MPI.COMM_WORLD.Get_size())


# For print
Print = PETSc.Sys.Print

def construct_operator(m, n):
    """
    Standard symmetric eigenproblem corresponding to the
    Laplacian operator in 2 dimensions.
    """
    # Create matrix for 2D Laplacian operator
    A = PETSc.Mat().create()
    A.setSizes([m*n, m*n])
    A.setFromOptions( )
    A.setUp()
    # Fill matrix
    hx = 1.0/(m-1) # x grid spacing
    hy = 1.0/(n-1) # y grid spacing
    diagv = 2.0*hy/hx + 2.0*hx/hy
    offdx = -1.0*hy/hx
    offdy = -1.0*hx/hy
    Istart, Iend = A.getOwnershipRange()
    print("Istart: ", Istart)
    print("Iend: ", Iend)
    for I in range(Istart, Iend) :
        A[I,I] = diagv
        i = I//n    # map row number to
        j = I - i*n # grid coordinates
        if i> 0  : J = I-n; A[I,J] = offdx
        if i< m-1: J = I+n; A[I,J] = offdx
        if j> 0  : J = I-1; A[I,J] = offdy
        if j< n-1: J = I+1; A[I,J] = offdy
    A.assemble()
    return A

def main():
    opts = PETSc.Options()
    N = opts.getInt('N', 96)
    m = opts.getInt('m', N)
    n = opts.getInt('n', m)
    Print("Symmetric Eigenproblem (sparse matrix), "
          "N=%d (%dx%d grid)" % (m*n, m, n))
    A = construct_operator(m,n)
Symmetric Eigenproblem (sparse matrix), N=9216 (96x96 grid)
Symmetric Eigenproblem (sparse matrix), N=9216 (96x96 grid)
2
Istart:  0
Iend:  9216
2
Istart:  0
Iend:  9216

if __name__ == '__main__':
    main()

it returns me the following output:

instead of the one i assumed to get from a local execution of my file:
2
2
Symmetric Eigenproblem (sparse matrix), N=9216 (96x96 grid)
Istart:  4608
Iend:  9216
Istart:  0
Iend:  4608

Therefore i assume somehow my MPI version is not linked correctly to my
file and i checked with "ldd" my petsc file:
linux-vdso.so.1 =>  (0x00007ffd8db6a000)
liblapack.so.3 => /lib64/liblapack.so.3 (0x00007f1bd95e8000)
libblas.so.3 => /lib64/libblas.so.3 (0x00007f1bd938e000)
libm.so.6 => /lib64/libm.so.6 (0x00007f1bd908c000)
libX11.so.6 => /lib64/libX11.so.6 (0x00007f1bd8d4e000)
libpthread.so.0 => /lib64/libpthread.so.0 (0x00007f1bd8b31000)
libstdc++.so.6 => /lib64/libstdc++.so.6 (0x00007f1bd8829000)
libdl.so.2 => /lib64/libdl.so.2 (0x00007f1bd8625000)
libgfortran.so.3 => /lib64/libgfortran.so.3 (0x00007f1bd8302000)
libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00007f1bd80ec000)
libquadmath.so.0 => /lib64/libquadmath.so.0 (0x00007f1bd7eb0000)
libc.so.6 => /lib64/libc.so.6 (0x00007f1bd7aec000)
/lib64/ld-linux-x86-64.so.2 (0x0000557325576000)
libxcb.so.1 => /lib64/libxcb.so.1 (0x00007f1bd78c4000)
libXau.so.6 => /lib64/libXau.so.6 (0x00007f1bd76bf000)
I assume that pip3 was for some reasons not able to link my mpi version to
it. Can i force pip to link mpi or is there another mistake somewhere?
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