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

Giovanni Samaey Giovanni.Samaey at cs.kuleuven.ac.be
Wed Nov 24 03:53:52 CST 2004


Since I don't use linalg myself, I do not have any problems using SciPy 
like this.
But I would appreciate this being solved before giving access to others.
Since we plan on encouraging new students to use this environment 
instead of matlab,
any help would be welcome.

Giovanni

Giovanni Samaey wrote:

> 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
>
>------------------------------------------------------------------------
>
>======================================================================
>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>
>  
>
>------------------------------------------------------------------------
>
>======================================================================
>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>
>  
>
>------------------------------------------------------------------------
>
>_______________________________________________
>SciPy-user mailing list
>SciPy-user at scipy.net
>http://www.scipy.net/mailman/listinfo/scipy-user
>  
>


-- 
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




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