On Fri, Jun 7, 2013 at 12:20 PM, colinbannister < colin.bannis...@nottingham.ac.uk> wrote:
> 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 ? > All that sounds very weird, and makes me wonder whether an MKL test program would compile on your system. Since the value of MKL is very limited, I would suggest compiling with FFTW for now. GROMACS 4.6.2 streamlined the MKL build process greatly for icc >= 11, but I would suggest waiting until GROMACS 4.6.3, because of a performance regression with MPI builds that we are working on fixing. Cheers, Mark > > 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 > -- 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
