Hi Gilles, The interconnect is Qlogic infiniband QDR. I was unable to compile latest UCX release on this CentOS6 based Rocks Cluster distribution when deploying OpenMPI 4.0.5 but I do not search a lot: I'm currently deploying a new cluster on CentOS8 and this old cluster will move to CentOS8 too as soon as the new one will be in production (using gcc10, OpenMPI 4.0.5 and UCX).
In attachment the ompi_info for OpenMPI 3.1 (version in production) and the dump requested on the kareline cluster using 16 processes. Patrick Le 04/12/2020 à 08:57, Gilles Gouaillardet via users a écrit : > Patrick, > > > the test points to a leak in the way the interconnect component > (pml/ucx ? pml/cm? mtl/psm2? btl/openib?) handles the datatype rather > than the datatype engine itself. > > > What interconnect is available on your cluster and which component(s) > are used? > > > mpirun --mca pml_base_verbose 10 --mca mtl_base_verbose 10 --mca > btl_base_verbose 10 ... > > will point you to the component(s) used. > > The output is pretty verbose, so feel free to compress and post it if > you cannot decipher it > > > Cheers, > > > Gilles > > On 12/4/2020 4:32 PM, Patrick Bégou via users wrote: >> Hi George and Gilles, >> >> Thanks George for your suggestion. Is it valuable for 4.05 and 3.1 >> OpenMPI Versions ? I will have a look today at these tables. May be >> writing a small piece of code juste creating and freeing subarray >> datatype. >> >> Thanks Gilles for suggesting disabling the interconnect. it is a good >> fast test and yes, *with "mpirun --mca pml ob1 --mca btl tcp,self" I >> have no memory leak*. So this explain the differences between my >> laptop and the cluster. >> The implementation of type management is so different from 1.7.3 ? >> >> A PhD student tells me he has also some trouble with this code on a >> cluster Omnipath based. I will have to investigate too but not sure >> it is the same problem. >> >> 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>> 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 >>>> >>
kareline.tgz
Description: application/compressed-tar
