[SciPy-user] problems with scipy.test() on Opteron 64-bit

Giovanni Samaey Giovanni.Samaey at cs.kuleuven.ac.be
Tue Nov 23 04:56:50 CST 2004


Hi again,

after all my trouble (reported above) I finally got a completed scipy build.
I got however errors in scipy.test(), which I presumed to be due to 
incorrect atlas libraries.
So I decided to compile those myself, following the instructions on 
www.scipy.org.

I had to make several modifications; namely adding -fPIC and -m64 as 
options to the make
files for blas and lapack.  (Otherwise, linking failed during scipy build.)

Running scipy.test(), I get the errors that are shown in 
file_atlas.txt.   I decided to give it a try
without atlas (which in my case worked without any difficulty).  I used 
the blas and lapack
routines that were compiled by myself and that are used to build atlas.  
As you will notice,
I get one error and one failure less in this case.

I am using cvs scipy and atlas3.6.0.  Everything is compiled using the 
gnu compilers with the
default options, to which -fPIC and -m64 are added for lapack and blas.
I googled and looked through this mailing list, but did not find 
anything directly applicable.
(If I overlooked it, I already apologize beforehand.)

Best,  Giovanni

-- 
Giovanni Samaey		 	http://www.cs.kuleuven.ac.be/~giovanni/ 
Katholieke Universiteit Leuven 	      email: giovanni at cs.kuleuven.ac.be 
Departement Computerwetenschappen                  phone: +32-16-327081
Celestijnenlaan 200A, B-3001 Heverlee, Belgium       fax: +32-16-327996
Office: A04.36


-------------- next part --------------
======================================================================
ERROR: check_simple_overdet (scipy.linalg.basic.test_basic.test_lstsq)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/data/home/giovanni/lib/python2.3/site-packages/scipy/linalg/tests/test_basic.py", line 361, in check_simple_overdet
    x,res,r,s = lstsq(a,b)
  File "/data/home/giovanni/lib/python2.3/site-packages/scipy/linalg/basic.py", line 353, in lstsq
    if rank==n: resids = sum(x[n:]**2)
ArithmeticError: Integer overflow in power.

======================================================================
ERROR: check_simple_sym (scipy.linalg.basic.test_basic.test_solve)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/data/home/giovanni/lib/python2.3/site-packages/scipy/linalg/tests/test_basic.py", line 80, in check_simple_sym
    x = solve(a,b,sym_pos=1,lower=lower)
  File "/data/home/giovanni/lib/python2.3/site-packages/scipy/linalg/basic.py", line 123, in solve
    raise LinAlgError, "singular matrix"
LinAlgError: singular matrix

======================================================================
FAIL: check_simple (scipy.linalg.decomp.test_decomp.test_cholesky)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/data/home/giovanni/lib/python2.3/site-packages/scipy/linalg/tests/test_decomp.py", line 260, in check_simple
    assert_array_almost_equal(dot(transpose(c),c),a)
  File "/data/home/giovanni/lib/python2.3/site-packages/scipy_test/testing.py", line 727, in assert_array_almost_equal
    assert cond,\
AssertionError:
Arrays are not almost equal (mismatch 100.0%):
        Array 1: [[-1885965976648932823  7796773222197633577  -761725725645001531]
 [ 7796773222197633577 -6619736815450336083  789149371...
        Array 2: [[8 2 3]
 [2 9 3]
 [3 3 6]]


======================================================================
FAIL: check_simple (scipy.linalg.decomp.test_decomp.test_eig)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/data/home/giovanni/lib/python2.3/site-packages/scipy/linalg/tests/test_decomp.py", line 88, in check_simple
    assert_array_almost_equal(w,exact_w)
  File "/data/home/giovanni/lib/python2.3/site-packages/scipy_test/testing.py", line 727, in assert_array_almost_equal
    assert cond,\
AssertionError:
Arrays are not almost equal (mismatch 66.6666666667%):
        Array 1: [ 9.4371906+0.j -0.1153653+0.j -0.3218254+0.j]
        Array 2: [ 9.3218254  0.        -0.3218254]


