[petsc-users] Warning while compiling Fortran with PETSc

Thu Feb 10 09:40:06 CST 2022

Thanks a lot, now I feel much better.

By the way, I can't get around the invalid magic cookie.  It is occurring
ever since I installed the OS (Ubuntu 20.04) so I eventually gave up and
decided to live with it :-D

    Cheers,

    Bojan

On Thu, Feb 10, 2022 at 4:37 PM Matthew Knepley <knepley at gmail.com> wrote:

> 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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