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 >>>>> >>> >>>>> >>> >>>>> >>> >>>>> >>> _________________________________________________ >>>>> >>> users mailing list >>>>> >>> us...@open-mpi.org <mailto:us...@open-mpi.org> >>>>> >>> Subscription: >>>>> >>> http://www.open-mpi.org/__mailman/listinfo.cgi/users >>>>> >>> <http://www.open-mpi.org/mailman/listinfo.cgi/users> >>>>> >>> Link to this post: >>>>> >>> >>>>> http://www.open-mpi.org/__community/lists/users/2015/01/__26171.php >>>>> >>> < >>>>> http://www.open-mpi.org/community/lists/users/2015/01/26171.php> >>>>> >>> >>>>> >>> >>>>> >>> _________________________________________________ >>>>> >>> users mailing list >>>>> >>> us...@open-mpi.org <mailto:us...@open-mpi.org> >>>>> >>> Subscription: >>>>> >>> http://www.open-mpi.org/__mailman/listinfo.cgi/users >>>>> >>> <http://www.open-mpi.org/mailman/listinfo.cgi/users> >>>>> >>> Link to this post: >>>>> >>> >>>>> http://www.open-mpi.org/__community/lists/users/2015/01/__26172.php >>>>> >>> < >>>>> http://www.open-mpi.org/community/lists/users/2015/01/26172.php> >>>>> >>> >>>>> >>> >>>>> >>> _______________________________________________ >>>>> >>> users mailing list >>>>> >>> us...@open-mpi.org <mailto:us...@open-mpi.org> >>>>> >>> Subscription: >>>>> http://www.open-mpi.org/mailman/listinfo.cgi/users >>>>> >>> Link to this post: >>>>> >>> http://www.open-mpi.org/community/lists/users/2015/01/26184.php >>>>> >> >>>>> >> >>>>> >> _______________________________________________ >>>>> >> users mailing list >>>>> >> us...@open-mpi.org <mailto:us...@open-mpi.org> >>>>> >> Subscription: http://www.open-mpi.org/mailman/listinfo.cgi/users >>>>> >> Link to this post: >>>>> >> http://www.open-mpi.org/community/lists/users/2015/01/26192.php >>>>> >> >>>>> >> >>>>> >> >>>>> >> >>>>> >> _______________________________________________ >>>>> >> users mailing list >>>>> >> us...@open-mpi.org >>>>> >> Subscription: http://www.open-mpi.org/mailman/listinfo.cgi/users >>>>> >> Link to this post: >>>>> http://www.open-mpi.org/community/lists/users/2015/01/26193.php >>>>> > >>>>> > _______________________________________________ >>>>> > users mailing list >>>>> > us...@open-mpi.org >>>>> > Subscription: http://www.open-mpi.org/mailman/listinfo.cgi/users >>>>> > Link to this post: >>>>> http://www.open-mpi.org/community/lists/users/2015/01/26194.php >>>>> _______________________________________________ >>>>> users mailing list >>>>> us...@open-mpi.org >>>>> Subscription: http://www.open-mpi.org/mailman/listinfo.cgi/users >>>>> Link to this post: >>>>> http://www.open-mpi.org/community/lists/users/2015/01/26195.php >>>>> >>>> >>>> >>>> _______________________________________________ >>>> users mailing list >>>> us...@open-mpi.org >>>> Subscription: http://www.open-mpi.org/mailman/listinfo.cgi/users >>>> Link to this post: >>>> http://www.open-mpi.org/community/lists/users/2015/01/26197.php >>>> >>> >>> >>> _______________________________________________ >>> users mailing list >>> us...@open-mpi.org >>> Subscription: http://www.open-mpi.org/mailman/listinfo.cgi/users >>> Link to this post: >>> http://www.open-mpi.org/community/lists/users/2015/01/26199.php >>> >> >> > _______________________________________________ > users mailing list > us...@open-mpi.org > Subscription: http://www.open-mpi.org/mailman/listinfo.cgi/users > Link to this post: > http://www.open-mpi.org/community/lists/users/2015/01/26201.php > > > > _______________________________________________ > users mailing list > us...@open-mpi.org > Subscription: http://www.open-mpi.org/mailman/listinfo.cgi/users > Link to this post: > http://www.open-mpi.org/community/lists/users/2015/01/26202.php >