======================================================================
FAIL: check_simple (scipy.linalg.decomp.test_decomp.test_eigvals)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/data/home/giovanni/lib/python2.3/site-packages/scipy/linalg/tests/test_decomp.py", line 36, in check_simple
    assert_array_almost_equal(w,exact_w)
  File "/data/home/giovanni/lib/python2.3/site-packages/scipy_test/testing.py", line 727, in assert_array_almost_equal
    assert cond,\
AssertionError:
Arrays are not almost equal (mismatch 66.6666666667%):
        Array 1: [ 9.4371906+0.j -0.1153653+0.j -0.3218254+0.j]
        Array 2: [ 9.3218254  0.        -0.3218254]


======================================================================
FAIL: check_simple_tr (scipy.linalg.decomp.test_decomp.test_eigvals)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/data/home/giovanni/lib/python2.3/site-packages/scipy/linalg/tests/test_decomp.py", line 44, in check_simple_tr
    assert_array_almost_equal(w,exact_w)
  File "/data/home/giovanni/lib/python2.3/site-packages/scipy_test/testing.py", line 727, in assert_array_almost_equal
    assert cond,\
AssertionError:
Arrays are not almost equal (mismatch 66.6666666667%):
        Array 1: [ 9.4371906+0.j -0.1153653+0.j -0.3218254+0.j]
        Array 2: [ 9.3218254  0.        -0.3218254]


======================================================================
FAIL: check_simple (scipy.linalg.basic.test_basic.test_det)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/data/home/giovanni/lib/python2.3/site-packages/scipy/linalg/tests/test_basic.py", line 273, in check_simple
    assert_almost_equal(a_det,-2.0)
  File "/data/home/giovanni/lib/python2.3/site-packages/scipy_test/testing.py", line 649, in assert_almost_equal
    assert round(abs(desired - actual),decimal) == 0, msg
AssertionError:
Items are not equal:
DESIRED: -2.0
ACTUAL: -0.0

======================================================================
FAIL: check_simple (scipy.linalg.basic.test_basic.test_inv)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/data/home/giovanni/lib/python2.3/site-packages/scipy/linalg/tests/test_basic.py", line 202, in check_simple
    [[1,0],[0,1]])
  File "/data/home/giovanni/lib/python2.3/site-packages/scipy_test/testing.py", line 727, in assert_array_almost_equal
    assert cond,\
AssertionError:
Arrays are not almost equal (mismatch 100.0%):
        Array 1: [[9216616637413720064   -4503599627370496]
 [9207609438158979072   -9007199254740992]]
        Array 2: [[1 0]
 [0 1]]


======================================================================
FAIL: check_simple_exact (scipy.linalg.basic.test_basic.test_lstsq)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/data/home/giovanni/lib/python2.3/site-packages/scipy/linalg/tests/test_basic.py", line 356, in check_simple_exact
    assert_array_almost_equal(Numeric.matrixmultiply(a,x),b)
  File "/data/home/giovanni/lib/python2.3/site-packages/scipy_test/testing.py", line 727, in assert_array_almost_equal
    assert cond,\
AssertionError:
Arrays are not almost equal (mismatch 50.0%):
        Array 1: [0 0]
        Array 2: [1 0]


======================================================================
FAIL: check_simple (scipy.linalg.basic.test_basic.test_solve)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/data/home/giovanni/lib/python2.3/site-packages/scipy/linalg/tests/test_basic.py", line 74, in check_simple
    assert_array_almost_equal(Numeric.matrixmultiply(a,x),b)
  File "/data/home/giovanni/lib/python2.3/site-packages/scipy_test/testing.py", line 727,
in assert_array_almost_equal
    assert cond,\
AssertionError:
Arrays are not almost equal (mismatch 100.0%):
        Array 1: [[             nan              nan]
 [             nan              nan]]
        Array 2: [[1 0]
 [0 1]]


======================================================================
FAIL: check_matvec (scipy.sparse.Sparse.test_Sparse.test_csc)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/data/home/giovanni/lib/python2.3/site-packages/scipy/sparse/tests/test_Sparse.py", line 66, in check_matvec
    assert_array_almost_equal([1,2,3,4]*b,dot([1,2,3,4],b.todense()))
  File "/data/home/giovanni/lib/python2.3/site-packages/scipy_test/testing.py", line 727,
in assert_array_almost_equal
    assert cond,\
AssertionError:
Arrays are not almost equal (mismatch 100.0%):
        Array 1: [  8.3991160e-323   6.9169190e-323   4.4465908e-323]
        Array 2: [ 17.  14.   9.]


