BUG: tighten alignment for complex types. by cournape · Pull Request #5365 · numpy/numpy

cournape · 2014-12-11T11:54:22Z

Complex types memory representations in C for a given type are guaranteed to be equivalent to type[2]. As such, the alignment of complex<type> should be the same as type.

I tested scipy 0.14.x (at scipy/scipy@d6c3206, containing the f2py workaround) in the following setups:

numpy 1.9.1, w/ this patch

one genuine error (all platforms). Unlikely to be related to numpy.

[192.168.33.13] out: ======================================================================
[192.168.33.13] out: ERROR: test_antiderivative_of_constant (test_interpolate.TestPPoly)
[192.168.33.13] out: ----------------------------------------------------------------------
[192.168.33.13] out: Traceback (most recent call last):
[192.168.33.13] out:   File "/home/vagrant/src/master-env/lib/python2.7/site-packages/scipy/interpolate/tests/test_interpolate.py", line 659, in test_antiderivative_of_constant
[192.168.33.13] out:     assert_equal(p.antiderivative().c, PPoly([[1], [0]], [0, 1]).c)
[192.168.33.13] out:   File "/home/vagrant/src/master-env/lib/python2.7/site-packages/scipy/interpolate/interpolate.py", line 821, in antiderivative
[192.168.33.13] out:     self.x, nu)
[192.168.33.13] out:   File "_ppoly.pyx", line 142, in scipy.interpolate._ppoly.fix_continuity (scipy/interpolate/_ppoly.c:5462)
[192.168.33.13] out: ValueError: order too large

a few minor precision issues that have been here for a while otherwise.

numpy 1.9.1, w/o this patch

Same results as above for rh5 and osx and windows 64 bits, but a dozen new errors for windows 32 bits:

