[Numpy-discussion] numpy error with mkl 10.1

Olivier Delalleau shish@keba...
Wed Nov 2 20:24:50 CDT 2011


I believe they are optional, but I'm not sure.

Note that this system I copied the distutils from is not one I setup myself
so I'm not sure how numpy was installed exactly. I just know it works and
it's using MKL :) It's an 8 core Intel(R) Xeon(R) CPU E5462  @ 2.80GHz
(x86_64 as well).

-=- Olivier

2011/11/2 akshar bhosale <akshar.bhosale@gmail.com>

> hi,
> are amd,fftw and umfpack required? my architecture is : intel xeon x_86_64.
>
> On Thu, Nov 3, 2011 at 6:30 AM, Olivier Delalleau <shish@keba.be> wrote:
>
>> 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 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 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 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 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 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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