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

From: Jerry Ebalunode (jebalunode_at_UH.EDU)
Date: Wed Aug 17 2005 - 13:58:40 CDT

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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