[gmx-users] 4.6.3 and MKL

Éric Germaneau germaneau at zoho.com
Thu Jul 11 01:17:53 CEST 2013 

I have the same feeling too but I'm not in charge of it unfortunately.
Thank you, I appreciate.

On 07/11/2013 07:15 AM, Mark Abraham wrote:
> No problems :-) (For the record, the fact that you had to brute-force
> static libraries in another thread does not fill me with confidence
> that your compiler is installed correctly. But that is for you to
> judge! :-)
>
> On Thu, Jul 11, 2013 at 1:11 AM, Éric Germaneau <germaneau at zoho.com> wrote:
>> I see.
>> Thank you.
>>
>>
>> On 07/11/2013 07:08 AM, Mark Abraham wrote:
>>> On Thu, Jul 11, 2013 at 1:02 AM, Éric Germaneau <germaneau at zoho.com>
>>> wrote:
>>>> Yes, as one can see in my first post.
>>> No, because we can't guess whether your icc is 11 or not. If so, you
>>> have a bunch of stuff that is not required. icc 11 has a magic flag
>>> for using MKL, which GROMACS will use if given the chance. But I guess
>>> I wasted my time implementing and documenting it :-)
>>>
>>>> One thing is I don't know what libraries I need and in which order.
>>> ... and neither does anybody else who can't see the documentation for
>>> your system. That's why if you have icc before version 11, the GROMACS
>>> instructions suggest you look at them! That is the price of using mkl
>>> before icc-11.
>>>
>>> Mark
>>>
>>>> Thanks,
>>>>
>>>>                  Eric.
>>>>
>>>>
>>>> On 07/11/2013 06:58 AM, Mark Abraham wrote:
>>>>> Are you following the advice here?
>>>>>
>>>>> http://www.gromacs.org/Documentation/Installation_Instructions#3.4.2._MKL
>>>>>
>>>>> On Thu, Jul 11, 2013 at 12:24 AM, Éric Germaneau <germaneau at zoho.com>
>>>>> wrote:
>>>>>> Dear all,
>>>>>>
>>>>>> Anyone have successfully built the 4.6.3 release using MKL?
>>>>>> I keep getting the following error message:
>>>>>>
>>>>>>       -- Looking for DftiCreateDescriptor - not found
>>>>>>       CMake Error at CMakeLists.txt:1018 (message):
>>>>>>          Linking with MKL was requested, but was not successful.  The
>>>>>>       include path
>>>>>>          to mkl.h in MKL_INCLUDE_DIR, and the link libraries in
>>>>>>
>>>>>>
>>>>>>
>>>>>> MKL_LIBRARIES=/lustre/utility/intel/mkl/lib/intel64/libmkl_intel_thread.so;/lustre/utility/intel/mkl/lib/intel64/libmkl_core.so;/lustre/utility/intel/mkl/lib/intel64/libfftw2xf_double_intel.a;/lustre/utility/intel/mkl/lib/intel64/libmkl_avx2.so;/lustre/utility/intel/mkl/lib/intel64/libmkl_scalapack_lp64.so;/lustre/utility/intel/mkl/lib/intel64/libmkl_intel_lp64.so
>>>>>>          need to match what the MKL documentation says you need for your
>>>>>>       system.
>>>>>>          Use full paths to library files, in the right order, and
>>>>>> separated
>>>>>> by
>>>>>>          semicolons.
>>>>>>
>>>>>> Here is how I use CMAKE:
>>>>>>
>>>>>>       CC=mpicc CXX=mpicxx
>>>>>>       CMAKE_PREFIX_PATH=$CUDAPATH/include:$CUDAPATH/lib64:$CUDAPATH/bin
>>>>>> \
>>>>>>          /lustre/utility/bin/cmake \
>>>>>>           -DGMX_FFT_LIBRARY=mkl \
>>>>>>
>>>>>>
>>>>>>
