Yes, opening an issue would be great -- thanks!
On Dec 14, 2020, at 11:32 AM, Patrick Bégou via users <users@lists.open-mpi.org<mailto:users@lists.open-mpi.org>> wrote: OK, Thanks Gilles. Does it still require that I open an issue for tracking ? Patrick Le 14/12/2020 à 14:56, Gilles Gouaillardet via users a écrit : 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<mailto: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 <patch.png> 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> <mailto:users@lists.open-mpi.org><mailto: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 -- Jeff Squyres jsquy...@cisco.com<mailto:jsquy...@cisco.com>
