I am trying to build Gromacs 4.6 on a Linux machine, running Scientific Linux 6.2. I am doing an MPI build with Intel-MPI, and Intel compilers, and MKL.
Commands I issue to set environment, and run cmake (available as cmake28) are: [cczcb@login02 gromacs-build-nocuda]$ module load intel/compiler/64 [cczcb@login02 gromacs-build-nocuda]$ module load intel-mpi/64/4.1.0 [cczcb@login02 gromacs-build-nocuda]$ module load intel/mkl/64 [cczcb@login02 gromacs-build-nocuda]$ export CC=mpicc [cczcb@login02 gromacs-build-nocuda]$ export CXX=mpicxx [cczcb@login02 gromacs-build-nocuda]$ mklvars_intel64.sh [cczcb@login02 gromacs-build-nocuda]$ cmake28 ../gromacs-4.6 -DCMAKE_INSTALL_PREFIX=/home/cczcb/gromacs-install -DGMX_MPI=ON -DGMX_FFT_LIBRARY=mkl -DMKL_INCLUDE_DIR=/cm/shared/apps/intel/composer_xe/2011_sp1.11.339/mkl/include -DMKL_LIBRARIES=/cm/shared/apps/intel/composer_xe/2011_sp1.11.339/mkl/lib/intel64/libmkl_intel_lp64.so;/cm/shared/apps/intel/composer_xe/2011_sp1.11.339/mkl/lib/intel64/libmkl_sequential.so;/cm/shared/apps/intel/composer_xe/2011_sp1.11.339/mkl/lib/intel64/libmkl_core.so This completes, but gives Segmentation fault messages at the end. Output attached as 'cmake28.out' When I type 'make', it gets to 53% then gives a large number of 'undefined reference' errors, see 'make.out'. I have also tried only putting the libmkl_core.so library path as the setting for MKL_LIBRARIES. This avoids the Segmentation faults, but again results in many undefined references, as you might expect. Any idea what could be happening here ? Is Cmake messing up in parsing the command in some way ? Is there a different approach I could use to build Gromacs ? Any assistance much appreciated! Colin cmake28.out <http://gromacs.5086.x6.nabble.com/file/n5008889/cmake28.out> make.out <http://gromacs.5086.x6.nabble.com/file/n5008889/make.out> -- View this message in context: http://gromacs.5086.x6.nabble.com/Problems-building-gromacs-4-6-tp5008889.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
