George, Yes that's what I understood after struggling with it over a week. I need to send such messages frequently so creating and destroying the data type each time may be expensive. What would be the best alternative for sending such malloced data ? Though I can always pack the data in a long array and unpack at the opposite end as I know the structure of the data at each node. Anything more efficient and elegant will be better.
Thanks for the help. Jitendra George Bosilca wrote: > Jitendra, > > You will not be able to reuse the same data-type. All internal arrays > are malloced and their position in memory will be completely random > from call to call (or use to use of the data-type). Therefore, even if > your structure looks the same, as you use non static arrays in your > structure, you will have to recreate the data-type for every new > structure (of type individual). > > george. > > On Aug 19, 2008, at 5:12 PM, Jitendra Kumar wrote: > >> George, >> Thanks for your reply. However, I am still not able to resolve the >> issue. I have been looking at one of your old post >> http://www.open-mpi.org/community/lists/users/2005/08/0123.php >> (I have tried to explain the issues below with snippets of codes and on >> screen debugging messages) >> >> I am trying not to use MPI_BOTTOM because I wish to use the same >> declared data type again and again for sending any struct of that type. >> So I specified the addresses as follows. >> 521 MPI_Get_address(&parentPop[0].indiv, &origin); >> 522 printf("origin %ld \n", origin); >> 523 MPI_Get_address(&parentPop[0].indiv[0].intvar[0], >> &disp[0]); >> 524 printf("disp 0 %ld \n", disp[0]); >> 525 MPI_Get_address(&parentPop[0].indiv[0].realvar[0], >> &disp[1]); >> 526 printf("disp 1 %ld\n", disp[1]); >> 527 MPI_Get_address(&parentPop[0].indiv[0].binvar[0], >> &disp[2]); >> 528 printf("disp 2 %ld\n", disp[2]); >> 529 MPI_Get_address(&parentPop[0].indiv[0].gene[0][0], >> &disp[3]); >> 530 printf("disp 3 %ld\n", disp[3]); >> 531 MPI_Get_address(&parentPop[0].indiv[0].obj[0], &disp[4]); >> 532 printf("disp 4 %ld %ld\n", disp[4], >> &parentPop[0].indiv[0].obj[0]); >> 533 MPI_Get_address(&parentPop[0].indiv[0].constr[0], >> &disp[5]); >> 534 printf("disp 5 %ld\n", disp[5]); >> 535 MPI_Get_address(&parentPop[0].indiv[0].constr_violation, >> &disp[6]); >> 536 printf("disp 6 %ld\n", disp[6]); >> 537 MPI_Get_address(&parentPop[0].indiv[0].crowd_dist, >> &disp[7]); >> 538 printf("disp 7 %ld\n", disp[7]); >> 539 MPI_Get_address(&parentPop[0].indiv[0].rank, &disp[8]); >> 540 printf("disp 8 %ld\n", disp[8]); >> 541 >> MPI_Get_address(&parentPop[0].indiv[0].strategyParameter[0], &disp[9]); >> 542 printf("disp 9 %ld\n", disp[9]); >> 543 // base = disp[0]; >> 544 base = origin; >> >> The values of displacements looks like this: >> 3: origin 6088720 >> 3: disp 0 6089648 >> 3: disp 1 6089680 >> 3: disp 2 6089712 >> 3: disp 3 6089776 >> 3: disp 4 6089808 >> 3: disp 5 6089840 >> 3: disp 6 6090672 >> 3: disp 7 6090680 >> 3: disp 8 6090688 >> 3: disp 9 6089872 >> >> after subtracting origin from the displacement to get relative >> displacements. >> 569 for(i=0; i<10; i++) >> 570 { >> 571 disp[i] -= base; >> 572 fprintf(stdout, "Rank %d: disp[%d] %d\n", rank, i, >> disp[i]); >> 573 } >> >> 3: Rank 3: disp[0] 928 >> 3: Rank 3: disp[1] 960 >> 3: Rank 3: disp[2] 992 >> 3: Rank 3: disp[3] 1056 >> 3: Rank 3: disp[4] 1088 >> 3: Rank 3: disp[5] 1120 >> 3: Rank 3: disp[6] 1952 >> 3: Rank 3: disp[7] 1960 >> 3: Rank 3: disp[8] 1968 >> 3: Rank 3: disp[9] 1152 >> >> 574 