[Numpy-discussion] Fwd: numpy error with mkl 10.1

akshar bhosale akshar.bhosale@gmail....
Wed Nov 2 22:23:26 CDT 2011


thanks once again. how can i use ur distutils directly (ur supplied files
etc)

On Thu, Nov 3, 2011 at 8:15 AM, Olivier Delalleau <shish@keba.be> wrote:

> Yes they pass:
>
> Ran 2030 tests in 6.672s
>
> OK (KNOWNFAIL=1)
> <nose.result.TextTestResult run=2030 errors=0 failures=0>
>
> Google "einsum hang".... I know you're not the first one with this bug
> (but I'm not sure exactly how to fix it).
>
> -=- Olivier
>
> 2011/11/2 akshar bhosale <akshar.bhosale@gmail.com>
>
>> my numpy.test hangs here
>>
>> Test whether equivalent subarray dtypes hash the same. ... ok
>> Test whether different subarray dtypes hash differently. ... ok
>> Test some data types that are equal ... ok
>> Test some more complicated cases that shouldn't be equal ... ok
>> Test some simple cases that shouldn't be equal ... ok
>> test_single_subarray (test_dtype.TestSubarray) ... ok
>> test_einsum_errors (test_einsum.TestEinSum) ... ok
>> test_einsum_sums_cfloat128 (test_einsum.TestEinSum) ...
>>
>>
>> ---------- Forwarded message ----------
>> From: akshar bhosale <akshar.bhosale@gmail.com>
>> Date: Thu, Nov 3, 2011 at 8:00 AM
>> Subject: Re: [Numpy-discussion] numpy error with mkl 10.1
>> To: Discussion of Numerical Python <numpy-discussion@scipy.org>
>>
>>
>> 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 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
>>>>>>>>> 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
>>>>>>>>> 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 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 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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