[petsc-users] PETSc initialization error

[Junchao Zhang]

Sam,
   The MPI_Comm_create_keyval() error was fixed in maint/master. From the
error message, it seems you need to configure --with-log=1
   Otherwise, please send your full error stack trace and configure.log.
  Thanks.
--Junchao Zhang


On Thu, Jun 25, 2020 at 2:18 PM Sam Guo <sam.guo at cd-adapco.com> wrote:

> Hi Junchao,
>    I now encountered the same error with parallel. I am wondering if there
> is a need for parallel fix as well.
> [1]PETSC ERROR: #1 PetscInitialize() line 969 in
> ../../../petsc/src/sys/objects/pinit.c
> PETSC ERROR: Logging has not been enabled.
> You might have forgotten to call PetscInitialize().
> PETSC ERROR: Logging has not been enabled.
> You might have forgotten to call PetscInitialize().
>
> On Sat, Jun 20, 2020 at 7:35 PM Sam Guo <sam.guo at cd-adapco.com> wrote:
>
>> Hi Junchao,
>>    Your patch works.
>>
>> Thanks,
>> Sam
>>
>> On Sat, Jun 20, 2020 at 4:23 PM Junchao Zhang <junchao.zhang at gmail.com>
>> wrote:
>>
>>>
>>>
>>> On Sat, Jun 20, 2020 at 12:24 PM Barry Smith <bsmith at petsc.dev> wrote:
>>>
>>>>
>>>>    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) {
>>>>
>>> attr_keyval[i].extra_state is provided by user (could be NULL). We can
>>> not rely on it.
>>>
>>>>         /* 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> 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> 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>
>>>>>> 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>
>>>>>>> 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>
>>>>>>>> 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
>>>>>>>>>
>>>>>>>>
>>>>
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