>>>>>> -DMKL_LIBRARIES="${MKL}/lib/intel64/libmkl_intel_thread.so;${MKL}/lib/intel64/libmkl_core.so;${MKL}/lib/intel64/libfftw2xf_double_intel.a;${MKL}/lib/intel64/libmkl_avx2.so;${MKL}/lib/intel64/libmkl_scalapack_lp64.so;${MKL}/lib/intel64/libmkl_intel_lp64.so"
>>>>>>       \
>>>>>>           -DMKL_INCLUDE_DIR="${MKL}/include" \
>>>>>>           -DGMX_MPI=ON \
>>>>>>           -DGMX_GPU=OFF [-DCUDA_TOOLKIT_ROOT_DIR=$CUDAPATH] \
>>>>>>           -DCMAKE_INSTALL_PREFIX=$INSTALL_DIR \
>>>>>>           -DGMX_X11=OFF ../$APP \
>>>>>>           -DGMX_THREADS=OFF
>>>>>>
>>>>>> Any hints here?
>>>>>> I thank you in advance,
>>>>>>
>>>>>>                                                  'Eric.
>>>>>>
>>>>>> --
>>>>>> /Be the change you wish to see in the world
>>>>>> / --- Mahatma Gandhi ---
>>>>>>
>>>>>> Éric Germaneau <http://hpc.sjtu.edu.cn/index.htm>
>>>>>>
>>>>>> Shanghai Jiao Tong University
>>>>>> Network & Information Center
>>>>>> room 205
>>>>>> Minhang Campus
>>>>>> 800 Dongchuan Road
>>>>>> Shanghai 200240
>>>>>> China
>>>>>>
>>>>>> View Éric Germaneau's profile on LinkedIn
>>>>>> <http://cn.linkedin.com/pub/%C3%A9ric-germaneau/30/931/986>
>>>>>>
>>>>>> /Please, if possible, don't send me MS Word or PowerPoint attachments
>>>>>> Why? See: http://www.gnu.org/philosophy/no-word-attachments.html/
>>>>>>
>>>>>> --
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>>>> --
>>>> /Be the change you wish to see in the world
>>>> / --- Mahatma Gandhi ---
>>>>
>>>> Éric Germaneau <http://hpc.sjtu.edu.cn/index.htm>
>>>>
>>>> Shanghai Jiao Tong University
>>>> Network & Information Center
>>>> room 205
>>>> Minhang Campus
>>>> 800 Dongchuan Road
>>>> Shanghai 200240
>>>> China
>>>>
>>>> View Éric Germaneau's profile on LinkedIn
>>>> <http://cn.linkedin.com/pub/%C3%A9ric-germaneau/30/931/986>
>>>>
>>>> /Please, if possible, don't send me MS Word or PowerPoint attachments
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>>>>
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>>
>> --
>> /Be the change you wish to see in the world
>> / --- Mahatma Gandhi ---
>>
>> Éric Germaneau <http://hpc.sjtu.edu.cn/index.htm>
>>
>> Shanghai Jiao Tong University
>> Network & Information Center
>> room 205
>> Minhang Campus
>> 800 Dongchuan Road
>> Shanghai 200240
>> China
>>
>> View Éric Germaneau's profile on LinkedIn
>> <http://cn.linkedin.com/pub/%C3%A9ric-germaneau/30/931/986>
>>
>> /Please, if possible, don't send me MS Word or PowerPoint attachments
>> Why? See: http://www.gnu.org/philosophy/no-word-attachments.html/
>>
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-- 
/Be the change you wish to see in the world
/ --- Mahatma Gandhi ---

Éric Germaneau <http://hpc.sjtu.edu.cn/index.htm>

Shanghai Jiao Tong University
Network & Information Center
room 205
Minhang Campus
800 Dongchuan Road
Shanghai 200240
China

View Éric Germaneau's profile on LinkedIn 
<http://cn.linkedin.com/pub/%C3%A9ric-germaneau/30/931/986>

/Please, if possible, don't send me MS Word or PowerPoint attachments
Why? See: http://www.gnu.org/philosophy/no-word-attachments.html/

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