[MOAB-dev] linking issues

Thu May 14 11:59:23 CDT 2015

WOW, sorry! I checked out the master branch and the linking issue is gone. Sorry for that.
I wrongly assumed that you keep updating the old website with a link to latest stable release.

Since we are discussing compilation issues...
Are you able to build moab with an HDF5 release newer than 1.8.10? I’m not, see attached config.log.
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Is this an issue related to szip? With 1.8.10 szip dependency can be avoided. 
Is it mandatory now?

Thanks a lot.
Lorenzo

> On 14 May 2015, at 17:21, Vijay S. Mahadevan <vijay.m at gmail.com> wrote:
> 
> Thanks for the clarification Lorenzo. The MOAB_LIBS_LINK variable only
> contains dependencies for compiling C++ based MOAB drivers and so
> -lstdc++ is redundant here since the C++ compiler can resolve the
> paths correctly. We specifically check for the standard C++ library
> only when linking fortran codes. This should be in the FLIBS variable
> which we currently don't write out to moab.make. Additionally, for
> Intel compilers, using the flag "-cxxlib" during both compile/link
> stages will resolve this issue without stdc++. This is available from
> current master branch.
> 
> I also noticed that you are using MOAB 4.6.3 which is more than a year
> old. We've made quite a few modifications to the current release
> version MOAB 4.8.1 which contains several fixes for fortran linkage
> among other things. Can you upgrade your MOAB installation ? Is there
> a reason why you want the older versions specifically ?
> 
> Vijay
> 
> On Thu, May 14, 2015 at 4:13 AM, Lorenzo Alessio Botti
> <bottilorenzo at gmail.com> wrote:
>> Dear Vijay,
>> in attachment the config.log file.
>> I don’t think there’s a failure here. Indeed libMOAB.la is correct and MOAB
>> tests compile and run.
>> 
>> The problem is that the path for libstdc++ is not included in the
>> MOAB_LIBS_LINK in moab.make. Since I use moab.make to link MOAB to my
>> application I need to add it manually
>> 
>> MOAB_LIBS_LINK = ${MOAB_LDFLAGS} -L${MOAB_LIBDIR} -lMOAB  -lm    -lhdf5
>> -lgpfs  -lz -ldl /cineca/prod/compilers/gnu/4.9.2/none/lib64/libstdc++.a
>> 
>> 
>> Is there an other (more correct) way to link MOAB?
>> 
>> Thanks for help.
>> Lorenzo
>> 
>> 
>> 
>> 
>> On 12 May 2015, at 21:49, Vijay S. Mahadevan <vijay.m at gmail.com> wrote:
>> 
>> Lorenzo,
>> 
>> In our autoconf configuration, we do find and add -lstdc++ when
>> compiling with fortran enabled. But we have not tested with GNU 4.9.2
>> AFAIK and so possibly the behavior is slightly different because in
>> older versions, libstdc++ is typically available in a system or
>> compiler dependent path. I've never had to specify a libtool path to
>> libstdc++ before. Can you send us the config.log so that we can
>> decipher where this failed ?
>> 
>> You can also take a look at config/compilers.m4 (search for stdc++) to
>> see where we add the flag currently and why it might possibly fail the
>> checks. If you are comfortable with autoconf, we would also be very
>> happy to accept a patch.
>> 
>> Vijay
>> 
>> On Tue, May 12, 2015 at 12:34 PM, Lorenzo Alessio Botti
>> <bottilorenzo at gmail.com> wrote:
>> 
>> 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
>> 
>> 
>> 
>> 
>> 