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