======================================================================
FAIL: check_matvec (scipy.sparse.Sparse.test_Sparse.test_csr)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/data/home/giovanni/lib/python2.3/site-packages/scipy/sparse/tests/test_Sparse.py", line 66, in check_matvec
    assert_array_almost_equal([1,2,3,4]*b,dot([1,2,3,4],b.todense()))
  File "/data/home/giovanni/lib/python2.3/site-packages/scipy_test/testing.py", line 727,
in assert_array_almost_equal
    assert cond,\
AssertionError:
Arrays are not almost equal (mismatch 100.0%):
        Array 1: [  8.3991160e-323   6.9169190e-323   4.4465908e-323]
        Array 2: [ 17.  14.   9.]


======================================================================
FAIL: check_matvec (scipy.sparse.Sparse.test_Sparse.test_dok)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/data/home/giovanni/lib/python2.3/site-packages/scipy/sparse/tests/test_Sparse.py", line 66, in check_matvec
    assert_array_almost_equal([1,2,3,4]*b,dot([1,2,3,4],b.todense()))
  File "/data/home/giovanni/lib/python2.3/site-packages/scipy_test/testing.py", line 727,
in assert_array_almost_equal
    assert cond,\
AssertionError:
Arrays are not almost equal (mismatch 100.0%):
        Array 1: [  8.3991160e-323   6.9169190e-323   4.4465908e-323]
        Array 2: [ 17.  14.   9.]


----------------------------------------------------------------------
Ran 1080 tests in 1.265s

FAILED (failures=11, errors=2)
<unittest.TextTestRunner object at 0x2a9e3be710>
-------------- next part --------------
======================================================================
ERROR: check_simple_overdet (scipy.linalg.basic.test_basic.test_lstsq)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/data/home/giovanni/lib/python2.3/site-packages/scipy/linalg/tests/test_basic.py", line 361, in check_simple_overdet
    x,res,r,s = lstsq(a,b)
  File "/data/home/giovanni/lib/python2.3/site-packages/scipy/linalg/basic.py", line 353, in lstsq
    if rank==n: resids = sum(x[n:]**2)
ArithmeticError: Integer overflow in power.

======================================================================
FAIL: check_simple (scipy.linalg.decomp.test_decomp.test_eig)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/data/home/giovanni/lib/python2.3/site-packages/scipy/linalg/tests/test_decomp.py", line 88, in check_simple
    assert_array_almost_equal(w,exact_w)
  File "/data/home/giovanni/lib/python2.3/site-packages/scipy_test/testing.py", line 727, in assert_array_almost_equal
    assert cond,\
AssertionError:
Arrays are not almost equal (mismatch 66.6666666667%):
        Array 1: [ 9.4371906+0.j -0.1153653+0.j -0.3218254+0.j]
        Array 2: [ 9.3218254  0.        -0.3218254]


======================================================================
FAIL: check_simple (scipy.linalg.decomp.test_decomp.test_eigvals)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/data/home/giovanni/lib/python2.3/site-packages/scipy/linalg/tests/test_decomp.py", line 36, in check_simple
    assert_array_almost_equal(w,exact_w)
  File "/data/home/giovanni/lib/python2.3/site-packages/scipy_test/testing.py", line 727, in assert_array_almost_equal
    assert cond,\
AssertionError:
Arrays are not almost equal (mismatch 66.6666666667%):
        Array 1: [ 9.4371906+0.j -0.1153653+0.j -0.3218254+0.j]
        Array 2: [ 9.3218254  0.        -0.3218254]


======================================================================
FAIL: check_simple_tr (scipy.linalg.decomp.test_decomp.test_eigvals)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/data/home/giovanni/lib/python2.3/site-packages/scipy/linalg/tests/test_decomp.py", line 44, in check_simple_tr
    assert_array_almost_equal(w,exact_w)
  File "/data/home/giovanni/lib/python2.3/site-packages/scipy_test/testing.py", line 727, in assert_array_almost_equal
    assert cond,\
AssertionError:
Arrays are not almost equal (mismatch 66.6666666667%):
        Array 1: [ 9.4371906+0.j -0.1153653+0.j -0.3218254+0.j]
        Array 2: [ 9.3218254  0.        -0.3218254]


======================================================================
FAIL: check_simple (scipy.linalg.basic.test_basic.test_det)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/data/home/giovanni/lib/python2.3/site-packages/scipy/linalg/tests/test_basic.py", line 273, in check_simple
    assert_almost_equal(a_det,-2.0)
  File "/data/home/giovanni/lib/python2.3/site-packages/scipy_test/testing.py", line 649, in assert_almost_equal
    assert round(abs(desired - actual),decimal) == 0, msg
AssertionError:
Items are not equal:
DESIRED: -2.0
ACTUAL: inf

