[Numpy-discussion] [SciPy-Dev] numpy.test hangs

akshar bhosale akshar.bhosale@gmail....
Sun Oct 23 04:45:07 CDT 2011


Hi,

i changed site.cfg :
####site.cfg####
[MKL}

mkl_libs = mkl_def, mkl_intel_lp64, mkl_intel_thread, mkl_core, mkl_mc

lapack_libs = mkl_lapack95_lp64, mkl_lapack, mkl_scalapack_ilp64,
mkl_scalapack_lp64


#lapack_libs
=mkl_lapack,mkl_scalapack_ilp64,mkl_scalapack_lp64,mkl_lapack95_lp64
library_dirs =
/opt/intel/Compiler/11.0/069/mkl/lib/em64t:/opt/intel/Compiler/11.0/069/lib/intel64/
include_dirs =
/opt/intel/Compiler/11.0/069/mkl/include:/opt/intel/Compiler/11.0/069/include/


and now numpy.test hangs at :

python
Python 2.6 (r26:66714, May 29 2011, 15:10:47)
[GCC 4.1.2 20071124 (Red Hat 4.1.2-42)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import numpy
>>> numpy.test(verbose=3)
Running unit tests for numpy
NumPy version 1.6.0
NumPy is installed in
/home/aksharb/Python-2.6/lib/python2.6/site-packages/numpy
Python version 2.6 (r26:66714, May 29 2011, 15:10:47) [GCC 4.1.2 20071124
(Red Hat 4.1.2-42)]
nose version 1.0.0
nose.config: INFO: Excluding tests matching ['f2py_ext', 'f2py_f90_ext',
'gen_ext', 'pyrex_ext', 'swig_ext']
nose.selector: INFO:
/home/external/unipune/gadre/Python-2.6/lib/python2.6/site-packages/numpy/core/multiarray.so
is executable; skipped
nose.selector: INFO:
/home/external/unipune/gadre/Python-2.6/lib/python2.6/site-packages/numpy/core/scalarmath.so
is executable; skipped
nose.selector: INFO:
/home/external/unipune/gadre/Python-2.6/lib/python2.6/site-packages/numpy/core/umath.so
is executable; skipped
nose.selector: INFO:
/home/external/unipune/gadre/Python-2.6/lib/python2.6/site-packages/numpy/core/multiarray_tests.so
is executable; skipped
nose.selector: INFO:
/home/external/unipune/gadre/Python-2.6/lib/python2.6/site-packages/numpy/core/umath_tests.so
is executable; skipped
nose.selector: INFO:
/home/external/unipune/gadre/Python-2.6/lib/python2.6/site-packages/numpy/fft/fftpack_lite.so
is executable; skipped
nose.selector: INFO:
/home/external/unipune/gadre/Python-2.6/lib/python2.6/site-packages/numpy/linalg/lapack_lite.so
is executable; skipped
nose.selector: INFO:
/home/external/unipune/gadre/Python-2.6/lib/python2.6/site-packages/numpy/random/mtrand.so
is executable; skipped
test_api.test_fastCopyAndTranspose ... ok
test_arrayprint.TestArrayRepr.test_nan_inf ... ok
test_str (test_arrayprint.TestComplexArray) ... ok
Ticket 844. ... ok
test_blasdot.test_blasdot_used ... ok
test_blasdot.test_dot_2args ... ok
test_blasdot.test_dot_3args ... ok
test_blasdot.test_dot_3args_errors ... ok
.
.
.
Test if an appropriate exception is raised when passing bad values to ... ok
Test whether equivalent subarray dtypes hash the same. ... ok
Test whether different subarray dtypes hash differently. ... ok
Test some data types that are equal ... ok
Test some more complicated cases that shouldn't be equal ... ok
Test some simple cases that shouldn't be equal ... ok
test_single_subarray (test_dtype.TestSubarray) ... ok
test_einsum_errors (test_einsum.TestEinSum) ... ok
test_einsum_sums_cfloat128 (test_einsum.TestEinSum) ...

#######################

On Sat, Oct 22, 2011 at 1:46 PM, <numpy-discussion-owner@scipy.org> wrote:

