[Numpy-discussion] Complex matrix seg fault
Dag Sverre Seljebotn
dagss at student.matnat.uio.no
Fri Feb 4 09:32:43 EST 2011
On 02/04/2011 03:13 PM, Jonathan Tu wrote:
> Hi,
>
> When I run the following code, I get a seg fault on certain cluster nodes, but not others:
>
Is it a homogenous cluster or not? Try to look for differences in
/proc/cpuinfo between crashing and non-crashing nodes, in particular in
the flags.
Dag
>
>>>> import numpy as N
>>>> A = N.random.rand(262144,10)+1j*N.random.rand(262144,10)
>>>> x = N.random.rand(262144,)
>>>> d, res, rank, s = N.linalg.lstsq( A, x )
>>>>
> My numpy is configured as such:
>
> lapack_opt_info:
> libraries = ['mkl_lapack', 'mkl_intel_lp64', 'mkl_intel_thread', 'mkl_core', 'mkl_def', 'mkl_mc', 'iomp5', 'pthread']
> library_dirs = ['/home/jhtu/local/lib/mkl_links']
> define_macros = [('SCIPY_MKL_H', None)]
> include_dirs = ['/opt/intel/Compiler/11.1/072/mkl/include']
> blas_opt_info:
> libraries = ['mkl_intel_lp64', 'mkl_intel_thread', 'mkl_core', 'mkl_def', 'mkl_mc', 'iomp5', 'pthread']
> library_dirs = ['/home/jhtu/local/lib/mkl_links']
> define_macros = [('SCIPY_MKL_H', None)]
> include_dirs = ['/opt/intel/Compiler/11.1/072/mkl/include']
> lapack_mkl_info:
> libraries = ['mkl_lapack', 'mkl_intel_lp64', 'mkl_intel_thread', 'mkl_core', 'mkl_def', 'mkl_mc', 'iomp5', 'pthread']
> library_dirs = ['/home/jhtu/local/lib/mkl_links']
> define_macros = [('SCIPY_MKL_H', None)]
> include_dirs = ['/opt/intel/Compiler/11.1/072/mkl/include']
> blas_mkl_info:
> libraries = ['mkl_intel_lp64', 'mkl_intel_thread', 'mkl_core', 'mkl_def', 'mkl_mc', 'iomp5', 'pthread']
> library_dirs = ['/home/jhtu/local/lib/mkl_links']
> define_macros = [('SCIPY_MKL_H', None)]
> include_dirs = ['/opt/intel/Compiler/11.1/072/mkl/include']
> mkl_info:
> libraries = ['mkl_intel_lp64', 'mkl_intel_thread', 'mkl_core', 'mkl_def', 'mkl_mc', 'iomp5', 'pthread']
> library_dirs = ['/home/jhtu/local/lib/mkl_links']
> define_macros = [('SCIPY_MKL_H', None)]
> include_dirs = ['/opt/intel/Compiler/11.1/072/mkl/include']
>
> All unit tests pass except the following, but I was told (by this mailing list) that this shouldn't be an issue:
>
> ======================================================================
> FAIL: test_special_values (test_umath_complex.TestClog)
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File "/home/jhtu/local/lib/python2.7/site-packages/numpy/testing/decorators.py", line 215, in knownfailer
> return f(*args, **kwargs)
> File "/home/jhtu/local/lib/python2.7/site-packages/numpy/core/tests/test_umath_complex.py", line 312, in test_special_values
> assert_almost_equal(np.log(np.conj(xa[i])), np.conj(np.log(xa[i])))
> File "/home/jhtu/local/lib/python2.7/site-packages/numpy/testing/utils.py", line 443, in assert_almost_equal
> raise AssertionError(msg)
> AssertionError:
> Arrays are not almost equal
> ACTUAL: array([-inf+3.14159265j])
> DESIRED: array([-inf-3.14159265j])
>
> ----------------------------------------------------------------------
> Ran 2648 tests in 15.852s
>
> FAILED (KNOWNFAIL=4, SKIP=1, failures=1)
> <nose.result.TextTestResult run=2648 errors=0 failures=1>
>
> Anyone have ideas why this would fail on some nodes but not others? (I mean the code snippet fails on some nodes. The above unit test always fails.)
>
>
>
>
>
>
> Thanks,
>
>
>
> Jonathan Tu
>
>
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