[gmx-users] V2018.1 building issues

Mark Abraham mark.j.abraham at gmail.com
Fri May 11 15:23:59 CEST 2018


I'm surprised that was able to work in 2016, but nevertheless it was never
designed to work and should not be relied upon. Build a separate binary for
each hardware flavor and have the module system choose the correct one to
load, per our installation guide


On Thu, May 10, 2018 at 4:17 PM kevin chen <fch6699 at gmail.com> wrote:

> Hi  Gromacs Users,
> I'm having this weird issue while trying to build the new V2018.1 on
> Stampede2, which has both SKX amd KNL nodes on it. For V2016 and older, in
> order to run the same executable(mdrun_mpi), we have to build the "fat"
> binary with " -DGMX_SIMD=AVX_512" and "-DCMAKE_C_FLAGS="-O3 -xCORE-AVX2
> -axCORE-AVX512,MIC-AVX512 ". That actually worked just fine for V2016. We
> can actually run simulation on both skx and knl without any issues using
> the same binary. However, for some reason the same trick no longer works
> with V2018.1. We tried to build V2018.1 with the exactly same building
> script with " -DGMX_SIMD=AVX_512" option applied. This time around the
> binary(mdrun_mpi) only works on skx node but no on knls. So I was wondering
> is there any thing change since V2016 causing this issue or am I missing
> anything here? Thanks advanced for any pointers you guys might provide.
> Our building environment,
> Currently Loaded Modules:
>   1) intel/17.0.4   3) git/2.9.0       5) python/2.7.13   7) TACC
>   2) impi/17.0.3    4) autotools/1.1   6) xalt/1.7.7      8) cmake/3.10.2
> Best,
> Kevin
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