[gmx-developers] Fortran acceleration + OpenMP strangeness

[Alexey Shvetsov]

Szilárd Páll писал 2012-05-31 19:09:
> Hi,
>
> I bumped into a strange issue when verifying the nbnxn code with
> Jenkins. Using the Fortran kernels, while the appropriate OpenMP flag
> is used and mdrun compiles fine, some tools fail to compile with a
> weird message complaining about missing symbols:
>
> ../gmxlib/libgmx.so.6: undefined reference to `omp_get_thread_num'
> ../gmxlib/libgmx.so.6: undefined reference to `GOMP_parallel_end'
> ../gmxlib/libgmx.so.6: undefined reference to `omp_get_num_threads'
> ../gmxlib/libgmx.so.6: undefined reference to `omp_set_num_threads'
> ../gmxlib/libgmx.so.6: undefined reference to `GOMP_parallel_start'
> ../gmxlib/libgmx.so.6: undefined reference to `omp_get_max_threads'
>
> i) Does anybody have an idea what could be wrong?
>
> ii) For what platforms are the fortran kernels still useful? If there
> is any platform where they provide a faster alternative to the plain 
> C
> kernels, we should definitely keep them. Otherwise, deprecating them
> is an option.
>
> Cheers,
> --
> Szilárd

Looks like something doesn link with -lgomp
Does build system forces "-fopenmp" for tools in case fortran kernel 
build?
-- 
Best Regards,
Alexey 'Alexxy' Shvetsov
Petersburg Nuclear Physics Institute, NRC Kurchatov Institute, 
Gatchina, Russia
Department of Molecular and Radiation Biophysics
Gentoo Team Ru
Gentoo Linux Dev
mailto:alexxyum at gmail.com
mailto:alexxy at gentoo.org
mailto:alexxy at omrb.pnpi.spb.ru