[gmx-developers] Fortran acceleration + OpenMP strangeness

Szilárd Páll szilard.pall at cbr.su.se
Fri Jun 1 03:01:51 CEST 2012

On Thu, May 31, 2012 at 5:29 PM, Alexey Shvetsov
<alexxy at omrb.pnpi.spb.ru> wrote:
> 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?

Yes, -fopnemp is simply added to the CFLAGS. I thought that was
harmless, moreover, some tools do use OpenMP. Could this be the issue?

> --
> 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
> --
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