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 <[email protected]> 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 < > > > [email protected]> 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 <[email protected]> > > wrote: > > > > > > > >> On Thu, Feb 10, 2022 at 10:34 AM Bojan Niceno < > > > >> [email protected]> 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 <[email protected]> > > 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/> > > > >> > > > > > > > > > > > > >
