[Numpy-discussion] numpy error with mkl 10.1

akshar bhosale akshar.bhosale@gmail....
Wed Nov 2 21:30:52 CDT 2011


hi,
on your machine, is numpy.test passed?

On Thu, Nov 3, 2011 at 6:54 AM, Olivier Delalleau <shish@keba.be> wrote:

> 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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