> This is a members-only list.  Your message has been automatically
> rejected, since it came from a non-member's email address.  Please
> make sure to use the email account that you used to join this list.
>
>
>
> ---------- Forwarded message ----------
> From: akshar bhosale <akshar.bhosale@gmail.com>
> To: SciPy Developers List <scipy-dev@scipy.org>, Discussion of Numerical
> Python <numpy-discussion@scipy.org>
> Date: Sat, 22 Oct 2011 13:46:49 +0530
> Subject: Re: [SciPy-Dev] numpy.test hangs
> <charlesr.harris@gmail.com>Hi,
>
> python
> Python 2.6 (r26:66714, May 29 2011, 15:10:47)
> [GCC 4.1.2 20071124 (Red Hat 4.1.2-42)] on linux2
> Type "help", "copyright", "credits" or "license" for more information.
> >>> import numpy
> >>> numpy.show_config()
> lapack_opt_info:
>     libraries = ['mkl_lapack95_lp64', 'mkl_def', 'mkl_intel_lp64',
> 'mkl_intel_thread', 'mkl_core', 'mkl_mc', 'pthread']
>     library_dirs = ['/opt/intel/Compiler/11.0/069/mkl/lib/em64t']
>     define_macros = [('SCIPY_MKL_H', None)]
>     include_dirs = ['/opt/intel/Compiler/11.0/069/mkl/include',
> '/opt/intel/Compiler/11.0/069/include/']
> blas_opt_info:
>     libraries = ['mkl_def', 'mkl_intel_lp64', 'mkl_intel_thread',
> 'mkl_core', 'mkl_mc', 'pthread']
>     library_dirs = ['/opt/intel/Compiler/11.0/069/mkl/lib/em64t']
>     define_macros = [('SCIPY_MKL_H', None)]
>     include_dirs = ['/opt/intel/Compiler/11.0/069/mkl/include',
> '/opt/intel/Compiler/11.0/069/include/']
> lapack_mkl_info:
>     libraries = ['mkl_lapack95_lp64', 'mkl_def', 'mkl_intel_lp64',
> 'mkl_intel_thread', 'mkl_core', 'mkl_mc', 'pthread']
>     library_dirs = ['/opt/intel/Compiler/11.0/069/mkl/lib/em64t']
>     define_macros = [('SCIPY_MKL_H', None)]
>     include_dirs = ['/opt/intel/Compiler/11.0/069/mkl/include',
> '/opt/intel/Compiler/11.0/069/include/']
> blas_mkl_info:
>     libraries = ['mkl_def', 'mkl_intel_lp64', 'mkl_intel_thread',
> 'mkl_core', 'mkl_mc', 'pthread']
>     library_dirs = ['/opt/intel/Compiler/11.0/069/mkl/lib/em64t']
>     define_macros = [('SCIPY_MKL_H', None)]
>     include_dirs = ['/opt/intel/Compiler/11.0/069/mkl/include',
> '/opt/intel/Compiler/11.0/069/include/']
> mkl_info:
>     libraries = ['mkl_def', 'mkl_intel_lp64', 'mkl_intel_thread',
> 'mkl_core', 'mkl_mc', 'pthread']
>     library_dirs = ['/opt/intel/Compiler/11.0/069/mkl/lib/em64t']
>     define_macros = [('SCIPY_MKL_H', None)]
>     include_dirs = ['/opt/intel/Compiler/11.0/069/mkl/include',
> '/opt/intel/Compiler/11.0/069/include/']
>
> Akshar
>
>
> On Sat, Oct 22, 2011 at 11:54 AM, akshar bhosale <akshar.bhosale@gmail.com
> > wrote:
>
>> yes sure..
>> i have intel cluster toolkit installed on my system. (11/069 version and
>> mkl 10.3). i have machine having intel xeon processor and rhel 5.2 x86_64
>> platform. i am trying with intel compilers.
>> if i do
>>
>> python -c 'import numpy;numpy.matrix([[1, 5, 10], [1.0, 3j, 4]],
>> numpy.complex128).T.I.H'
>> python: symbol lookup error:
>> /opt/intel/Compiler/11.0/069/mkl/lib/em64/libmkl_lapack.so: undefined
>> symbol: mkl_lapack_zgeqrf
>>
>> my site.cfg is :
>> ####################
>> [mkl]
>>
>> mkl_libs = mkl_def, mkl_intel_lp64, mkl_intel_thread, mkl_core, mkl_mc
>> lapack_libs = mkl_lapack95_lp64
>>
>> library_dirs =
>> /opt/intel/Compiler/11.0/069/mkl/lib/em64t:/opt/intel/Compiler/11.0/069/lib/intel64/
>> include_dirs =
>> /opt/intel/Compiler/11.0/069/mkl/include:/opt/intel/Compiler/11.0/069/include/
>> ####################
>> and intelcompiler.py is :
>> ############################
>> from distutils.unixccompiler import UnixCCompiler
>> from numpy.distutils.exec_command import find_executable
>> import sys
>>
>> class IntelCCompiler(UnixCCompiler):
>>     """ A modified Intel compiler compatible with an gcc built Python."""
>>     compiler_type = 'intel'
>>     cc_exe = 'icc'
>>     cc_args = 'fPIC'
>>
>>     def __init__ (self, verbose=0, dry_run=0, force=0):
