[Numpy-discussion] numpy error with mkl 10.1

akshar bhosale akshar.bhosale@gmail....
Wed Nov 2 20:11:03 CDT 2011


hi,
are amd,fftw and umfpack required? my architecture is : intel xeon x_86_64.

On Thu, Nov 3, 2011 at 6:30 AM, Olivier Delalleau <shish@keba.be> wrote:

> It's inside the distutils folder.
>
> -=- Olivier
>
> 2011/11/2 akshar bhosale <akshar.bhosale@gmail.com>
>
>> thanks..what about site.cfg?
>>
>> On Thu, Nov 3, 2011 at 1:27 AM, Olivier Delalleau <shish@keba.be> wrote:
>>
>>> Sorry, no clue :/
>>>
>>> I made a tarball with my distutils folder here:
>>> http://www.iro.umontreal.ca/~delallea/tmp/distutils.tar.bz2
>>> Hope this helps...
>>>
>>> -=- Olivier
>>>
>>> 2011/11/2 akshar bhosale <akshar.bhosale@gmail.com>
>>>
>>>>  hi,
>>>> thanks for the reply
>>>> none of them is linked with libmkl_lapack.so.
>>>> what can be the problem?
>>>> libmkl_lapack.so is present in its location.
>>>>
>>>> if possible, can you send your site.cfg and other related files like
>>>> intelccompilers.py / system_config.py etc...and configure/build options, i
>>>> will try the same?
>>>>
>>>> On Wed, Nov 2, 2011 at 11:51 PM, Olivier Delalleau <shish@keba.be>wrote:
>>>>
>>>>>  Hmm that's interesting, it's not linked against libmkl_lapack. On my
>>>>> system with MKL it says:
>>>>>
>>>>> ldd linalg/lapack_lite.so
>>>>>         libmkl_lapack.so => /opt/intel/mkl/*MailScanner soupçonne le
>>>>> lien suivant d'être une tentative de fraude de la part de "10.1.3.027"
>>>>> * *MailScanner warning: numerical links are often malicious:
>>>>> 10.1.3.027/lib/em64t/libmkl_lapack.so*<http://10.1.3.027/lib/em64t/libmkl_lapack.so>(0x00002acf0e25a000)
>>>>>         libmkl_intel_lp64.so => /opt/intel/mkl/*MailScanner soupçonne
>>>>> le lien suivant d'être une tentative de fraude de la part de "10.1.3.027"
>>>>> * *MailScanner warning: numerical links are often malicious:
>>>>> 10.1.3.027/lib/em64t/libmkl_intel_lp64.so*<http://10.1.3.027/lib/em64t/libmkl_intel_lp64.so>(0x00002acf0ebb8000)
>>>>>         libmkl_intel_thread.so => /opt/intel/mkl/*MailScanner
>>>>> soupçonne le lien suivant d'être une tentative de fraude de la part de
>>>>> "10.1.3.027" * *MailScanner warning: numerical links are often
>>>>> malicious: 10.1.3.027/lib/em64t/libmkl_intel_thread.so*<http://10.1.3.027/lib/em64t/libmkl_intel_thread.so>(0x00002acf0ef2e000)
>>>>>         libmkl_def.so => /opt/intel/mkl/*MailScanner soupçonne le
>>>>> lien suivant d'être une tentative de fraude de la part de "10.1.3.027"
>>>>> * *MailScanner warning: numerical links are often malicious:
>>>>> 10.1.3.027/lib/em64t/libmkl_def.so*<http://10.1.3.027/lib/em64t/libmkl_def.so>(0x00002acf0fc93000)
>>>>>         libmkl_core.so => /opt/intel/mkl/*MailScanner soupçonne le
>>>>> lien suivant d'être une tentative de fraude de la part de "10.1.3.027"
>>>>> * *MailScanner warning: numerical links are often malicious:
>>>>> 10.1.3.027/lib/em64t/libmkl_core.so*<http://10.1.3.027/lib/em64t/libmkl_core.so>(0x00002acf1080e000)
>>>>>
>>>>>         libguide.so => /opt/intel/cce/10.1.026/lib/libguide.so
>>>>> (0x00002acf10a03000)
>>>>>         libpthread.so.0 => /lib64/libpthread.so.0 (0x00002acf10ba6000)
>>>>>         libm.so.6 => /lib64/libm.so.6 (0x00002acf10dc1000)
>>>>>         libpython2.6.so.1.0 =>
>>>>> /opt/python64/2.6.4/lib/libpython2.6.so.1.0 (0x00002acf11044000)
>>>>>         libc.so.6 => /lib64/libc.so.6 (0x00002acf113f3000)
>>>>>         libdl.so.2 => /lib64/libdl.so.2 (0x00002acf1174b000)
>>>>>         /lib64/ld-linux-x86-64.so.2 (0x0000003d90400000)
>>>>>         libutil.so.1 => /lib64/libutil.so.1 (0x00002acf1194f000)
>>>>>
>>>>> So to clarify, what I was trying to achieve is find which of numpy's
>>>>> shared libraries was trying to load libmkl_lapack.so, and if it could be
>>>>> found properly with ldd. Just to make sure it's not another .so, can you
>>>>> run from within your numpy directory:
>>>>>    find -name "*.so" -exec ldd \{} \; | grep lapack
>>>>>
>>>>> If the output is not empty, try to run ldd on all .so within numpy to
>>>>> see which one is linked against libmkl_lapack.so. Then hopefully something
>>>>> will stand out (I admit that's not guaranteed though ;).