[172.17.5.102] err: ======================================================================
[172.17.5.102] err: FAIL: test_x_and_y_stride (test_fblas.TestZaxpy)
[172.17.5.102] err: ----------------------------------------------------------------------
[172.17.5.102] err: Traceback (most recent call last):
[172.17.5.102] err:   File "C:\Users\vagrant\src\master-env\lib\site-packages\scipy\lib\blas\tests\test_fblas.py", line 85, in test_x_and_y_stride
[172.17.5.102] err:     assert_array_almost_equal(real_y,y[::2])
[172.17.5.102] err:   File "C:\Users\vagrant\src\master-env\lib\site-packages\numpy\testing\utils.py", line 842, in assert_array_almost_equal
[172.17.5.102] err:     precision=decimal)
[172.17.5.102] err:   File "C:\Users\vagrant\src\master-env\lib\site-packages\numpy\testing\utils.py", line 665, in assert_array_compare
[172.17.5.102] err:     raise AssertionError(msg)
[172.17.5.102] err: AssertionError:
[172.17.5.102] err: Arrays are not almost equal to 6 decimals
[172.17.5.102] err: 
[172.17.5.102] err: (mismatch 66.6666666667%)
[172.17.5.102] err:  x: array([  0.+0.j,  12.+0.j,  24.+0.j])
[172.17.5.102] err:  y: array([ 0.+0.j,  0.+0.j,  0.+0.j])
[172.17.5.102] err: 
[172.17.5.102] err: ======================================================================
[172.17.5.102] err: FAIL: test_x_stride (test_fblas.TestZaxpy)
[172.17.5.102] err: ----------------------------------------------------------------------
[172.17.5.102] err: Traceback (most recent call last):
[172.17.5.102] err:   File "C:\Users\vagrant\src\master-env\lib\site-packages\scipy\lib\blas\tests\test_fblas.py", line 71, in test_x_stride
[172.17.5.102] err:     assert_array_almost_equal(real_y,y)
[172.17.5.102] err:   File "C:\Users\vagrant\src\master-env\lib\site-packages\numpy\testing\utils.py", line 842, in assert_array_almost_equal
[172.17.5.102] err:     precision=decimal)
[172.17.5.102] err:   File "C:\Users\vagrant\src\master-env\lib\site-packages\numpy\testing\utils.py", line 665, in assert_array_compare
[172.17.5.102] err:     raise AssertionError(msg)
[172.17.5.102] err: AssertionError:
[172.17.5.102] err: Arrays are not almost equal to 6 decimals
[172.17.5.102] err: 
[172.17.5.102] err: (mismatch 66.6666666667%)
[172.17.5.102] err:  x: array([  0.+0.j,   7.+0.j,  14.+0.j])
[172.17.5.102] err:  y: array([ 0.+0.j,  1.+0.j,  2.+0.j])
[172.17.5.102] err: 
[172.17.5.102] err: ======================================================================
[172.17.5.102] err: FAIL: test_y_stride (test_fblas.TestZaxpy)
[172.17.5.102] err: ----------------------------------------------------------------------
[172.17.5.102] err: Traceback (most recent call last):
[172.17.5.102] err:   File "C:\Users\vagrant\src\master-env\lib\site-packages\scipy\lib\blas\tests\test_fblas.py", line 78, in test_y_stride
[172.17.5.102] err:     assert_array_almost_equal(real_y,y[::2])
[172.17.5.102] err:   File "C:\Users\vagrant\src\master-env\lib\site-packages\numpy\testing\utils.py", line 842, in assert_array_almost_equal
[172.17.5.102] err:     precision=decimal)
[172.17.5.102] err:   File "C:\Users\vagrant\src\master-env\lib\site-packages\numpy\testing\utils.py", line 665, in assert_array_compare
[172.17.5.102] err:     raise AssertionError(msg)
[172.17.5.102] err: AssertionError:
[172.17.5.102] err: Arrays are not almost equal to 6 decimals
[172.17.5.102] err: 
[172.17.5.102] err: (mismatch 66.6666666667%)
[172.17.5.102] err:  x: array([ 0.+0.j,  3.+0.j,  6.+0.j])
[172.17.5.102] err:  y: array([ 0.+0.j,  0.+0.j,  0.+0.j])
[172.17.5.102] err: 
[172.17.5.102] err: ======================================================================
[172.17.5.102] err: FAIL: test_x_and_y_stride (test_fblas.TestZcopy)
[172.17.5.102] err: ----------------------------------------------------------------------
[172.17.5.102] err: Traceback (most recent call last):
[172.17.5.102] err:   File "C:\Users\vagrant\src\master-env\lib\site-packages\scipy\lib\blas\tests\test_fblas.py", line 219, in test_x_and_y_stride
[172.17.5.102] err:     assert_array_almost_equal(x[::4],y[::2])
[172.17.5.102] err:   File "C:\Users\vagrant\src\master-env\lib\site-packages\numpy\testing\utils.py", line 842, in assert_array_almost_equal
[172.17.5.102] err:     precision=decimal)
[172.17.5.102] err:   File "C:\Users\vagrant\src\master-env\lib\site-packages\numpy\testing\utils.py", line 665, in assert_array_compare
[172.17.5.102] err:     raise AssertionError(msg)
[172.17.5.102] err: AssertionError:
