<div dir="ltr"><div class="gmail_default" style="font-size:large">Hi Satish,</div><div class="gmail_default" style="font-size:large"><br></div><div class="gmail_default" style="font-size:large">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:</div><div class="gmail_default" style="font-size:large">/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)<br>/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)<br>/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)<br>/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)<br>/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)<br></div><div class="gmail_default" style="font-size:large"><br></div><div class="gmail_default" style="font-size:large">Not sure if it is related to discussion in this post (<a href="https://gitlab.com/petsc/petsc/-/issues/997">https://gitlab.com/petsc/petsc/-/issues/997</a>), but after I tried the configure option --with-cxx=0, I still got the same errors. </div><div class="gmail_default" style="font-size:large">My make.log file for compiling petsc is attached here. Also, the dependencies of the compiled petsc is:</div><div class="gmail_default" style="font-size:large"><br></div><div class="gmail_default" style="font-size:large">>>: ldd arch-linux-c-debug/lib/libpetsc.so<br> linux-vdso.so.1 => (0x00007ffd80348000)<br> libflexiblas.so.3 => /cluster/software/FlexiBLAS/3.0.4-GCC-11.2.0/lib/libflexiblas.so.3 (0x00007f6e8b93f000)<br> libpthread.so.0 => /usr/lib64/libpthread.so.0 (0x00007f6e8b723000)<br> libm.so.6 => /usr/lib64/libm.so.6 (0x00007f6e8b421000)<br> libdl.so.2 => /usr/lib64/libdl.so.2 (0x00007f6e8b21d000)<br> libmpi_usempif08.so.40 => /cluster/software/OpenMPI/4.1.1-GCC-11.2.0/lib/libmpi_usempif08.so.40 (0x00007f6e8fd92000)<br> libmpi_usempi_ignore_tkr.so.40 => /cluster/software/OpenMPI/4.1.1-GCC-11.2.0/lib/libmpi_usempi_ignore_tkr.so.40 (0x00007f6e8fd84000)<br> libmpi_mpifh.so.40 => /cluster/software/OpenMPI/4.1.1-GCC-11.2.0/lib/libmpi_mpifh.so.40 (0x00007f6e8fd0c000)<br> libmpi.so.40 => /cluster/software/OpenMPI/4.1.1-GCC-11.2.0/lib/libmpi.so.40 (0x00007f6e8fbfa000)<br> libgfortran.so.5 => /cluster/software/GCCcore/11.2.0/lib64/libgfortran.so.5 (0x00007f6e8af70000)<br> libgcc_s.so.1 => /cluster/software/GCCcore/11.2.0/lib64/libgcc_s.so.1 (0x00007f6e8fbe0000)<br> libquadmath.so.0 => /cluster/software/GCCcore/11.2.0/lib64/libquadmath.so.0 (0x00007f6e8af28000)<br> libc.so.6 => /usr/lib64/libc.so.6 (0x00007f6e8ab5a000)<br> /lib64/ld-linux-x86-64.so.2 (0x00007f6e8fbb3000)<br> libopen-rte.so.40 => /cluster/software/OpenMPI/4.1.1-GCC-11.2.0/lib/libopen-rte.so.40 (0x00007f6e8aa9e000)<br> libopen-orted-mpir.so => /cluster/software/OpenMPI/4.1.1-GCC-11.2.0/lib/libopen-orted-mpir.so (0x00007f6e8fbdb000)<br> libopen-pal.so.40 => /cluster/software/OpenMPI/4.1.1-GCC-11.2.0/lib/libopen-pal.so.40 (0x00007f6e8a9ea000)<br> librt.so.1 => /lib64/librt.so.1 (0x00007f6e8a7d5000)<br> libutil.so.1 => /lib64/libutil.so.1 (0x00007f6e8a5d2000)<br> libhwloc.so.15 => /cluster/software/hwloc/2.5.0-GCCcore-11.2.0/lib/libhwloc.so.15 (0x00007f6e8a575000)<br> libpciaccess.so.0 => /cluster/software/libpciaccess/0.16-GCCcore-11.2.0/lib/libpciaccess.so.0 (0x00007f6e8a56a000)<br> libxml2.so.2 => /cluster/software/libxml2/2.9.10-GCCcore-11.2.0/lib/libxml2.so.2 (0x00007f6e8a3f6000)<br> libz.so.1 => /cluster/software/zlib/1.2.11-GCCcore-11.2.0/lib/libz.so.1 (0x00007f6e8a3dd000)<br> liblzma.so.5 => /cluster/software/XZ/5.2.5-GCCcore-11.2.0/lib/liblzma.so.5 (0x00007f6e8a3b5000)<br> libevent_core-2.0.so.5 => /lib64/libevent_core-2.0.so.5 (0x00007f6e8a18a000)<br> libevent_pthreads-2.0.so.5 => /lib64/libevent_pthreads-2.0.so.5 (0x00007f6e89f87000)<br></div><div class="gmail_default" style="font-size:large"><br></div><div class="gmail_default" style="font-size:large">Thanks very much,</div><div class="gmail_default" style="font-size:large">Jianbo</div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Mon, Nov 7, 2022 at 6:01 PM Satish Balay <<a href="mailto:balay@mcs.anl.gov">balay@mcs.anl.gov</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">Glad you have it working. Thanks for the update.<br>
<br>
Satish<br>
<br>
On Mon, 7 Nov 2022, Jianbo Long wrote:<br>
<br>
> Hi Satish and Barry,<br>
> <br>
> Thanks very much for the feedback !<br>
> <br>
> It looks like my include file path was not correct !<br>
> <br>
> Bests,<br>
> Jianbo<br>
> <br>
> <br>
> On Fri, Nov 4, 2022 at 6:08 AM Satish Balay <<a href="mailto:balay@mcs.anl.gov" target="_blank">balay@mcs.anl.gov</a>> wrote:<br>
> <br>
> > For ex83f.F90:<br>
> ><br>
> > >>>>><br>
> > balay@p1 /home/balay/test<br>
> > $ ls<br>
> > ex83f.F90<br>
> > balay@p1 /home/balay/test<br>
> > $ ls<br>
> > ex83f.F90<br>
> > balay@p1 /home/balay/test<br>
> > $ export PETSC_DIR=$HOME/petsc<br>
> > balay@p1 /home/balay/test<br>
> > $ cp $PETSC_DIR/src/ksp/ksp/tests/makefile .<br>
> > balay@p1 /home/balay/test<br>
> > $ make ex83f<br>
> > mpif90 -fPIC -Wall -ffree-line-length-none -ffree-line-length-0<br>
> > -Wno-lto-type-mismatch -Wno-unused-dummy-argument -g -O0<br>
> > -I/home/balay/petsc/include<br>
> > -I/home/balay/petsc/arch-linux-c-debug/include ex83f.F90<br>
> > -Wl,-rpath,/home/balay/petsc/arch-linux-c-debug/lib<br>
> > -L/home/balay/petsc/arch-linux-c-debug/lib<br>
> > -Wl,-rpath,/home/balay/soft/mpich-4.0.1/lib<br>
> > -L/home/balay/soft/mpich-4.0.1/lib<br>
> > -Wl,-rpath,/usr/lib/gcc/x86_64-redhat-linux/12<br>
> > -L/usr/lib/gcc/x86_64-redhat-linux/12 -lpetsc -llapack -lblas -lm -lX11<br>
> > -lstdc++ -ldl -lmpifort -lmpi -lgfortran -lm -lgfortran -lm -lgcc_s<br>
> > -lquadmath -lstdc++ -ldl -o ex83f<br>
> > balay@p1 /home/balay/test<br>
> > $<br>
> > <<<<<<<br>
> ><br>
> > Also when you are adding PETSc to your current project - are you using<br>
> > source files with .f or .f90 suffix? If so rename them to .F or .F90 suffix.<br>
> ><br>
> > If you still have issues send more details - As Barry indicated - the<br>
> > makefile [with the sources compiled by this makefile] - and the compile log<br>
> > when you attempt to build these sources with this makefile.<br>
> ><br>
> > Satish<br>
> ><br>
> > On Thu, 3 Nov 2022, Barry Smith wrote:<br>
> ><br>
> > ><br>
> > > Please send your attempted makefile and we'll see if we can get it<br>
> > working.<br>
> > ><br>
> > > I am not sure if we can organize the include files as Fortran compiler<br>
> > include files easily. We've always used the preprocessor approach. The<br>
> > Intel compiler docs indicate the procedure for finding the Fortran compiler<br>
> > include files<br>
> > <a href="https://www.intel.com/content/www/us/en/develop/documentation/fortran-compiler-oneapi-dev-guide-and-reference/top/program-structure/use-include-files.html" rel="noreferrer" target="_blank">https://www.intel.com/content/www/us/en/develop/documentation/fortran-compiler-oneapi-dev-guide-and-reference/top/program-structure/use-include-files.html</a><br>
