[petsc-dev] PETSC_WITH_EXTERNAL_LIB is not including the correct gcc directories

[Balay, Satish]

My general suggestion to avoid such issues is use either:

gcc/g++/gfortran

or

icc/icpc/ifort

You can also modify petscvariables manually - and see if your changes don't break examples - and then run your application/cmake

Or tweak and specify the correct LIBS option [which is also a manual process anyway - so might aswell modify petscvariables manually]

Satish

On Tue, 23 Oct 2018, Hector E Barrios Molano wrote:

> Satish,
> 
> My problem is that my application links with PETSc and another library
> (Iphreeqc) that uses libstdc++. I compiled this other library with a newer gcc
> (6.1). Then, during the configuration of my application (with CMake) it looks
> into petscvariables to get the additional libraries required and  there it
> gets the old gcc path.
> 
> When I am linking my  application the linker gets libstdc++ from the old path
> instead of the new path and it breaks.
> 
> This is not a problem if I use the default gcc (but for the system I am
> working now it is quite old) or if I do not link another library which
> requirements can conflict.
> 
> Best regards,
> 
> Hector
> 
> 
> On 10/23/18 4:34 PM, Balay, Satish wrote:
> > BTW: You have not stated what problem you are encountering due to this
> > reference to old gcc libraries from ifort.
> >
> > Satish
> >
> > On Tue, 23 Oct 2018, Balay, Satish wrote:
> >
> >> You can check 'ifort -v test.F' - to see how its using gcc internally.
> >>
> >> configure.log will have the details on where the path is coming from. [you
> >> can send us this log]
> >>
> >> PETSc configure attempts to determine the compiler libraries - and this
> >> part could show
> >> up with some paths that are not needed.
> >>
> >> Workaround is to manually specify these paths to petsc configure - so that
> >> it doesn't
> >> try to determine from 'ifort -v' - and pick up unneed stuff.
> >>
> >> ./configure LIBS=/path_to/libifcore.a
> >>
> >> [but then ifort changes this from libifcore.a to libifcoremt.a - if openmp
> >> is enabled]
> >>
> >> Satish
> >>
> >>
> >> On Tue, 23 Oct 2018, Hector E Barrios Molano wrote:
> >>
> >>> Thank you Satish for your response,
> >>>
> >>> Yes I am intended to use ifort with gcc.
> >>>
> >>> I changed ifort versions to one that does not include tbb.
> >>>
> >>> However, PETSc is still including -L/usr/lib/gcc/x86_64-redhat-linux/4.1.2
> >>> in
> >>> petscvariables, attached you will find an updated petscvariables file.
> >>>
> >>> ifort is not including any gcc, neither there is reference to this
> >>> directory
> >>> in $PATH or $LD_LIBRARY_PATH, why is PETSc still including it?
> >>>
> >>> Thanks for your help,
> >>>
> >>> Hector
> >>>
> >>>
> >>> On 10/18/18 5:28 PM, Balay, Satish wrote:
> >>>>> -L/share/apps/intel3/compilers_and_libraries_2016.2.181/linux/tbb/lib/intel64/gcc4.1
> >>>>> -L/usr/lib/gcc/x86_64-redhat-linux/4.1.2
> >>>> Its likely the gcc-4.1 stuff is coming from ifort.
> >>>>
> >>>> Did you intend to use ifort with gcc? [instead of gfortran?]
> >>>>
> >>>> Satish
> >>>>
> >>>> On Thu, 18 Oct 2018, Hector E Barrios Molano wrote:
> >>>>
> >>>>> Hi PETSc Experts!
> >>>>>
> >>>>> I am building PETSc from the git repository and it is strange that once
> >>>>> PETSc
> >>>>> is installed the petscvariables (PETSC_WITH_EXTERNAL_LIB) file shows a
