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/> >> > -- 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/>
