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but StackOverflow seems to be down for maintenance at the moment :-( I did manage to find that "include mpif.h" is obsolete, which I didn't know before :-) On Fri, Feb 11, 2022 at 5:29 AM Satish Balay <[email protected]> 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 < > > [email protected]> 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 <[email protected]> > 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 <[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/> > > >> > > > >> > > >> > > > > > > >> > > > > > >> > > > > > >> > > > > >> > > > >> > > > > > >
