import sys import os import gc import threading import numpy as np from numpy.testing import assert_equal, assert_, assert_allclose from scipy.sparse import (_sparsetools, coo_matrix, csr_matrix, csc_matrix, bsr_matrix, dia_matrix) from scipy.sparse.sputils import supported_dtypes, matrix from scipy._lib._testutils import check_free_memory import pytest from pytest import raises as assert_raises def test_exception(): assert_raises(MemoryError, _sparsetools.test_throw_error) def test_threads(): # Smoke test for parallel threaded execution; doesn't actually # check that code runs in parallel, but just that it produces # expected results. nthreads = 10 niter = 100 n = 20 a = csr_matrix(np.ones([n, n])) bres = [] class Worker(threading.Thread): def run(self): b = a.copy() for j in range(niter): _sparsetools.csr_plus_csr(n, n, a.indptr, a.indices, a.data, a.indptr, a.indices, a.data, b.indptr, b.indices, b.data) bres.append(b) threads = [Worker() for _ in range(nthreads)] for thread in threads: thread.start() for thread in threads: thread.join() for b in bres: assert_(np.all(b.toarray() == 2)) def test_regression_std_vector_dtypes(): # Regression test for gh-3780, checking the std::vector typemaps # in sparsetools.cxx are complete. for dtype in supported_dtypes: ad = matrix([[1, 2], [3, 4]]).astype(dtype) a = csr_matrix(ad, dtype=dtype) # getcol is one function using std::vector typemaps, and should not fail assert_equal(a.getcol(0).todense(), ad[:,0]) @pytest.mark.slow def test_nnz_overflow(): # Regression test for gh-7230 / gh-7871, checking that coo_todense # with nnz > int32max doesn't overflow. nnz = np.iinfo(np.int32).max + 1 # Ensure ~20 GB of RAM is free to run this test. check_free_memory((4 + 4 + 1) * nnz / 1e6 + 0.5) # Use nnz duplicate entries to keep the dense version small. row = np.zeros(nnz, dtype=np.int32) col = np.zeros(nnz, dtype=np.int32) data = np.zeros(nnz, dtype=np.int8) data[-1] = 4 s = coo_matrix((data, (row, col)), shape=(1, 1), copy=False) # Sums nnz duplicates to produce a 1x1 array containing 4. d = s.toarray() assert_allclose(d, [[4]]) @pytest.mark.skipif(not (sys.platform.startswith('linux') and np.dtype(np.intp).itemsize >= 8), reason="test requires 64-bit Linux") class TestInt32Overflow(object): """ Some of the sparsetools routines use dense 2D matrices whose total size is not bounded by the nnz of the sparse matrix. These routines used to suffer from int32 wraparounds; here, we try to check that the wraparounds don't occur any more. """ # choose n large enough n = 50000 def setup_method(self): assert self.n**2 > np.iinfo(np.int32).max # check there's enough memory even if everything is run at the # same time try: parallel_count = int(os.environ.get('PYTEST_XDIST_WORKER_COUNT', '1')) except ValueError: parallel_count = np.inf check_free_memory(3000 * parallel_count) def teardown_method(self): gc.collect() def test_coo_todense(self): # Check *_todense routines (cf. gh-2179) # # All of them in the end call coo_matrix.todense n = self.n i = np.array([0, n-1]) j = np.array([0, n-1]) data = np.array([1, 2], dtype=np.int8) m = coo_matrix((data, (i, j))) r = m.todense() assert_equal(r[0,0], 1) assert_equal(r[-1,-1], 2) del r gc.collect() @pytest.mark.slow def test_matvecs(self): # Check *_matvecs routines n = self.n i = np.array([0, n-1]) j = np.array([0, n-1]) data = np.array([1, 2], dtype=np.int8) m = coo_matrix((data, (i, j))) b = np.ones((n, n), dtype=np.int8) for sptype in (csr_matrix, csc_matrix, bsr_matrix): m2 = sptype(m) r = m2.dot(b) assert_equal(r[0,0], 1) assert_equal(r[-1,-1], 2) del r gc.collect() del b gc.collect() @pytest.mark.slow def test_dia_matvec(self): # Check: huge dia_matrix _matvec n = self.n data = np.ones((n, n), dtype=np.int8) offsets = np.arange(n) m = dia_matrix((data, offsets), shape=(n, n)) v = np.ones(m.shape[1], dtype=np.int8) r = m.dot(v) assert_equal(r[0], np.int8(n)) del data, offsets, m, v, r gc.collect() _bsr_ops = [pytest.param("matmat", marks=pytest.mark.xslow), pytest.param("matvecs", marks=pytest.mark.xslow), "matvec", "diagonal", "sort_indices", pytest.param("transpose", marks=pytest.mark.xslow)] @pytest.mark.slow @pytest.mark.parametrize("op", _bsr_ops) def test_bsr_1_block(self, op): # Check: huge bsr_matrix (1-block) # # The point here is that indices inside a block may overflow. def get_matrix(): n = self.n data = np.ones((1, n, n), dtype=np.int8) indptr = np.array([0, 1], dtype=np.int32) indices = np.array([0], dtype=np.int32) m = bsr_matrix((data, indices, indptr), blocksize=(n, n), copy=False) del data, indptr, indices return m gc.collect() try: getattr(self, "_check_bsr_" + op)(get_matrix) finally: gc.collect() @pytest.mark.slow @pytest.mark.parametrize("op", _bsr_ops) def test_bsr_n_block(self, op): # Check: huge bsr_matrix (n-block) # # The point here is that while indices within a block don't # overflow, accumulators across many block may. def get_matrix(): n = self.n data = np.ones((n, n, 1), dtype=np.int8) indptr = np.array([0, n], dtype=np.int32) indices = np.arange(n, dtype=np.int32) m = bsr_matrix((data, indices, indptr), blocksize=(n, 1), copy=False) del data, indptr, indices return m gc.collect() try: getattr(self, "_check_bsr_" + op)(get_matrix) finally: gc.collect() def _check_bsr_matvecs(self, m): m = m() n = self.n # _matvecs r = m.dot(np.ones((n, 2), dtype=np.int8)) assert_equal(r[0,0], np.int8(n)) def _check_bsr_matvec(self, m): m = m() n = self.n # _matvec r = m.dot(np.ones((n,), dtype=np.int8)) assert_equal(r[0], np.int8(n)) def _check_bsr_diagonal(self, m): m = m() n = self.n # _diagonal r = m.diagonal() assert_equal(r, np.ones(n)) def _check_bsr_sort_indices(self, m): # _sort_indices m = m() m.sort_indices() def _check_bsr_transpose(self, m): # _transpose m = m() m.transpose() def _check_bsr_matmat(self, m): m = m() n = self.n # _bsr_matmat m2 = bsr_matrix(np.ones((n, 2), dtype=np.int8), blocksize=(m.blocksize[1], 2)) m.dot(m2) # shouldn't SIGSEGV del m2 # _bsr_matmat m2 = bsr_matrix(np.ones((2, n), dtype=np.int8), blocksize=(2, m.blocksize[0])) m2.dot(m) # shouldn't SIGSEGV @pytest.mark.skip(reason="64-bit indices in sparse matrices not available") def test_csr_matmat_int64_overflow(): n = 3037000500 assert n**2 > np.iinfo(np.int64).max # the test would take crazy amounts of memory check_free_memory(n * (8*2 + 1) * 3 / 1e6) # int64 overflow data = np.ones((n,), dtype=np.int8) indptr = np.arange(n+1, dtype=np.int64) indices = np.zeros(n, dtype=np.int64) a = csr_matrix((data, indices, indptr)) b = a.T assert_raises(RuntimeError, a.dot, b) def test_upcast(): a0 = csr_matrix([[np.pi, np.pi*1j], [3, 4]], dtype=complex) b0 = np.array([256+1j, 2**32], dtype=complex) for a_dtype in supported_dtypes: for b_dtype in supported_dtypes: msg = "(%r, %r)" % (a_dtype, b_dtype) if np.issubdtype(a_dtype, np.complexfloating): a = a0.copy().astype(a_dtype) else: a = a0.real.copy().astype(a_dtype) if np.issubdtype(b_dtype, np.complexfloating): b = b0.copy().astype(b_dtype) else: b = b0.real.copy().astype(b_dtype) if not (a_dtype == np.bool_ and b_dtype == np.bool_): c = np.zeros((2,), dtype=np.bool_) assert_raises(ValueError, _sparsetools.csr_matvec, 2, 2, a.indptr, a.indices, a.data, b, c) if ((np.issubdtype(a_dtype, np.complexfloating) and not np.issubdtype(b_dtype, np.complexfloating)) or (not np.issubdtype(a_dtype, np.complexfloating) and np.issubdtype(b_dtype, np.complexfloating))): c = np.zeros((2,), dtype=np.float64) assert_raises(ValueError, _sparsetools.csr_matvec, 2, 2, a.indptr, a.indices, a.data, b, c) c = np.zeros((2,), dtype=np.result_type(a_dtype, b_dtype)) _sparsetools.csr_matvec(2, 2, a.indptr, a.indices, a.data, b, c) assert_allclose(c, np.dot(a.toarray(), b), err_msg=msg) def test_endianness(): d = np.ones((3,4)) offsets = [-1,0,1] a = dia_matrix((d.astype('f8'), offsets), (4, 4)) v = np.arange(4) assert_allclose(a.dot(v), [1, 3, 6, 5]) assert_allclose(b.dot(v), [1, 3, 6, 5])