Re: [petsc-users] [petsc-maint] Issues linking petsc header files and lib from FORTRAN codes
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-compil... 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>
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-compil... 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>
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-compil... 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>
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-compil... 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>
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-compil...
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>
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-compil...
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>
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-compil...
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>
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 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-compil...
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>
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-compil...
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>
Here are the ldd outputs:
ldd petsc_3.18_gnu/arch-linux-c-debug/lib/libpetsc.so linux-vdso.so.1 => (0x00007f23e5ff2000) libflexiblas.so.3 => /cluster/software/FlexiBLAS/3.0.4-GCC-11.2.0/lib/libflexiblas.so.3 (0x00007f23e1b60000) libpthread.so.0 => /usr/lib64/libpthread.so.0 (0x00007f23e1944000) libm.so.6 => /usr/lib64/libm.so.6 (0x00007f23e1642000) libdl.so.2 => /usr/lib64/libdl.so.2 (0x00007f23e143e000) libmpi_usempif08.so.40 => /cluster/software/OpenMPI/4.1.1-GCC-11.2.0/lib/libmpi_usempif08.so.40 (0x00007f23e5fb0000) libmpi_usempi_ignore_tkr.so.40 => /cluster/software/OpenMPI/4.1.1-GCC-11.2.0/lib/libmpi_usempi_ignore_tkr.so.40 (0x00007f23e5fa2000) libmpi_mpifh.so.40 => /cluster/software/OpenMPI/4.1.1-GCC-11.2.0/lib/libmpi_mpifh.so.40 (0x00007f23e5f2a000) libmpi.so.40 => /cluster/software/OpenMPI/4.1.1-GCC-11.2.0/lib/libmpi.so.40 (0x00007f23e5e18000) libgfortran.so.5 => /cluster/software/GCCcore/11.2.0/lib64/libgfortran.so.5 (0x00007f23e1191000) libgcc_s.so.1 => /cluster/software/GCCcore/11.2.0/lib64/libgcc_s.so.1 (0x00007f23e5dfe000) libquadmath.so.0 => /cluster/software/GCCcore/11.2.0/lib64/libquadmath.so.0 (0x00007f23e1149000) libc.so.6 => /usr/lib64/libc.so.6 (0x00007f23e0d7b000) /lib64/ld-linux-x86-64.so.2 (0x00007f23e5dd3000) libopen-rte.so.40 => /cluster/software/OpenMPI/4.1.1-GCC-11.2.0/lib/libopen-rte.so.40 (0x00007f23e0cbf000) libopen-orted-mpir.so => /cluster/software/OpenMPI/4.1.1-GCC-11.2.0/lib/libopen-orted-mpir.so (0x00007f23e5df9000) libopen-pal.so.40 => /cluster/software/OpenMPI/4.1.1-GCC-11.2.0/lib/libopen-pal.so.40 (0x00007f23e0c0b000) librt.so.1 => /lib64/librt.so.1 (0x00007f23e09f6000) libutil.so.1 => /lib64/libutil.so.1 (0x00007f23e07f3000) libhwloc.so.15 => /cluster/software/hwloc/2.5.0-GCCcore-11.2.0/lib/libhwloc.so.15 (0x00007f23e0796000) libpciaccess.so.0 => /cluster/software/libpciaccess/0.16-GCCcore-11.2.0/lib/libpciaccess.so.0 (0x00007f23e078b000) libxml2.so.2 => /cluster/software/libxml2/2.9.10-GCCcore-11.2.0/lib/libxml2.so.2 (0x00007f23e0617000) libz.so.1 => /cluster/software/zlib/1.2.11-GCCcore-11.2.0/lib/libz.so.1 (0x00007f23e05fe000) liblzma.so.5 => /cluster/software/XZ/5.2.5-GCCcore-11.2.0/lib/liblzma.so.5 (0x00007f23e05d6000) libevent_core-2.0.so.5 => /lib64/libevent_core-2.0.so.5 (0x00007f23e03ab000) libevent_pthreads-2.0.so.5 => /lib64/libevent_pthreads-2.0.so.5 (0x00007f23e01a8000)
And /cluster/software/GCCcore/11.2.0 is pretty recent (around 2020/2021). You can see that I am using openmpi. Now I am trying compiling petsc without MPI. On Tue, Nov 8, 2022 at 4:43 PM Satish Balay <[email protected]> wrote:
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-compil...
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>
On Tue, Nov 8, 2022 at 10:28 AM Jianbo Long <[email protected]> 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 <[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-compil...
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>
-- 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/>
participants (4)
-
Barry Smith -
Jianbo Long -
Matthew Knepley -
Satish Balay