[gmx-users] Version 5.1.4: cannot open source file "mkl_dfti.h"

[Loris Bennett]

Hi,

I deleted my 'build' directory and tried again without the MKL variables:

ccmake -DGMX_MPI=on \
       -DGMX_FFT_LIBRARY=mkl \
       -DCMAKE_INSTALL_PREFIX="/cm/shared/apps/gromacs/openmpi/intel/64/5.1.4" \
       -DCMAKE_C_COMPILER=icc \
       -DCMAKE_CXX_COMPILER=icpc \
       -DMPI_C_COMPILER=mpicc \
       -DMPI_CXX_COMPILER=mpicpc \
       ..

However, I got exactly the same error as before.

I then added the include directory explicitly via the environment
variable CCXFLAGS:

export CXXFLAGS=-I/cm/shared/apps/intel/compilers_and_libraries_2016.1.150/linux/mkl/include

With this I was able to build the binary successfully.

Cheers,

Loris

Mark Abraham <mark.j.abraham at gmail.com> writes:

> Hi,
>
> Specifying MKL variables hasn't been necessary since its version 11
> introduced -qmkl, but I don't know why your build isn't working. Different
> shell when you configured, perhaps? Run Intel's compilervars.sh script as
> you are doing, and let GMX_FFT_LIBRARY=mkl do the job.
>
> Mark
>
> On Thu, Jan 26, 2017 at 11:15 AM Loris Bennett <loris.bennett at fu-berlin.de>
> wrote:
>
>> Hi,
>>
>> I am trying to install version 5.1.4 for one of our users with the Intel
>> compiler 2016.1.150 and MKL:
>>
>> module add intel/compiler/64/16.0 boost/1.61
>> compilervars.sh intel64
>> mkdir build
>> cd build
>> ccmake -DGMX_MPI=on \
>>        -DGMX_FFT_LIBRARY=mkl \
>>
>>  -DMKL_LIBRARIES="/cm/shared/apps/intel/compilers_and_libraries_2016.1.150/linux/mkl/lib/intel64/libmkl_rt.so"
>> \
>>
>>  -DMKL_INCLUDE_DIR="/cm/shared/apps/intel/compilers_and_libraries_2016.1.150/linux/mkl/include"
>> \
>>
>>  -DCMAKE_INSTALL_PREFIX="/cm/shared/apps/gromacs/openmpi/intel/64/5.1.4" \
>>        -DCMAKE_C_COMPILER=icc \
>>        -DCMAKE_CXX_COMPILER=icpc \
>>        -DMPI_C_COMPILER=mpicc \
>>        -DMPI_CXX_COMPILER=mpicpc \
>>        ..
>>
>> When I then run 'make VERBOSE=1' I get the following error:
>>
>> [  0%] Building CXX object
>> src/gromacs/CMakeFiles/libgromacs.dir/fft/fft_mkl.cpp.o
>> cd /home/BUILD/gromacs/gromacs-5.1.4/build/src/gromacs &&
>> /cm/shared/apps/intel/compilers_and_libraries_2016.1.150/linux/bin/intel64/icpc
>>  -DHAVE_CONFIG_H -Dlibgromacs_EXPORTS -msse4.1    -w3 -wd177 -wd271 -wd304
>> -wd383 -wd424 -wd444 -wd522 -wd593 -wd869 -wd981 -wd1418 -wd1419 -wd1572
>> -wd1599 -wd2259 -wd2415 -wd2547 -wd2557 -wd3280 -wd3346 -wd11074 -wd11076
>> -wd1782 -wd2282  -O3 -DNDEBUG -ip -funroll-all-loops -alias-const
>> -ansi-alias   -fPIC
>> -I/home/BUILD/gromacs/gromacs-5.1.4/build/src/external/tng_io/include
>> -I/home/BUILD/gromacs/gromacs-5.1.4/src/external/tng_io/include
>> -I/home/BUILD/gromacs/gromacs-5.1.4/build/src
>> -I/home/BUILD/gromacs/gromacs-5.1.4/src/external/thread_mpi/include
>> -I/home/BUILD/gromacs/gromacs-5.1.4/src
>> -I/cm/shared/apps/intel/compilers_and_libraries_2016.1.150/linux/mpi/intel64/include
>> -I/cm/shared/apps/boost/1.61/include    -openmp -o
>> CMakeFiles/libgromacs.dir/fft/fft_mkl.cpp.o -c
>> /home/BUILD/gromacs/gromacs-5.1.4/src/gromacs/fft/fft_mkl.cpp
>> /home/BUILD/gromacs/gromacs-5.1.4/src/gromacs/fft/fft_mkl.cpp(41):
>> catastrophic error: cannot open source file "mkl_dfti.h"
>>   #include <mkl_dfti.h>
>>
>> It seems that the directory defined by MKL_INCLUDE_DIR is not being
>> passed to the compiler via a '-I' option.
>>
>> What am I doing wrong?
>>
>> Cheers,
>>
>> Loris
>>
>> --
>> Dr. Loris Bennett (Mr.)
>> ZEDAT, Freie Universität Berlin         Email loris.bennett at fu-berlin.de
>> --
>> Gromacs Users mailing list
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-- 
Dr. Loris Bennett (Mr.)
ZEDAT, Freie Universität Berlin         Email loris.bennett at fu-berlin.de