[OMPI users] 1D and 2D arrays allocate memory by maloc() and MPI_Send and MPI_Recv problem.
Hello all
Sorry, may be this is a stupid question, bat a have a big problem with
maloc() and matrix arrays.
I want to make a program that do very simple thing like matriA *
matrixB = matrixC.
Because I need more matrix size than 100x100 (5000x5000), I have to
use maloc() for memory allocation.
First I tried this way:
The typical form for dynamically allocating an NxM array of type T is:
T **a = malloc(sizeof *a * N);
if (a)
{
for (i = 0; i < N; i++)
{
a[i] = malloc(sizeof *a[i] * M);
}
}
// the arrays are created before split to nodes
No problem with create, fill array,but the problem started when I have
send and receive it.
Of course before send I calculated "cont" for MPI_Send.
To be shore, that the count for MPI_Send i MPI_Recv is the same I also
send "count".
count = rows*matrix_size*sizeof (double); //part of matrix
MPI_Send(&count, 1, MPI_INT, dest, mtype,MPI_COMM_WORLD);
MPI_Send(&matrixA[offset][0], count, MPI_DOUBLE, dest, mtype, MPI_COMM_WORLD);
from worker side the code looks like:
MPI_Recv(&countA, 1, MPI_INT, source, mtype, MPI_COMM_WORLD, &status);
MPI_Recv(&matrixA[0][0], countA, MPI_DOUBLE, source, mtype,
MPI_COMM_WORLD, &status);
An error looks like:
[pawcioj-VirtualBox:01700] *** Process received signal ***
[pawcioj-VirtualBox:01700] Signal: Segmentation fault (11)
[pawcioj-VirtualBox:01700] Signal code: Address not mapped (1)
[pawcioj-VirtualBox:01700] Failing at address: 0x88fa000
[pawcioj-VirtualBox:01700] [ 0] [0xc2740c]
[pawcioj-VirtualBox:01700] [ 1]
/usr/lib/openmpi/lib/openmpi/mca_pml_ob1.so(+0x906c) [0x17606c]
[pawcioj-VirtualBox:01700] [ 2]
/usr/lib/openmpi/lib/openmpi/mca_pml_ob1.so(+0x6a1b) [0x173a1b]
[pawcioj-VirtualBox:01700] [ 3]
/usr/lib/openmpi/lib/openmpi/mca_btl_sm.so(+0x3ae6) [0x7b7ae6]
[pawcioj-VirtualBox:01700] [ 4]
/usr/lib/libopen-pal.so.0(opal_progress+0x81) [0x406fa1]
[pawcioj-VirtualBox:01700] [ 5]
/usr/lib/openmpi/lib/openmpi/mca_pml_ob1.so(+0x48e5) [0x1718e5]
[pawcioj-VirtualBox:01700] [ 6] /usr/lib/libmpi.so.0(MPI_Recv+0x165) [0x1ef9d5]
[pawcioj-VirtualBox:01700] [ 7] macierz_V.02(main+0x927) [0x8049870]
[pawcioj-VirtualBox:01700] [ 8] /lib/libc.so.6(__libc_start_main+0xe7)
[0xddfce7]
[pawcioj-VirtualBox:01700] [ 9] macierz_V.02() [0x8048b71]
[pawcioj-VirtualBox:01700] *** End of error message ***
--
mpirun noticed that process rank 1 with PID 1700 on node
pawcioj-VirtualBox exited on signal 11 (Segmentation fault).
Because I have no result, I tied do that by 1D array but the problem
seems similar.
Probably I do something wrong, so I would like to ask you about advice
how do that proper or maybe link to useful tutorial.
I spend two weeks to find out how do that but unfortunately without result :(.
--
--
pozdrawiam
Paweł Jaromin
Re: [OMPI users] 1D and 2D arrays allocate memory by maloc() and MPI_Send and MPI_Recv problem.
All MPI operations (including MPI_Send and MPI_Recv) consider any type of
buffers (input and output) as a contiguous entity.
Therefore, you have two options:
1. Have a loop around MPI_Send & MPI_Recv similar to the allocation section.
2. Build an MPI Datatype representing the non-contiguous memory layout you
really intend to send between peers.
george.
On Aug 7, 2012, at 10:33 , Paweł Jaromin wrote:
> Hello all
>
> Sorry, may be this is a stupid question, bat a have a big problem with
> maloc() and matrix arrays.
