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

[Lyudmyla Dorosh]

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
>
> --
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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