>>>>>
>>>>>
>>>>> -=- Olivier
>>>>>
>>>>> 2011/11/2 akshar bhosale <akshar.bhosale@gmail.com>
>>>>>
>>>>>> Hi,
>>>>>>
>>>>>> ldd
>>>>>> Python-2.6/lib/python2.6/site-packages/numpy/linalg/lapack_lite.so
>>>>>>     libstdc++.so.6 => /usr/lib64/libstdc++.so.6 (0x00002b1199349000)
>>>>>>     libmkl_def.so =>
>>>>>> /opt/intel/Compiler/11.0/069/mkl/lib/em64t/libmkl_def.so
>>>>>> (0x00002b1199653000)
>>>>>>     libmkl_intel_lp64.so =>
>>>>>> /opt/intel/Compiler/11.0/069/mkl/lib/em64t/libmkl_intel_lp64.so
>>>>>> (0x00002b119a1a8000)
>>>>>>     libmkl_intel_thread.so =>
>>>>>> /opt/intel/Compiler/11.0/069/mkl/lib/em64t/libmkl_intel_thread.so
>>>>>> (0x00002b119a503000)
>>>>>>     libmkl_core.so =>
>>>>>> /opt/intel/Compiler/11.0/069/mkl/lib/em64t/libmkl_core.so
>>>>>> (0x00002b119b22c000)
>>>>>>     libmkl_mc.so =>
>>>>>> /opt/intel/Compiler/11.0/069/mkl/lib/em64t/libmkl_mc.so (0x00002b119b420000)
>>>>>>     libpthread.so.0 => /lib64/libpthread.so.0 (0x00002b119c176000)
>>>>>>     libimf.so => /opt/intel/Compiler/11.0/069/lib/intel64/libimf.so
>>>>>> (0x00002b119c392000)
>>>>>>     libsvml.so => /opt/intel/Compiler/11.0/069/lib/intel64/libsvml.so
>>>>>> (0x00002b119c6e9000)
>>>>>>     libm.so.6 => /lib64/libm.so.6 (0x00002b119c8a6000)
>>>>>>     libiomp5.so =>
>>>>>> /opt/intel/Compiler/11.0/069/lib/intel64/libiomp5.so (0x00002b119cb2b000)
>>>>>>     libintlc.so.5 =>
>>>>>> /opt/intel/Compiler/11.0/069/lib/intel64/libintlc.so.5 (0x00002b119ccbc000)
>>>>>>     libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00002b119cdf9000)
>>>>>>     libc.so.6 => /lib64/libc.so.6 (0x00002b119d007000)
>>>>>>     libdl.so.2 => /lib64/libdl.so.2 (0x00002b119d37e000)
>>>>>>     /lib64/ld-linux-x86-64.so.2 (0x0000003fb8000000)
>>>>>>
>>>>>>
>>>>>>
>>>>>> On Wed, Nov 2, 2011 at 11:26 PM, Olivier Delalleau <shish@keba.be>wrote:
>>>>>>
>>>>>>> Doh I'm sorry, I forgot the problem was with lapack, what about ldd
>>>>>>> numpy/linalg/lapack_lite.so?
