Re: [OMPI users] MPI_type_free question

[George Bosilca via users]

On Fri, Dec 4, 2020 at 2:33 AM Patrick Bégou via users <
users@lists.open-mpi.org> 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.
>

Patrick,

If you use Gilles' suggestion to go through the type_f2c function when
listing the datatypes should give you a portable datatype iterator across
all versions of OMPI. The call to dump a datatype content,
ompi_datatype_dump, has been there for a very long time, so the combination
of the two should work everywhere.

Thinking a little more about this, you don't necessarily have to dump the
content of the datatype, you only need to check if they are different from
MPI_DATATYPE_NULL. Thus, you can have a solution using only the MPI API.

  George.


>
> 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 
> > 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
> 10 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
>
>
>

Re: [OMPI users] MPI_type_free question

[Patrick Bégou via users]

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
 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
     10 temporal iterations)

     MPI_type_free manual says that it "/Marks the datatype 

Re: [OMPI users] MPI_type_free question

[Gilles Gouaillardet via users]

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 
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
    10 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