Re: [gmx-users] Need help with installation of Gromacs-2019.3 with Intell compilers
Hi,
It needs to be on its own line prior to the void.
What will be in next version of GROMACS (2019.6 and 2020.1) is:
https://gerrit.gromacs.org/c/gromacs/+/15218/4/src/gromacs/pulling/pullutil.cpp
You don't need the #ifdef/#endif if you only care about compiling with ICC.
Roland
> -Original Message-
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
> On Behalf Of
> Cardenas, Alfredo E
> Sent: Friday, January 10, 2020 12:00 PM
> To: gromacs.org_gmx-users@maillist.sys.kth.se
> Subject: [gmx-users] Need help with installation of Gromacs-2019.3 with
> Intell compilers
>
> Hi Roland and others gmx-users,
> I am also getting a similar compilation error regarding pullutil.cpp:
>
> icpc: error #10106: Fatal error in
> /opt/intel/compilers_and_libraries_2019.5.281/linux/bin/intel64/mcpcom,
> terminated by floating point exception compilation aborted for
> /home1/01247/alfredo/Software/gromacs-
> 2019.4/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
>
> using optimization for AVX512. I saw this post where you suggested a work-
> around adding "#pragma intel optimization_level 2" in front of
> pull_calc_coms. I see the line in pullutil.cpp:
>
> void pull_calc_coms(const t_commrec *cr,
> pull_t *pull,
> const t_mdatoms *md,
> t_pbc *pbc,
> double t,
> const rvec x[], rvec *xp) {
>
> I tried putting the pragma before void and it gave me a bunch of errors.
> Where exactly should it be added?
> Thanks,
>
> Alfredo
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Re: [gmx-users] Need help with installation of Gromacs-2019.3 with Intell compilers
Hi, As a work-around it is possible to put "#pragma intel optimization_level 2" in front pull_calc_coms in file src/gromacs/pulling/pullutil.cpp or use Intel compiler 2019u4 which doesn't have the problem. Lowering the optimization for the one function shouldn't have a significant impact on performance even if you use pulling because this function isn't compute intensive. A full fix is in the works. Roland > -Original Message- > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se > On Behalf Of Rajib > Biswas > Sent: Monday, December 30, 2019 6:13 AM > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] Need help with installation of Gromacs-2019.3 with > Intell compilers > > 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/int > el64/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
Re: [gmx-users] Need help with installation of Gromacs-2019.3 with Intell compilers
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 >
Re: [gmx-users] Need help with installation of Gromacs-2019.3 with Intell compilers
Here are some details I gathered over some time and how I overcame the issue of *slow running gromacs* due to not using all threads in the intel processor. * Install according to following videos* https://www.youtube.com/watch?v=vOJsmtFeSGk https://www.youtube.com/watch?v=BZNzYt_DUB0 SIMD value different for various processors. If this value is not given during gromacs dirty installation the run will be very slow. Problem of slow running gromacs https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2014-October/092874.html -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_USE_RDTSCP=ON -DGMX_SIMD=AVX2_256 Add above line when doing command during dirty installation of gromacs cmake *gromacs_extraction_folder_location* -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_USE_RDTSCP=ON -DGMX_SIMD=AVX2_256 Windows installation after enabling Linux subsystem cmake /mnt/d/gmx/gromacs-2018.7/ -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_USE_RDTSCP=ON -DGMX_SIMD=AVX2_256 http://manual.gromacs.org/documentation/2018/install-guide/index.html With tar xfz gromacs-2018.tar.gz cd gromacs-2018 mkdir build cd build cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_USE_RDTSCP=ON -DGMX_SIMD=AVX2_256 make make check sudo make install source /usr/local/gromacs/bin/GMXRC Email Thread on profiles...@gmaill.com https://mail.google.com/mail/u/0/#sent/QgrcJHsbfmGnwcmrVLLsVwCnxXgGcqBRJLg https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2017-June/114030.html To remove gromacs https://www.thelinuxfaq.com/ubuntu/ubuntu-17-04-zesty-zapus/gromacs?type=uninstall Gromacs dirty installation http://manual.gromacs.org/documentation/2018/install-guide/index.html On Mon, Dec 30, 2019 at 7:45 PM 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 > >
Re: [gmx-users] Need help with installation of Gromacs-2019.3 with Intell compilers
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 > 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 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: dor...@ualberta.ca
Re: [gmx-users] Need help with installation of Gromacs-2019.3 with Intell compilers
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 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 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: dor...@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! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Regards, Lyudmyla Dorosh, PhD University of Alberta Department of Electrical and Computer Engineering, 4-021 ECERF Edmonton, AB, T6G 2G8 Canada Email: dor...@ualberta.ca -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Need help with installation of Gromacs-2019.3 with Intell compilers
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: dor...@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! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
