[gmx-users] 4.6.3 and MKL

[Mark Abraham]

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>
>>>
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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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