Dear Rajib,
Originally I have made too many irreversible changes to my ubuntu trying to
fit requirements, including nvidia cuda and openMPI. Hence segmentation
fault and system started crushing in general. Since then I re-installed
Ununtu, Intel drivers and libraries, newest version of cmake.
Ubuntu 18.04.3 LTS
Intel® Parallel Studio XE 2019
gromacs-2018.8.tar.gz
fftw-3.3.8.tar.gz
cmake-3.16.0-rc1-Linux-x86_64.tar.gz
Sourced Intel compilers:
source /opt/intel/bin/compilervars.sh intel64
source /opt/intel/impi/2019.5.281/intel64/bin/mpivars.sh
source /opt/intel/mkl/bin/mklvars.sh intel64
Runned cmake install using the flags:
sudo cmake .. -DBUILD_SHARED_LIBS=off -DGMX_FFT_LIBRARY=mkl
-DCMAKE_INSTALL_PREFIX=$installDir -DGMX_MPI=on -DGMX_OPENMP=on
-DGMX_CYCLE_SUBCOUNTERS=on -DGMX_GPU=off -DGMX_SIMD=SSE2
-DCMAKE_C_COMPILER="/opt/intel/bin/icc"
-DCMAKE_CXX_COMPILER="/opt/intel/bin/icpc" -DREGRESSIONTEST_DOWNLOAD=on
Now it works perfectly, performance just great.
Fantastic reply from Quin K - THANKS.
Hope it helps,
Lyudmyla
On Mon, Dec 30, 2019 at 7:15 AM Rajib Biswas wrote:
> Dear Gromacs-Users,
>
> Is there any update on this issue? I have used the following flags for
> version 2019.3
>
> /apps/codes/cmake/3.15.4/bin/cmake ..
> -DCMAKE_INSTALL_PREFIX=/opt/gromacs/2019.3 -DGMX_FFT_LIBRARY=fftw3
> -DCMAKE_PREFIX_PATH=/apps/libs/fftw/3.3.8 -DBUILD_SHARED_LIBS=OFF
> -DGMX_DOUBLE=ON -DGMX_SIMD=AVX2_256 -DCMAKE_C_COMPILER=mpiicc
> -DCMAKE_CXX_COMPILER=mpiicpc -DGMX_MPI=ON -DGMX_OPENMP=ON
> -DGMX_BUILD_MDRUN_ONLY=ON
>
> and getting compilation error which says:
>
> [ 58%] Building CXX object
> src/gromacs/CMakeFiles/libgromacs.dir/awh/pointstate.cpp.o
> icpc: error #10105:
> /apps/intel/compilers_and_libraries_2019.5.281/linux/bin/intel64/mcpcom:
> core dumped
> icpc: warning #10102: unknown signal(-497903120)
> icpc: error #10106: Fatal error in
> /apps/intel/compilers_and_libraries_2019.5.281/linux/bin/intel64/mcpcom,
> terminated by unknown
> compilation aborted for
> /storage/rajib/opt/gromacs-2019.3/src/gromacs/pulling/pullutil.cpp (code 1)
> make[2]: *** [src/gromacs/CMakeFiles/libgromacs.dir/pulling/pullutil.cpp.o]
> Error 1
> make[2]: *** Waiting for unfinished jobs
> make[1]: *** [src/gromacs/CMakeFiles/libgromacs.dir/all] Error 2
> make: *** [all] Error 2
>
> Your help will be highly appreciated.
>
> Thanking you.
>
> With regards,
> Rajib
>
>
>
> On Wed, Oct 9, 2019 at 4:03 AM Lyudmyla Dorosh wrote:
>
> > I have tried this command line:
> > sudo cmake .. -DBUILD_SHARED_LIBS=OFF -DGMX_FFT_LIBRARY=mkl
> > -DCMAKE_INSTALL_PREFIX=$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 ..***Failed0.00
> 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
>
