On Aug 19, 2008, at 11:12 AM, 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
Jitendra,
1) The memory in the structure you're using to declare the derived
data type must be contiguous. In your struct declaration you have a
pointer to a dynamically allocated area, so the number you're getting
from MPI_Get_address is the location of the pointer itself, not the
dynamically allocated memory which I think you want to use. That
memory is not part of the structure and MPI_Type_create_struct can't
create the definition you're expecting.
2) disp[0] must be 0. I see you subtract base from disp[0] but for
some reason the output says disp[0] = 928?
3) Although it shouldn't change the value returned by
MPI_Get_address, try to remove the indexing of your pointers, just to
isolate the problem for now:
MPI_Get_address(parentPop[0].indiv[0].intvar, &disp[0]);
MPI_Get_address(parentPop[0].indiv[0].realvar, &disp[1]);
...
4) I would first try to send the message to a different process to
make sure the derived type is correct (the 'canonical' use for
MPI_Send + derived data type), then try with the same process through
MPI_Sendrecv as per your example.
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);
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