[Numpy-discussion] numpy error with mkl 10.1

akshar bhosale akshar.bhosale@gmail....
Wed Nov 2 13:44:18 CDT 2011


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/
> 10.1.3.027/lib/em64t/libmkl_lapack.so (0x00002acf0e25a000)
>         libmkl_intel_lp64.so => /opt/intel/mkl/
> 10.1.3.027/lib/em64t/libmkl_intel_lp64.so (0x00002acf0ebb8000)
>         libmkl_intel_thread.so => /opt/intel/mkl/
> 10.1.3.027/lib/em64t/libmkl_intel_thread.so (0x00002acf0ef2e000)
>         libmkl_def.so => /opt/intel/mkl/10.1.3.027/lib/em64t/libmkl_def.so(0x00002acf0fc93000)
>         libmkl_core.so => /opt/intel/mkl/
> 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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