> > is the same as for the preprocessor include files so I don't understand how<br>
> > the using the Fortran compiler include file approach would make the<br>
> > makefiles any simpler for users?<br>
> > ><br>
> > ><br>
> > > Barry<br>
> > ><br>
> > ><br>
> > > > On Nov 3, 2022, at 8:58 PM, Jianbo Long <<a href="mailto:longtuteng249@gmail.com" target="_blank">longtuteng249@gmail.com</a>><br>
> > wrote:<br>
> > > ><br>
> > > > Hello,<br>
> > > ><br>
> > > > I'm struggling to make my FORTRAN code work with petsc as I cannot<br>
> > link the required header files (e.g., petscksp.h) and compiled library<br>
> > files to my FORTRAN code.<br>
> > > ><br>
> > > > Compiling petsc was not a problem. However, even with the fortran<br>
> > examples (see those on <a href="https://petsc.org/main/docs/manual/fortran/" rel="noreferrer" target="_blank">https://petsc.org/main/docs/manual/fortran/</a>) and<br>
> > the guide on using petsc in c++ and fortran codes (see Section "Writing<br>
> > C/C++ or Fortran Applications" at<br>
> > <a href="https://petsc.org/main/docs/manual/getting_started/" rel="noreferrer" target="_blank">https://petsc.org/main/docs/manual/getting_started/</a>), I still cannot make<br>
> > my FORTRAN code work.<br>
> > > ><br>
> > > > The Fortran test code is exactly the example code ex83f.F90 (see<br>
> > attached files). Aftering following the 2nd method in the Guide (see the<br>
> > picture below), I still get errors:<br>
> > > ><br>
> > > > petsc/finclude/petscksp.h: No such file or directory<br>
> > > ><br>
> > > > Even if I set up the path of the header file correctly in my own<br>
> > makefile without using environment variables, I still can only find the<br>
> > file "petscksp.h" for my code. Of course, the trouble is that all other<br>
> > headers files required by KSP are recursively included in this petscksp.h<br>
> > file, and I have no way to link them together for my Fortran code.<br>
> > > ><br>
> > > > So, here are my questions:<br>
> > > > 1) in the Guide, how exactly are we supposed to set up the environment<br>
> > variables PETSC_DIR and PETSC_ARCH ? More details and examples would be<br>
> > extremely helpful !<br>
> > > > 2) Is there a way to get rid of the preprocessor statement<br>
> > > > #include <petsc/finclude/petscvec.h><br>
> > > > when using c++/Fortran codes ?<br>
> > > ><br>
> > > > For example, when using MUMPS package in a Fortran code, we can simply<br>
> > use compiler 'include', rather than a preprocessor, to extract all required<br>
> > variables for the user's codes :<br>
> > > > INCLUDE 'zmumps_struc.h'<br>
> > > > where the header file zmumps_struc.h is already provided in the<br>
> > package. Similarly, I think it's much more portable and easier when using<br>
> > petsc in other codes if we can make it work to use petsc.<br>
> > > ><br>
> > > > (Note: similar issues were discussed before, see<br>
> > <a href="https://lists.mcs.anl.gov/mailman/htdig/petsc-users/2019-January/037499.html" rel="noreferrer" target="_blank">https://lists.mcs.anl.gov/mailman/htdig/petsc-users/2019-January/037499.html</a>.<br>
> > Unfortunately, I have no clue about the solution archived there ...)<br>
> > > ><br>
> > > > Any thoughts and solutions would be much appreciated !<br>
> > > ><br>
> > > > Thanks,<br>
> > > > Jianbo Long<br>
> > > ><br>
> > > > <image.png><br>
> > > > <ex83f.F90><br>
> > ><br>
> > ><br>
> ><br>
> ><br>
> <br>
<br>
</blockquote></div>