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Hi,
Am 07.04.2017 um 19:11 schrieb Christof Koehler:
> […]
>
> On top, all OpenMPI libraries when checked with ldd (gcc 6.3 module
> still loaded) reference the /usr/lib64/libstdc++.so.6 and not
> /cluster/comp/gcc/6.3.0/lib64/libstdc++.so.6 which leads to the idea
> that the OpenMPI installation might be the reason we have the
> /usr/lib64/libstdc++.so.6 dependency in the mpi4py libraries as well.
>
> What we would like to have is that libstdc++.so.6 resolves to the
> libstdc++ provided by the gcc 6.3 compiler for the mpi4py, which would be
> available in its installation directory, i.e.
> /cluster/comp/gcc/6.3.0/lib64/libstdc++.so.6.
>
> So, am I missing options in my OpenMPI build ? Should I explicitely do a
> ./configure CC=/cluster/comp/gcc/6.3.0/bin/gcc
> CXX=/cluster/comp/gcc/6.3.0/bin/g++ ...
> or similar ? Am I building it correctly with a gcc contained in a
> separate module anyway ? Or do we have a problem with our ld configuration ?
I have a default GCC 4.7.2 in the system, and I just prepend PATH and
LD_LIBRARY_PATH with the paths to my private GCC 6.2.0 compilation in my home
directory by a plain `export`. I can spot:
$ ldd libmpi_cxx.so.20
…
libstdc++.so.6 =>
/home/reuti/local/gcc-6.2.0/lib64/../lib64/libstdc++.so.6 (0x00007f184d2e2000)
So this looks fine (although /lib64/../lib64/ looks nasty). In the library, the
RPATH and RUNPATH are set:
$ readelf -a libmpi_cxx.so.20
…
0x000000000000000f (RPATH) Library rpath:
[/home/reuti/local/openmpi-2.1.0_gcc-6.2.0_shared/lib64:/home/reuti/local/gcc-6.2.0/lib64/../lib64]
0x000000000000001d (RUNPATH) Library runpath:
[/home/reuti/local/openmpi-2.1.0_gcc-6.2.0_shared/lib64:/home/reuti/local/gcc-6.2.0/lib64/../lib64]
Can you check the order in your PATH and LD_LIBRARY_PATH – are they as expected
when loading the module?
- -- Reuti
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