[petsc-users] Warning while compiling Fortran with PETSc

Satish Balay balay at mcs.anl.gov
Thu Feb 10 22:29:43 CST 2022 

1. you can call MPI_Init() before calling PetscInitialize() For
example - check src/sys/tutorials/ex4f90.F90

2. Are you using -i8 -r8 type flags when compiling your code? That
might case issues when using mpif.h. Perhaps you can switch from
"include 'mpif.h'" to "use mpi" - in your module file - and see if
that helps.

Satish

On Fri, 11 Feb 2022, Bojan Niceno wrote:

> Dear both,
> 
> Allow me to update you on the issue.  I tried to re-compile PETSc with
> different configuration options as Satish suggested, and went further on by
> specifying exact location of OpenMPI libraries and include files to the
> ones installed by PETSc (for those configurations for which I used
> "--download-openmpi=1") and the original problem, the warning Named COMMON
> block ‘mpi_fortran_bottom’ at (1) shall be of the same size as elsewhere (4
> vs 8 bytes), prevailed.
> 
> In desperation, I completely removed OpenMPI from my workstation to make
> sure that only those which are downloaded with PETSc are used, yet the
> warning was still there.  (That resolved the Invalid MIT-MAGIC-COOKIE-1
> warning at least)
> 
> Now I am wondering if the problem originates from the fact that I already
> have all the necessary MPI routines developed in Fortran?  All calls,
> including the basic MPI_Init, MPI_Comm_Size and MPI_Comm_Rank, are done
> from Fortran.  I actually have a module called Comm_Mod which does all
> MPI-related calls, and this module contains line include 'mpif.h'.  That
> include statement does take the file from PETSc installation as no other
> MPI installation is left on my system, but still it somehow seems to be the
> origin of the warning on common blocks I observe.  Now I am wondering if
> the include 'mpif.h' from Fortran somehow collides with the option include
> ${PETSC_DIR}/lib/petsc/conf/variables I put in my makefile in order to
> compile with PETSc.
> 
> I am really not sure if it is possible to have main program and all MPI
> initialization done from Fortran (as I have now) and then plug PETSc on top
> of it?  Should that be possible?
> 
>     Kind regards,
> 
>     Bojan
> 
> P.S. The sequential version works fine, I can compile without warning and
> can call PETSc solvers from Fortran without a glitch.
> 
> On Thu, Feb 10, 2022 at 5:08 PM Bojan Niceno <
> bojan.niceno.scientist at gmail.com> wrote:
> 
> > 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/>
> >> > > > >>
> >> > > > >
> >> > > >
> >> > > >
> >> > >
> >> >
> >>
> >
>

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