>>         sys.exit(0)
>>         UnixCCompiler.__init__ (self, verbose,dry_run, force)
>>         self.cc_exe = 'icc -fPIC '
>>         compiler = self.cc_exe
>>         self.set_executables(compiler=compiler,
>>                              compiler_so=compiler,
>>                              compiler_cxx=compiler,
>>                              linker_exe=compiler,
>>                              linker_so=compiler + ' -shared -lstdc++')
>>
>> class IntelItaniumCCompiler(IntelCCompiler):
>>     compiler_type = 'intele'
>>
>>     # On Itanium, the Intel Compiler used to be called ecc, let's search
>> for
>>     # it (now it's also icc, so ecc is last in the search).
>>     for cc_exe in map(find_executable,['icc','ecc']):
>>         if cc_exe:
>>             break
>>
>> class IntelEM64TCCompiler(UnixCCompiler):
>>     """ A modified Intel x86_64 compiler compatible with a 64bit gcc built
>> Python.
>>     """
>>     compiler_type = 'intelem'
>>     cc_exe = 'icc -m64 -fPIC'
>>     cc_args = "-fPIC -openmp"
>>     def __init__ (self, verbose=0, dry_run=0, force=0):
>>         UnixCCompiler.__init__ (self, verbose,dry_run, force)
>>         self.cc_exe = 'icc -m64 -fPIC -openmp '
>>         compiler = self.cc_exe
>>         self.set_executables(compiler=compiler,
>>                              compiler_so=compiler,
>>                              compiler_cxx=compiler,
>>                              linker_exe=compiler,
>>                              linker_so=compiler + ' -shared -lstdc++')
>> ##########################
>> LD_LIBRARY_PATH is :
>> #########################
>>
>> /opt/intel/Compiler/11.0/069/mkl/lib/em64t:/opt/scalasca-1.3.3/lib:/opt/PBS/lib:/opt/intel/mpi/lib64:/opt/maui/lib:/opt/jdk1.6.0_23/lib:/opt/intel/Compiler/11.0/069/ipp/em64t/sharedlib:/opt/intel/Compiler/11.0/069/mkl/lib/em64t:/opt/intel/Compiler/11.0/069/tbb/em64t/cc4.1.0_libc2.4_kernel2.6.16.21/lib:/opt/intel/Compiler/11.0/069/lib/intel64:/opt/intel/Compiler/11.0/069/ipp/em64t/sharedlib:/opt/intel/Compiler/11.0/069/mkl/lib/em64t:/opt/intel/Compiler/11.0/069/tbb/em64t/cc4.1.0_libc2.4_kernel2.6.16.21/lib:/opt/intel/Compiler/11.0/069/lib/intel64:/usr/local/lib
>> #########################
>>
>> -AKSHAR
>>
>>
>>
>> On Sat, Oct 22, 2011 at 11:32 AM, Charles R Harris <
>> charlesr.harris@gmail.com> wrote:
>>
>>>
>>>
>>> On Fri, Oct 21, 2011 at 11:49 PM, akshar bhosale <
>>> akshar.bhosale@gmail.com> wrote:
>>>
>>>> Hi,
>>>>
>>>> unfortunately 1.6.1 also hangs on the same place. Can i move ahead with
>>>> installing scipy?
>>>>
>>>>
>>> Hmm. Well, give scipy a try, but it would be nice to know what the
>>> problem is with einsum. I'm thinking compiler, GCC 4.1.2 might be a bit
>>> old, but it could easily be something else. Can you give us more information
>>> about your system?
>>>
>>> Chuck
>>>
>>>>
>>>> On Sat, Oct 22, 2011 at 12:19 AM, Charles R Harris <
>>>> charlesr.harris@gmail.com> wrote:
>>>>
>>>>>
>>>>>
>>>>> On Fri, Oct 21, 2011 at 5:25 AM, akshar bhosale <
>>>>> akshar.bhosale@gmail.com> wrote:
>>>>>
>>>>>> Hi,
>>>>>> does this mean that numpy is not configured properly or i can ignore
>>>>>> this and go ahead with scipy installation?
>>>>>>
>>>>>
>>>>> Scipy will probably work, but you should really install numpy 1.6.1
>>>>> instead of 1.6.0.
>>>>>
>>>>> <snip>
>>>>>
>>>>> Chuck
>>>>>
>>>>> _______________________________________________
>>>>> SciPy-Dev mailing list
>>>>> SciPy-Dev@scipy.org
>>>>> http://mail.scipy.org/mailman/listinfo/scipy-dev
>>>>>
>>>>>
>>>>
>>>> _______________________________________________
>>>> SciPy-Dev mailing list
>>>> SciPy-Dev@scipy.org
>>>> http://mail.scipy.org/mailman/listinfo/scipy-dev
>>>>
>>>>
>>>
>>> _______________________________________________
>>> SciPy-Dev mailing list
>>> SciPy-Dev@scipy.org
>>> http://mail.scipy.org/mailman/listinfo/scipy-dev
>>>
>>>
>>
>
>
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