[Numpy-discussion] numpy error with mkl 10.1

Olivier Delalleau shish@keba...
Wed Nov 2 13:21:48 CDT 2011


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
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> NumPy-Discussion mailing list
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>>>>>>>
>>>>>>>
>>>>>>
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>>>>>>
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