Sorry to take so long to reply ...
On Thu, 2015-12-17 at 11:53 -0500, Tony Schreiner wrote:
Did you load the compat-openmpi environment module?
module load mpi/compat-openmpi16-x86_64
Yes, but you can't load both mpi/openmpi-x86_64 and mpi/compat- openmpi16-x86_64 as they are labelled as conflicting.
As I said, if you load just mpi/compat-openmpi16-x86_64 it can't find the boost-openmpi library; if you load just mpi/openmpi-x86_64 it can't find the correct libmpi version.
P.
Tony
On Thu, Dec 17, 2015 at 10:57 AM, Pete Biggs pete@biggs.org.uk wrote:
After the 7.2 upgrade boost-openmpi-1.53.0-25 was installed, along with openmpi-1.10.0-10. The old openmpi was then replaced with compat- openmpi16-1.6.4-10. All fine.
Except boost-openmpi has a dependency on the old libmpi.so.1 and the new openmpi has libmpi.so.12:
# ldd libboost_mpi-mt.so.1.53.0 linux-vdso.so.1 => (0x00007ffe8c182000) libboost_serialization-mt.so.1.53.0 => /lib64/libboost_serialization-mt.so.1.53.0 (0x00007f39da4d2000) libmpi.so.1 => not found libmpi_cxx.so.1 => /usr/lib64/openmpi/lib/libmpi_cxx.so.1 (0x00007f39da2b6000) librt.so.1 => /lib64/librt.so.1 (0x00007f39da0ae000) libstdc++.so.6 => /lib64/libstdc++.so.6 (0x00007f39d9da5000) libm.so.6 => /lib64/libm.so.6 (0x00007f39d9aa3000) libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00007f39d988d000) libpthread.so.0 => /lib64/libpthread.so.0 (0x00007f39d9670000) libc.so.6 => /lib64/libc.so.6 (0x00007f39d92af000) libmpi.so.12 => /usr/lib64/openmpi/lib/libmpi.so.12 (0x00007f39d8fcc000) libopen-rte.so.12 => /usr/lib64/openmpi/lib/libopen-rte.so.12 (0x00007f39d8d4f000) libopen-pal.so.13 => /usr/lib64/openmpi/lib/libopen-pal.so.13 (0x00007f39d8aac000) libdl.so.2 => /lib64/libdl.so.2 (0x00007f39d88a8000) libutil.so.1 => /lib64/libutil.so.1 (0x00007f39d86a4000) libhwloc.so.5 => /lib64/libhwloc.so.5 (0x00007f39d8476000) /lib64/ld-linux-x86-64.so.2 (0x00007f39da987000) libnuma.so.1 => /lib64/libnuma.so.1 (0x00007f39d8269000) libpciaccess.so.0 => /lib64/libpciaccess.so.0 (0x00007f39d805f000) libxml2.so.2 => /lib64/libxml2.so.2 (0x00007f39d7cf6000) libz.so.1 => /lib64/libz.so.1 (0x00007f39d7adf000) liblzma.so.5 => /lib64/liblzma.so.5 (0x00007f39d78ba000)
We have tried switching to using compat-openmpi - but then the programs don't find the boost library.
There are other ways around it (setting the LD_LIBRARY_PATH variable or putting in symlinks so things are found), but they seem to throw segfaults with the code.
Presumably this is just a packaging/compiling error - is there anyway to trigger an update for the boost-openmpi package?
Pete _______________________________________________ CentOS mailing list CentOS@centos.org https://lists.centos.org/mailman/listinfo/centos