[172.17.5.102] err: Arrays are not almost equal to 6 decimals
[172.17.5.102] err: 
[172.17.5.102] err: (mismatch 66.6666666667%)
[172.17.5.102] err:  x: array([ 0.+0.j,  4.+0.j,  8.+0.j])
[172.17.5.102] err:  y: array([ 0.+0.j,  0.+0.j,  0.+0.j])
[172.17.5.102] err: 
[172.17.5.102] err: ======================================================================
[172.17.5.102] err: FAIL: test_y_stride (test_fblas.TestZcopy)
[172.17.5.102] err: ----------------------------------------------------------------------
[172.17.5.102] err: Traceback (most recent call last):
[172.17.5.102] err:   File "C:\Users\vagrant\src\master-env\lib\site-packages\scipy\lib\blas\tests\test_fblas.py", line 213, in test_y_stride
[172.17.5.102] err:     assert_array_almost_equal(x,y[::2])
[172.17.5.102] err:   File "C:\Users\vagrant\src\master-env\lib\site-packages\numpy\testing\utils.py", line 842, in assert_array_almost_equal
[172.17.5.102] err:     precision=decimal)
[172.17.5.102] err:   File "C:\Users\vagrant\src\master-env\lib\site-packages\numpy\testing\utils.py", line 665, in assert_array_compare
[172.17.5.102] err:     raise AssertionError(msg)
[172.17.5.102] err: AssertionError:
[172.17.5.102] err: Arrays are not almost equal to 6 decimals
[172.17.5.102] err: 
[172.17.5.102] err: (mismatch 66.6666666667%)
[172.17.5.102] err:  x: array([ 0.+0.j,  1.+0.j,  2.+0.j])
[172.17.5.102] err:  y: array([ 0.+0.j,  0.+0.j,  0.+0.j])
[172.17.5.102] err: 
[172.17.5.102] err: ======================================================================
[172.17.5.102] err: FAIL: test_simple (test_fblas.TestZscal)
[172.17.5.102] err: ----------------------------------------------------------------------
[172.17.5.102] err: Traceback (most recent call last):
[172.17.5.102] err:   File "C:\Users\vagrant\src\master-env\lib\site-packages\scipy\lib\blas\tests\test_fblas.py", line 145, in test_simple
[172.17.5.102] err:     assert_array_almost_equal(real_x,x)
[172.17.5.102] err:   File "C:\Users\vagrant\src\master-env\lib\site-packages\numpy\testing\utils.py", line 842, in assert_array_almost_equal
[172.17.5.102] err:     precision=decimal)
[172.17.5.102] err:   File "C:\Users\vagrant\src\master-env\lib\site-packages\numpy\testing\utils.py", line 665, in assert_array_compare
[172.17.5.102] err:     raise AssertionError(msg)
[172.17.5.102] err: AssertionError:
[172.17.5.102] err: Arrays are not almost equal to 6 decimals
[172.17.5.102] err: 
[172.17.5.102] err: (mismatch 66.6666666667%)
[172.17.5.102] err:  x: array([ 0.+0.j,  3.+0.j,  6.+0.j])
[172.17.5.102] err:  y: array([ 0.+0.j,  1.+0.j,  2.+0.j])
[172.17.5.102] err: 
[172.17.5.102] err: ======================================================================
[172.17.5.102] err: FAIL: test_simple (test_fblas.TestZswap)
[172.17.5.102] err: ----------------------------------------------------------------------
[172.17.5.102] err: Traceback (most recent call last):
[172.17.5.102] err:   File "C:\Users\vagrant\src\master-env\lib\site-packages\scipy\lib\blas\tests\test_fblas.py", line 288, in test_simple
[172.17.5.102] err:     assert_array_almost_equal(desired_x,x)
[172.17.5.102] err:   File "C:\Users\vagrant\src\master-env\lib\site-packages\numpy\testing\utils.py", line 842, in assert_array_almost_equal
[172.17.5.102] err:     precision=decimal)
[172.17.5.102] err:   File "C:\Users\vagrant\src\master-env\lib\site-packages\numpy\testing\utils.py", line 665, in assert_array_compare
[172.17.5.102] err:     raise AssertionError(msg)
[172.17.5.102] err: AssertionError:
[172.17.5.102] err: Arrays are not almost equal to 6 decimals
[172.17.5.102] err: 
[172.17.5.102] err: (mismatch 66.6666666667%)
[172.17.5.102] err:  x: array([ 0.+0.j,  0.+0.j,  0.+0.j])
[172.17.5.102] err:  y: array([ 0.+0.j,  1.+0.j,  2.+0.j])
[172.17.5.102] err: 
[172.17.5.102] err: ======================================================================
[172.17.5.102] err: FAIL: test_x_and_y_stride (test_fblas.TestZswap)
[172.17.5.102] err: ----------------------------------------------------------------------
[172.17.5.102] err: Traceback (most recent call last):
[172.17.5.102] err:   File "C:\Users\vagrant\src\master-env\lib\site-packages\scipy\lib\blas\tests\test_fblas.py", line 315, in test_x_and_y_stride
[172.17.5.102] err:     assert_array_almost_equal(desired_x,x[::4])
[172.17.5.102] err:   File "C:\Users\vagrant\src\master-env\lib\site-packages\numpy\testing\utils.py", line 842, in assert_array_almost_equal
[172.17.5.102] err:     precision=decimal)
