[Numpy-discussion] Complex matrix seg fault

Dag Sverre Seljebotn dagss@student.matnat.uio...
Fri Feb 4 08:32:43 CST 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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>    



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