[petsc-users] Warning while compiling Fortran with PETSc

Thu Feb 10 09:43:52 CST 2022

On Thu, Feb 10, 2022 at 10:40 AM Bojan Niceno <
bojan.niceno.scientist at gmail.com> wrote:

> 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
>

https://unix.stackexchange.com/questions/199891/invalid-mit-magic-cookie-1-key-when-trying-to-run-program-remotely

  Thanks,

    Matt

>     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/>
>>
>

-- 
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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