[gmx-developers] Fortran acceleration + OpenMP strangeness

[Szilárd Páll]

On Fri, Jun 1, 2012 at 3:45 AM, Christoph Junghans <junghans at votca.org> wrote:
> 2012/5/31 Szilárd Páll <szilard.pall at cbr.su.se>:
>> 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?
> That is strange. Usually -lgomp is added internally by gcc automatically.
> $ echo "int main() { return 0; }" > test.c
> $ gcc -fopenmp test.c -o test
> $ ldd test | grep omp
> libgomp.so.1 => /usr/lib/gcc/i686-pc-linux-gnu/4.6.3/libgomp.so.1
>
> Did we add -fopenmp to the Fortran Flags as well?

No, only to the CFLAGS. However, AFAIK only the kernels are compiled
with a fortran, the rest by the C compiler.

>> --
>> Szilárd
>>
>>> --
>>> 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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>
>
>
> --
> Christoph Junghans
> Web: http://www.compphys.de
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