[petsc-users] Memory growth issue

[Zhang, Junchao]

Hi, Sanjay,
  Could you send your modified data exchange code (psetb.F) with MPI_Waitall? See other inlined comments below. Thanks.

On Thu, May 30, 2019 at 1:49 PM Sanjay Govindjee via petsc-users <petsc-users at mcs.anl.gov<mailto:petsc-users at mcs.anl.gov>> wrote:
Lawrence,
Thanks for taking a look!  This is what I had been wondering about -- my
knowledge of MPI is pretty minimal and
this origins of the routine were from a programmer we hired a decade+
back from NERSC.  I'll have to look into
VecScatter.  It will be great to dispense with our roll-your-own
routines (we even have our own reduceALL scattered around the code).
Petsc VecScatter has a very simple interface and you definitely should go with.  With VecScatter, you can think in familiar vectors and indices instead of the low level MPI_Send/Recv. Besides that, PETSc has optimized VecScatter so that communication is efficient.

Interestingly, the MPI_WaitALL has solved the problem when using OpenMPI
but it still persists with MPICH.  Graphs attached.
I'm going to run with openmpi for now (but I guess I really still need
to figure out what is wrong with MPICH and WaitALL;
I'll try Barry's suggestion of
--download-mpich-configure-arguments="--enable-error-messages=all
--enable-g" later today and report back).

Regarding MPI_Barrier, it was put in due a problem that some processes
were finishing up sending and receiving and exiting the subroutine
before the receiving processes had completed (which resulted in data
loss as the buffers are freed after the call to the routine).
MPI_Barrier was the solution proposed
to us.  I don't think I can dispense with it, but will think about some
more.
After MPI_Send(), or after MPI_Isend(..,req) and MPI_Wait(req), you can safely free the send buffer without worry that the receive has not completed. MPI guarantees the receiver can get the data, for example, through internal buffering.

I'm not so sure about using MPI_IRecv as it will require a bit of
rewriting since right now I process the received
data sequentially after each blocking MPI_Recv -- clearly slower but
easier to code.

Thanks again for the help.

-sanjay

On 5/30/19 4:48 AM, Lawrence Mitchell wrote:
> Hi Sanjay,
>
>> On 30 May 2019, at 08:58, Sanjay Govindjee via petsc-users <petsc-users at mcs.anl.gov<mailto:petsc-users at mcs.anl.gov>> wrote:
>>
>> The problem seems to persist but with a different signature.  Graphs attached as before.
>>
>> Totals with MPICH (NB: single run)
>>
>> For the CG/Jacobi          data_exchange_total = 41,385,984; kspsolve_total = 38,289,408
>> For the GMRES/BJACOBI      data_exchange_total = 41,324,544; kspsolve_total = 41,324,544
>>
>> Just reading the MPI docs I am wondering if I need some sort of MPI_Wait/MPI_Waitall before my MPI_Barrier in the data exchange routine?
>> I would have thought that with the blocking receives and the MPI_Barrier that everything will have fully completed and cleaned up before
>> all processes exited the routine, but perhaps I am wrong on that.
>
> Skimming the fortran code you sent you do:
>
> for i in ...:
>     call MPI_Isend(..., req, ierr)
>
> for i in ...:
>     call MPI_Recv(..., ierr)
>
> But you never call MPI_Wait on the request you got back from the Isend. So the MPI library will never free the data structures it created.
>
> The usual pattern for these non-blocking communications is to allocate an array for the requests of length nsend+nrecv and then do:
>
> for i in nsend:
>     call MPI_Isend(..., req[i], ierr)
> for j in nrecv:
>     call MPI_Irecv(..., req[nsend+j], ierr)
>
> call MPI_Waitall(req, ..., ierr)
>
> I note also there's no need for the Barrier at the end of the routine, this kind of communication does neighbourwise synchronisation, no need to add (unnecessary) global synchronisation too.
>
> As an aside, is there a reason you don't use PETSc's VecScatter to manage this global to local exchange?
>
> Cheers,
>
> Lawrence

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