[Numpy-discussion] Fwd: numpy error with mkl 10.1
akshar bhosale
akshar.bhosale at gmail.com
Wed Nov 2 23:32:45 EDT 2011
thank you very much for your kind help.
On Thu, Nov 3, 2011 at 8:58 AM, Olivier Delalleau <shish at keba.be> wrote:
> I'm sorry, I don't know. I'm not at all an expert about numpy
> installation, I just happened to have access to a computer with a working
> install of numpy with MKL, so I thought it might help... but I'm afraid
> that's all I can do for you :/
>
> -=- Olivier
>
> 2011/11/2 akshar bhosale <akshar.bhosale at gmail.com>
>
>> 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 at 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 at 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 at 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 at scipy.org>
>>>>
>>>>
>>>> hi,
>>>> on your machine, is numpy.test passed?
>>>>
>>>>
>>>> On Thu, Nov 3, 2011 at 6:54 AM, Olivier Delalleau <shish at 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 at 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 at keba.be>wrote:
>>>>>>
>>>>>>> It's inside the distutils folder.
>>>>>>>
>>>>>>> -=- Olivier
>>>>>>>
>>>>>>> 2011/11/2 akshar bhosale <akshar.bhosale at gmail.com>
>>>>>>>
>>>>>>>> thanks..what about site.cfg?
>>>>>>>>
>>>>>>>> On Thu, Nov 3, 2011 at 1:27 AM, Olivier Delalleau <shish at 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 at 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 at 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 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 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 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
>>>>>>>>>>> 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
>>>>>>>>>>> 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 at 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 at 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 at 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 at keba.be> wrote:
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Ok, can you print the output of ldd numpy/core/_dotblas.so?
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> -=- Olivier
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> 2011/11/2 akshar bhosale <akshar.bhosale at 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 at 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 at 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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