Hi Patrick, Glad to hear you are now able to move forward.
Please keep in mind this is not a fix but a temporary workaround. At first glance, I did not spot any issue in the current code. It turned out that the memory leak disappeared when doing things differently Cheers, Gilles On Mon, Dec 14, 2020 at 7:11 PM Patrick Bégou via users < users@lists.open-mpi.org> wrote: > Hi Gilles, > > you catch the bug! With this patch, on a single node, the memory leak > disappear. The cluster is actualy overloaded, as soon as possible I will > launch a multinode test. > Below the memory used by rank 0 before (blue) and after (red) the patch. > > Thanks > > Patrick > > > Le 10/12/2020 à 10:15, Gilles Gouaillardet via users a écrit : > > Patrick, > > > First, thank you very much for sharing the reproducer. > > > Yes, please open a github issue so we can track this. > > > I cannot fully understand where the leak is coming from, but so far > > - the code fails on master built with --enable-debug (the data engine > reports an error) but not with the v3.1.x branch > > (this suggests there could be an error in the latest Open MPI ... or in > the code) > > - the attached patch seems to have a positive effect, can you please give > it a try? > > > Cheers, > > > Gilles > > > > On 12/7/2020 6:15 PM, Patrick Bégou via users wrote: > > Hi, > > I've written a small piece of code to show the problem. Based on my > application but 2D and using integers arrays for testing. > The figure below shows the max RSS size of rank 0 process on 20000 > iterations on 8 and 16 cores, with openib and tcp drivers. > The more processes I have, the larger the memory leak. I use the same > binaries for the 4 runs and OpenMPI 3.1 (same behavior with 4.0.5). > The code is in attachment. I'll try to check type deallocation as soon as > possible. > > Patrick > > > > > Le 04/12/2020 à 01:34, Gilles Gouaillardet via users a écrit : > > Patrick, > > > based on George's idea, a simpler check is to retrieve the Fortran index > via the (standard) MPI_Type_c2() function > > after you create a derived datatype. > > > If the index keeps growing forever even after you MPI_Type_free(), then > this clearly indicates a leak. > > Unfortunately, this simple test cannot be used to definitely rule out any > memory leak. > > > Note you can also > > mpirun --mca pml ob1 --mca btl tcp,self ... > > in order to force communications over TCP/IP and hence rule out any memory > leak that could be triggered by your fast interconnect. > > > > In any case, a reproducer will greatly help us debugging this issue. > > > Cheers, > > > Gilles > > > > On 12/4/2020 7:20 AM, George Bosilca via users wrote: > > Patrick, > > I'm afraid there is no simple way to check this. The main reason being > that OMPI use handles for MPI objects, and these handles are not tracked by > the library, they are supposed to be provided by the user for each call. In > your case, as you already called MPI_Type_free on the datatype, you cannot > produce a valid handle. > > There might be a trick. If the datatype is manipulated with any Fortran > MPI functions, then we convert the handle (which in fact is a pointer) to > an index into a pointer array structure. Thus, the index will remain used, > and can therefore be used to convert back into a valid datatype pointer, > until OMPI completely releases the datatype. Look into > the ompi_datatype_f_to_c_table table to see the datatypes that exist and > get their pointers, and then use these pointers as arguments to > ompi_datatype_dump() to see if any of these existing datatypes are the ones > you define. > > George. > > > > > On Thu, Dec 3, 2020 at 4:44 PM Patrick Bégou via users < > users@lists.open-mpi.org <mailto:users@lists.open-mpi.org> > <users@lists.open-mpi.org>> wrote: > > Hi, > > I'm trying to solve a memory leak since my new implementation of > communications based on MPI_AllToAllW and MPI_type_Create_SubArray > calls. Arrays of SubArray types are created/destroyed at each > time step and used for communications. > > On my laptop the code runs fine (running for 15000 temporal > itérations on 32 processes with oversubscription) but on our > cluster memory used by the code increase until the OOMkiller stop > the job. On the cluster we use IB QDR for communications. > > Same Gcc/Gfortran 7.3 (built from sources), same sources of > OpenMPI (3.1 or 4.0.5 tested), same sources of the fortran code on > the laptop and on the cluster. > > Using Gcc/Gfortran 4.8 and OpenMPI 1.7.3 on the cluster do not > show the problem (resident memory do not increase and we ran > 100000 temporal iterations) > > MPI_type_free manual says that it "/Marks the datatype object > associated with datatype for deallocation/". But how can I check > that the deallocation is really done ? > > Thanks for ant suggestions. > > Patrick > > > >