> >>>>> different gcc library path that the one from the compiler used and the
> >>>>> one
> >>>>> defined in LD_LIBRARY_PATH. This is causing me troubles when using PETSc
> >>>>> with
> >>>>> other library that requires libstdc++
> >>>>>
> >>>>> Here is the command used to build PETSc:
> >>>>> ./configure --prefix=$DEV_lib_dir/petsc_git-debug
> >>>>> --PETSC_DIR=/home/hector/dwnld_prog/petsc --PETSC_ARCH=linux-intel-debug
> >>>>> --CC=mpicc --FC=mpifort --CXX=mpicxx --with-openmp=1 --with-valgrind=1
> >>>>> --with-valgri
> >>>>> nd-dir=/home/hector/installed --with-parmetis-dir=$DEV_lib_dir/parmetis/
> >>>>> --with-metis-dir=$DEV_lib_dir/parmetis/
> >>>>> --with-zoltan-dir=$DEV_lib_dir/zoltan/
> >>>>> --with-hypre-dir=$DEV_lib_dir/hypre --download-ptscotch
> >>>>> --with-blas-lapack-lib=\[${MKLR
> >>>>> OOT}/lib/intel64/libmkl_intel_lp64.a,${MKLROOT}/lib/intel64/libmkl_core.a,${MKLROOT}/lib/intel64/libmkl_intel_thread.a\]
> >>>>> --with-scalapack-include=${MKLROOT}/include
> >>>>> --with-scalapack-lib=\[${MKLROOT}/lib/intel64/libmkl_scalapack_lp64.a,${MK
> >>>>> LROOT}/lib/intel64/libmkl_blacs_intelmpi_lp64.a\]
> >>>>> --with-shared-libraries=0
> >>>>> --FC_LINKER_FLAGS="-qopenmp -qopenmp-link static" --FFLAGS="-qopenmp
> >>>>> -qopenmp-link static" --LIBS="-Wl,--start-group
> >>>>> ${MKLROOT}/lib/intel64/libmkl_intel_lp64.a ${M
> >>>>> KLROOT}/lib/intel64/libmkl_core.a
> >>>>> ${MKLROOT}/lib/intel64/libmkl_intel_thread.a
> >>>>> -Wl,--end-group -liomp5 -ldl -lpthread -lm"
> >>>>>
> >>>>> Here is LD_LIBRARY_PATH:
> >>>>> echo $LD_LIBRARY_PATH
> >>>>> /home/hector/installed/gcc-6.1/lib64:/home/hector/installed/gcc-5.1/lib64://home/hector/installed/lib:/home/hector/installed/libraries_intel/openmpi/lib:/share/apps/intel3/compilers_and_libraries_2016.2.181/linux/compiler/lib/intel64:/share/apps/intel3/compilers_and_libraries_2016.2.181/linux/compiler/lib/intel64_lin:/share/apps/intel3/compilers_and_libraries_2016.2.181/linux/mpi/intel64/lib:/share/apps/intel3/compilers_and_libraries_2016.2.181/linux/mpi/mic/lib:/share/apps/intel3/compilers_and_libraries_2016.2.181/linux/ipp/lib/intel64:/share/apps/intel3/compilers_and_libraries_2016.2.181/linux/compiler/lib/intel64:/share/apps/intel3/compilers_and_libraries_2016.2.181/linux/mkl/lib/intel64:/share/apps/intel3/compilers_and_libraries_2016.2.181/linux/tbb/lib/intel64/gcc4.1:/share/apps/intel3/debugger_2016/libipt/intel64/lib:/share/apps/intel3/compilers_and_libraries_2016.2.181/linux/daal/lib/intel64_lin:/share/apps/intel3/compilers_and_libraries_2016.2.181/linux/daal/../
> >>>>> tbb
> >>>>> /li
> >>>>> b/intel64_lin/gcc4.4:/share/apps/intel3/compilers_and_libraries_2016.2.181/linux/daal/../compiler/lib/intel64_lin:/home/hector/installed/gcc-6.1/lib64:/home/hector/installed/gcc-5.1/lib64://home/hector/installed/lib:/home/hector/installed/gcc-6.1/lib64:/home/hector/installed/gcc-5.1/lib64://home/hector/installed/lib:/opt/gridengine/lib/lx26-amd64:/opt/openmpi/lib
> >>>>>
> >>>>>
> >>>>> Attached you will find the resulting petscvariables file. There in the
> >>>>> definition of PETSC_WITH_EXTERNAL_LIB it is not included the gcc-6.1
> >>>>> directory
> >>>>> and instead gcc4.1 directory is included.
> >>>>>
> >>>>>
> >>>>> What could be the problem? Thank you for your help.
> >>>>>
> >>>>> Best regards,
> >>>>>
> >>>>> Hector
> >>>>>
> >>>>>
> >>>
> 
>