[petsc-users] Warning while compiling Fortran with PETSc

Bojan Niceno bojan.niceno.scientist at gmail.com
Thu Feb 10 10:08:50 CST 2022 

Dear Satish,

Thanks for the advice.  I will try in a few hours because it is almost
dinner time with me (I am in Europe) and I am supposed to go out with a
friend this evening.

Will let you know.  Thanks for help, I highly appreciate it.


    Kind regards,

    Bojan


On Thu, Feb 10, 2022 at 5:06 PM Satish Balay <balay at mcs.anl.gov> wrote:

> Hm - this is strange.
>
> Do you have 'xauth' installed?
>
> I would make sure xauth is installed, delete ~/.Xauthority - and reboot
> [or restart the X server]
>
> Yeah - it might not work - but perhaps worth a try..
>
> Or perhaps its not X11 related..
>
> I would also try 'strace' on an application that is producing this message
> - to see if I can narrow down further..
>
> Do you get this message with both (runs)?:
>
> cd src/ksp/ksp/tutorials
> make ex2
> mpiexec -n 1 ./ex2
> ./ex2
>
> Satish
>
> On Thu, 10 Feb 2022, Bojan Niceno wrote:
>
> > Dear both,
> >
> > I work on an ASUS ROG laptop and don't use any NFS.  Everything is on one
> > computer, one disk.  That is why I couldn't resolve the Invalid Magic
> > Cookie, because all the advice I've found about it concerns the remote
> > access/display.  It is not an issue for me.  My laptop has an Nvidia
> > GeForce RTX graphical card, maybe Ubuntu drivers are simply not able to
> > cope with it.  I am out of ideas, really.
> >
> >
> >     Cheers,
> >
> >     Bojan
> >
> > On Thu, Feb 10, 2022 at 4:53 PM Satish Balay <balay at mcs.anl.gov> wrote:
> >
> > > Do the compute nodes and frontend share the same NFS?
> > >
> > > I would try the following [to see if they work):
> > >
> > > - delete ~/.Xauthority [first check with 'xauth list')
> > > - setup ssh to not use X - i.e add the following to ~/.ssh/config
> > >
> > > ForwardX11 no
> > > ForwardX11Trusted no
> > >
> > > [this can be tailored to apply only to your specific compute nodes - if
> > > needed]
> > >
> > > Satish
> > >
> > > On Thu, 10 Feb 2022, Matthew Knepley wrote:
> > >
> > > > 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/>
> > > > >>
> > > > >
> > > >
> > > >
> > >
> >
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20220210/f366aa59/attachment-0001.html>

More information about the petsc-users mailing list