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

[Mark Abraham]

Hi,

OK. I would mention this to the people who manage the modules. Needing to
do that is atypical behaviour for icc.

Mark

On Thu, Jan 26, 2017 at 1:45 PM Loris Bennett <loris.bennett at fu-berlin.de>
wrote:

> 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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> >>
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> >>
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>
> --
> Dr. Loris Bennett (Mr.)
> ZEDAT, Freie Universität Berlin         Email loris.bennett at fu-berlin.de
> --
> Gromacs Users mailing list
>
> * Please search the archive at
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> posting!
>
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>
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