[petsc-users] Warning while compiling Fortran with PETSc

[Bojan Niceno]

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 <balay at mcs.anl.gov> 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
> > >
> > >
> > >
> > >
> >
> >
>
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