[molpro-user] Linking problem with molpro.2012.1.4

Fri Sep 6 12:35:34 BST 2013

Dear Molproers
I've had problems trying to install Molpro2012 patch level 4 using GA 
(ga-5-2) built with MPI (mpich2-1.5)
on our ia64/RedHat el5 cluster.  Everything worked alright with 
compilation but  the program failed to link
with the following error message:
........................
linking ../bin/molpro.exe
failed
/home/soft/molpro2012.1.4/src/boost-install/lib/libboost_thread.a(once.o): 
In function `boost::thread_detail::commit_once_region(boost::once_flag&)':
once.cpp:(.text+0x142): undefined reference to 
`boost::atomics::detail::lockpool::get_lock_for(void const volatile*)'
/home/soft/molpro2012.1.4/src/boost-install/lib/libboost_thread.a(once.o): 
In function `boost::thread_detail::rollback_once_region(boost::once_flag&)':
once.cpp:(.text+0x852): undefined reference to 
`boost::atomics::detail::lockpool::get_lock_for(void const volatile*)'
/home/soft/molpro2012.1.4/src/boost-install/lib/libboost_thread.a(once.o): 
In function `boost::thread_detail::enter_once_region(boost::once_flag&)':
once.cpp:(.text+0xf42): undefined reference to 
`boost::atomics::detail::lockpool::get_lock_for(void const volatile*)'
once.cpp:(.text+0x1012): undefined reference to 
`boost::atomics::detail::lockpool::get_lock_for(void const volatile*)'
once.cpp:(.text+0x10d2): undefined reference to 
`boost::atomics::detail::lockpool::get_lock_for(void const volatile*)'
make[2]: [../bin/molpro.exe] Error 1 (ignored)
failure
/home/soft/molpro2012.1.4/src/boost-install/lib/libboost_thread.a(once.o): 
In function `boost::thread_detail::commit_once_region(boost::once_flag&)':
once.cpp:(.text+0x142): undefined reference to 
`boost::atomics::detail::lockpool::get_lock_for(void const volatile*)'
/home/soft/molpro2012.1.4/src/boost-install/lib/libboost_thread.a(once.o): 
In function `boost::thread_detail::rollback_once_region(boost::once_flag&)':
once.cpp:(.text+0x852): undefined reference to 
`boost::atomics::detail::lockpool::get_lock_for(void const volatile*)'
/home/soft/molpro2012.1.4/src/boost-install/lib/libboost_thread.a(once.o): 
In function `boost::thread_detail::enter_once_region(boost::once_flag&)':
once.cpp:(.text+0xf42): undefined reference to 
`boost::atomics::detail::lockpool::get_lock_for(void const volatile*)'
once.cpp:(.text+0x1012): undefined reference to 
`boost::atomics::detail::lockpool::get_lock_for(void const volatile*)'
once.cpp:(.text+0x10d2): undefined reference to 
`boost::atomics::detail::lockpool::get_lock_for(void const volatile*)'
make[2]: *** [../bin/molpro.exe] Error 1
make[2]: Leaving directory `/home/soft/molpro2012.1.4/src'
make[1]: *** [default] Error 2
make[1]: Leaving directory `/home/soft/molpro2012.1.4/src'
make: *** [src] Error 2
............................................................................
Any ideas would be deeply appreciated. CONFIG file is also attached.
Thanks

A. Papakondylis

-- 
_________________________________
Aristotle Papakondylis
Assistant Professor
Physical Chemistry Laboratory
Department of Chemistry
University of Athens
Panepistimiopolis Zografou
157 71 Athens, Greece
Phone:(+30210)7274565
Fax:  (+30210)7274752
e-mail: papakondylis at chem.uoa.gr
_________________________________

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# MOLPRO CONFIG generated at Thu Sep  5 20:51:16 EEST 2013, for host nodeib_01, SHA1=906ff95322ac2640f501d5a110d03f1abf60e5f2

CONFIGURE_OPTIONS="-mpp" "-mppbase" "/home/soft/ga-5-2" "-var" "PREFIX=/home/soft/molpro2012.1.4" "-var" "INSTBIN=/home/soft/molpro2012.1.4/bin"