[172.17.5.102] err:   File "C:\Users\vagrant\src\master-env\lib\site-packages\numpy\testing\utils.py", line 665, in assert_array_compare
[172.17.5.102] err:     raise AssertionError(msg)
[172.17.5.102] err: AssertionError:
[172.17.5.102] err: Arrays are not almost equal to 6 decimals
[172.17.5.102] err: 
[172.17.5.102] err: (mismatch 66.6666666667%)
[172.17.5.102] err:  x: array([ 0.+0.j,  0.+0.j,  0.+0.j])
[172.17.5.102] err:  y: array([ 0.+0.j,  4.+0.j,  8.+0.j])
[172.17.5.102] err: 
[172.17.5.102] err: ======================================================================
[172.17.5.102] err: FAIL: test_x_stride (test_fblas.TestZswap)
[172.17.5.102] err: ----------------------------------------------------------------------
[172.17.5.102] err: Traceback (most recent call last):
[172.17.5.102] err:   File "C:\Users\vagrant\src\master-env\lib\site-packages\scipy\lib\blas\tests\test_fblas.py", line 297, in test_x_stride
[172.17.5.102] err:     assert_array_almost_equal(desired_x,x[::2])
[172.17.5.102] err:   File "C:\Users\vagrant\src\master-env\lib\site-packages\numpy\testing\utils.py", line 842, in assert_array_almost_equal
[172.17.5.102] err:     precision=decimal)
[172.17.5.102] err:   File "C:\Users\vagrant\src\master-env\lib\site-packages\numpy\testing\utils.py", line 665, in assert_array_compare
[172.17.5.102] err:     raise AssertionError(msg)
[172.17.5.102] err: AssertionError:
[172.17.5.102] err: Arrays are not almost equal to 6 decimals
[172.17.5.102] err: 
[172.17.5.102] err: (mismatch 66.6666666667%)
[172.17.5.102] err:  x: array([ 0.+0.j,  0.+0.j,  0.+0.j])
[172.17.5.102] err:  y: array([ 0.+0.j,  2.+0.j,  4.+0.j])
[172.17.5.102] err: 
[172.17.5.102] err: ======================================================================
[172.17.5.102] err: FAIL: test_y_stride (test_fblas.TestZswap)
[172.17.5.102] err: ----------------------------------------------------------------------
[172.17.5.102] err: Traceback (most recent call last):
[172.17.5.102] err:   File "C:\Users\vagrant\src\master-env\lib\site-packages\scipy\lib\blas\tests\test_fblas.py", line 307, in test_y_stride
[172.17.5.102] err:     assert_array_almost_equal(desired_y,y[::2])
[172.17.5.102] err:   File "C:\Users\vagrant\src\master-env\lib\site-packages\numpy\testing\utils.py", line 842, in assert_array_almost_equal
[172.17.5.102] err:     precision=decimal)
[172.17.5.102] err:   File "C:\Users\vagrant\src\master-env\lib\site-packages\numpy\testing\utils.py", line 665, in assert_array_compare
[172.17.5.102] err:     raise AssertionError(msg)
[172.17.5.102] err: AssertionError:
[172.17.5.102] err: Arrays are not almost equal to 6 decimals
[172.17.5.102] err: 
[172.17.5.102] err: (mismatch 66.6666666667%)
[172.17.5.102] err:  x: array([ 0.+0.j,  1.+0.j,  2.+0.j])
[172.17.5.102] err:  y: array([ 0.+0.j,  0.+0.j,  0.+0.j])
[172.17.5.102] err: 
[172.17.5.102] err: ======================================================================
[172.17.5.102] err: FAIL: test_x_and_y_stride (test_fblas.TestZaxpy)
[172.17.5.102] err: ----------------------------------------------------------------------
[172.17.5.102] err: Traceback (most recent call last):
[172.17.5.102] err:   File "C:\Users\vagrant\src\master-env\lib\site-packages\scipy\linalg\tests\test_fblas.py", line 87, in test_x_and_y_stride
[172.17.5.102] err:     assert_array_equal(real_y,y[::2])
[172.17.5.102] err:   File "C:\Users\vagrant\src\master-env\lib\site-packages\numpy\testing\utils.py", line 739, in assert_array_equal
[172.17.5.102] err:     verbose=verbose, header='Arrays are not equal')
[172.17.5.102] err:   File "C:\Users\vagrant\src\master-env\lib\site-packages\numpy\testing\utils.py", line 665, in assert_array_compare
[172.17.5.102] err:     raise AssertionError(msg)
[172.17.5.102] err: AssertionError:
[172.17.5.102] err: Arrays are not equal
[172.17.5.102] err: 
[172.17.5.102] err: (mismatch 66.6666666667%)
[172.17.5.102] err:  x: array([  0.+0.j,  12.+0.j,  24.+0.j])
[172.17.5.102] err:  y: array([ 0.+0.j,  0.+0.j,  0.+0.j])
[172.17.5.102] err: 
[172.17.5.102] err: ======================================================================
[172.17.5.102] err: FAIL: test_y_stride (test_fblas.TestZaxpy)
[172.17.5.102] err: ----------------------------------------------------------------------
[172.17.5.102] err: Traceback (most recent call last):
[172.17.5.102] err:   File "C:\Users\vagrant\src\master-env\lib\site-packages\scipy\linalg\tests\test_fblas.py", line 80, in test_y_stride
