[petsc-users] Warning while compiling Fortran with PETSc

Bojan Niceno bojan.niceno.scientist at gmail.com
Thu Feb 10 23:51:21 CST 2022 

Thanks for the example.

I do use -i8 -r8 (I know it is a bad practice and am planning to get rid of
it in mid terms), and I did suspect that, but when I tried to compile
without those options, the warning remained.

When I switched from "include mpif.h" to:

use mpi,

or even:

#include <petsc/finclude/petscsys.h>

  use petscmpi

  use petscsys


I get the following type of messages:

Error: There is no specific subroutine for the generic ‘mpi_barrier’ at (1)
Comm_Mod/Parallel/Start.f90:11:22:

Error: There is no specific subroutine for the generic ‘mpi_init’ at (1)
Comm_Mod/Parallel/Start.f90:14:52:

Error: There is no specific subroutine for the generic ‘mpi_comm_size’ at
(1)
Comm_Mod/Parallel/Start.f90:17:54:

I was googling for a solution, but StackOverflow seems to be down for
maintenance at the moment :-(

I did manage to find that "include mpif.h" is obsolete, which I didn't know
before :-)









On Fri, Feb 11, 2022 at 5:29 AM Satish Balay <balay at mcs.anl.gov> wrote:

> 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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