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/> > >> > > > >