MPI_Type_create_struct(10, blockcounts, disp, types, >> &Individual); >> 575 >> 576 /* Check that the datatype has correct extent */ >> 577 MPI_Type_extent(Individual, &extent); >> 578 if(extent != sizeof(individual)) >> 579 { >> 580 printf("Rank %d: adjusting the extent (%d) of the >> data type %d\n", rank, extent, sizeof(individual)); >> 581 MPI_Datatype indold = Individual; >> 582 MPI_Type_create_resized(indold, 0, >> sizeof(individual), &Individual); >> 583 MPI_Type_free(&indold); >> 584 } >> 585 MPI_Type_commit(&Individual); >> 586 /* MPI derived datatype for indivdual declared */ >> >> After creating the datatype, for test I tried to send and receive a >> struct to itself and save it to a variable of the same struct type. But >> the value of the variables in the receiving struct remains unchanged. >> Though the MPI_Get_elements shows the correct number of elements in the >> received datatype. >> >> 588 int count; >> 589 individual recvind; >> 590 allocateMemoryInd(&parentPop[0], &recvind); >> 591 initializeInd(&parentPop[0], &recvind); >> 592 >> 593 fprintf(stdout, "Rank %d: before receive recvind.nobj %f >> recvind.numreal %f\n", rank, recvind.obj[0], recvind.realvar[0]); >> 594 MPI_Sendrecv(&parentPop[0].indiv[0], 1, Individual, >> rank, rank, &recvind, 1, Individual, rank, rank, MPI_COMM_WORLD, >> &status); >> 595 count = 0; >> 596 MPI_Get_elements(&status, Individual, &count); >> 597 fprintf(stdout, "Rank %d: after receive recvind.nobj %f >> (expected value %f) recvind.numreal %f (expected value %f) count %d\n", >> rank, recvind.obj[0], parentPo p[0].indiv[0].obj[0], >> recvind.realvar[0], parentPop[0].indiv[0].realvar[0], count); >> >> 3: Rank 3: adjusting the extent (1048) of the data type 80 >> 3: Rank 3: before receive recvind.nobj 0.000000 recvind.numreal >> -26.938538 >> 3: Rank 3: after receive recvind.nobj 0.000000 (expected value 0.000000) >> recvind.numreal -26.938538 (expected value -126.740479) count 16 >> >> I highly appreciate your help resolving the issue. >> >> Thanks, >> Jitendra >>> Message: 1 >>> Date: Sun, 17 Aug 2008 23:30:54 +0200 >>> From: George Bosilca <bosi...@eecs.utk.edu> >>> Subject: Re: [OMPI users] MPI_Type_struct for structs with dynamic >>> arrays >>> To: Open MPI Users <us...@open-mpi.org> >>> Message-ID: <b9dd8054-97d1-47ba-a88c-27f0c5529...@eecs.utk.edu> >>> Content-Type: text/plain; charset="us-ascii"; Format="flowed"; >>> DelSp="yes" >>> >>> Jitendra, >>> >>> There is a problem with the addresses you provide to MPI_Type_struct. >>> For all arrays instead of giving the pointer to the array, you provide >>> a pointer to the pointer in the individual struct. >>> >>> Try the following >>> MPI_Get_address(&parentPop[0].indiv[0].intvar[0], &disp[0]); >>> instead of >>> MPI_Get_address(&parentPop[0].indiv[0].intvar, &disp[0]); >>> >>> Please note the [0] after the array name. Please do the same to all >>> arrays and I think the MPI_Type_struct will do the rest. >>> >>> Btw, you dont have to substract the disp[0] from all addresses. >>> Instead you can use MPI_BOTTOM and all your addresses can be absolute. >>> >>> george. >>> >>> On Aug 11, 2008, at 1:07 AM, Jitendra Kumar wrote: >>> >>> >>>> Hi, >>>> I am trying to use MPI derived datatype doutines for sending a struct >>>> which contains dynamically allocated arrays. I tried implementing it >>>> using MPI_Type_struct. It doesn't throws any error but messages being >>>> received (of the declared datatype) aren't correct. Some memory >>>> corruption seems to be going on as the value of 'rank' at receive end >>>> are changed to 0 right after the