> I want to make a program that do very simple thing like matriA *
> matrixB = matrixC.
> Because I need more matrix size than 100x100 (5000x5000), I have to
> use maloc() for memory allocation.
> First I tried this way:
>
> The typical form for dynamically allocating an NxM array of type T is:
> T **a = malloc(sizeof *a * N);
> if (a)
> {
> for (i = 0; i < N; i++)
> {
>a[i] = malloc(sizeof *a[i] * M);
> }
> }
> // the arrays are created before split to nodes
>
> No problem with create, fill array,but the problem started when I have
> send and receive it.
> Of course before send I calculated "cont" for MPI_Send.
> To be shore, that the count for MPI_Send i MPI_Recv is the same I also
> send "count".
>
> count = rows*matrix_size*sizeof (double); //part of matrix
> MPI_Send(&count, 1, MPI_INT, dest, mtype,MPI_COMM_WORLD);
> MPI_Send(&matrixA[offset][0], count, MPI_DOUBLE, dest, mtype, MPI_COMM_WORLD);
>
> from worker side the code looks like:
>
> MPI_Recv(&countA, 1, MPI_INT, source, mtype, MPI_COMM_WORLD, &status);
> MPI_Recv(&matrixA[0][0], countA, MPI_DOUBLE, source, mtype,
> MPI_COMM_WORLD, &status);
>
>
> An error looks like:
>
> [pawcioj-VirtualBox:01700] *** Process received signal ***
> [pawcioj-VirtualBox:01700] Signal: Segmentation fault (11)
> [pawcioj-VirtualBox:01700] Signal code: Address not mapped (1)
> [pawcioj-VirtualBox:01700] Failing at address: 0x88fa000
> [pawcioj-VirtualBox:01700] [ 0] [0xc2740c]
> [pawcioj-VirtualBox:01700] [ 1]
> /usr/lib/openmpi/lib/openmpi/mca_pml_ob1.so(+0x906c) [0x17606c]
> [pawcioj-VirtualBox:01700] [ 2]
> /usr/lib/openmpi/lib/openmpi/mca_pml_ob1.so(+0x6a1b) [0x173a1b]
> [pawcioj-VirtualBox:01700] [ 3]
> /usr/lib/openmpi/lib/openmpi/mca_btl_sm.so(+0x3ae6) [0x7b7ae6]
> [pawcioj-VirtualBox:01700] [ 4]
> /usr/lib/libopen-pal.so.0(opal_progress+0x81) [0x406fa1]
> [pawcioj-VirtualBox:01700] [ 5]
> /usr/lib/openmpi/lib/openmpi/mca_pml_ob1.so(+0x48e5) [0x1718e5]
> [pawcioj-VirtualBox:01700] [ 6] /usr/lib/libmpi.so.0(MPI_Recv+0x165)
> [0x1ef9d5]
> [pawcioj-VirtualBox:01700] [ 7] macierz_V.02(main+0x927) [0x8049870]
> [pawcioj-VirtualBox:01700] [ 8] /lib/libc.so.6(__libc_start_main+0xe7)
> [0xddfce7]
> [pawcioj-VirtualBox:01700] [ 9] macierz_V.02() [0x8048b71]
> [pawcioj-VirtualBox:01700] *** End of error message ***
> --
> mpirun noticed that process rank 1 with PID 1700 on node
> pawcioj-VirtualBox exited on signal 11 (Segmentation fault).
>
>
> Because I have no result, I tied do that by 1D array but the problem
> seems similar.
>
> Probably I do something wrong, so I would like to ask you about advice
> how do that proper or maybe link to useful tutorial.
> I spend two weeks to find out how do that but unfortunately without result :(.
>
>
>
> --
> --
> pozdrawiam
>
> Paweł Jaromin
>
> ___
> users mailing list
> us...@open-mpi.org
> http://www.open-mpi.org/mailman/listinfo.cgi/users
Re: [OMPI users] 1D and 2D arrays allocate memory by maloc() and MPI_Send and MPI_Recv problem.
Hi
2012/8/7 George Bosilca :
> All MPI operations (including MPI_Send and MPI_Recv) consider any type of
> buffers (input and output) as a contiguous entity.
I tried use 1D array (instead of 2D) to have contiguous data - but
result was the same :(
>
> Therefore, you have two options:
>
> 1. Have a loop around MPI_Send & MPI_Recv similar to the allocation section.