AR=ar
ARCHNAME=Linux/ia64
ARFLAGS=-rS
AWK=awk
BIBTEX=
BLASLIB=-L/opt/intel/Compiler/11.1/059/mkl/lib/64 -lmkl_intel_ilp64 -lmkl_sequential -lmkl_core
BUILD=p
CAT=cat
CC=/usr/bin/gcc
CCVERSION=4.1.1
CC_FRONT=
CDEBUG=-g $(addprefix $(CDEFINE),_DEBUG)
CDEFINE=-D
CFLAGS=-Wcast-align -Wcast-qual -Wchar-subscripts -Wcomment -Wdeclaration-after-statement -Wformat -Wimplicit -Wimplicit-function-declaration -Wimplicit-int -Wmain -Wmissing-braces -Wmultichar -Wnested-externs -Wparentheses -Wpointer-arith -Wreturn-type -Wsequence-point -Wsign-compare -Wswitch -Wtrigraphs -Wunknown-pragmas -Wunused-function -Wunused-label -Wunused-value -Wunused-variable -Wwrite-strings -pedantic -Wno-long-long -I/home/soft/mpich2-1-5/include
CLDFLAGS=
CLEAN=echo 'target clean only available with git cloned versions, please unpack the tarball again'
CMPPINCLUDE=/home/soft/ga-5-2/include
COPT=-O3
COPT0=-O0
COPT1=-O1
COPT2=-O2
COPT3=-O3
CP=cp -p
CPROFILE=-p
CUDACC=
CUDACCVERSION=
CUDACDEBUG=-g $(addprefix $(CUDACDEFINE),_DEBUG)
CUDACDEFINE=-D
CUDACFLAGS=
CUDACOPT=
CUDACOPT0=-O0
CUDACOPT1=-O1
CUDACOPT2=-O2
CUDACOPT3=-O3
CUDACPROFILE=-p
CXX=/usr/bin/g++
CXXFLAGS=$(filter-out -Wdeclaration-after-statement -Wimplicit -Wimplicit-function-declaration -Wimplicit-int -Wmain -Wnested-externs -Wpointer-sign,$(CFLAGS))
DOXYGEN=/usr/bin/doxygen
ECHO=/bin/echo
EXPORT=export
F90FLAGS=-stand f03 -diag-disable 5268
FC=/opt/intel/Compiler/11.1/059/bin/ia64/ifort
FCVERSION=11.1
FDEBUG=-g $(addprefix $(FDEFINE),_DEBUG)
FDEFINE=-D
FFLAGS=-i8 -r8 -auto -Vaxlib -WB -ftz -align -cxxlib
FLDFLAGS=
FOPT=-O2
FOPT0=-O0
FOPT1=-O1
FOPT2=-O2
FOPT3=-O3
FPROFILE=-p
FSTATIC=
HOSTFILE_FORMAT=%N
INSTALL_FILES_EXTRA=
INSTBIN=/home/soft/molpro2012.1.4/bin
INST_PL=0
INTEGER=8
LAPACKLIB=
LATEX2HTML=
LAUNCHER=/home/soft/mpich2-1-5/bin/mpiexec -machinefile %h -np %n %x
LD_ENV=/opt/intel/Compiler/11.1/059/mkl/lib/64
LD_ENVNAME=LD_LIBRARY_PATH
LIBRARY_SUFFIX=a
LIBS=-lpthread /home/soft/molpro2012.1.4/src/boost-install/lib/libboost_system.a /home/soft/molpro2012.1.4/src/boost-install/lib/libboost_thread.a -lrt
LN=ln -s
MACROS=MOLPRO MOLPRO_f2003 GA_MPI HAVE_BOOST_THREADS _I8_ MOLPRO_INT=8 BLAS_INT=8 LAPACK_INT=8 MOLPRO_AIMS MOLPRO_NECI _MOLCAS_MPP_ MOLPRO_BLAS MOLPRO_LAPACK
MAKEDEPEND_OPTIONS=-M
MAKEINDEX=
MAPLE=
MAX_INCREMENT_LIBRARY=0
MKDIR=mkdir -p
MODULE_FLAG=-I
MODULE_SUFFIX=mod
MPILIB=-I/home/soft/mpich2-1-5/include -L/home/soft/mpich2-1-5/lib -lmpich -lopa -lmpl -lrt -lpthread
MPPLIB=-L/home/soft/ga-5-2/lib -lga -larmci
OBJECT_SUFFIX=o
OPT0=ccabc.F mxmadd.F response.F90 vcff2d.F copyc6.F
OPT1=
OPT2=rdip.F cigps.F drv2el_pg.F t2tran.F ucckext.F cicon.F
OPT3=
PAPER=a4paper
PARSE=parse-Linux-ia64-i8.o
PDFLATEX=
PNAME=molprop_2012_1_Linux_ia64_i8
PREFIX=/home/soft/molpro2012.1.4/molprop_2012_1_Linux_ia64_i8
PTSIZE=11
PYTHON=/usr/bin/python
RANLIB=ranlib
RM=rm -rf
SHELL=/bin/sh
STRIP=strip
SUFFIXES=F F90 c cpp
TAR=tar -cf
UNTAR=tar -xf
VERBOSE=@
VERSION=2012.1
XSD=/usr/bin/xmllint --noout --schema
XSLT=/usr/bin/xsltproc
YACC=bison -b y
bug3990=0

.SUFFIXES:
MAKEFLAGS+=-r
ifneq ($(LD_ENVNAME),)
$(LD_ENVNAME):=$(LD_ENV):$($(LD_ENVNAME))
endif