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
Did you load the compat-openmpi environment module? module load mpi/compat-openmpi16-x86_64 Tony On Thu, Dec 17, 2015 at 10:57 AM, Pete Biggs <pete at 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 at centos.org > https://lists.centos.org/mailman/listinfo/centos >
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_64Yes, 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 at 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 at centos.org > > https://lists.centos.org/mailman/listinfo/centos > > >