How do You see this loop - byte per byte ??
>
> 2. Build an MPI Datatype representing the non-contiguous memory layout you
> really intend to send between peers.
>
I'm not enough good programmer to do that :( - as You can see I'm a a
beginner. Maybe more details how do that ?? an example ??
> george.
>
> On Aug 7, 2012, at 10:33 , Paweł Jaromin wrote:
>
>> Hello all
>>
>> Sorry, may be this is a stupid question, bat a have a big problem with
>> maloc() and matrix arrays.
>> I want to make a program that do very simple thing like matriA *
>> matrixB = matrixC.
>> Because I need more matrix size than 100x100 (5000x5000), I have to
>> use maloc() for memory allocation.
>> First I tried this way:
>>
>> The typical form for dynamically allocating an NxM array of type T is:
>> T **a = malloc(sizeof *a * N);
>> if (a)
>> {
>> for (i = 0; i < N; i++)
>> {
>>a[i] = malloc(sizeof *a[i] * M);
>> }
>> }
>> // the arrays are created before split to nodes
>>
>> No problem with create, fill array,but the problem started when I have
>> send and receive it.
>> Of course before send I calculated "cont" for MPI_Send.
>> To be shore, that the count for MPI_Send i MPI_Recv is the same I also
>> send "count".
>>
>> count = rows*matrix_size*sizeof (double); //part of matrix
>> MPI_Send(&count, 1, MPI_INT, dest, mtype,MPI_COMM_WORLD);
>> MPI_Send(&matrixA[offset][0], count, MPI_DOUBLE, dest, mtype,
>> MPI_COMM_WORLD);
>>
>> from worker side the code looks like:
>>
>> MPI_Recv(&countA, 1, MPI_INT, source, mtype, MPI_COMM_WORLD, &status);
>> MPI_Recv(&matrixA[0][0], countA, MPI_DOUBLE, source, mtype,
>> MPI_COMM_WORLD, &status);
>>
>>
>> An error looks like:
>>
>> [pawcioj-VirtualBox:01700] *** Process received signal ***
>> [pawcioj-VirtualBox:01700] Signal: Segmentation fault (11)
>> [pawcioj-VirtualBox:01700] Signal code: Address not mapped (1)
>> [pawcioj-VirtualBox:01700] Failing at address: 0x88fa000
>> [pawcioj-VirtualBox:01700] [ 0] [0xc2740c]
>> [pawcioj-VirtualBox:01700] [ 1]
>> /usr/lib/openmpi/lib/openmpi/mca_pml_ob1.so(+0x906c) [0x17606c]
>> [pawcioj-VirtualBox:01700] [ 2]
>> /usr/lib/openmpi/lib/openmpi/mca_pml_ob1.so(+0x6a1b) [0x173a1b]
>> [pawcioj-VirtualBox:01700] [ 3]
>> /usr/lib/openmpi/lib/openmpi/mca_btl_sm.so(+0x3ae6) [0x7b7ae6]
>> [pawcioj-VirtualBox:01700] [ 4]
>> /usr/lib/libopen-pal.so.0(opal_progress+0x81) [0x406fa1]
>> [pawcioj-VirtualBox:01700] [ 5]
>> /usr/lib/openmpi/lib/openmpi/mca_pml_ob1.so(+0x48e5) [0x1718e5]
>> [pawcioj-VirtualBox:01700] [ 6] /usr/lib/libmpi.so.0(MPI_Recv+0x165)
>> [0x1ef9d5]
>> [pawcioj-VirtualBox:01700] [ 7] macierz_V.02(main+0x927) [0x8049870]
>> [pawcioj-VirtualBox:01700] [ 8] /lib/libc.so.6(__libc_start_main+0xe7)
>> [0xddfce7]
>> [pawcioj-VirtualBox:01700] [ 9] macierz_V.02() [0x8048b71]
>> [pawcioj-VirtualBox:01700] *** End of error message ***
>> --
>> mpirun noticed that process rank 1 with PID 1700 on node
>> pawcioj-VirtualBox exited on signal 11 (Segmentation fault).
>>
>>
>> Because I have no result, I tied do that by 1D array but the problem
>> seems similar.
>>
>> Probably I do something wrong, so I would like to ask you about advice
>> how do that proper or maybe link to useful tutorial.
>> I spend two weeks to find out how do that but unfortunately without result
>> :(.