[172.17.5.102] err:     assert_array_equal(real_y,y[::2])
[172.17.5.102] err:   File "C:\Users\vagrant\src\master-env\lib\site-packages\numpy\testing\utils.py", line 739, in assert_array_equal
[172.17.5.102] err:     verbose=verbose, header='Arrays are not equal')
[172.17.5.102] err:   File "C:\Users\vagrant\src\master-env\lib\site-packages\numpy\testing\utils.py", line 665, in assert_array_compare
[172.17.5.102] err:     raise AssertionError(msg)
[172.17.5.102] err: AssertionError:
[172.17.5.102] err: Arrays are not equal
[172.17.5.102] err: 
[172.17.5.102] err: (mismatch 66.6666666667%)
[172.17.5.102] err:  x: array([ 0.+0.j,  3.+0.j,  6.+0.j])
[172.17.5.102] err:  y: array([ 0.+0.j,  0.+0.j,  0.+0.j])
[172.17.5.102] err: 
[172.17.5.102] err: ======================================================================
[172.17.5.102] err: FAIL: test_x_and_y_stride (test_fblas.TestZcopy)
[172.17.5.102] err: ----------------------------------------------------------------------
[172.17.5.102] err: Traceback (most recent call last):
[172.17.5.102] err:   File "C:\Users\vagrant\src\master-env\lib\site-packages\scipy\linalg\tests\test_fblas.py", line 219, in test_x_and_y_stride
[172.17.5.102] err:     assert_array_equal(x[::4],y[::2])
[172.17.5.102] err:   File "C:\Users\vagrant\src\master-env\lib\site-packages\numpy\testing\utils.py", line 739, in assert_array_equal
[172.17.5.102] err:     verbose=verbose, header='Arrays are not equal')
[172.17.5.102] err:   File "C:\Users\vagrant\src\master-env\lib\site-packages\numpy\testing\utils.py", line 665, in assert_array_compare
[172.17.5.102] err:     raise AssertionError(msg)
[172.17.5.102] err: AssertionError:
[172.17.5.102] err: Arrays are not equal
[172.17.5.102] err: 
[172.17.5.102] err: (mismatch 66.6666666667%)
[172.17.5.102] err:  x: array([ 0.+0.j,  4.+0.j,  8.+0.j])
[172.17.5.102] err:  y: array([ 0.+0.j,  0.+0.j,  0.+0.j])
[172.17.5.102] err: 
[172.17.5.102] err: ======================================================================
[172.17.5.102] err: FAIL: test_y_stride (test_fblas.TestZcopy)
[172.17.5.102] err: ----------------------------------------------------------------------
[172.17.5.102] err: Traceback (most recent call last):
[172.17.5.102] err:   File "C:\Users\vagrant\src\master-env\lib\site-packages\scipy\linalg\tests\test_fblas.py", line 213, in test_y_stride
[172.17.5.102] err:     assert_array_equal(x,y[::2])
[172.17.5.102] err:   File "C:\Users\vagrant\src\master-env\lib\site-packages\numpy\testing\utils.py", line 739, in assert_array_equal
[172.17.5.102] err:     verbose=verbose, header='Arrays are not equal')
[172.17.5.102] err:   File "C:\Users\vagrant\src\master-env\lib\site-packages\numpy\testing\utils.py", line 665, in assert_array_compare
[172.17.5.102] err:     raise AssertionError(msg)
[172.17.5.102] err: AssertionError:
[172.17.5.102] err: Arrays are not equal
[172.17.5.102] err: 
[172.17.5.102] err: (mismatch 66.6666666667%)
[172.17.5.102] err:  x: array([ 0.+0.j,  1.+0.j,  2.+0.j])
[172.17.5.102] err:  y: array([ 0.+0.j,  0.+0.j,  0.+0.j])
[172.17.5.102] err: 
[172.17.5.102] err: ======================================================================
[172.17.5.102] err: FAIL: test_simple (test_fblas.TestZscal)
[172.17.5.102] err: ----------------------------------------------------------------------
[172.17.5.102] err: Traceback (most recent call last):
[172.17.5.102] err:   File "C:\Users\vagrant\src\master-env\lib\site-packages\scipy\linalg\tests\test_fblas.py", line 146, in test_simple
[172.17.5.102] err:     assert_array_equal(real_x,x)
[172.17.5.102] err:   File "C:\Users\vagrant\src\master-env\lib\site-packages\numpy\testing\utils.py", line 739, in assert_array_equal
[172.17.5.102] err:     verbose=verbose, header='Arrays are not equal')
[172.17.5.102] err:   File "C:\Users\vagrant\src\master-env\lib\site-packages\numpy\testing\utils.py", line 665, in assert_array_compare
[172.17.5.102] err:     raise AssertionError(msg)
[172.17.5.102] err: AssertionError:
[172.17.5.102] err: Arrays are not equal
[172.17.5.102] err: 
[172.17.5.102] err: (mismatch 66.6666666667%)
[172.17.5.102] err:  x: array([ 0.+0.j,  3.+0.j,  6.+0.j])
[172.17.5.102] err:  y: array([ 0.+0.j,  1.+0.j,  2.+0.j])
[172.17.5.102] err: 
[172.17.5.102] err: ======================================================================
[172.17.5.102] err: FAIL: test_simple (test_fblas.TestZswap)
[172.17.5.102] err: ----------------------------------------------------------------------
