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
