On Tue, 8 Nov 2022, Satish Balay via petsc-users wrote: > You don't see 'libstdc++' in the output from 'ldd libptsc.so' below - so > there is no reference > to libstdc++ from petsc > > Try a clean build of PETSc and see if you still have these issues. > > ./configure --with-cc=gcc --with-cxx=0 --with-fc=gfortran > --download-fblaslapack --download-mpich
Perhaps good to also add: --with-hwloc=0 Satish > > Another way to avoid this issue is to use /usr/bin/gcc, gfortran - i.e avoid > using tools from /cluster/software/GCCcore > Are they super old versions - that are not suitable? > > Satish > > > > On Tue, 8 Nov 2022, Jianbo Long wrote: > > > I am suspecting something else as well ... > > > > Could you elaborate more about "mixing c++ codes compiled with /usr/bin/g++ > > and compilers in /cluster/software/GCCcore/11.2.0" ? My own Fortran code > > does not have any c++ codes, and for some reason, the compiled petsc > > library is dependent on this libstdc++.so.6. I am sure about this because > > without linking the petsc, I don't have this libstdc++ trouble. > > > > Thanks, > > Jianbo > > > > On Mon, Nov 7, 2022 at 7:10 PM Satish Balay <[email protected]> wrote: > > > > > Likely due to mixing c++ codes compiled with /usr/bin/g++ and compilers in > > > /cluster/software/GCCcore/11.2.0 > > > > > > if you still get this with --with-cxx=0 - then the issue with some other > > > [non-petsc library] > > > > > > Satish > > > > > > On Mon, 7 Nov 2022, Jianbo Long wrote: > > > > > > > Hi Satish, > > > > > > > > I wonder if you know anything about another issue: after compiling petsc > > > on > > > > a cluster, when I tried to link my Fortran code with compiled > > > libpetsc.so, > > > > the shared library, I got the following errors: > > > > /cluster/software/binutils/2.37-GCCcore-11.2.0/bin/ld.gold: > > > > /lib64/libstdc++.so.6: version `CXXABI_1.3.9' not found (required by > > > > /cluster/software/binutils/2.37-GCCcore-11.2.0/bin/ld.gold) > > > > /cluster/software/binutils/2.37-GCCcore-11.2.0/bin/ld.gold: > > > > /lib64/libstdc++.so.6: version `GLIBCXX_3.4.21' not found (required by > > > > /cluster/software/binutils/2.37-GCCcore-11.2.0/bin/ld.gold) > > > > /cluster/software/binutils/2.37-GCCcore-11.2.0/bin/ld.gold: > > > > /lib64/libstdc++.so.6: version `GLIBCXX_3.4.29' not found (required by > > > > /cluster/software/binutils/2.37-GCCcore-11.2.0/bin/ld.gold) > > > > /cluster/software/binutils/2.37-GCCcore-11.2.0/bin/ld.gold: > > > > /lib64/libstdc++.so.6: version `GLIBCXX_3.4.20' not found (required by > > > > /cluster/software/binutils/2.37-GCCcore-11.2.0/bin/ld.gold) > > > > /cluster/software/binutils/2.37-GCCcore-11.2.0/bin/ld.gold: > > > > /lib64/libstdc++.so.6: version `CXXABI_1.3.8' not found (required by > > > > /cluster/software/binutils/2.37-GCCcore-11.2.0/bin/ld.gold) > > > > > > > > Not sure if it is related to discussion in this post ( > > > > https://gitlab.com/petsc/petsc/-/issues/997), but after I tried the > > > > configure option --with-cxx=0, I still got the same errors. > > > > My make.log file for compiling petsc is attached here. Also, the > > > > dependencies of the compiled petsc is: > > > > > > > > >>: ldd arch-linux-c-debug/lib/libpetsc.so > > > > linux-vdso.so.1 => (0x00007ffd80348000) > > > > libflexiblas.so.3 => > > > > /cluster/software/FlexiBLAS/3.0.4-GCC-11.2.0/lib/libflexiblas.so.3 > > > > (0x00007f6e8b93f000) > > > > libpthread.so.0 => /usr/lib64/libpthread.so.0 (0x00007f6e8b723000) > > > > libm.so.6 => /usr/lib64/libm.so.6 (0x00007f6e8b421000) > > > > libdl.so.2 => /usr/lib64/libdl.so.2 (0x00007f6e8b21d000) > > > > libmpi_usempif08.so.40 => > > > > /cluster/software/OpenMPI/4.1.1-GCC-11.2.0/lib/libmpi_usempif08.so.40 > > > > (0x00007f6e8fd92000) > > > > libmpi_usempi_ignore_tkr.so.40 => > > > > > > > /cluster/software/OpenMPI/4.1.1-GCC-11.2.0/lib/libmpi_usempi_ignore_tkr.so.40 > > > > (0x00007f6e8fd84000) > > > > libmpi_mpifh.so.40 => > > > > /cluster/software/OpenMPI/4.1.1-GCC-11.2.0/lib/libmpi_mpifh.so.40 > > > > (0x00007f6e8fd0c000) > > > > libmpi.so.40 => > > > /cluster/software/OpenMPI/4.1.1-GCC-11.2.0/lib/libmpi.so.40 > > > > (0x00007f6e8fbfa000) > > > > libgfortran.so.5 => > > > /cluster/software/GCCcore/11.2.0/lib64/libgfortran.so.5 > > > > (0x00007f6e8af70000) > > > > libgcc_s.so.1 => /cluster/software/GCCcore/11.2.0/lib64/libgcc_s.so.1 > > > > (0x00007f6e8fbe0000) > > > > libquadmath.so.0 => > > > /cluster/software/GCCcore/11.2.0/lib64/libquadmath.so.0 > > > > (0x00007f6e8af28000) > > > > libc.so.6 => /usr/lib64/libc.so.6 (0x00007f6e8ab5a000) > > > > /lib64/ld-linux-x86-64.so.2 (0x00007f6e8fbb3000) > > > > libopen-rte.so.40 => > > > > /cluster/software/OpenMPI/4.1.1-GCC-11.2.0/lib/libopen-rte.so.40 > > > > (0x00007f6e8aa9e000) > > > > libopen-orted-mpir.so => > > > > /cluster/software/OpenMPI/4.1.1-GCC-11.2.0/lib/libopen-orted-mpir.so > > > > (0x00007f6e8fbdb000) > > > > libopen-pal.so.40 => > > > > /cluster/software/OpenMPI/4.1.1-GCC-11.2.0/lib/libopen-pal.so.40 > > > > (0x00007f6e8a9ea000) > > > > librt.so.1 => /lib64/librt.so.1 (0x00007f6e8a7d5000) > > > > libutil.so.1 => /lib64/libutil.so.1 (0x00007f6e8a5d2000) > > > > libhwloc.so.15 => > > > > /cluster/software/hwloc/2.5.0-GCCcore-11.2.0/lib/libhwloc.so.15 > > > > (0x00007f6e8a575000) > > > > libpciaccess.so.0 => > > > > /cluster/software/libpciaccess/0.16-GCCcore-11.2.0/lib/libpciaccess.so.0 > > > > (0x00007f6e8a56a000) > > > > libxml2.so.2 => > > > > /cluster/software/libxml2/2.9.10-GCCcore-11.2.0/lib/libxml2.so.2 > > > > (0x00007f6e8a3f6000) > > > > libz.so.1 => /cluster/software/zlib/1.2.11-GCCcore-11.2.0/lib/libz.so.1 > > > > (0x00007f6e8a3dd000) > > > > liblzma.so.5 => > > > /cluster/software/XZ/5.2.5-GCCcore-11.2.0/lib/liblzma.so.5 > > > > (0x00007f6e8a3b5000) > > > > libevent_core-2.0.so.5 => /lib64/libevent_core-2.0.so.5 > > > (0x00007f6e8a18a000) > > > > libevent_pthreads-2.0.so.5 => /lib64/libevent_pthreads-2.0.so.5 > > > > (0x00007f6e89f87000) > > > > > > > > Thanks very much, > > > > Jianbo > > > > > > > > On Mon, Nov 7, 2022 at 6:01 PM Satish Balay <[email protected]> wrote: > > > > > > > > > Glad you have it working. Thanks for the update. > > > > > > > > > > Satish > > > > > > > > > > On Mon, 7 Nov 2022, Jianbo Long wrote: > > > > > > > > > > > Hi Satish and Barry, > > > > > > > > > > > > Thanks very much for the feedback ! > > > > > > > > > > > > It looks like my include file path was not correct ! > > > > > > > > > > > > Bests, > > > > > > Jianbo > > > > > > > > > > > > > > > > > > On Fri, Nov 4, 2022 at 6:08 AM Satish Balay <[email protected]> > > > wrote: > > > > > > > > > > > > > For ex83f.F90: > > > > > > > > > > > > > > >>>>> > > > > > > > balay@p1 /home/balay/test > > > > > > > $ ls > > > > > > > ex83f.F90 > > > > > > > balay@p1 /home/balay/test > > > > > > > $ ls > > > > > > > ex83f.F90 > > > > > > > balay@p1 /home/balay/test > > > > > > > $ export PETSC_DIR=$HOME/petsc > > > > > > > balay@p1 /home/balay/test > > > > > > > $ cp $PETSC_DIR/src/ksp/ksp/tests/makefile . > > > > > > > balay@p1 /home/balay/test > > > > > > > $ make ex83f > > > > > > > mpif90 -fPIC -Wall -ffree-line-length-none -ffree-line-length-0 > > > > > > > -Wno-lto-type-mismatch -Wno-unused-dummy-argument -g -O0 > > > > > > > -I/home/balay/petsc/include > > > > > > > -I/home/balay/petsc/arch-linux-c-debug/include ex83f.F90 > > > > > > > -Wl,-rpath,/home/balay/petsc/arch-linux-c-debug/lib > > > > > > > -L/home/balay/petsc/arch-linux-c-debug/lib > > > > > > > -Wl,-rpath,/home/balay/soft/mpich-4.0.1/lib > > > > > > > -L/home/balay/soft/mpich-4.0.1/lib > > > > > > > -Wl,-rpath,/usr/lib/gcc/x86_64-redhat-linux/12 > > > > > > > -L/usr/lib/gcc/x86_64-redhat-linux/12 -lpetsc -llapack -lblas -lm > > > -lX11 > > > > > > > -lstdc++ -ldl -lmpifort -lmpi -lgfortran -lm -lgfortran -lm > > > > > > > -lgcc_s > > > > > > > -lquadmath -lstdc++ -ldl -o ex83f > > > > > > > balay@p1 /home/balay/test > > > > > > > $ > > > > > > > <<<<<< > > > > > > > > > > > > > > Also when you are adding PETSc to your current project - are you > > > using > > > > > > > source files with .f or .f90 suffix? If so rename them to .F or > > > .F90 > > > > > suffix. > > > > > > > > > > > > > > If you still have issues send more details - As Barry indicated - > > > the > > > > > > > makefile [with the sources compiled by this makefile] - and the > > > > > compile log > > > > > > > when you attempt to build these sources with this makefile. > > > > > > > > > > > > > > Satish > > > > > > > > > > > > > > On Thu, 3 Nov 2022, Barry Smith wrote: > > > > > > > > > > > > > > > > > > > > > > > Please send your attempted makefile and we'll see if we can get > > > it > > > > > > > working. > > > > > > > > > > > > > > > > I am not sure if we can organize the include files as Fortran > > > > > compiler > > > > > > > include files easily. We've always used the preprocessor approach. > > > The > > > > > > > Intel compiler docs indicate the procedure for finding the Fortran > > > > > compiler > > > > > > > include files > > > > > > > > > > > > > > > https://www.intel.com/content/www/us/en/develop/documentation/fortran-compiler-oneapi-dev-guide-and-reference/top/program-structure/use-include-files.html > > > > > > > is the same as for the preprocessor include files so I don't > > > > > understand how > > > > > > > the using the Fortran compiler include file approach would make > > > > > > > the > > > > > > > makefiles any simpler for users? > > > > > > > > > > > > > > > > > > > > > > > > Barry > > > > > > > > > > > > > > > > > > > > > > > > > On Nov 3, 2022, at 8:58 PM, Jianbo Long < > > > [email protected]> > > > > > > > wrote: > > > > > > > > > > > > > > > > > > Hello, > > > > > > > > > > > > > > > > > > I'm