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Subject: Re: [OMPI users] EXTERNAL: Re: Unresolved reference 'mbind' and 'get_mempolicy'
From: Blosch, Edwin L (edwin.l.blosch_at_[hidden])
Date: 2011-09-28 17:02:25


I've tried it now adding --without-libnuma. Actually that did NOT fix the problem, so I can send you the full output from configure if you want, to understand why this "hwloc" function is trying to use a function which appears to be unavailable. The answers to some of your questions:

The configure command was this:

./configure --prefix=/release/cfd/openmpi-intel --without-tm --without-sge --without-lsf --without-psm --without-portals --without-elan --without-slurm --without-loadleveler --without-libnuma --enable-mpirun-prefix-by-default --enable-contrib-no-build=vt --enable-mca-no-build=maffinity --disable-per-user-config-files --disable-io-romio --enable-static --disable-shared --without-openib CXX=/appserv/intel/cce/10.1.021/bin/icpc CC=/appserv/intel/cce/10.1.021/bin/icc 'CFLAGS= -O2' 'CXXFLAGS= -O2' F77=/appserv/intel/fce/10.1.021/bin/ifort 'FFLAGS=-D_GNU_SOURCE -traceback -O2' FC=/appserv/intel/fce/10.1.021/bin/ifort 'FCFLAGS=-D_GNU_SOURCE -traceback -O2' 'LDFLAGS= -static-intel

The error messages upon linking the application are unchanged:
> /scratch1/bloscel/builds/release/openmpi-intel/lib/libmpi.a(topology-linux.o): In function `hwloc_linux_alloc_membind':
> topology-linux.c:(.text+0x1da): undefined reference to `mbind'

Re: NUMA: It appears there is a /usr/lib64/ but no static version. There is /usr/include/numa.h and /usr/include/numaif.h.

I don't understand about make V=1. What tree? Somewhere in the OpenMPI build, or in the application compilation itself? Is "V=1" something in the OpenMPI makefile structure?



-----Original Message-----
From: users-bounces_at_[hidden] [mailto:users-bounces_at_[hidden]] On Behalf Of Jeff Squyres
Sent: Wednesday, September 28, 2011 11:05 AM
To: Open MPI Users
Subject: EXTERNAL: Re: [OMPI users] Unresolved reference 'mbind' and 'get_mempolicy'

Yowza; that sounds like a configury bug. :-(

What line were you using to configure Open MPI? Do you have libnuma installed? If so, do you have the .h and .so files? Do you have the .a file?

Can you send the last few lines of output from a failed "make V=1" in that tree? (it'll show us the exact commands used to compile/link, etc.)

On Sep 28, 2011, at 11:55 AM, Blosch, Edwin L wrote:

> I am getting some undefined references in building OpenMPI 1.5.4 and I would like to know how to work around it.
> The errors look like this:
> /scratch1/bloscel/builds/release/openmpi-intel/lib/libmpi.a(topology-linux.o): In function `hwloc_linux_alloc_membind':
> topology-linux.c:(.text+0x1da): undefined reference to `mbind'
> topology-linux.c:(.text+0x213): undefined reference to `mbind'
> /scratch1/bloscel/builds/release/openmpi-intel/lib/libmpi.a(topology-linux.o): In function `hwloc_linux_set_area_membind':
> topology-linux.c:(.text+0x414): undefined reference to `mbind'
> topology-linux.c :(.text+0x46c): undefined reference to `mbind'
> /scratch1/bloscel/builds/release/openmpi-intel/lib/libmpi.a(topology-linux.o): In function `hwloc_linux_get_thisthread_membind':
> topology-linux.c:(.text+0x4ff): undefined reference to `get_mempolicy'
> topology-linux.c:(.text+0x5ff): undefined reference to `get_mempolicy'
> /scratch1/bloscel/builds/release/openmpi-intel/lib/libmpi.a(topology-linux.o): In function `hwloc_linux_set_thisthread_membind':
> topology-linux.c:(.text+0x7b5): undefined reference to `migrate_pages'
> topology-linux.c:(.text+0x7e9): undefined reference to `set_mempolicy'
> topology-linux.c:(.text+0x831): undefined reference to `set_mempolicy'
> make: *** [main] Error 1
> S ome configure output that is probably relevant:
> checking numaif.h usability... yes
> checking numaif.h presence... yes
> checking for numaif.h... yes
> checking for set_mempolicy in -lnuma... yes
> checking for mbind in -lnuma... yes
> checking for migrate_pages in -lnuma... yes
> The FAQ says that I should have to give -with-libnuma explicitly, but I did not do that. Is there a problem with configure? Or the FAQ? Or perhaps the system has a configuration peculiarity?
> On another system, the configure output is different, and there are no unresolved references:
> checking numaif.h usability... no
> checking numaif.h presence... no
> checking for numaif.h... no
> What is the configure option that will make the unresolved references go away?
> Thanks,
> Ed
> _______________________________________________
> users mailing list
> users_at_[hidden]

Jeff Squyres
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