On Tuesday 10 May 2005 3:37 pm, Christopher G. Traylor wrote: > Sorry, if this has been addressed before. We're trying to build scipy on > an dual opteron box in 64 bit mode. With the r1 ebuild, it fails > complaining that it can't find some symbol. If I take the atlas-3.6.0 > requirement out, it builds fine, but during the test phase, it gives > these errors. My guess is that having atlas in there is causing some > sort of multilib problem, and that blas-atlas provides all the required > symbols, but doesn't have the proper internal support to return the > answers that the scipy test suite is expecting. I guess my confusion > stems from the whole "odd" virtual atlas set up. Any guidance would be > appreciated.
sci-libs/atlas will, if installed after lapack-atlas, overwrite a symlink in /usr/lib with an incomplete lapack library. atlas should not be in the ebuild. Only lapack-atlas should be in there, which still provides the atlas libraries. I wrote about this in the bug report. Try running ls -l /usr/lib/liblapack.*, they should all be symlinks to files in /usr/lib/lapack/atlas/. If, in /usr/lib, liblapack.a (I think .a) is not a symlink, it is probably smaller than ~5.5MB, and isnt a full lapack implementation. I am going to update the scipy ebuild as soon as the numeric ebuild is settled (it appears that this will happen soon.) There are also two patches that needs to be applied. I'll post them at the bug page: http://bugs.gentoo.org/show_bug.cgi?id=24593 > > <snip> > ====================================================================== > ERROR: check_simple_overdet (scipy.linalg.basic.test_basic.test_lstsq) > ---------------------------------------------------------------------- > Traceback (most recent call last): > File > "/usr/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 "/usr/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.basic.test_basic.test_det) > ---------------------------------------------------------------------- > Traceback (most recent call last): > File > "/usr/lib/python2.3/site-packages/scipy/linalg/tests/test_basic.py", > line 273, in check_simple > assert_almost_equal(a_det,-2.0) > File "/usr/lib/python2.3/site-packages/scipy_test/testing.py", line > 606, 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_exact (scipy.linalg.basic.test_basic.test_lstsq) > ---------------------------------------------------------------------- > Traceback (most recent call last): > File > "/usr/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 "/usr/lib/python2.3/site-packages/scipy_test/testing.py", line > 684, 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 > "/usr/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 "/usr/lib/python2.3/site-packages/scipy_test/testing.py", line > 684, in assert_array_almost_equal > assert cond,\ > AssertionError: > Arrays are not almost equal (mismatch 50.0%): > Array 1: [-9223372036854775808 0] > Array 2: [1 0] > > > ====================================================================== > FAIL: check_simple_sym (scipy.linalg.basic.test_basic.test_solve) > ---------------------------------------------------------------------- > Traceback (most recent call last): > File > "/usr/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 "/usr/lib/python2.3/site-packages/scipy_test/testing.py", line > 684, in assert_array_almost_equal > assert cond,\ > AssertionError: > Arrays are not almost equal (mismatch 100.0%): > Array 1: [-9223372036854775784 -9223372036854775770] > Array 2: [1 0] > > > ---------------------------------------------------------------------- > <snip> -- Darren S. Dale Bard Hall Department of Materials Science and Engineering Cornell University Ithaca, NY. 14850 [EMAIL PROTECTED]
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