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METIS partitioner for mesh and graph

License: MIT License

Python 4.27% C 94.28% Cython 1.45%

scientific-computing graph-algorithms metis partitioning-algorithms mesh

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mgmetis's Issues

How to disable the mpi during the installation.

I have installed it successfully, but wheni run it. it feeds back the following error:
OSError: libmpi.so.20: cannot open shared object file: No such file or directory

Install with error.

The feedbacks are about " /usr/lib64/mpi/gcc/openmpi2/bin/mpicc: no such file or directory". I only use mpich and i have intalled it.
I want to know how to disable the use of openmpi or disable it.

Parmetis error

ParMETIS is not available, please install mpi4py and rebuild mgmetis

OpenMP METIS

Multithreading is definitely useful, it should be enabled in mgmetis.

TODO Tasks

Support MPI as stated in #2
Support OpenMP as stated in #3

Bad output with Python 3.6.7

Hi.

I tried to use mgmetis inside a Docker container that uses Python 3.6.7 and NumPy 1.18.1. When I attempt to partition a mesh with 8 cells into 4 parts with the following script,

from mgmetis import metis
import numpy as np
cells = np.array([[0, 1, 4], [0, 3, 4], [1, 2, 5], [1, 4, 5], [3, 4, 7], [3, 6, 7], [4, 5, 8], [4, 7, 8]], dtype = 'int64')
print(cells.dtype)
parts = 4
objval, epart, npart = metis.part_mesh_dual(parts, cells, ncommon = 2)
print('objval:', objval)
print('epart:', epart)

I get a bad partition:

When I run the same script locally with Python 3.8.2 and NumPy 1.18.1, I get a good partition:

Do you know what my problem may be?
Thank you.

Segmentation fault with parmetis

Hi, I am trying to use parmetis but I am having a segmentation fault.

OS: Ubuntu 7.5.0-3ubuntu1~18.04
MPI: mpirun (Open MPI) 4.0.5

First, I check MPI is properly installed:

$ env MPICC=$(which mpicc) python3 -m pip install mpi4py
$ mpiexec -n 5 python -m mpi4py.bench helloworld
Hello, World! I am process 0 of 5 on localhost.
Hello, World! I am process 1 of 5 on localhost.
Hello, World! I am process 2 of 5 on localhost.
Hello, World! I am process 3 of 5 on localhost.
Hello, World! I am process 4 of 5 on localhost.

Next, I install mgmetis:

$ python3 -m pip install --upgrade pip setuptools wheel
$ git clone https://github.com/chiao45/mgmetis.git
$ cd mgmetis
$ python setup.py build
$ python setup.py install

Finally, I tried running a simple example, my_test.py, inspired from the unittest test_part_kway.py:

import numpy as np
from mgmetis.parmetis import part_kway
from mpi4py import MPI

comm = MPI.COMM_WORLD
has_mpi = True
rank = comm.rank

xadj = [int(x) for x in "0 2 5 8 11 13 16 20 24 28 31 33 36 39 42 44".split()]
adjncy = [
    int(x)
    for x in "1 5 0 2 6 1 3 7 2 4 8 3 9 0 6 10 1 5 7 11 2 6 8 12 3 7 9 13 4 8 14 5 11 6 10 12 7 11 13 8 12 14 9 13".split()
]
xadj, adjncy = np.asarray(xadj, dtype=int), np.asarray(adjncy, dtype=int)
n = xadj.size // 2

xadj0 = xadj[: n + 1].copy()
adjs0 = adjncy[: xadj0[-1]].copy()
xadj, adjs = np.asarray(xadj0, dtype=int), np.asarray(adjs0, dtype=int)
_, part = part_kway(4, xadj, adjs, comm=comm)

But I get this segmentation fault:

$ python my_test.py
[localhost:222298] *** Process received signal ***
[localhost:222298] Signal: Segmentation fault (11)
[localhost:222298] Signal code:  (128)
[localhost:222298] Failing at address: (nil)
[localhost:222298] [ 0] /lib/x86_64-linux-gnu/libc.so.6(+0x3ef10)[0x7fdab870af10]
[localhost:222298] [ 1] /my_project/mgmetis/_cython/./metis64.cpython-36m-x86_64-linux-gnu.so(libmetis__CreateCoarseGraphNoMask+0x1df)[0x7fd897e6749f]
[localhost:222298] [ 2] /myproject/mgmetis/mgmetis/_cython/./metis64.cpython-36m-x86_64-linux-gnu.so(libmetis__Match_RM+0x33a)[0x7fd897e6840a]
[localhost:222298] [ 3] /myproject/mgmetis/mgmetis/_cython/./metis64.cpython-36m-x86_64-linux-gnu.so(libmetis__CoarsenGraph+0x123)[0x7fd897e68e93]
[localhost:222298] [ 4] /myproject/mgmetis/mgmetis/_cython/./metis64.cpython-36m-x86_64-linux-gnu.so(libmetis__MlevelKWayPartitioning+0xf1)[0x7fd897e763b1]
[localhost:222298] [ 5] /myproject/mgmetis/mgmetis/_cython/./metis64.cpython-36m-x86_64-linux-gnu.so(METIS_PartGraphKway+0x2af)[0x7fd897e7678f]
[localhost:222298] [ 6] /myproject/mgmetis/mgmetis/_cython/parmetis64.cpython-36m-x86_64-linux-gnu.so(ParMETIS_V3_PartKway+0x4f8)[0x7fd8980e0ce8]
[localhost:222298] [ 7] /usr/lib/x86_64-linux-gnu/libffi.so.6(ffi_call_unix64+0x4c)[0x7fd89c542dae]
[localhost:222298] [ 8] /usr/lib/x86_64-linux-gnu/libffi.so.6(ffi_call+0x22f)[0x7fd89c54271f]
[localhost:222298] [ 9] /my_venv_3.6.9/lib/python3.6/lib-dynload/_ctypes.cpython-36m-x86_64-linux-gnu.so(_ctypes_callproc+0x2b4)[0x7fd89c7565a4]
[localhost:222298] [10] /my_venv_3.6.9/lib/python3.6/lib-dynload/_ctypes.cpython-36m-x86_64-linux-gnu.so(+0x11d34)[0x7fd89c756d34]
[localhost:222298] [11] python(_PyObject_FastCallKeywords+0x19c)[0x5aa9ac]
[localhost:222298] [12] python[0x50af03]
[localhost:222298] [13] python(_PyEval_EvalFrameDefault+0x444)[0x50c924]
[localhost:222298] [14] python[0x508675]
[localhost:222298] [15] python[0x50a3e0]
[localhost:222298] [16] python[0x50adcd]
[localhost:222298] [17] python(_PyEval_EvalFrameDefault+0x12a4)[0x50d784]
[localhost:222298] [18] python[0x508675]
[localhost:222298] [19] python(PyEval_EvalCode+0x23)[0x50b7d3]
[localhost:222298] [20] python[0x6352e2]
[localhost:222298] [21] python(PyRun_FileExFlags+0x97)[0x635397]
[localhost:222298] [22] python(PyRun_SimpleFileExFlags+0x17f)[0x638b4f]
[localhost:222298] [23] python(Py_Main+0x591)[0x6396f1]
[localhost:222298] [24] python(main+0xe0)[0x4b0e50]
[localhost:222298] [25] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xe7)[0x7fdab86edc87]
[localhost:222298] [26] python(_start+0x2a)[0x5b30ea]
[localhost:222298] *** End of error message ***
Segmentation fault

Add support MPI with ParMETIS

We need to add support for ParMETIS to enable using mgmetis in parallel with MPI.

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