struggling to make my FORTRAN code work with petsc as I > > > cannot > > > > > > > link the required header files (e.g., petscksp.h) and compiled > > > library > > > > > > > files to my FORTRAN code. > > > > > > > > > > > > > > > > > > Compiling petsc was not a problem. However, even with the > > > fortran > > > > > > > examples (see those on https://petsc.org/main/docs/manual/fortran/ > > > ) > > > > > and > > > > > > > the guide on using petsc in c++ and fortran codes (see Section > > > "Writing > > > > > > > C/C++ or Fortran Applications" at > > > > > > > https://petsc.org/main/docs/manual/getting_started/), I still > > > cannot > > > > > make > > > > > > > my FORTRAN code work. > > > > > > > > > > > > > > > > > > The Fortran test code is exactly the example code ex83f.F90 > > > (see > > > > > > > attached files). Aftering following the 2nd method in the Guide > > > (see > > > > > the > > > > > > > picture below), I still get errors: > > > > > > > > > > > > > > > > > > petsc/finclude/petscksp.h: No such file or directory > > > > > > > > > > > > > > > > > > Even if I set up the path of the header file correctly in my > > > own > > > > > > > makefile without using environment variables, I still can only > > > find the > > > > > > > file "petscksp.h" for my code. Of course, the trouble is that all > > > other > > > > > > > headers files required by KSP are recursively included in this > > > > > petscksp.h > > > > > > > file, and I have no way to link them together for my Fortran code. > > > > > > > > > > > > > > > > > > So, here are my questions: > > > > > > > > > 1) in the Guide, how exactly are we supposed to set up the > > > > > environment > > > > > > > variables PETSC_DIR and PETSC_ARCH ? More details and examples > > > would > > > > > be > > > > > > > extremely helpful ! > > > > > > > > > 2) Is there a way to get rid of the preprocessor statement > > > > > > > > > #include <petsc/finclude/petscvec.h> > > > > > > > > > when using c++/Fortran codes ? > > > > > > > > > > > > > > > > > > For example, when using MUMPS package in a Fortran code, we > > > > > > > > > can > > > > > simply > > > > > > > use compiler 'include', rather than a preprocessor, to extract all > > > > > required > > > > > > > variables for the user's codes : > > > > > > > > > INCLUDE 'zmumps_struc.h' > > > > > > > > > where the header file zmumps_struc.h is already provided in > > > > > > > > > the > > > > > > > package. Similarly, I think it's much more portable and easier > > > > > > > when > > > > > using > > > > > > > petsc in other codes if we can make it work to use petsc. > > > > > > > > > > > > > > > > > > (Note: similar issues were discussed before, see > > > > > > > > > > > > > > > https://lists.mcs.anl.gov/mailman/htdig/petsc-users/2019-January/037499.html > > > > > . > > > > > > > Unfortunately, I have no clue about the solution archived there > > > ...) > > > > > > > > > > > > > > > > > > Any thoughts and solutions would be much appreciated ! > > > > > > > > > > > > > > > > > > Thanks, > > > > > > > > > Jianbo Long > > > > > > > > > > > > > > > > > > <image.png> > > > > > > > > > <ex83f.F90> > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > >
