Re: undefined symbol errors:__builtin_bzero and _alloca building mpi-ppc-darwin version of namd2.6b1

From: Gengbin Zheng (gzheng_at_ks.uiuc.edu)
Date: Wed Aug 17 2005 - 14:14:43 CDT

Hi Jerry,

Please try downloading charm-5.9 from:
http://charm.cs.uiuc.edu/download/downloads.phtml

I hope this is fixed in the newer version of charm-5.9 in our cvs.

Gengbin

Jerry Ebalunode wrote:

> Hi all,
>
> I’m currently trying to build an mpich2 capable version of namd2.6b1
> on an Xserve cluster, using the ibm xlc 6.0 advanced c/c++ compiler
> and MPICH2 which was also built with the ibm xlc c/c++ compiler. After
> making changes to the cc-xlc.sh and
> “src/arch/mpi-ppc-darwin/conv-mach.sh” shown below, I finally managed
> to build charm++ with the “./build charm++ mpi-ppc-darwin xlc”
> command. Upon completion of the charm++ build I tried to build
> namd2.6b1 with mpicxx or xlC_r and my compilation exited with the
> following errors
>
> ld: Undefined symbols:
>
> ___builtin_bzero
>
> _alloca
>
> Fatal Error by charmc in directory
> /Users/briggstest/src/namd/namd2/MacOSX-PPC-MPI-c++
>
> Any assistance on how to resolve this problem would be appreciated,
> below are other specs and modifications not mentioned before.
>
> OS and architecture info = Mac OS Tiger 10.4, and xserve with dual G5 cpus
>
> #uname -a
>
> Darwin vbchs.uh.edu 8.2.0 Darwin Kernel Version 8.2.0: Fri Jun 24
> 17:46:54 PDT 2005; root:xnu-792.2.4.obj~3/RELEASE_PPC Power Macintosh
> powerpc
>
> T
>
> src/arch/mpi-ppc-darwin/conv-mach.sh
>
> ----------------------------------------------------------------
>
> # preprocess mpicxx which include mpich before ampi
>
> # this default conv-mach does not work with linking ampi
>
> CMK_CPP_CHARM="/lib/cpp -P"
>
> CMK_CPP_C="/common/mpich2/bin/mpicc -E"
>
> OPTS_CC="$OPTS_CC "
>
> CMK_CC="/common/mpich2/bin/mpicc "
>
> CMK_CXX="/common/mpich2/bin/mpicxx "
>
> CMK_CXXPP="/common/mpich2/bin/mpicxx -E "
>
> OPTS_LD="$OPTS_LD "
>
> CMK_LD="$CMK_CC "
>
> OPTS_LDXX="$OPTS_LDXX "
>
> CMK_LDXX="$CMK_CXX "
>
> CMK_LIBS=" -lckqt "
>
> CMK_RANLIB="ranlib"
>
> # Assumes IBM xlf90 compiler:
>
> CMK_CF77="f77 -qnocommon -qextname -qthreaded "
>
> CMK_CF90="f90 -qnocommon -qextname -qthreaded "
>
> CMK_CF90_FIXED="xlf90 -qnocommon -qextname -qthreaded -qsuffix=f=f"
>
> CMK_F90LIBS="-L/opt/ibmcmp/xlf/8.1/lib -lxlf90 -lxlopt -lxl -lxlfmath"
>
> CMK_MOD_EXT="mod"
>
> # native compilers
>
> CMK_NATIVE_LIBS=""
>
> CMK_NATIVE_CC="/common/mpich2/bin/mpicc "
>
> CMK_NATIVE_LD="/common/mpich2/bin/mpicc "
>
> CMK_NATIVE_CXX="/common/mpich2/bin/mpicxx "
>
> CMK_NATIVE_LDXX="/common/mpich2/bin/mpicxx "
>
> CMK_NATIVE_CC="/common/mpich2/bin/mpicc "
>
> CMK_NATIVE_CXX="/common/mpich2/bin/mpicxx "
>
> # setting for shared lib
>
> # need -lstdc++ for c++ reference, and it needs to be put at very last
>
> # of command line.
>
> # need 10.3 in this Mac environment varaible
>
> export MACOSX_DEPLOYMENT_TARGET=10.4
>
> CMK_SHARED_SUF="dylib"
>
> CMK_LD_SHARED=" "
>
> CMK_LD_SHARED_LIBS="-lstdc++"
>
> CMK_LD_SHARED_ABSOLUTE_PATH=true
>
> ../arch/MacOSX-PPC-MPI-c++.arch
>
> NAMD_ARCH = MacOSX-PPC
>
> CHARMARCH = mpi-ppc-darwin-xlc
>
> CXX = /common/mpich2/bin/mpicxx -O3 -D_NO_MALLOC_H -DNO_STRSTREAM_H
>
> CXXOPTS = -O3 -qaggrcopy=nooverlap -qalias=addrtaken:typeptr:ansi
>
> CXXNOALIASOPTS = -O3 -qaggrcopy=nooverlap
> -qalias=addrtaken:allptrs:typeptr:ansi
>
> CC = xlc
>
> COPTS = -O3
>
> ./tmp/cc-xlc.sh
>
> CMK_CC='xlc_r '
>
> CMK_CXX='xlC_r -qstaticinline '
>
> CMK_LD="$CMK_CC "
>
> CMK_LDXX="$CMK_CXX "
>
> CMK_NATIVE_CC='xlc_r '
>
> CMK_NATIVE_LD='xlc_r '
>
> CMK_NATIVE_CXX='xlC_r -qstaticinline '
>
> CMK_NATIVE_LDXX='xlC_r '
>
> CMK_CF77='xlf_r '
>
> CMK_CF90='xlf90_r -qsuffix=f=f90'
>
> CMK_CF90_FIXED='xlf90_r '
>
> CMK_C_OPTIMIZE='-O3 -qstrict -Q '
>
> CMK_CXX_OPTIMIZE='-O3 -qstrict -Q '
>
> CMK_AR='ar cq'
>
> CMK_NM='nm '
>

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