From owner-nwchem-users@emsl.pnl.gov Fri Apr 25 11:14:14 2008 Received: from odyssey.emsl.pnl.gov (localhost [127.0.0.1]) by odyssey.emsl.pnl.gov (8.14.1/8.14.1) with ESMTP id m3PIEDao017935 for ; Fri, 25 Apr 2008 11:14:13 -0700 (PDT) Received: (from majordom@localhost) by odyssey.emsl.pnl.gov (8.14.1/8.14.1/Submit) id m3PIECii017934 for nwchem-users-outgoing-0915; Fri, 25 Apr 2008 11:14:12 -0700 (PDT) X-Authentication-Warning: odyssey.emsl.pnl.gov: majordom set sender to owner-nwchem-users@emsl.pnl.gov using -f X-Ironport-SG: Throttle X-Ironport-SBRS: 1.5 X-IronPort-Anti-Spam-Filtered: true X-IronPort-Anti-Spam-Result: As8AAIO8EUhA6aazc2dsb2JhbACRWQEMAwQECQ+bHA X-IronPort-AV: E=Sophos;i="4.25,708,1199692800"; d="scan'208";a="51776125" Message-ID: <48121F3F.3070006@hope.edu> Date: Fri, 25 Apr 2008 14:13:19 -0400 From: Paul Van Allsburg User-Agent: Thunderbird 1.5.0.14 (Windows/20071210) MIME-Version: 1.0 To: ",NWChem users mailing list" Subject: Re: [NWCHEM] nwchem5.1 install error undefined reference with openmpi 1.2.6 References: <48060A47.3000009@hope.edu> <4806249C.1090500@pnl.gov> <48063267.2070407@hope.edu> <48064563.8090408@pnl.gov> <48076BE9.6040909@hope.edu> <480776BE.8080407@pnl.gov> <48079E97.5020607@hope.edu> In-Reply-To: Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Sender: owner-nwchem-users@emsl.pnl.gov Precedence: bulk Giacomo Mulas wrote: > On Thu, 17 Apr 2008, Paul Van Allsburg wrote: > >> Hi Dunyou, >> I still get all the same errors. >> /usr/local/openmpi-1.2.1_intel/lib/libopen-rte.a(rmgr_base_check_context.o)(.text+0x366): >> In function `orte_rmgr_base_purge_mca_params': >> : undefined reference to `opal_setenv' >> /usr/local/openmpi-1.2.1_intel/lib/libopen-rte.a(rmgr_base_check_context.o)(.text+0x394): >> In function `orte_rmgr_base_purge_mca_params': >> : undefined reference to `opal_setenv' >> make: *** [all] Error 1 >> >> What might be wrong with the mpi installation? > > invert the order between -lopen-pal and -lopen-rte. You are using static > libraries. When you link against a static libraries, only the unresolved > functions at the moment it is encountered by the linker are included > in the > result. In your case, you link first against libopen-pal, and the > function > "opal_setenv", which is at that moment not needed, is not included; > then you > link against libopen-rte, which does need that function, which was not > included and cannot be resolved. So: either you swap their order, or > you use > dynamic libs, for which that particular problem (the order of linking) > does > not exist. > > Bye > Giacomo > Hi, I've worked on the order of the libs and reduced the errors to the following small set. I'm using static libs because that's how I could get openmpi to link with the installed version of pbs. I'm running NWCHEM_TOP=/home/vanallp/nwchem/5.1/nwchem-5.1;export NWCHEM_TOP NWCHEM_TARGET=LINUX64;export NWCHEM_TARGET cd $NWCHEM_TOP/src NWCHEM_MODULES="all python"; export NWCHEM_MODULES PYTHONHOME=/usr/bin; export PYTHONHOME PYTHONVERSION=2.3; export PYTHONVERSION USE_MPI="y"; export USE_MPI LIBMPI="-lmpi -lopen-rte -lopen-pal -lpbs"; export LIBMPI MPI_LIB=/usr/local/openmpi-1.2.6_intel/lib; export MPI_LIB MPI_INCLUDE=/usr/local/openmpi-1.2.6_intel/include; export MPI_INCLUDE source /opt/intel/fce/9.1.045/bin/ifortvars.sh source /opt/intel/cce/9.1.049/bin/iccvars.sh FC=ifort;export FC CC=icc; export CC And I'm getting undefined aio_error64, aio_return64, aio_write64, aio_read64, aio_suspend64 references: /usr/local/openmpi-1.2.6_intel/lib/libmpi.a(io_romio_ad_nfs_done.o)(.text+0xb3): In function `mca_io_romio_dist_ADIOI_NFS_ReadDone': : undefined reference to `aio_error64' /usr/local/openmpi-1.2.6_intel/lib/libmpi.a(io_romio_ad_nfs_done.o)(.text+0xe0): In function `mca_io_romio_dist_ADIOI_NFS_ReadDone': : undefined reference to `aio_return64' /usr/local/openmpi-1.2.6_intel/lib/libmpi.a(io_romio_ad_nfs_done.o)(.text+0xf6): In function `mca_io_romio_dist_ADIOI_NFS_ReadDone': : undefined reference to `aio_error64' /usr/local/openmpi-1.2.6_intel/lib/libmpi.a(io_romio_ad_nfs_iwrite.o)(.text+0xe0): In function `mca_io_romio_dist_ADIOI_NFS_IwriteContig': : undefined reference to `aio_write64' /usr/local/openmpi-1.2.6_intel/lib/libmpi.a(io_romio_ad_nfs_iwrite.o)(.text+0x1e2): In function `mca_io_romio_dist_ADIOI_NFS_IwriteContig': : undefined reference to `aio_write64' Any suggestions as to where these references are hiding? Thanks, Paul -- Paul Van Allsburg Computational Science & Modeling Facilitator Natural Sciences Division, Hope College 35 East 12th Street Holland, Michigan 49423 616-395-7292 http://www.hope.edu/academic/csm/