receive . Below are the snippets of >>>> my >>>> struct and implementation of the derived datatype. >>>> I am not sure where things are going wrong. I would highly appreciate >>>> any pointers or suggestions. Is there any better alternative way >>>> instead >>>> of MPI_Type_struct considering that frequent communication of these >>>> structs are needed? >>>> >>>> Thanks, >>>> Jitendra >>>> >>>> The struct looks like this: >>>> 51 typedef struct >>>> 52 { >>>> 53 int *intvar; >>>> 54 double *realvar; >>>> 55 double *binvar; >>>> 56 int **gene; >>>> 57 >>>> 58 double *obj; >>>> 59 double *constr; >>>> 60 double constr_violation; >>>> 61 double crowd_dist; >>>> 62 int rank; >>>> 63 double *strategyParameter; >>>> 64 } >>>> 65 individual; >>>> >>>> Implementation of the derived datatype: >>>> >>>> 483 blockcounts[0] = parentPop[0].numInteger; >>>> 484 blockcounts[1] = parentPop[0].numReal; >>>> 485 blockcounts[2] = parentPop[0].numBinary; >>>> 486 sum = 0; >>>> 487 for(i=0; i<parentPop[0].numBinary; i++) >>>> 488 { >>>> 489 sum = sum + parentPop[0].nbits[i]; >>>> 490 } >>>> 491 >>>> 492 blockcounts[3] = sum; >>>> 493 blockcounts[4] = parentPop[0].nobj; >>>> 494 blockcounts[5] = parentPop[0].ncon; >>>> 495 blockcounts[6] = 1; >>>> 496 blockcounts[7] = 1; >>>> 497 blockcounts[8] = 1; >>>> 498 blockcounts[9] = parentPop[0].numInteger + >>>> parentPop[0].numReal; >>>> >>>> 506 types[0] = MPI_INT; >>>> 507 types[1] = MPI_DOUBLE; >>>> 508 types[2] = MPI_DOUBLE; >>>> 509 types[3] = MPI_INT; >>>> 510 types[4] = MPI_DOUBLE; >>>> 511 types[5] = MPI_DOUBLE; >>>> 512 types[6] = MPI_DOUBLE; >>>> 513 types[7] = MPI_DOUBLE; >>>> 514 types[8] = MPI_INT; >>>> 515 types[9] = MPI_DOUBLE; >>>> 516 >>>> 517 MPI_Get_address(&parentPop[0].indiv[0].intvar, >>>> &disp[0]); >>>> 518 printf("parentpop.indiv0 %ld disp %ld (%ld)\n", >>>> &parentPop[0].indiv[0], disp, disp[0]); >>>> 519 MPI_Get_address(&parentPop[0].indiv[0].realvar, >>>> &disp[1]); >>>> 520 printf("disp 1 %ld\n", disp[1]); >>>> 521 MPI_Get_address(&parentPop[0].indiv[0].binvar, >>>> &disp[2]); >>>> 522 printf("disp 2 %ld\n", disp[2]); >>>> 523 MPI_Get_address(&parentPop[0].indiv[0].gene, &disp[3]); >>>> 524 MPI_Get_address(&parentPop[0].indiv[0].obj, &disp[4]); >>>> 525 MPI_Get_address(&parentPop[0].indiv[0].constr, >>>> &disp[5]); >>>> 526 >>>> MPI_Get_address(&parentPop[0].indiv[0].constr_violation, >>>> &disp[6]); >>>> 527 MPI_Get_address(&parentPop[0].indiv[0].crowd_dist, >>>> &disp[7]); >>>> 528 MPI_Get_address(&parentPop[0].indiv[0].rank, &disp[8]); >>>> 529 >>>> MPI_Get_address(&parentPop[0].indiv[0].strategyParameter, &disp[9]); >>>> 530 base = disp[0]; >>>> 531 for(i=0; i<10; i++) >>>> 532 { >>>> 533 disp[i] -= base; >>>> 534 } >>>> 535 >>>> 536 MPI_Type_create_struct(10, blockcounts, disp, types, >>>> &Individual); >>>> 537 >>>> 538 /* Check that the datatype has correct extent */ >>>> 539 MPI_Type_extent(Individual, &extent); >>>> 540 if(extent != sizeof(individual)) >>>> 541 { >>>> 542 MPI_Datatype indold = Individual; >>>> 543 MPI_Type_create_resized(indold, 0, >>>> sizeof(individual), &Individual); >>>> 544 MPI_Type_free(&indold); >>>> 545 } >>>> 546 MPI_Type_commit(&Individual); >>>> >>>> >> >> _______________________________________________ >> users mailing list >> us...@open-mpi.org >> http://www.open-mpi.org/mailman/listinfo.cgi/users > > ------------------------------------------------------------------------ > > _______________________________________________ > users mailing list > us...@open-mpi.org > http://www.open-mpi.org/mailman/listinfo.cgi/users
