Bizarrely enough I can build on my machine with the exact same configuration as the jenkins auto-build uses (<a href="http://goo.gl/e3Ku1">http://goo.gl/e3Ku1</a>).<div><br></div><div>The only difference is the OS version, but not the compiler used (in both cases gcc/gfortran 4.6 was used).</div>
<div><br></div><div>Any idea what could cause this discrepancy?</div><div><br></div><div>--<br>Szilárd<br>
<br><br><div class="gmail_quote">On Fri, Jun 1, 2012 at 11:05 AM, Szilárd Páll <span dir="ltr"><<a href="mailto:szilard.pall@cbr.su.se" target="_blank">szilard.pall@cbr.su.se</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div class="HOEnZb"><div class="h5">On Fri, Jun 1, 2012 at 3:45 AM, Christoph Junghans <<a href="mailto:junghans@votca.org">junghans@votca.org</a>> wrote:<br>
> 2012/5/31 Szilárd Páll <<a href="mailto:szilard.pall@cbr.su.se">szilard.pall@cbr.su.se</a>>:<br>
>> On Thu, May 31, 2012 at 5:29 PM, Alexey Shvetsov<br>
>> <<a href="mailto:alexxy@omrb.pnpi.spb.ru">alexxy@omrb.pnpi.spb.ru</a>> wrote:<br>
>>> Szilárd Páll писал 2012-05-31 19:09:<br>
>>><br>
>>>> Hi,<br>
>>>><br>
>>>> I bumped into a strange issue when verifying the nbnxn code with<br>
>>>> Jenkins. Using the Fortran kernels, while the appropriate OpenMP flag<br>
>>>> is used and mdrun compiles fine, some tools fail to compile with a<br>
>>>> weird message complaining about missing symbols:<br>
>>>><br>
>>>> ../gmxlib/libgmx.so.6: undefined reference to `omp_get_thread_num'<br>
>>>> ../gmxlib/libgmx.so.6: undefined reference to `GOMP_parallel_end'<br>
>>>> ../gmxlib/libgmx.so.6: undefined reference to `omp_get_num_threads'<br>
>>>> ../gmxlib/libgmx.so.6: undefined reference to `omp_set_num_threads'<br>
>>>> ../gmxlib/libgmx.so.6: undefined reference to `GOMP_parallel_start'<br>
>>>> ../gmxlib/libgmx.so.6: undefined reference to `omp_get_max_threads'<br>
>>>><br>
>>>> i) Does anybody have an idea what could be wrong?<br>
>>>><br>
>>>> ii) For what platforms are the fortran kernels still useful? If there<br>
>>>> is any platform where they provide a faster alternative to the plain C<br>
>>>> kernels, we should definitely keep them. Otherwise, deprecating them<br>
>>>> is an option.<br>
>>>><br>
>>>> Cheers,<br>
>>>> --<br>
>>>> Szilárd<br>
>>><br>
>>><br>
>>> Looks like something doesn link with -lgomp<br>
>>> Does build system forces "-fopenmp" for tools in case fortran kernel build?<br>
>><br>
>> Yes, -fopnemp is simply added to the CFLAGS. I thought that was<br>
>> harmless, moreover, some tools do use OpenMP. Could this be the issue?<br>
> That is strange. Usually -lgomp is added internally by gcc automatically.<br>
> $ echo "int main() { return 0; }" > test.c<br>
> $ gcc -fopenmp test.c -o test<br>
> $ ldd test | grep omp<br>
> libgomp.so.1 => /usr/lib/gcc/i686-pc-linux-gnu/4.6.3/libgomp.so.1<br>
><br>
> Did we add -fopenmp to the Fortran Flags as well?<br>
<br>
</div></div>No, only to the CFLAGS. However, AFAIK only the kernels are compiled<br>
with a fortran, the rest by the C compiler.<br>
<div class="HOEnZb"><div class="h5"><br>
>> --<br>
>> Szilárd<br>
>><br>
>>> --<br>
>>> Best Regards,<br>
>>> Alexey 'Alexxy' Shvetsov<br>
>>> Petersburg Nuclear Physics Institute, NRC Kurchatov Institute, Gatchina,<br>
>>> Russia<br>
>>> Department of Molecular and Radiation Biophysics<br>
>>> Gentoo Team Ru<br>
>>> Gentoo Linux Dev<br>
>>> mailto:<a href="mailto:alexxyum@gmail.com">alexxyum@gmail.com</a><br>
>>> mailto:<a href="mailto:alexxy@gentoo.org">alexxy@gentoo.org</a><br>
>>> mailto:<a href="mailto:alexxy@omrb.pnpi.spb.ru">alexxy@omrb.pnpi.spb.ru</a><br>
>>> --<br>
>>> gmx-developers mailing list<br>
>>> <a href="mailto:gmx-developers@gromacs.org">gmx-developers@gromacs.org</a><br>
>>> <a href="http://lists.gromacs.org/mailman/listinfo/gmx-developers" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-developers</a><br>
>>> Please don't post (un)subscribe requests to the list. Use the www interface<br>
>>> or send it to <a href="mailto:gmx-developers-request@gromacs.org">gmx-developers-request@gromacs.org</a>.<br>
>> --<br>
>> gmx-developers mailing list<br>
>> <a href="mailto:gmx-developers@gromacs.org">gmx-developers@gromacs.org</a><br>
>> <a href="http://lists.gromacs.org/mailman/listinfo/gmx-developers" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-developers</a><br>
>> Please don't post (un)subscribe requests to the list. Use the<br>
>> www interface or send it to <a href="mailto:gmx-developers-request@gromacs.org">gmx-developers-request@gromacs.org</a>.<br>
><br>
><br>
><br>
> --<br>
> Christoph Junghans<br>
> Web: <a href="http://www.compphys.de" target="_blank">http://www.compphys.de</a><br>
> --<br>
> gmx-developers mailing list<br>
> <a href="mailto:gmx-developers@gromacs.org">gmx-developers@gromacs.org</a><br>
> <a href="http://lists.gromacs.org/mailman/listinfo/gmx-developers" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-developers</a><br>
> Please don't post (un)subscribe requests to the list. Use the<br>
> www interface or send it to <a href="mailto:gmx-developers-request@gromacs.org">gmx-developers-request@gromacs.org</a>.<br>
</div></div></blockquote></div><br></div>