======================================================================
FAIL: check_simple_exact (scipy.linalg.basic.test_basic.test_lstsq)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/data/home/giovanni/lib/python2.3/site-packages/scipy/linalg/tests/test_basic.py", line 356, in check_simple_exact
    assert_array_almost_equal(Numeric.matrixmultiply(a,x),b)
  File "/data/home/giovanni/lib/python2.3/site-packages/scipy_test/testing.py", line 727, in assert_array_almost_equal
    assert cond,\
AssertionError:
Arrays are not almost equal (mismatch 50.0%):
        Array 1: [0 0]
        Array 2: [1 0]


======================================================================
FAIL: check_simple (scipy.linalg.basic.test_basic.test_solve)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/data/home/giovanni/lib/python2.3/site-packages/scipy/linalg/tests/test_basic.py", line 74, in check_simple
    assert_array_almost_equal(Numeric.matrixmultiply(a,x),b)
  File "/data/home/giovanni/lib/python2.3/site-packages/scipy_test/testing.py", line 727, in assert_array_almost_equal
    assert cond,\
AssertionError:
Arrays are not almost equal (mismatch 50.0%):
        Array 1: [0 0]
        Array 2: [1 0]


======================================================================
FAIL: check_simple_sym (scipy.linalg.basic.test_basic.test_solve)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/data/home/giovanni/lib/python2.3/site-packages/scipy/linalg/tests/test_basic.py", line 81, in check_simple_sym
    assert_array_almost_equal(Numeric.matrixmultiply(a,x),b)
  File "/data/home/giovanni/lib/python2.3/site-packages/scipy_test/testing.py", line 727,
in assert_array_almost_equal
    assert cond,\
AssertionError:
Arrays are not almost equal (mismatch 100.0%):
        Array 1: [-9223372036854775784 -9223372036854775770]
        Array 2: [1 0]


======================================================================
FAIL: check_matvec (scipy.sparse.Sparse.test_Sparse.test_csc)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/data/home/giovanni/lib/python2.3/site-packages/scipy/sparse/tests/test_Sparse.py", line 66, in check_matvec
    assert_array_almost_equal([1,2,3,4]*b,dot([1,2,3,4],b.todense()))
  File "/data/home/giovanni/lib/python2.3/site-packages/scipy_test/testing.py", line 727,
in assert_array_almost_equal
    assert cond,\
AssertionError:
Arrays are not almost equal (mismatch 100.0%):
        Array 1: [  8.3991160e-323   6.9169190e-323   4.4465908e-323]
        Array 2: [ 17.  14.   9.]


======================================================================
FAIL: check_matvec (scipy.sparse.Sparse.test_Sparse.test_csr)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/data/home/giovanni/lib/python2.3/site-packages/scipy/sparse/tests/test_Sparse.py", line 66, in check_matvec
    assert_array_almost_equal([1,2,3,4]*b,dot([1,2,3,4],b.todense()))
  File "/data/home/giovanni/lib/python2.3/site-packages/scipy_test/testing.py", line 727,
in assert_array_almost_equal
    assert cond,\
AssertionError:
Arrays are not almost equal (mismatch 100.0%):
        Array 1: [  8.3991160e-323   6.9169190e-323   4.4465908e-323]
        Array 2: [ 17.  14.   9.]


======================================================================
FAIL: check_matvec (scipy.sparse.Sparse.test_Sparse.test_dok)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/data/home/giovanni/lib/python2.3/site-packages/scipy/sparse/tests/test_Sparse.py", line 66, in check_matvec
    assert_array_almost_equal([1,2,3,4]*b,dot([1,2,3,4],b.todense()))
  File "/data/home/giovanni/lib/python2.3/site-packages/scipy_test/testing.py", line 727,
in assert_array_almost_equal
    assert cond,\
AssertionError:
Arrays are not almost equal (mismatch 100.0%):
        Array 1: [  8.3991160e-323   6.9169190e-323   4.4465908e-323]
        Array 2: [ 17.  14.   9.]


----------------------------------------------------------------------
Ran 1080 tests in 1.189s

FAILED (failures=10, errors=1)
<unittest.TextTestRunner object at 0x2a9aa7f710>


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