[Numpy-discussion] numpy error with mkl 10.1

Olivier Delalleau shish@keba...
Wed Nov 2 20:00:03 CDT 2011


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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