[petsc-users] [petsc-maint] Issues linking petsc header files and lib from FORTRAN codes

Tue Nov 8 09:41:49 CST 2022

On Tue, Nov 8, 2022 at 10:28 AM Jianbo Long <longtuteng249 at gmail.com> 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.
>

Are you sure it is not MPI that is bringing in C++? With --with-cxx=0,
there should be no C++ in PETSc. However, we can test this.
Can you

  ldd ${PETSC_ARCH}/lib/libpetsc.so

  Thanks,

    Matt

> Thanks,
> Jianbo
>
> On Mon, Nov 7, 2022 at 7:10 PM Satish Balay <balay at mcs.anl.gov> 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 <balay at mcs.anl.gov> 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 <balay at mcs.anl.gov>
>> wrote:
>> > > >
>> > > > > For ex83f.F90:
>> > > > >
>> > > > > >>>>>
>> > > > > balay at p1 /home/balay/test
>> > > > > $ ls
>> > > > > ex83f.F90
>> > > > > balay at p1 /home/balay/test
>> > > > > $ ls
>> > > > > ex83f.F90
>> > > > > balay at p1 /home/balay/test
>> > > > > $ export PETSC_DIR=$HOME/petsc
>> > > > > balay at p1 /home/balay/test
>> > > > > $ cp $PETSC_DIR/src/ksp/ksp/tests/makefile .
>> > > > > balay at 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 at 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 <
>> longtuteng249 at gmail.com>
>> > > > > 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>
>> > > > > >
>> > > > > >
>> > > > >
>> > > > >
>> > > >
>> > >
>> > >
>> >
>>
>>

-- 
What most experimenters take for granted before they begin their
experiments is infinitely more interesting than any results to which their
experiments lead.
-- Norbert Wiener

https://www.cse.buffalo.edu/~knepley/ <http://www.cse.buffalo.edu/~knepley/>
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