Dear all,
here the 3D example, but unfortunately it does not work.
I believe that there is some problem with the stride.
What do you think?
Thanks again to everyone
Diego
On 16 January 2015 at 19:20, Diego Avesani <diego.aves...@gmail.com> wrote:
> Dear All,
> in the attachment the 2D example, Now I will try the 3D example.
>
> What do you think of it? is it correct?
> The idea is to build a 2D data_type, to sent 3D data
>
> Diego
>
>
> On 16 January 2015 at 18:19, Diego Avesani <diego.aves...@gmail.com>
> wrote:
>
>> Dear George, Dear All,
>>
>> and what do you think about the previous post?
>>
>> Thanks again
>>
>> Diego
>>
>>
>> On 16 January 2015 at 18:11, George Bosilca <bosi...@icl.utk.edu> wrote:
>>
>>> You could but you don’t need to. The datatype engine of Open MPI is
>>> doing a fair job of packing/unpacking the data on the flight, so you don’t
>>> have to.
>>>
>>> George.
>>>
>>> On Jan 16, 2015, at 11:32 , Diego Avesani <diego.aves...@gmail.com>
>>> wrote:
>>>
>>> Dear all,
>>>
>>> Could I use MPI_PACK?
>>>
>>>
>>> Diego
>>>
>>>
>>> On 16 January 2015 at 16:26, Diego Avesani <diego.aves...@gmail.com>
>>> wrote:
>>>
>>>> Dear George, Dear all,
>>>>
>>>> I have been studying. It's clear for 2D case QQ(:,:).
>>>>
>>>> For example if
>>>> real :: QQ(npt,9) , with 9 the characteristic of each particles.
>>>>
>>>> I can simple:
>>>>
>>>> call MPI_TYPE_VECTOR(QQ(1:50), 9, 9, MPI_REAL, my_2D_type, ierr)
>>>>
>>>> I send 50 element of QQ. I am in fortran so a two dimensional array is
>>>> organized in a 1D array and a new row start after the 9 elements of a colum
>>>>
>>>> The problem is a 3D array. I belive that I have to create a sort of *vector
>>>> of vectors.*
>>>> More or less like:
>>>>
>>>> call MPI_TYPE_VECTOR(xxx, xxx, xxx, MPI_REAL, my_row, ierr)
>>>>
>>>> and then
>>>>
>>>> call MPI_TYPE_VECTOR(xxx, xxx, xxx, *my_row*, my_type, ierr).
>>>>
>>>> You can note that in the second case I have *my_row *instead of
>>>> mpi_real.
>>>>
>>>> I found somethind about it in a tutorial but I am not able to find it
>>>> again in google. I think that is not convinient the use of struct in this
>>>> case, I have only real. Moreover, mpi_struct is think to emulate
>>>> Fortran90 and C structures, as Gus' suggestion.
>>>>
>>>> Let's me look to that tutorial
>>>> What do you think?
>>>>
>>>> Thanks again
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> Diego
>>>>
>>>>
>>>> On 16 January 2015 at 16:02, George Bosilca <bosi...@icl.utk.edu>
>>>> wrote:
>>>>
>>>>> The operation you describe is a pack operation, agglomerating together
>>>>> in a contiguous buffer originally discontinuous elements. As a result
>>>>> there
>>>>> is no need to use the MPI_TYPE_VECTOR, but instead you can just use the
>>>>> type you created so far (MPI_my_STRUCT) with a count.
>>>>>
>>>>> George.
>>>>>
>>>>>
>>>>> On Fri, Jan 16, 2015 at 5:32 AM, Diego Avesani <
>>>>> diego.aves...@gmail.com> wrote:
>>>>>
>>>>>> Dear All,
>>>>>> I'm sorry to insist, but I am not able to understand. Moreover, I
>>>>>> have realized that I have to explain myself better.
>>>>>>
>>>>>> I try to explain in may program. Each CPU has *npt* particles. My
>>>>>> program understand how many particles each CPU has to send, according to
>>>>>> their positions. Then I can do:
>>>>>>
>>>>>> *icount=1*
>>>>>> * DO i=1,npt*
>>>>>> * IF(i is a particle to send)THEN*
>>>>>>
>>>>>> * DATASEND(icount)%ip = PART(ip)%ip*
>>>>>> * DATASEND(icount)%mc = PART(ip)%mc*
>>>>>>
>>>>>> * DATASEND(icount)%RP = PART(ip)%RP*
>>>>>> * DATASEND(icount)%QQ = PART(ip)%QQ*
>>>>>>
>>>>>> * icount=icount+1*
>>>>>> * ENDIF*
>>>>>> * ENDDO*
>>>>>>
>>>>>> After that, I can send *DATASEND*
>>>>>>
>>>>>> I *DATASEND* is a *MPI_my_STRUCT.* I can allocate it according to
>>>>>> the number of particles that I have to send:
>>>>>>
>>>>>> TYPE(tParticle) ,ALLOCATABLE,DIMENSION(:) :: DATASEND,DATARECV
>>>>>>
>>>>>> This means that the number of particles which I have to send can
>>>>>> change every time.
>>>>>>
>>>>>> After that, I compute for each particles, somethins called
>>>>>> QQmls(:,:,:).
>>>>>> QQmls has all real elements. Now I would like to to the same that I
>>>>>> did with PART, but in this case:
>>>>>>
>>>>>> *icount=1*
>>>>>> *DO i=1,npt*
>>>>>> * IF(i is a particle to send)THEN*
>>>>>>
>>>>>> *DATASEND_REAL(:,icount,:)=QQmls(:,i,:)*
>>>>>> * icount=icount+1*
>>>>>>
>>>>>> * ENDIF*
>>>>>> *ENDDO*
>>>>>>
>>>>>> I would like to have a sort *MPI_my_TYPE to do that (like *
>>>>>> *MPI_my_STRUCT**) *and not to create every time *MPI_TYPE_VECTOR *
>>>>>> because *DATASEND_REAL *changes size every time.
>>>>>>
>>>>>> I hope to make myself clear.
>>>>>>
>>>>>> So is it correct to use *MPI_TYPE_VECTOR?, *Can I do what I want?
>>>>>>
>>>>>> In the meantime, I will study some examples.
>>>>>>
>>>>>> Thanks again
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> Diego
>>>>>>
>>>>>>
>>>>>> On 16 January 2015 at 07:39, George Bosilca <bosi...@icl.utk.edu>
>>>>>> wrote:
>>>>>>
>>>>>>> The subarray creation is an multi-dimension extension of the vector
>>>>>>> type. You can see it as a vector of vector of vector and so on, one
>>>>>>> vector
>>>>>>> per dimension. The stride array is used to declare on each dimension
>>>>>>> what
>>>>>>> is the relative displacement (in number of elements) from the beginning
>>>>>>> of
>>>>>>> the dimension array.
>>>>>>>
>>>>>>> It is important to use regular type creation when you can take
>>>>>>> advantage of such regularity instead of resorting to use of struct or
>>>>>>> h*.
>>>>>>> This insure better packing/unpacking performance, as well as possible
>>>>>>> future support for one-sided communications.
>>>>>>>
>>>>>>> George.
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> > On Jan 15, 2015, at 19:31, Gus Correa <g...@ldeo.columbia.edu>
>>>>>>> wrote:
>>>>>>> >
>>>>>>> > I never used MPI_Type_create_subarray, only MPI_Type_Vector.
>>>>>>> > What I like about MPI_Type_Vector is that you can define a stride,
>>>>>>> > hence you can address any regular pattern in memory.
>>>>>>> > However, it envisages the array layout in memory as a big 1-D
>>>>>>> array,
>>>>>>> > with a linear index progressing in either Fortran or C order.
>>>>>>> >
>>>>>>> > Somebody correct me please if I am wrong, but at first sight
>>>>>>> MPI_Type_Vector sounds more flexible to me than
>>>>>>> MPI_Type_create_subarray,
>>>>>>> exactly because the latter doesn't have strides.
>>>>>>> >
>>>>>>> > The downside is that you need to do some index arithmetic to figure
>>>>>>> > the right strides, etc, to match the corresponding
>>>>>>> > Fortran90 array sections.
>>>>>>> >
>>>>>>> > There are good examples in the "MPI - The complete reference"
>>>>>>> books I suggested to you before (actually in vol 1).
>>>>>>> >
>>>>>>> > Online I could find the two man pages (good information, but no
>>>>>>> example):
>>>>>>> >
>>>>>>> > http://www.open-mpi.org/doc/v1.8/man3/MPI_Type_vector.3.php
>>>>>>> >
>>>>>>> http://www.open-mpi.org/doc/v1.8/man3/MPI_Type_create_subarray.3.php
>>>>>>> >
>>>>>>> > There is a very simple 2D example of MPI_Type_vector using strides
>>>>>>> here:
>>>>>>> >
>>>>>>> > https://computing.llnl.gov/tutorials/mpi/#Derived_Data_Types
>>>>>>> >
>>>>>>> > and a similar one here:
>>>>>>> >
>>>>>>> >
>>>>>>> http://static.msi.umn.edu/tutorial/scicomp/general/MPI/content6.html
>>>>>>> >
>>>>>>> > Gus Correa
>>>>>>> >
>>>>>>> >> On 01/15/2015 06:53 PM, Diego Avesani wrote:
>>>>>>> >> dear George, dear Gus, dear all,
>>>>>>> >> Could you please tell me where I can find a good example?
>>>>>>> >> I am sorry but I can not understand the 3D array.
>>>>>>> >>
>>>>>>> >>
>>>>>>> >> Really Thanks
>>>>>>> >>
>>>>>>> >> Diego
>>>>>>> >>
>>>>>>> >>
>>>>>>> >> On 15 January 2015 at 20:13, George Bosilca <bosi...@icl.utk.edu
>>>>>>> >> <mailto:bosi...@icl.utk.edu>> wrote:
>>>>>>> >>
>>>>>>> >>
>>>>>>> >>> On Jan 15, 2015, at 06:02 , Diego Avesani <
>>>>>>> diego.aves...@gmail.com
>>>>>>> >>> <mailto:diego.aves...@gmail.com>> wrote:
>>>>>>> >>>
>>>>>>> >>> Dear Gus, Dear all,
>>>>>>> >>> Thanks a lot.
>>>>>>> >>> MPI_Type_Struct works well for the first part of my problem,
>>>>>>> so I
>>>>>>> >>> am very happy to be able to use it.
>>>>>>> >>>
>>>>>>> >>> Regarding MPI_TYPE_VECTOR.
>>>>>>> >>>
>>>>>>> >>> I have studied it and for simple case it is clear to me what
>>>>>>> id
>>>>>>> >>> does (at least I believe). Foe example if I have a matrix
>>>>>>> define as:
>>>>>>> >>> REAL, ALLOCATABLE (AA(:,:))
>>>>>>> >>> ALLOCATE AA(100,5)
>>>>>>> >>>
>>>>>>> >>> I could send part of it defining
>>>>>>> >>>
>>>>>>> >>> CALL MPI_TYPE_VECTOR(5,1,5,MPI_DOUBLE_PRECISION,/MY_NEW_TYPE/)
>>>>>>> >>>
>>>>>>> >>> after that I can send part of it with
>>>>>>> >>>
>>>>>>> >>> CALL MPI_SEND( AA(1:/10/,:), /10/, /MY_NEW_TYPE/, 1, 0,
>>>>>>> >>> MPI_COMM_WORLD );
>>>>>>> >>>
>>>>>>> >>> Have I understood correctly?
>>>>>>> >>>
>>>>>>> >>> What I can do in case of three dimensional array? for example
>>>>>>> >>> AA(:,:,:), I am looking to MPI_TYPE_CREATE_SUBARRAY.
>>>>>>> >>> Is that the correct way?
>>>>>>> >>>
>>>>>>> >>> Thanks again
>>>>>>> >>
>>>>>>> >> Indeed, using the subarray is the right approach independent
>>>>>>> on the
>>>>>>> >> number of dimensions of the data (you can use it instead of
>>>>>>> >> MPI_TYPE_VECTOR as well).
>>>>>>> >>
>>>>>>> >> George.
>>>>>>> >>
>>>>>>> >>
>>>>>>> >>>
>>>>>>> >>>
>>>>>>> >>>
>>>>>>> >>>
>>>>>>> >>> Diego
>>>>>>> >>>
>>>>>>> >>>
>>>>>>> >>> On 13 January 2015 at 19:04, Gus Correa <
>>>>>>> g...@ldeo.columbia.edu
>>>>>>> >>> <mailto:g...@ldeo.columbia.edu>> wrote:
>>>>>>> >>>
>>>>>>> >>> Hi Diego
>>>>>>> >>> I guess MPI_Type_Vector is the natural way to send and
>>>>>>> receive
>>>>>>> >>> Fortran90 array sections (e.g. your QQMLS(:,50:100,:)).
>>>>>>> >>> I used that before and it works just fine.
>>>>>>> >>> I think that is pretty standard MPI programming style.
>>>>>>> >>> I guess MPI_Type_Struct tries to emulate Fortran90 and C
>>>>>>> >>> structures
>>>>>>> >>> (as you did in your previous code, with all the surprises
>>>>>>> >>> regarding alignment, etc), not array sections.
>>>>>>> >>> Also, MPI type vector should be more easy going (and
>>>>>>> probably
>>>>>>> >>> more efficient) than MPI type struct, with less memory
>>>>>>> >>> alignment problems.
>>>>>>> >>> I hope this helps,
>>>>>>> >>> Gus Correa
>>>>>>> >>>
>>>>>>> >>> PS - These books have a quite complete description and
>>>>>>> several
>>>>>>> >>> examples
>>>>>>> >>> of all MPI objects and functions, including MPI types
>>>>>>> (native
>>>>>>> >>> and user defined):
>>>>>>> >>> http://mitpress.mit.edu/books/__mpi-complete-reference-0
>>>>>>> >>> <http://mitpress.mit.edu/books/mpi-complete-reference-0>
>>>>>>> >>> http://mitpress.mit.edu/books/__mpi-complete-reference-1
>>>>>>> >>> <http://mitpress.mit.edu/books/mpi-complete-reference-1>
>>>>>>> >>>
>>>>>>> >>> [They cover MPI 1 and 2. I guess there is a new/upcoming
>>>>>>> book
>>>>>>> >>> with MPI 3, but for what you're doing 1 and 2 are more
>>>>>>> than
>>>>>>> >>> enough.]
>>>>>>> >>>
>>>>>>> >>>
>>>>>>> >>> On 01/13/2015 09:22 AM, Diego Avesani wrote:
>>>>>>> >>>
>>>>>>> >>> Dear all,
>>>>>>> >>>
>>>>>>> >>> I had some wonderful talking about
>>>>>>> MPI_type_create_struct adn
>>>>>>> >>> isend\irecv with
>>>>>>> >>> Gilles, Gustavo, George, Gus, Tom and Jeff. Now all is
>>>>>>> >>> more clear and my
>>>>>>> >>> program works.
>>>>>>> >>>
>>>>>>> >>> Now I have another question. In may program I have
>>>>>>> matrix:
>>>>>>> >>>
>>>>>>> >>> /QQMLS(:,:,:) /that is allocate as
>>>>>>> >>>
>>>>>>> >>> /ALLOCATE(QQMLS(9,npt,18)/), where npt is the number
>>>>>>> of
>>>>>>> >>> particles
>>>>>>> >>>
>>>>>>> >>> QQMLS is double precision.
>>>>>>> >>>
>>>>>>> >>> I would like to sent form a CPU to another part of
>>>>>>> it, for
>>>>>>> >>> example,
>>>>>>> >>> sending QQMLS(:,50:100,:). I mean sending the QQMLS
>>>>>>> of the
>>>>>>> >>> particles
>>>>>>> >>> between 50 to 100.
>>>>>>> >>> I suppose that i could use MPI_Type_vector but I am
>>>>>>> not
>>>>>>> >>> sure. The
>>>>>>> >>> particle that I want to sent could be from 25 to 50
>>>>>>> ecc..
>>>>>>> >>> ecc..so
>>>>>>> >>> blocklength changes everytime.
>>>>>>> >>>
>>>>>>> >>> Do I have to use MPI_type_create_struct?
>>>>>>> >>> Do I have correctly understood MPI_Type_vector?
>>>>>>> >>>
>>>>>>> >>> Thanks a lot
>>>>>>> >>>
>>>>>>> >>>
>>>>>>> >>> Diego
>>>>>>> >>>
>>>>>>> >>>
>>>>>>> >>>
>>>>>>> >>> _________________________________________________
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>
MODULE MOD_PRECISION
integer, parameter :: dp = selected_real_kind(15, 307)
ENDMODULE MOD_PRECISION
PROGRAM test_2Darray_send
USE MOD_PRECISION
USE MPI
IMPLICIT NONE
INTEGER :: iCPU,icount,iTag,ip,sendcount,sendrecv,i,iStart,iEnd
INTEGER :: NPT
INTEGER :: status(MPI_STATUS_SIZE)
TYPE tMPI
INTEGER :: myrank, nCPU, iErr, status
END TYPE tMPI
TYPE(tMPI) :: MPIdata
INTEGER :: MPI_TYPE_VECTOR_1D,MPI_TYPE_VECTOR_2D
REAL(DP),ALLOCATABLE,DIMENSION(:,:,:) :: AA
CALL MPI_INIT(MPIdata%iErr)
CALL MPI_COMM_RANK(MPI_COMM_WORLD, MPIdata%myrank, MPIdata%iErr)
CALL MPI_COMM_SIZE(MPI_COMM_WORLD, MPIdata%nCPU, MPIdata%iErr)
NPT=10
ALLOCATE(AA(NPT,2,2))
AA=0.d0
CALL MPI_TYPE_VECTOR(2, 1, 1, MPI_DOUBLE_PRECISION, MPI_TYPE_VECTOR_1D,MPIdata%iErr)
CALL MPI_TYPE_COMMIT(MPI_TYPE_VECTOR_1D,MPIdata%iErr)
CALL MPI_TYPE_VECTOR(2, 1, 1, MPI_TYPE_VECTOR_1D, MPI_TYPE_VECTOR_2D,MPIdata%iErr)
CALL MPI_TYPE_COMMIT(MPI_TYPE_VECTOR_2D,MPIdata%iErr)
IF(MPIdata%myrank==0)THEN
DO I=1,NPT
AA(I,1,1)=REAL(I,DP)
AA(I,1,2)=10.d0*REAL(I,DP)
AA(I,2,1)=REAL(I,DP)*2.d0
AA(I,2,2)=10.d0*REAL(I,DP)*2.d0
ENDDO
WRITE(*,*) '-------------'
WRITE(*,*) MPIdata%myrank
WRITE(*,*) AA(1:3,2,2)
WRITE(*,*) '-------------'
WRITE(*,*) SIZE(aa(1,:,:))
!
CALL MPI_SEND(AA(1:3,:,:),3*4,MPI_TYPE_VECTOR_2D,1,5,MPI_COMM_WORLD,MPIdata%iErr)
!
ENDIF
CALL MPI_BARRIER(MPI_COMM_WORLD,MPIdata%iErr)
IF(MPIdata%myrank==1)THEN
!
CALL MPI_RECV(AA(1:3,:,:),3*4,MPI_TYPE_VECTOR_1D,0,5,MPI_COMM_WORLD,status,MPIdata%iErr)
WRITE(*,*) AA(1:3,2,2)
!
ENDIF
CALL MPI_Finalize(MPIdata%iErr)
ENDPROGRAM
