Dear Satish, Thanks for the answer. Your suggestion makes a lot of sense, but this is what I get as a result of that:
Running check examples to verify correct installation Using PETSC_DIR=/home/niceno/Development/petsc-debug and PETSC_ARCH=arch-linux-c-debug Possible error running C/C++ src/snes/tutorials/ex19 with 1 MPI process See http://www.mcs.anl.gov/petsc/documentation/faq.html Invalid MIT-MAGIC-COOKIE-1 keylid velocity = 0.0016, prandtl # = 1., grashof # = 1. Number of SNES iterations = 2 Possible error running C/C++ src/snes/tutorials/ex19 with 2 MPI processes See http://www.mcs.anl.gov/petsc/documentation/faq.html Invalid MIT-MAGIC-COOKIE-1 keylid velocity = 0.0016, prandtl # = 1., grashof # = 1. Number of SNES iterations = 2 Possible error running Fortran example src/snes/tutorials/ex5f with 1 MPI process See http://www.mcs.anl.gov/petsc/documentation/faq.html Invalid MIT-MAGIC-COOKIE-1 keyNumber of SNES iterations = 4 Completed test examples I am getting the "Possible error running Fortran example" warning with this. This somehow looks more severe to me. But I could be wrong. Any suggestions what to do? Kind regards, Bojan On Wed, Feb 9, 2022 at 5:49 PM Satish Balay <[email protected]> wrote: > To clarify: > > you are using --download-openmpi=yes with petsc. However you say: > > > > The mpif90 command which > > > I use to compile the code, wraps gfortran with OpenMPI > > This suggests a different install of OpenMPI is used to build your code. > > One way to resolve this is - delete current build of PETSc - and rebuild > it with this same MPI [that you are using with your application] > > ./configure --with-cc=mpicc --with-cxx=mpicxx --with-fc=mpif90 > --download-fblaslapack --download-metis --download-parmetis --download-cmake > > Also PETSc provides makefile format that minimizes such conflicts.. > > > https://petsc.org/release/docs/manual/getting_started/#writing-c-c-or-fortran-applications > > Satish > > On Wed, 9 Feb 2022, Balay, Satish via petsc-users wrote: > > > Are you using the same MPI to build both PETSc and your appliation? > > > > Satish > > > > On Wed, 2022-02-09 at 05:21 +0100, Bojan Niceno wrote: > > > To whom it may concern, > > > > > > > > > I am working on a Fortran (2003) computational fluid dynamics solver, > > > which is actually quite mature, was parallelized with MPI from the > > > very beginning and it comes with its own suite of Krylov solvers. > > > Although the code is self-sustained, I am inclined to believe that it > > > would be better to use PETSc instead of my own home-grown solvers. > > > > > > In the attempt to do so, I have installed PETSc 3.16.4 with following > > > options: > > > > > > ./configure --with-debugging=yes --download-openmpi=yes --download- > > > fblaslapack=yes --download-metis=yes --download-parmetis=yes -- > > > download-cmake=yes > > > > > > on a workstation running Ubuntu 20.04 LTS. The mpif90 command which > > > I use to compile the code, wraps gfortran with OpenMPI, hence the > > > option "--download-openmpi=yes" when configuring PETSc. > > > > > > Anyhow, installation of PETSc went fine, I managed to link and run it > > > with my code, but I am getting the following messages during > > > compilation: > > > > > > Petsc_Mod.f90:18:6: > > > > > > 18 | use PetscMat, only: tMat, MAT_FINAL_ASSEMBLY > > > | 1 > > > Warning: Named COMMON block ‘mpi_fortran_bottom’ at (1) shall be of > > > the same size as elsewhere (4 vs 8 bytes) > > > > > > Petsc_Mod.f90 is a module I wrote for interfacing PETSc. All works, > > > but these messages give me a reason to worry. > > > > > > Can you tell what causes this warnings? I would guess they might > > > appear if one mixes OpenMPI with MPICH, but I don't think I even have > > > MPICH on my system. > > > > > > Please let me know what you think about it? > > > > > > Cheers, > > > > > > Bojan > > > > > > > > > > > > > > > > >
