[SciPy-Dev] numpy.test hangs

akshar bhosale akshar.bhosale@gmail....
Sat Oct 22 01:24:36 CDT 2011


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
>>>
>>>
>>
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>
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