[172.17.5.102] err: Traceback (most recent call last):
[172.17.5.102] err:   File "C:\Users\vagrant\src\master-env\lib\site-packages\scipy\linalg\tests\test_fblas.py", line 287, in test_simple
[172.17.5.102] err:     assert_array_equal(desired_x,x)
[172.17.5.102] err:   File "C:\Users\vagrant\src\master-env\lib\site-packages\numpy\testing\utils.py", line 739, in assert_array_equal
[172.17.5.102] err:     verbose=verbose, header='Arrays are not equal')
[172.17.5.102] err:   File "C:\Users\vagrant\src\master-env\lib\site-packages\numpy\testing\utils.py", line 665, in assert_array_compare
[172.17.5.102] err:     raise AssertionError(msg)
[172.17.5.102] err: AssertionError:
[172.17.5.102] err: Arrays are not equal
[172.17.5.102] err: 
[172.17.5.102] err: (mismatch 66.6666666667%)
[172.17.5.102] err:  x: array([ 0.+0.j,  0.+0.j,  0.+0.j])
[172.17.5.102] err:  y: array([ 0.+0.j,  1.+0.j,  2.+0.j])
[172.17.5.102] err: 
[172.17.5.102] err: ======================================================================
[172.17.5.102] err: FAIL: test_x_and_y_stride (test_fblas.TestZswap)
[172.17.5.102] err: ----------------------------------------------------------------------
[172.17.5.102] err: Traceback (most recent call last):
[172.17.5.102] err:   File "C:\Users\vagrant\src\master-env\lib\site-packages\scipy\linalg\tests\test_fblas.py", line 314, in test_x_and_y_stride
[172.17.5.102] err:     assert_array_equal(desired_x,x[::4])
[172.17.5.102] err:   File "C:\Users\vagrant\src\master-env\lib\site-packages\numpy\testing\utils.py", line 739, in assert_array_equal
[172.17.5.102] err:     verbose=verbose, header='Arrays are not equal')
[172.17.5.102] err:   File "C:\Users\vagrant\src\master-env\lib\site-packages\numpy\testing\utils.py", line 665, in assert_array_compare
[172.17.5.102] err:     raise AssertionError(msg)
[172.17.5.102] err: AssertionError:
[172.17.5.102] err: Arrays are not equal
[172.17.5.102] err: 
[172.17.5.102] err: (mismatch 66.6666666667%)
[172.17.5.102] err:  x: array([ 0.+0.j,  0.+0.j,  0.+0.j])
[172.17.5.102] err:  y: array([ 0.+0.j,  4.+0.j,  8.+0.j])
[172.17.5.102] err: 
[172.17.5.102] err: ======================================================================
[172.17.5.102] err: FAIL: test_x_stride (test_fblas.TestZswap)
[172.17.5.102] err: ----------------------------------------------------------------------
[172.17.5.102] err: Traceback (most recent call last):
[172.17.5.102] err:   File "C:\Users\vagrant\src\master-env\lib\site-packages\scipy\linalg\tests\test_fblas.py", line 297, in test_x_stride
[172.17.5.102] err:     assert_array_equal(desired_y,y)
[172.17.5.102] err:   File "C:\Users\vagrant\src\master-env\lib\site-packages\numpy\testing\utils.py", line 739, in assert_array_equal
[172.17.5.102] err:     verbose=verbose, header='Arrays are not equal')
[172.17.5.102] err:   File "C:\Users\vagrant\src\master-env\lib\site-packages\numpy\testing\utils.py", line 665, in assert_array_compare
[172.17.5.102] err:     raise AssertionError(msg)
[172.17.5.102] err: AssertionError:
[172.17.5.102] err: Arrays are not equal
[172.17.5.102] err: 
[172.17.5.102] err: (mismatch 66.6666666667%)
[172.17.5.102] err:  x: array([ 0.+0.j,  2.+0.j,  4.+0.j])
[172.17.5.102] err:  y: array([ 0.+0.j,  0.+0.j,  0.+0.j])
[172.17.5.102] err: 
[172.17.5.102] err: ======================================================================
[172.17.5.102] err: FAIL: test_y_stride (test_fblas.TestZswap)
[172.17.5.102] err: ----------------------------------------------------------------------
[172.17.5.102] err: Traceback (most recent call last):
[172.17.5.102] err:   File "C:\Users\vagrant\src\master-env\lib\site-packages\scipy\linalg\tests\test_fblas.py", line 305, in test_y_stride
[172.17.5.102] err:     assert_array_equal(desired_x,x)
[172.17.5.102] err:   File "C:\Users\vagrant\src\master-env\lib\site-packages\numpy\testing\utils.py", line 739, in assert_array_equal
[172.17.5.102] err:     verbose=verbose, header='Arrays are not equal')
[172.17.5.102] err:   File "C:\Users\vagrant\src\master-env\lib\site-packages\numpy\testing\utils.py", line 665, in assert_array_compare
[172.17.5.102] err:     raise AssertionError(msg)
[172.17.5.102] err: AssertionError:
[172.17.5.102] err: Arrays are not equal
[172.17.5.102] err: 
[172.17.5.102] err: (mismatch 66.6666666667%)
[172.17.5.102] err:  x: array([ 0.+0.j,  0.+0.j,  0.+0.j])
[172.17.5.102] err:  y: array([ 0.+0.j,  1.+0.j,  2.+0.j])
[172.17.5.102] err:

Complex types memory representations in C are guaranteed to be equivalent to type[2]. As such, the alignment of complex<type> should be the same as type.

juliantaylor · 2014-12-11T17:54:28Z

test failure is real, should be the same you see on sparc

juliantaylor · 2014-12-11T18:23:07Z

confirmed the bus error on sparc with this patch,, see I told you I tried this :)
that said that this crashes even though the alignment should be sufficient is an issue in numpy, a fix for that would be great.

pv · 2014-12-11T19:47:24Z

The real problem apparently is that the logic in the loop selection in
lowlevel_strided_loops.c.src:PyArray_GetStridedCopyFn is correct only
if the alignment is the same as for the integer type of the same itemsize.
.
In particular, complex64 on gcc/linux/x86_64 has alignment 4 and
itemsize 8. The loop selector sees the array is aligned and selects
itemsize-8 loop. However, the itemsize-8 loop itself assumes the data
is aligned according to uint64 -> boom. (On x86 this doesn't matter,
apart from the asserts.)

juliantaylor · 2014-12-11T19:49:35Z

yes thats why I introduced the copy alignment variable to account for this, one could also add special complex code or only use copy alignment for copy operations.

pv · 2014-12-11T19:54:00Z

Yes, the problem is that PyArray_ISALIGNED has nothing to do with the alignment that the copy loops want to know about. Nevertheless, PyArray_ISALIGNED is used to in ndarray_constr.c to decide this. I'll try to see if this it's easy to come up with a patch...

pv · 2014-12-11T21:18:34Z

I won't finish it today (or tomorrow), but the suggested fix would be to restore descr->alignment to be the alignment given by the C compiler --- this is a public API in numpy, and this is how it used to be. Then, add an internal function PyArray_DescrGetCopyAlignment(desrc) that returns the appropriate alignment for the copy loops, and use that in all code paths that end up choosing copy loops. There are a number of them, and various variants of alignment checks are littered here and there, so there's some cleanup to do. (There are also some FIXMEs there along these lines :)

juliantaylor · 2014-12-11T21:22:26Z

do we really care that a complex float32 from 8 byte unaligned memory is not flagged as 4 byte aligned?
if not my other pr is somewhat simpler

charris · 2014-12-11T21:27:00Z

I haven't worked on this so my opinion might be totally irrelevant, but if I understand correctly, it makes sense to distinguish the types of alignment if one is specific to the needs of copying.

