[Numpy-discussion] numpy error with mkl 10.1

Olivier Delalleau shish@keba...
Wed Nov 2 14:57:29 CDT 2011


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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>>>>>>>>>
>>>>>>>>>
>>>>>>>>
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