[Numpy-discussion] numpy error with mkl 10.1

akshar bhosale akshar.bhosale@gmail....
Wed Nov 2 19:49:03 CDT 2011


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 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 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 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 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 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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