[gmx-users] Need help with installation of Gromacs-2019.3 with Intell compilers
Lyudmyla Dorosh
dorosh at ualberta.ca
Thu Jan 2 04:54:56 CET 2020
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=$installDir -DGMX_MPI=on -DGMX_OPENMP=on
-DGMX_CYCLE_SUBCOUNTERS=on -DGMX_GPU=off -DGMX_SIMD=SSE2
-DCMAKE_C_COMPILER="/opt/intel/bin/icc"
-DCMAKE_CXX_COMPILER="/opt/intel/bin/icpc" -DREGRESSIONTEST_DOWNLOAD=on
Now it works perfectly, performance just great.
Fantastic reply from Quin K - THANKS.
Hope it helps,
Lyudmyla
On Mon, Dec 30, 2019 at 7:15 AM Rajib Biswas <chemrajib at gmail.com> wrote:
> Dear Gromacs-Users,
>
> Is there any update on this issue? I have used the following flags for
> version 2019.3
>
> /apps/codes/cmake/3.15.4/bin/cmake ..
> -DCMAKE_INSTALL_PREFIX=/opt/gromacs/2019.3 -DGMX_FFT_LIBRARY=fftw3
> -DCMAKE_PREFIX_PATH=/apps/libs/fftw/3.3.8 -DBUILD_SHARED_LIBS=OFF
> -DGMX_DOUBLE=ON -DGMX_SIMD=AVX2_256 -DCMAKE_C_COMPILER=mpiicc
> -DCMAKE_CXX_COMPILER=mpiicpc -DGMX_MPI=ON -DGMX_OPENMP=ON
> -DGMX_BUILD_MDRUN_ONLY=ON
>
> and getting compilation error which says:
>
> [ 58%] Building CXX object
> src/gromacs/CMakeFiles/libgromacs.dir/awh/pointstate.cpp.o
> icpc: error #10105:
> /apps/intel/compilers_and_libraries_2019.5.281/linux/bin/intel64/mcpcom:
> core dumped
> icpc: warning #10102: unknown signal(-497903120)
> icpc: error #10106: Fatal error in
> /apps/intel/compilers_and_libraries_2019.5.281/linux/bin/intel64/mcpcom,
> terminated by unknown
> compilation aborted for
> /storage/rajib/opt/gromacs-2019.3/src/gromacs/pulling/pullutil.cpp (code 1)
> make[2]: *** [src/gromacs/CMakeFiles/libgromacs.dir/pulling/pullutil.cpp.o]
> Error 1
> make[2]: *** Waiting for unfinished jobs....
> make[1]: *** [src/gromacs/CMakeFiles/libgromacs.dir/all] Error 2
> make: *** [all] Error 2
>
> Your help will be highly appreciated.
>
> Thanking you.
>
> With regards,
> Rajib
>
>
>
> On Wed, Oct 9, 2019 at 4:03 AM Lyudmyla Dorosh <dorosh at ualberta.ca> wrote:
>
> > I have tried this command line:
> > sudo cmake .. -DBUILD_SHARED_LIBS=OFF -DGMX_FFT_LIBRARY=mkl
> > -DCMAKE_INSTALL_PREFIX=$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
> > >
> > > * Please search the archive at
> > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > posting!
> > >
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> > > send a mail to gmx-users-request at gromacs.org.
> > >
> >
> >
> > --
> > 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
> > --
> > 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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