[gmx-users] 4.6.3 and MKL

[Éric Germaneau]

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
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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/