>>
>>
>>
>> --
>> --
>> pozdrawiam
>>
>> Paweł Jaromin
>>
>> ___
>> 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
--
--
pozdrawiam
Paweł Jaromin
Re: [OMPI users] 1D and 2D arrays allocate memory by maloc() and MPI_Send and MPI_Recv problem.
Look at this declaration:
int MPI_Send(void *buf, int count, MPI_Datatype datatype, int dest, int tag,
MPI_Comm comm)
here*"count" is the**number of elements* (not bytes!) in the send buffer
(nonnegative integer)
Your "count" was defined as
count = rows*matrix_size*sizeof (double);
and seems to be erroneous;
variable "count" cannot depend on the size of the matrix element!
Z Koza
On Aug 7, 2012, at 10:33 , Paweł Jaromin wrote:
Hello all
Sorry, may be this is a stupid question, bat a have a big problem with
maloc() and matrix arrays.
I want to make a program that do very simple thing like matriA *
matrixB = matrixC.
Because I need more matrix size than 100x100 (5000x5000), I have to
use maloc() for memory allocation.
First I tried this way:
The typical form for dynamically allocating an NxM array of type T is:
T **a = malloc(sizeof *a * N);
if (a)
{
for (i = 0; i < N; i++)
{
a[i] = malloc(sizeof *a[i] * M);
}
}
// the arrays are created before split to nodes
No problem with create, fill array,but the problem started when I have
send and receive it.
Of course before send I calculated "cont" for MPI_Send.
To be shore, that the count for MPI_Send i MPI_Recv is the same I also
send "count".
count = rows*matrix_size*sizeof (double); //part of matrix
MPI_Send(&count, 1, MPI_INT, dest, mtype,MPI_COMM_WORLD);
MPI_Send(&matrixA[offset][0], count, MPI_DOUBLE, dest, mtype, MPI_COMM_WORLD);
from worker side the code looks like:
MPI_Recv(&countA, 1, MPI_INT, source, mtype, MPI_COMM_WORLD, &status);
MPI_Recv(&matrixA[0][0], countA, MPI_DOUBLE, source, mtype,
MPI_COMM_WORLD, &status);
An error looks like:
[pawcioj-VirtualBox:01700] *** Process received signal ***
[pawcioj-VirtualBox:01700] Signal: Segmentation fault (11)
[pawcioj-VirtualBox:01700] Signal code: Address not mapped (1)
[pawcioj-VirtualBox:01700] Failing at address: 0x88fa000
[pawcioj-VirtualBox:01700] [ 0] [0xc2740c]
[pawcioj-VirtualBox:01700] [ 1]
/usr/lib/openmpi/lib/openmpi/mca_pml_ob1.so(+0x906c) [0x17606c]
[pawcioj-VirtualBox:01700] [ 2]
/usr/lib/openmpi/lib/openmpi/mca_pml_ob1.so(+0x6a1b) [0x173a1b]
[pawcioj-VirtualBox:01700] [ 3]
/usr/lib/openmpi/lib/openmpi/mca_btl_sm.so(+0x3ae6) [0x7b7ae6]
[pawcioj-VirtualBox:01700] [ 4]
/usr/lib/libopen-pal.so.0(opal_progress+0x81) [0x406fa1]
[pawcioj-VirtualBox:01700] [ 5]
/usr/lib/openmpi/lib/openmpi/mca_pml_ob1.so(+0x48e5) [0x1718e5]
[pawcioj-VirtualBox:01700] [ 6] /usr/lib/libmpi.so.0(MPI_Recv+0x165) [0x1ef9d5]
[pawcioj-VirtualBox:01700] [ 7] macierz_V.02(main+0x927) [0x8049870]
[pawcioj-VirtualBox:01700] [ 8] /lib/libc.so.6(__libc_start_main+0xe7)
[0xddfce7]
[pawcioj-VirtualBox:01700] [ 9] macierz_V.02() [0x8048b71]
[pawcioj-VirtualBox:01700] *** End of error message ***
--
mpirun noticed that process rank 1 with PID 1700 on node
pawcioj-VirtualBox exited on signal 11 (Segmentation fault).
Because I have no result, I tied do that by 1D array but the problem
seems similar.
Probably I do something wrong, so I would like to ask you about advice
how do that proper or maybe link to useful tutorial.
I spend two weeks to find out how do that but unfortunately without result :(.
--
--
pozdrawiam
Paweł Jaromin
___
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
