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 <[email protected]> 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 <[email protected]> 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 <[email protected]> >> wrote: >> >> >> >> >> On Thu, Aug 19, 2021 at 2:08 PM Feimi Yu <[email protected]> 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 <[email protected]> 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. >>> >> >>
