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 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 > us...@open-mpi.org > http://www.open-mpi.org/mailman/listinfo.cgi/users -- Jeff Squyres jsquy...@cisco.com For corporate legal information go to: http://www.cisco.com/web/about/doing_business/legal/cri/ _______________________________________________ users mailing list us...@open-mpi.org http://www.open-mpi.org/mailman/listinfo.cgi/users _______________________________________________ users mailing list us...@open-mpi.org http://www.open-mpi.org/mailman/listinfo.cgi/users
