[petsc-users] Warning while compiling Fortran with PETSc

[Matthew Knepley]

On Thu, Feb 10, 2022 at 10:34 AM Bojan Niceno <
bojan.niceno.scientist at gmail.com> 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 <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
>> > >
>> > >
>> > >
>> > >
>> >
>> >
>>
>

-- 
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/>
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