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

Olivier Delalleau shish@keba...
Wed Nov 2 21:45:23 CDT 2011


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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>>>>>>>>>>>>>>
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