Jeff, Bruce, Reuti, all:
If I add --without-hwloc in addition to --without-libnuma, then it builds. Is
that a reasonable thing to do? Is there a better workaround? This 'hwloc'
module looks like it might be important.
For what it's worth, if there's something wrong with my configure line, let me
know what to improve. Otherwise, as weird as "--enable-mca-no-build=maffinity
--disable-io-romio --enable-static --disable-shared" may look, I am not trying
to build fully static binaries. I have unavoidable need to build OpenMPI on
certain machines and then transfer the executables to other machines that are
compatable but not identical, and over the years these are the minimal set of
configure flags necessary to make that possible. I may revisit these choices at
some point, but if they are supposed to work, then I'd rather just keep using
them.
Thanks again,
Ed
-Original Message-
From: users-boun...@open-mpi.org [mailto:users-boun...@open-mpi.org] On Behalf
Of Blosch, Edwin L
Sent: Wednesday, September 28, 2011 4:02 PM
To: Open MPI Users
Subject: Re: [OMPI users] EXTERNAL: Re: Unresolved reference 'mbind' and
'get_mempolicy'
Jeff,
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/libnuma.so 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?
Thanks,
Ed
-Original Message-
From: users-boun...@open-mpi.org [mailto:users-boun...@open-mpi.org] 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