njsmith · 2014-12-11T21:42:30Z

"do we really care that a complex float32 from unaligned memory is not
flagged as aligned?" -- maybe I'm just not the audience for this question,
but FWIW I have no idea what you're asking :-)

Do I have it right that basically what the strided copy loop code should be
doing is, if (ptr % itemsize) == (stride % itemsize) == 0 then we use the
aligned loop, and otherwise we use the unaligned one?
On 11 Dec 2014 21:22, "Julian Taylor" [email protected] wrote:

do we really care that a complex float32 from unaligned memory is not
flagged as aligned?
if not my other pr is somewhat simpler

—
Reply to this email directly or view it on GitHub
#5365 (comment).

pv · 2014-12-11T21:43:56Z

The strided copy loop should be doing if (ptr % _ALIGN(@copytype@)) == 0 && (stride % _ALIGN(@copytype@)) == 0) where @copytype@ is uint8, uint16, uint32, uint64 and is chosen based on itemsize. Currently, it assumes this check is equivalent to checking the dtype alignment.

pv · 2014-12-11T22:08:53Z

@cournape: did you also test with Numpy 1.8.x? What I don't understand right now is that the complex alignment was doubled already in Numpy 1.8 (c9bf9b0), so one would expect to see f2py issues also there?

juliantaylor · 2014-12-11T22:09:51Z

1.8 didn't actually check the alignment, everything was aligned

pv · 2014-12-11T22:25:55Z

@juliantaylor: do you mean flags.aligned == True on all newly allocated arrays? Or just the thing of adding alignment checks to the transfer loops?

juliantaylor · 2014-12-11T22:28:18Z

the former, but also for arrays which where created by passing the constructor a pointer

cournape · 2014-12-11T23:31:59Z

@pv for numpy 1.8.1 on win-32, I had np.dtype("D").alignment == 8 true.

rgommers · 2014-12-22T20:35:16Z

@cournape test failure for Bento build

charris · 2015-01-19T19:52:33Z

Closing this. For 1.9.2 will backport #5316, and for 1.10.0 another fix is pending.

BUG: tighten alignment for complex types.

9fdcc60

Complex types memory representations in C are guaranteed to be equivalent to type[2]. As such, the alignment of complex<type> should be the same as type.

cournape mentioned this pull request Dec 11, 2014

BUG: sparse: work around alignment issue in f2py in Numpy 1.9.1 scipy/scipy#4241

Merged

pv mentioned this pull request Dec 14, 2014

Lots of arpack test failures on windows 32 bits with numpy 1.9.1 scipy/scipy#4168

Closed

ewmoore mentioned this pull request Jan 16, 2015

FAIL: test_syr_her (test_blas.TestFBLAS2Simple) on Windows python2.7.9 32 bit scipy0.15.0 numpy0.19.1 scipy/scipy#4410

Closed

charris mentioned this pull request Jan 19, 2015

fix 1.9 alignment issues #5316

Merged

charris closed this Jan 19, 2015

This was referenced Sep 26, 2015

Fix alignment issue for 1.10 #5656

Closed

BUG: define "uint-alignment", fixes complex64 alignment #6377

Merged

Conversation

cournape commented Dec 11, 2014

numpy 1.9.1, w/ this patch

numpy 1.9.1, w/o this patch

Uh oh!

juliantaylor commented Dec 11, 2014

Uh oh!

juliantaylor commented Dec 11, 2014

Uh oh!

pv commented Dec 11, 2014

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juliantaylor commented Dec 11, 2014

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pv commented Dec 11, 2014

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pv commented Dec 11, 2014

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juliantaylor commented Dec 11, 2014

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charris commented Dec 11, 2014

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njsmith commented Dec 11, 2014

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pv commented Dec 11, 2014

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pv commented Dec 11, 2014

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juliantaylor commented Dec 11, 2014

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pv commented Dec 11, 2014

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juliantaylor commented Dec 11, 2014

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cournape commented Dec 11, 2014

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rgommers commented Dec 22, 2014

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charris commented Jan 19, 2015

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