NumPy (& SciPy)

Read and print Matrix Market matrix files

SciPy provides an interface to read Matrix Market format files (.mtx), which can be generated, for example, by AMGX's AMGX_write_system function. However, it is important to note that AMGX_write_system, writes the matrix first, followed by the RHS and initial solution vectors within the same file. This format is not fully compatible with SciPy's binding which can only read the matrix. The .mtx file need to be edited, leaving only the matrix and keeping the full top banner, then it can be loaded using:

Pre-edited matrix fileUnedited full system file

import sys
from scipy.io import mmread
import numpy as np

mtx = mmread("AMGX_matrix.mtx")
mtx = mmread(buf).toarray() # Read data and convert to dense matrix
np.set_printoptions(linewidth=100, threshold=sys.maxsize)
print(mtx)

import io
import sys
from scipy.io import mmread
import numpy as np

n = 64 # Vector size

with open("AMGX_system.mtx", "r") as file_:
    lines = file_.readlines() # Read data

lines = lines[:-(n*2+2)] # Remove RHS and initial solution vectors (+ 2 for the headers)
buf = io.StringIO("".join(lines))

mtx = mmread(buf).toarray() # Read data and convert to dense matrix
np.set_printoptions(linewidth=100, threshold=sys.maxsize)
print(mtx)