[MOAB-dev] Fwd: linking issues

[Lorenzo Alessio Botti]

Hi all,
I’d like know your opinion on a problem I recently encountered compiling moab with intel compilers on a cluster at cineca (an Italian HPC facility)

When compiling my application linked to moab I got the following errors
/galileo/home/userexternal/lbotti00/moab/lib/libMOAB.a(ReaderWriterSet.o): In function `moab::ReaderWriterSet::get_file_extension_reader(std::string const&) const':
ReaderWriterSet.cpp:(.text+0xa22): undefined reference to `std::__throw_out_of_range_fmt(char const*, ...)'
/galileo/home/userexternal/lbotti00/moab/lib/libMOAB.a(ReaderWriterSet.o): In function `moab::ReaderWriterSet::get_file_extension_writer(std::string const&) const':
ReaderWriterSet.cpp:(.text+0xb72): undefined reference to `std::__throw_out_of_range_fmt(char const*, ...)'
/galileo/home/userexternal/lbotti00/moab/lib/libMOAB.a(ReaderWriterSet.o): In function `moab::ReaderWriterSet::extension_from_filename(std::string const&)':
ReaderWriterSet.cpp:(.text+0xcc7): undefined reference to `std::__throw_out_of_range_fmt(char const*, ...)'
/galileo/home/userexternal/lbotti00/moab/lib/libMOAB.a(ReadABAQUS.o): In function `moab::ReadABAQUS::get_keyword()':
ReadABAQUS.cpp:(.text+0x19c0): undefined reference to `std::__throw_out_of_range_fmt(char const*, ...)'
ReadABAQUS.cpp:(.text+0x19fb): undefined reference to `std::__throw_out_of_range_fmt(char const*, ...)'
/galileo/home/userexternal/lbotti00/moab/lib/libMOAB.a(ReadABAQUS.o):ReadABAQUS.cpp:(.text+0x285d): more undefined references to `std::__throw_out_of_range_fmt(char const*, ...)' follow

The problem seems to be related with  /cineca/prod/compilers/gnu/4.9.2/none/lib64/libstdc++.la
which is present in libMOAB.la but is missing in moab.make (see below) 

(libMOAB.la)

# libMOAB.la - a libtool library file
# Generated by libtool (GNU libtool) 2.4.2
#
# Please DO NOT delete this file!
# It is necessary for linking the library.

# The name that we can dlopen(3).
dlname=''

# Names of this library.
library_names=''

# The name of the static archive.
old_library='libMOAB.a'

# Linker flags that can not go in dependency_libs.
inherited_linker_flags=''

# Libraries that this one depends upon.
dependency_libs=' -L/galileo/home/userexternal/lbotti00/hdf5-1.8.10/hdf5/lib /galileo/home/userexternal/lbotti00/hdf5-1.8.10/hdf5/lib/libhdf5.la -lgpfs -lz /cineca/prod/compilers/gnu/4.9.2/none/lib64/libstdc++.la'

# Names of additional weak libraries provided by this library
weak_library_names=''

# Version information for libMOAB.
current=0
age=0
revision=0

# Is this an already installed library?
installed=no

# Should we warn about portability when linking against -modules?
shouldnotlink=no

# Files to dlopen/dlpreopen
dlopen=''
dlpreopen=''

# Directory that this library needs to be installed in:
libdir='/galileo/home/userexternal/lbotti00/moab/lib'
~                                                          



(maob.make)
# The values below are for an un-installed copy of MOAB used directly
# from its build build directory.  These values will be overridden below
# for installed copies of MOAB.
MOAB_LIBDIR = /galileo/home/userexternal/lbotti00/moab-4.6.3/src/.libs
MOAB_INCLUDES = -I/galileo/home/userexternal/lbotti00/moab-4.6.3/src \
                -I/galileo/home/userexternal/lbotti00/moab-4.6.3/src \
                -I/galileo/home/userexternal/lbotti00/moab-4.6.3/src/oldinc \
                -I/galileo/home/userexternal/lbotti00/moab-4.6.3/src/parallel \
                -I/galileo/home/userexternal/lbotti00/moab-4.6.3/src/parallel

MOAB_INCLUDES +=

MOAB_CPPFLAGS =  -DUNORDERED_MAP_NS=std::tr1 -DHAVE_UNORDERED_MAP=tr1/unordered_map -DHAVE_UNORDERED_SET=tr1/unordered_set       -I/galileo/home/userexternal/lbotti00/hdf5-1.8.10/hdf5/include -isystem /galileo/home/userexternal/lbotti00/hdf5-1.8.10/hdf5/include  -DTEMPLATE_SPECIALIZATION -DTEMPLATE_FUNC_SPECIALIZATION -DHAVE_VSNPRINTF -D_FILE_OFFSET_BITS=64   -DUSE_MPI -DHDF5_FILE -DHDF5_PARALLEL
MOAB_CXXFLAGS =  -Wall -wd981 -wd279 -wd1418 -wd383 -wd1572 -wd2259 -O2 -DNDEBUG
MOAB_CFLAGS =  -Wall -wd981 -wd279 -wd1418 -wd383 -wd1572 -O2 -DNDEBUG
MOAB_FFLAGS =   -O2
MOAB_FCFLAGS =   -O2
MOAB_LDFLAGS =          -L/galileo/home/userexternal/lbotti00/hdf5-1.8.10/hdf5/lib

MOAB_LIBS_LINK = ${MOAB_LDFLAGS} -L${MOAB_LIBDIR} -lMOAB  -lm    -lhdf5 -lgpfs  -lz -ldl

MOAB_CXX = /cineca/prod/compilers/intel/cs-xe-2015/binary/impi_5.0.2/intel64/bin/mpicxx
MOAB_CC  = /cineca/prod/compilers/intel/cs-xe-2015/binary/impi_5.0.2/intel64/bin/mpicc
MOAB_FC  = ifort
MOAB_F77  = ifort

# Override MOAB_LIBDIR and MOAB_INCLUDES from above with the correct
# values for the installed MOAB.

Adding the missing .la fixes the linking issue.

What do you guys think? I’m not an expert of this kind of problems...

Bests 
Lorenzo



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