Hi,
I'm attempting to build GROMACS 4.6.3 to run entirely within a single Xeon Phi (i.e. native) with either/both Intel MPI/OpenMP for parallelisation within the single Xeon Phi. I followed these instructions from Intel for cross compiling for Xeon Phi with cmake: http://software.intel.com/en-us/articles/cross-compilation-for-intel-xeon-phi-coprocessor-with-cmake which includes setting: export CC=icc export CXX=icpc export FC=ifort export CFLAGS="-mmic" export CXXFLAGS=$CFLAGS export FFLAGS=$CFLAGS export MPI_C=mpiicc export MPI_CXX=mpiicpc I then run cmake with: cmake .. -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_MPI=ON -DGMX_THREAD_MPI=OFF -DGMX_FFT_LIBRARY=mkl -DGMX_CPU_ACCELERATION=None -DCMAKE_INSTALL_PREFIX=~/gromacs Note -DGMX_THREAD_MPI=OFF. That seems to work fine (see attached cmake_output.txt), particularly, it finds the MIC Intel MPI: -- Found MPI_C: /opt/intel/impi/4.1.1.036/mic/lib/libmpigf.so;/opt/intel/impi/4.1.1.036/mic/lib/libmpi.so;/opt/i ntel/impi/4.1.1.036/mic/lib/libmpigi.a;/usr/lib64/libdl.so;/usr/lib64/librt.so;/usr/lib64/libpthread.so -- Checking for MPI_IN_PLACE -- Performing Test MPI_IN_PLACE_COMPILE_OK -- Performing Test MPI_IN_PLACE_COMPILE_OK - Success -- Checking for MPI_IN_PLACE - yes When I run make everything trundles along fine until: [ 20%] Building C object src/gmxlib/CMakeFiles/gmx.dir/thread_mpi/errhandler.c.o [ 20%] Building C object src/gmxlib/CMakeFiles/gmx.dir/thread_mpi/tmpi_malloc.c.o [ 22%] Building C object src/gmxlib/CMakeFiles/gmx.dir/thread_mpi/atomic.c.o [ 22%] Building C object src/gmxlib/CMakeFiles/gmx.dir/thread_mpi/pthreads.c.o /tmp/iccQqtl2Vas_.s: Assembler messages: /tmp/iccQqtl2Vas_.s:1773: Error: `sfence' is not supported on `k1om' make[2]: *** [src/gmxlib/CMakeFiles/gmx.dir/thread_mpi/pthreads.c.o] Error 1 make[1]: *** [src/gmxlib/CMakeFiles/gmx.dir/all] Error 2 make: *** [all] Error 2 Why is it still building thread_mpi given the -DGMX_THREAD_MPI=OFF at the cmake invocation above? Any suggestions how best to work around this? Thanks, Paul. cmake_output.txt <http://gromacs.5086.x6.nabble.com/file/n5011212/cmake_output.txt> -- View this message in context: http://gromacs.5086.x6.nabble.com/Cross-compiling-GROMACS-4-6-3-for-native-Xeon-Phi-thread-mpi-problem-tp5011212.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
