[petsc-users] PETSc initialization error

[Barry Smith]

   Junchao,

     This is a good bug fix. It solves the problem when PETSc initialize is called many times. 

     There is another fix you can do to limit PETSc mpiuni running out of attributes inside a single PETSc run:


int MPI_Comm_create_keyval(MPI_Copy_function *copy_fn,MPI_Delete_function *delete_fn,int *keyval,void *extra_state)
{
  
 if (num_attr >= MAX_ATTR){
   for (i=0; i<num_attr; i++) {
     if (!attr_keyval[i].extra_state) {
        /* reuse this slot */
        attr_keyval[i].extra_state = extra_state;
       attr_keyval[i.]del         = delete_fn;
       *keyval = i;
        return MPI_SUCCESS;
     }
  }
  return MPIUni_Abort(MPI_COMM_WORLD,1);
}
 return MPIUni_Abort(MPI_COMM_WORLD,1);
  attr_keyval[num_attr].extra_state = extra_state;
  attr_keyval[num_attr].del         = delete_fn;
  *keyval                           = num_attr++;
  return MPI_SUCCESS;
}

  This will work if the user creates tons of attributes but is constantly deleting some as they new ones. So long as the number outstanding at one time is < MAX_ATTR)

Barry





> On Jun 20, 2020, at 10:54 AM, Junchao Zhang <junchao.zhang at gmail.com> wrote:
> 
> I don't understand what your session means. Let's try this patch
> 
> diff --git a/src/sys/mpiuni/mpi.c b/src/sys/mpiuni/mpi.c
> index d559a513..c058265d 100644
> --- a/src/sys/mpiuni/mpi.c
> +++ b/src/sys/mpiuni/mpi.c
> @@ -283,6 +283,7 @@ int MPI_Finalize(void)
>    MPI_Comm_free(&comm);
>    comm = MPI_COMM_SELF;
>    MPI_Comm_free(&comm);
> +  num_attr = 1; /* reset the counter */
>    MPI_was_finalized = 1;
>    return MPI_SUCCESS;
>  }
> 
> 
> --Junchao Zhang
> 
> 
> On Sat, Jun 20, 2020 at 10:48 AM Sam Guo <sam.guo at cd-adapco.com <mailto:sam.guo at cd-adapco.com>> wrote:
> Typo: I mean “Assuming initializer is only needed once for entire session”
> 
> On Saturday, June 20, 2020, Sam Guo <sam.guo at cd-adapco.com <mailto:sam.guo at cd-adapco.com>> wrote:
> Assuming finalizer is only needed once for entire session(?), I can put initializer into the static block to call it once but where do I call finalizer?
> 
> 
> On Saturday, June 20, 2020, Junchao Zhang <junchao.zhang at gmail.com <mailto:junchao.zhang at gmail.com>> wrote:
> The counter num_attr should be recycled. But first try to call PETSc initialize/Finalize only once to see it fixes the error.
> --Junchao Zhang
> 
> 
> On Sat, Jun 20, 2020 at 12:48 AM Sam Guo <sam.guo at cd-adapco.com <mailto:sam.guo at cd-adapco.com>> wrote:
> To clarify, I call PETSc initialize and PETSc finalize everytime I call SLEPc:
> 
>   PetscInitializeNoPointers(argc,args,nullptr,nullptr);
>   SlepcInitialize(&argc,&args,static_cast<char*>(nullptr),help);
>   //calling slepc
>   SlepcFinalize();
>    PetscFinalize();  
> 
> 
> On Fri, Jun 19, 2020 at 10:32 PM Sam Guo <sam.guo at cd-adapco.com <mailto:sam.guo at cd-adapco.com>> wrote:
> Dear PETSc team,
>    When I called SLEPc multiple time, I eventually got following error: 
> 
> MPI operation not supported by PETSc's sequential MPI wrappers
> [0]PETSC ERROR: #1 PetscInitialize() line 967 in ../../../petsc/src/sys/objects/pinit.c
> [0]PETSC ERROR: #2 SlepcInitialize() line 262 in ../../../slepc/src/sys/slepcinit.c
> [0]PETSC ERROR: #3 SlepcInitializeNoPointers() line 359 in ../../../slepc/src/sys/slepcinit.c
> PETSC ERROR: Logging has not been enabled.
> You might have forgotten to call PetscInitialize().  
> 
>   I debugged: it is because of following in petsc/src/sys/mpiuni/mpi.c
> 
> if (num_attr >= MAX_ATTR)
> 
> in function int MPI_Comm_create_keyval(MPI_Copy_function *copy_fn,MPI_Delete_function *delete_fn,int *keyval,void *extra_state)
> 
> num_attr is declared static and keeps increasing every time MPI_Comm_create_keyval is called.
> 
> I am using petsc 3.11.3 but found 3.13.2 has the same logic.
> 
> Is this a bug or I didn't use it correctly?
> 
> Thanks,
> Sam

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20200620/6454bf05/attachment.html>