>>>>>>>
>>>>>>>
>>>>>>> 2011/11/2 akshar bhosale <akshar.bhosale@gmail.com>
>>>>>>>
>>>>>>>> Hi,
>>>>>>>> ldd _dotblas.so
>>>>>>>> libstdc++.so.6 => /usr/lib64/libstdc++.so.6 (0x00002b12f0692000)
>>>>>>>>     libmkl_def.so =>
>>>>>>>> /opt/intel/Compiler/11.0/069/mkl/lib/em64t/libmkl_def.so
>>>>>>>> (0x00002b12f099c000)
>>>>>>>>     libmkl_intel_lp64.so =>
>>>>>>>> /opt/intel/Compiler/11.0/069/mkl/lib/em64t/libmkl_intel_lp64.so
>>>>>>>> (0x00002b12f14f1000)
>>>>>>>>     libmkl_intel_thread.so =>
>>>>>>>> /opt/intel/Compiler/11.0/069/mkl/lib/em64t/libmkl_intel_thread.so
>>>>>>>> (0x00002b12f184c000)
>>>>>>>>     libmkl_core.so =>
>>>>>>>> /opt/intel/Compiler/11.0/069/mkl/lib/em64t/libmkl_core.so
>>>>>>>> (0x00002b12f2575000)
>>>>>>>>     libmkl_mc.so =>
>>>>>>>> /opt/intel/Compiler/11.0/069/mkl/lib/em64t/libmkl_mc.so (0x00002b12f2769000)
>>>>>>>>     libpthread.so.0 => /lib64/libpthread.so.0 (0x00002b12f34bf000)
>>>>>>>>     libimf.so => /opt/intel/Compiler/11.0/069/lib/intel64/libimf.so
>>>>>>>> (0x00002b12f36db000)
>>>>>>>>     libsvml.so =>
>>>>>>>> /opt/intel/Compiler/11.0/069/lib/intel64/libsvml.so (0x00002b12f3a32000)
>>>>>>>>     libm.so.6 => /lib64/libm.so.6 (0x00002b12f3bef000)
>>>>>>>>     libiomp5.so =>
>>>>>>>> /opt/intel/Compiler/11.0/069/lib/intel64/libiomp5.so (0x00002b12f3e74000)
>>>>>>>>     libintlc.so.5 =>
>>>>>>>> /opt/intel/Compiler/11.0/069/lib/intel64/libintlc.so.5 (0x00002b12f4005000)
>>>>>>>>     libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00002b12f4142000)
>>>>>>>>     libc.so.6 => /lib64/libc.so.6 (0x00002b12f4350000)
>>>>>>>>     libdl.so.2 => /lib64/libdl.so.2 (0x00002b12f46c7000)
>>>>>>>>     /lib64/ld-linux-x86-64.so.2 (0x0000003fb8000000)
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> On Wed, Nov 2, 2011 at 10:14 PM, Olivier Delalleau <shish@keba.be>wrote:
>>>>>>>>
>>>>>>>>> Ok, can you print the output of ldd numpy/core/_dotblas.so?
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> -=- Olivier
>>>>>>>>>
>>>>>>>>> 2011/11/2 akshar bhosale <akshar.bhosale@gmail.com>
>>>>>>>>>
>>>>>>>>>> HI,
>>>>>>>>>> It is already added in the LD_LIBRARY_PATH, thenalso it is
>>>>>>>>>> generating the same error.
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> On Wed, Nov 2, 2011 at 10:01 PM, Olivier Delalleau <shish@keba.be
>>>>>>>>>> > wrote:
>>>>>>>>>>
>>>>>>>>>>> Locate your libmkl_lapack.so and try to add the directory that
>>>>>>>>>>> contains it to your LD_LIBRARY_PATH environment variable.
>>>>>>>>>>>
>>>>>>>>>>> -=- Olivier
>>>>>>>>>>>
>>>>>>>>>>> 2011/11/2 akshar bhosale <akshar.bhosale@gmail.com>
>>>>>>>>>>>
>>>>>>>>>>>> Hi,
>>>>>>>>>>>>
>>>>>>>>>>>> i am getting following error.
>>>>>>>>>>>>    python -c 'import numpy;numpy.matrix([[1, 5, 10], [1.0, 3j,
>>>>>>>>>>>> 4]],
>>>>>>>>>>>>    numpy.complex128).T.I.H'
>>>>>>>>>>>>    MKL FATAL ERROR: Cannot load libmkl_lapack.so
>>>>>>>>>>>>
>>>>>>>>>>>>    have installed numpy 1.6.0 with python 2.6.
>>>>>>>>>>>>    i have intel cluster toolkit installed on my system. (11/069
>>>>>>>>>>>> version and mlk=10.1). i have machine having intel xeon processor and rhel
>>>>>>>>>>>> 5.2 x86_64
>>>>>>>>>>>>    platform.
>>>>>>>>>>>> Kindly help
>>>>>>>>>>>>
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