On Thu, Feb 10, 2022 at 10:34 AM Bojan Niceno < [email protected]> wrote:
> 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. > You are getting this message because your MPI implementation is printing Invalid MIT-MAGIC-COOKIE-1 key It is still running fine, but this is an MPI configuration issue. Thanks, Matt 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 >> > > >> > > >> > > >> > > >> > >> > >> > -- 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/>
