Dear Silard, cmake -DGMX_CPU_ACCELERATION=AVX_256 -DGMX_DEFAULT_SUFFIX=OFF -DGMX_BINARY_SUFFIX="_avx" -DGMX_OPENMP=ON -DGMX_MPI=ON -DGMX_DOUBLE=ON -DGMX_GPU=OFF -DGMX_PREFER_STATIC_LIBS=ON -DGMX_FFT_LIBRARY=mkl -DMKL_INCLUDE_DIR=$MKLROOT/include -DMKL_LIBRARIES="$MKLROOT/lib/intel64/libmkl_core.so;$MKLROOT/lib/intel64/l ibmkl_intel_lp64.so;$MKLROOT/lib/intel64/libmkl_sequential.so" -DCMAKE_INSTALL_PREFIX=$HOME/libs/gromacs
Compiled, linked and installed without warning using intel-suite/2013, mpi/intel-3.1, and cmake/2.8.9 I was compiling release-4-6 out of the git repository ( 06935659a3125d9b44b84c57e67cb6788fda42c1 ). The job using that executable is still in the queue, however, another one built using the sse2 kernels ran a minimisation on a single core without problems. How much faster fftw3 is than mkl for gromacs, is the difference likely to be on the scale of 1-2% or 10%? Thanks, Richard On 07/02/2013 02:17, "Szilárd Páll" <szilard.p...@cbr.su.se> wrote: >On Wed, Feb 6, 2013 at 6:03 PM, Richard Broadbent < >richard.broadben...@imperial.ac.uk> wrote: > >> Dear All, >> >> I would like to compile gromacs 4.6 to run with the correct acceleration >> on the compute nodes on our local cluster. Some of the nodes have intel >> sandy-bridge whilst others only have sse4.1 and some (including the >>login >> and single core job nodes) are still stuck on ssse3 (gmx would use sse2 >> acceleration here). >> >> Installing several versions is not a problem however, I'm not sure how >>to >> make cmake build a version of the code that is not using the >>acceleration >> for the system on which the code is being compiled. Restrictions on job >> sizes makes running the compilation on the sandy-bridge nodes almost >> impossible. Can anyone let me know which flags cmake needs to enable >> avx-256 acceleration? >> >> my standard cmake line is: >> >> $ CC=mpiicc CXX=mpiicpc ; cmake -DGMX_OPENMP=ON -DGMX_MPI=ON >> -DGMX_DOUBLE=ON -DGMX_GPU=OFF -DGMX_PREFER_STATIC_LIBS=ON >> -DGMX_FFT_LIBRARY=mkl -DMKL_INCLUDE_DIR=$MKLROOT/**include >> -DMKL_LIBRARIES="$MKLROOT/lib/**intel64/libmkl_core.so;$** >> >>MKLROOT/lib/intel64/libmkl_**intel_lp64.so;$MKLROOT/lib/**intel64/libmkl_ >>sequential.so" >> -DCMAKE_INSTALL_PREFIX=$HOME/**libs/gromacs ../ >> > >Note that MKL (without the fftw wrappers) is known to not work out of the >box. Making it work requires a fairly simple workaround described here: >http://redmine.gromacs.org/issues/1110#note-3 > >Additionally, note that FFTW is in most cases faster than MKL (but if you >find the contrary do let us know). > >-- >Szilárd > > > >> >> >> >> Thanks, >> >> Richard >> -- >> gmx-users mailing list gmx-users@gromacs.org >> >>http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromac >>s.org/mailman/listinfo/gmx-users> >> * Please search the archive at http://www.gromacs.org/** >> >>Support/Mailing_Lists/Search<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<http://www.gromacs.org/Sup >>port/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 -- 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
