[gmx-users] compiling on different architecture than the compute nodes architecture

Szilárd Páll szilard.pall at cbr.su.se
Thu Feb 7 03:17:55 CET 2013

On Wed, Feb 6, 2013 at 6:03 PM, Richard Broadbent <
richard.broadbent09 at 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
> -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:

Additionally, note that FFTW is in most cases faster than MKL (but if you
find the contrary do let us know).


> Thanks,
> Richard
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