[petsc-users] Reaching limit number of communicator with Spectrum MPI

[Junchao Zhang]

Feimi,
  I'm able to reproduce the problem. I will have a look. Thanks a lot for
the example.
--Junchao Zhang


On Fri, Aug 20, 2021 at 2:02 PM Feimi Yu <yuf2 at rpi.edu> wrote:

> Sorry, I forgot to destroy the matrix after the loop, but anyway, the
> in-loop preconditioners are destroyed. Updated the code here and the google
> drive.
>
> Feimi
> On 8/20/21 2:54 PM, Feimi Yu wrote:
>
> Hi Barry and Junchao,
>
> Actually I did a simple MPI "dup and free" test before with Spectrum MPI,
> but that one did not have any problem. I'm not a PETSc programmer as I
> mainly use deal.ii's PETSc wrappers, but I managed to write a minimal
> program based on petsc/src/mat/tests/ex98.c to reproduce my problem. This
> piece of code creates and destroys 10,000 instances of Hypre Parasail
> preconditioners (for my own code, it uses Euclid, but I don't think it
> matters). It runs fine with OpenMPI but reports the out of communicator
> error with Sepctrum MPI. The code is attached in the email. In case the
> attachment is not available, I also uploaded a copy on my google drive:
>
>
> https://drive.google.com/drive/folders/1DCf7lNlks8GjazvoP7c211ojNHLwFKL6?usp=sharing
>
> Thanks!
>
> Feimi
> On 8/20/21 9:58 AM, Junchao Zhang wrote:
>
> Feimi, if it is easy to reproduce, could you give instructions on how to
> reproduce that?
>
> PS: Spectrum MPI is based on OpenMPI.  I don't understand why it has the
> problem but OpenMPI does not.  It could be a bug in petsc or user's code.
> For reference counting on MPI_Comm, we already have petsc inner comm. I
> think we can reuse that.
>
> --Junchao Zhang
>
>
> On Fri, Aug 20, 2021 at 12:33 AM Barry Smith <bsmith at petsc.dev> wrote:
>
>>
>>   It sounds like maybe the Spectrum MPI_Comm_free() is not returning the
>> comm to the "pool" as available for future use; a very buggy MPI
>> implementation. This can easily be checked in a tiny standalone MPI program
>> that simply comm dups and frees thousands of times in a loop. Could even be
>> a configure test (that requires running an MPI program). I do not remember
>> if we ever tested this possibility; maybe and I forgot.
>>
>>   If this is the problem we can provide a "work around" that attributes
>> the new comm (to be passed to hypre) to the old comm with a reference count
>> value also in the attribute. When the hypre matrix is created that count is
>> (with the new comm) is set to 1, when the hypre matrix is freed that count
>> is set to zero (but the comm is not freed), in the next call to create the
>> hypre matrix when the attribute is found, the count is zero so PETSc knows
>> it can pass the same comm again to the new hypre matrix.
>>
>> This will only allow one simultaneous hypre matrix to be created from the
>> original comm. To allow multiply simultaneous hypre matrix one could have
>> multiple comms and counts in the attribute and just check them until one
>> finds an available one to reuse (or creates yet another one if all the
>> current ones are busy with hypre matrices). So it is the same model as
>> DMGetXXVector() where vectors are checked out and then checked in to be
>> available later. This would solve the currently reported problem (if it is
>> a buggy MPI that does not properly free comms), but not solve the MOOSE
>> problem where 10,000 comms are needed at the same time.
>>
>>   Barry
>>
>>
>>
>>
>>
>> On Aug 19, 2021, at 3:29 PM, Junchao Zhang <junchao.zhang at gmail.com>
>> wrote:
>>
>>
>>
>>
>> On Thu, Aug 19, 2021 at 2:08 PM Feimi Yu <yuf2 at rpi.edu> wrote:
>>
>>> Hi Jed,
>>>
>>> In my case, I only have 2 hypre preconditioners at the same time, and
>>> they do not solve simultaneously, so it might not be case 1.
>>>
>>> I checked the stack for all the calls of MPI_Comm_dup/MPI_Comm_free on
>>> my own machine (with OpenMPI), all the communicators are freed from my
>>> observation. I could not test it with Spectrum MPI on the clusters
>>> immediately because all the dependencies were built in release mode.
>>> However, as I mentioned, I haven't had this problem with OpenMPI before,
>>> so I'm not sure if this is really an MPI implementation problem, or just
>>> because Spectrum MPI has less limit for the number of communicators,
>>> and/or this also depends on how many MPI ranks are used, as only 2 out
>>> of 40 ranks reported the error.
>>>
>> You can add printf around MPI_Comm_dup/MPI_Comm_free sites on the two
>> ranks, e.g., if (myrank == 38) printf(...), to see if the dup/free are
>> paired.
>>
>>  As a workaround, I replaced the MPI_Comm_dup() at
>>
>>> petsc/src/mat/impls/hypre/mhypre.c:2120 with a copy assignment, and also
>>> removed the MPI_Comm_free() in the hypre destroyer. My code runs fine
>>> with Spectrum MPI now, but I don't think this is a long-term solution.
>>>
>>> Thanks!
>>>
>>> Feimi
>>>
>>> On 8/19/21 9:01 AM, Jed Brown wrote:
>>> > Junchao Zhang <junchao.zhang at gmail.com> writes:
>>> >
>>> >> Hi, Feimi,
>>> >>    I need to consult Jed (cc'ed).
>>> >>    Jed, is this an example of
>>> >>
>>> https://lists.mcs.anl.gov/mailman/htdig/petsc-dev/2018-April/thread.html#22663
>>> ?
>>> >> If Feimi really can not free matrices, then we just need to attach a
>>> >> hypre-comm to a petsc inner comm, and pass that to hypre.
>>> > Are there a bunch of solves as in that case?
>>> >
>>> > My understanding is that one should be able to
>>> MPI_Comm_dup/MPI_Comm_free as many times as you like, but the
>>> implementation has limits on how many communicators can co-exist at any one
>>> time. The many-at-once is what we encountered in that 2018 thread.
>>> >
>>> > One way to check would be to use a debugger or tracer to examine the
>>> stack every time (P)MPI_Comm_dup and (P)MPI_Comm_free are called.
>>> >
>>> > case 1: we'll find lots of dups without frees (until the end) because
>>> the user really wants lots of these existing at the same time.
>>> >
>>> > case 2: dups are unfreed because of reference counting
>>> issue/inessential references
>>> >
>>> >
>>> > In case 1, I think the solution is as outlined in the thread, PETSc
>>> can create an inner-comm for Hypre. I think I'd prefer to attach it to the
>>> outer comm instead of the PETSc inner comm, but perhaps a case could be
>>> made either way.
>>>
>>
>>
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