[gmx-users] Need help with installation of Gromacs-2019.3 with Intell compilers

Mon Dec 30 15:15:00 CET 2019

Dear Gromacs-Users,

Is there any update on this issue? I have used the following flags for
version 2019.3

/apps/codes/cmake/3.15.4/bin/cmake ..
-DCMAKE_INSTALL_PREFIX=/opt/gromacs/2019.3 -DGMX_FFT_LIBRARY=fftw3
-DCMAKE_PREFIX_PATH=/apps/libs/fftw/3.3.8 -DBUILD_SHARED_LIBS=OFF
 -DGMX_DOUBLE=ON -DGMX_SIMD=AVX2_256 -DCMAKE_C_COMPILER=mpiicc
-DCMAKE_CXX_COMPILER=mpiicpc -DGMX_MPI=ON -DGMX_OPENMP=ON
-DGMX_BUILD_MDRUN_ONLY=ON

and getting compilation error which says:

[ 58%] Building CXX object
src/gromacs/CMakeFiles/libgromacs.dir/awh/pointstate.cpp.o
icpc: error #10105:
/apps/intel/compilers_and_libraries_2019.5.281/linux/bin/intel64/mcpcom:
core dumped
icpc: warning #10102: unknown signal(-497903120)
icpc: error #10106: Fatal error in
/apps/intel/compilers_and_libraries_2019.5.281/linux/bin/intel64/mcpcom,
terminated by unknown
compilation aborted for
/storage/rajib/opt/gromacs-2019.3/src/gromacs/pulling/pullutil.cpp (code 1)
make[2]: *** [src/gromacs/CMakeFiles/libgromacs.dir/pulling/pullutil.cpp.o]
Error 1
make[2]: *** Waiting for unfinished jobs....
make[1]: *** [src/gromacs/CMakeFiles/libgromacs.dir/all] Error 2
make: *** [all] Error 2

Your help will be highly appreciated.

Thanking you.

With regards,
Rajib

On Wed, Oct 9, 2019 at 4:03 AM Lyudmyla Dorosh <dorosh at ualberta.ca> wrote:

> I have tried this command line:
> sudo cmake .. -DBUILD_SHARED_LIBS=OFF -DGMX_FFT_LIBRARY=mkl
> -DCMAKE_INSTALL_PREFIX=$installDir -DGMX_MPI=ON -DGMX_OPENMP=ON
> -DGMX_CYCLE_SUBCOUNTERS=ON -DGMX_GPU=OFF -DGMX_SIMD=SSE2
> -DCMAKE_C_COMPILER="/home/doroshl/apps/intel/bin/icc"
> -DCMAKE_CXX_COMPILER="/home/doroshl/apps/intel/bin/icpc"
> -DREGRESSIONTEST_DOWNLOAD=ON
> which had no errors for *cmake* or *make -j 4*, but *make check* gave me an
> error:
> ...
> [100%] Running all tests except physical validation
> Test project /home/doroshl/gromacs-2019.3/build
>       Start  1: TestUtilsUnitTests
>  1/46 Test  #1: TestUtilsUnitTests ..................***Failed    0.00 sec
> /home/doroshl/gromacs-2019.3/build/bin/testutils-test: error while loading
> shared libraries: libmkl_intel_lp64.so: cannot open shared object file: No
> such file or directory
> ...
> 0% tests passed, 46 tests failed out of 46
>
> so I included libmkl_intel_lp64.so:
> sudo cmake .. -DBUILD_SHARED_LIBS=OFF -DGMX_FFT_LIBRARY=mkl
> -DCMAKE_INSTALL_PREFIX=$installDir
>
> -DMKL_LIBRARIES="/home/doroshl/apps/intel/compilers_and_libraries_2019.5.281/linux/mkl/lib/intel64_lin/libmkl_intel_lp64.so"
> -DMKL_INCLUDE_DIR="/home/doroshl/apps/intel/intelpython2/lib"
> -DCMAKE_CXX_LINK_FLAGS="-Wl,-rpath,/usr/bin/gcc/lib64 -L/usr/bin/gcc/lib64"
> -DGMX_MPI=ON -DGMX_OPENMP=ON -DGMX_CYCLE_SUBCOUNTERS=ON -DGMX_GPU=OFF
> -DGMX_SIMD=SSE2 -DCMAKE_C_COMPILER="/home/doroshl/apps/intel/bin/icc"
> -DCMAKE_CXX_COMPILER="/home/doroshl/apps/intel/bin/icpc"
> -DREGRESSIONTEST_DOWNLOAD=ON &> cmake.out
> which doesn't give any error messages for cmake, but then in *sudo make -j
> 4 *results in
>
> [ 46%] Building CXX object
> src/gromacs/CMakeFiles/libgromacs.dir/pulling/pullutil.cpp.o
> icpc: error #10105:
>
> /home/doroshl/apps/intel/compilers_and_libraries_2019.5.281/linux/bin/intel64/mcpcom:
> core dumped
> icpc: warning #10102: unknown signal(694380720)
> icpc: error #10106: Fatal error in
>
> /home/doroshl/apps/intel/compilers_and_libraries_2019.5.281/linux/bin/intel64/mcpcom,
> terminated by unknown
> compilation aborted for
> /home/doroshl/gromacs-2019.3/src/gromacs/pulling/pullutil.cpp (code 1)
> src/gromacs/CMakeFiles/libgromacs.dir/build.make:2136: recipe for target
> 'src/gromacs/CMakeFiles/libgromacs.dir/pulling/pullutil.cpp.o' failed
> make[2]: *** [src/gromacs/CMakeFiles/libgromacs.dir/pulling/pullutil.cpp.o]
> Error 1
> make[2]: *** Waiting for unfinished jobs....
> CMakeFiles/Makefile2:2499: recipe for target
> 'src/gromacs/CMakeFiles/libgromacs.dir/all' failed
> make[1]: *** [src/gromacs/CMakeFiles/libgromacs.dir/all] Error 2
> Makefile:162: recipe for target 'all' failed
> make: *** [all] Error 2
> Thanks for any help
>
>
> On Tue, Oct 8, 2019 at 2:21 AM Paul bauer <paul.bauer.q at gmail.com> wrote:
>
> > Hej,
> >
> > I can't access the repository, so I can't say for certain what happened.
> > Can you share your cmake command line?
> >
> > Cheers
> >
> > Paul
> >
> > On 07/10/2019 21:25, Lyudmyla Dorosh wrote:
> > > Hello Gromacs Developers/Users,
> > >
> > > I'm trying to install Gromacs-2019.3 on Intel Xeon W-2175 with Intel
> > > compilers (+MKL+MPI).
> > > First I compiled cmake with Intel compilers. All output files are
> > attached.
> > > cmake, make seemed to go ok, but all check test failed. What do I do
> > wrong?
> > >
> >
> https://drive.google.com/file/d/1M8aOaq7ocmK4UOAzcRb5AqWMihIhVtmn/view?usp=sharing
> > >
> > > Thank you,
> > >
> > > Lyudmyla Dorosh, PhD
> > > ------------------------------------------------------------
> > > University of Alberta
> > > Department of Electrical and Computer Engineering,
> > > 4-021 ECERF
> > > Edmonton, AB, T6G 2G8
> > > Canada
> > > Email: dorosh at ualberta.ca
> > >
> >
> > --
> > Paul Bauer, PhD
> > GROMACS Release Manager
> > KTH Stockholm, SciLifeLab
> > 0046737308594
> >
> > --
> > Gromacs Users mailing list
> >
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> >
>
>
> --
> Regards,
>
> Lyudmyla Dorosh, PhD
> ------------------------------------------------------------
> University of Alberta
> Department of Electrical and Computer Engineering,
> 4-021 ECERF
> Edmonton, AB, T6G 2G8
> Canada
> Email: dorosh at ualberta.ca
> --
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