[petsc-users] Warning while compiling Fortran with PETSc

Thu Feb 10 09:53:08 CST 2022

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/>
> >>
> >
> 
> 