[petsc-users] Warning while compiling Fortran with PETSc

Satish Balay balay at mcs.anl.gov
Mon Feb 14 07:59:42 CST 2022 

Thanks for the update. Glad you were able to find a fix for this issue.

Satish

On Mon, 14 Feb 2022, Bojan Niceno wrote:

> Dear both,
> 
> It was the compiler options for integer lengths after all, thanks,  Now I
> corrected it all in my code, all integers have explicitly defined lengths,
> and I am using the MPI_F08 module instead of obsolete mpi.f.  It was a
> daunting task (> 800 files, > 64000 lines of code), but I am happy with the
> outcome.  Now I can continue with PETSc :-)
> 
>     Cheers
> 
>     Bojan
> 
> 
> 
> 
> On Fri, Feb 11, 2022 at 7:26 AM Bojan Niceno <
> bojan.niceno.scientist at gmail.com> wrote:
> 
> > What does seem to work is:
> >
> > use mpi_f08
> >
> > and using:
> >
> >   call Mpi_Init_08(error)
> >
> >   call Mpi_Comm_Size_08(MPI_COMM_WORLD, n_proc, error)·
> >
> >   call Mpi_Comm_Rank_08(MPI_COMM_WORLD, this_proc, error)
> >
> >
> > That is, function calls with extension _08
> >
> >
> >
> >
> >
> > On Fri, Feb 11, 2022 at 6:51 AM Bojan Niceno <
> > bojan.niceno.scientist at gmail.com> wrote:
> >
> >> 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 I did manage to find that "include mpif.h" is obsolete, which I didn't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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