The following sequence of errors is received when I try to run a problem on four processors. The MPI command I use is mpirun -np 4
I apologize for posting the error message as is (Primarily due a lack of knowledge on deciphering the information given). Would appreciate your input on the following:
What does the error message mean? At what point does one receive it? Is it because of the system memory (hardware) or is it due to a communication error (something related to MPI_Isend/Irecv?, i.e. Software issue).
Finally, how do I fix this?
Thanks!
ERROR message received follows below:: - - *PLEASE NOTE: This error is received only when the time is large*. Code computes fine when time required to compute data is small (i.e, 300 time steps compared to 1000 time steps)
aborting job:
Fatal error in MPI_Irecv: Other MPI error, error stack:
MPI_Irecv(143): MPI_Irecv(buf=0x8294a60, count=48, MPI_DOUBLE, src=2, tag=-1, MPI_COMM_WORLD, request=0xffffd68c) failed
MPID_Irecv(64): Out of memory
aborting job:
Fatal error in MPI_Irecv: Other MPI error, error stack:
MPI_Irecv(143): MPI_Irecv(buf=0x8295080, count=48, MPI_DOUBLE, src=3, tag=-1, MPI_COMM_WORLD, request=0xffffd690) failed
MPID_Irecv(64): Out of memory
aborting job: Fatal error in MPI_Isend: Internal MPI error!, error stack:
MPI_Isend(142): MPI_Isend(buf=0x8295208, count=48, MPI_DOUBLE, dest=3, tag=0, MPI_COMM_WORLD, request=0xffffd678) failed
(unknown)(): Internal MPI error!
aborting job: Fatal error in MPI_Irecv: Other MPI error, error stack:
MPI_Irecv(143): MPI_Irecv(buf=0x82959b0, count=48, MPI_DOUBLE, src=2, tag=-1, MPI_COMM_WORLD, request=0xffffd678) failed
MPID_Irecv(64): Out of memory
rank 3 in job 1 myocyte80_37021 caused collective abort of all ranks exit status of rank 3: return code 13
rank 1 in job 1 myocyte80_37021 caused collective abort of all ranks exit status of rank 1: return code 13
EDIT: (SOURCE CODE)
Header files
Variable declaration
TOTAL TIME =
...
...
double *A = new double[Rows];
double *AA = new double[Rows];
double *B = new double[Rows;
double *BB = new double[Rows];
....
....
int Rmpi;
int my_rank;
int p;
int source;
int dest;
int tag = 0;
function declaration
int main (int argc, char *argv[])
{
MPI_Status status[8];
MPI_Request request[8];
MPI_Init (&argc, &argv);
MPI_Comm_size(MPI_COMM_WORLD, &p);
MPI_Comm_rank(MPI_COMM_WORLD, &my_rank);
//PROBLEM SPECIFIC PROPERTIES. VARY BASED ON NODE
if (Flag = 1)
{
if (my_rank == 0)
{
Defining boundary (start/stop) for special elements in tissue (Rows x Column)
}
if (my_rank == 2)
..
if (my_rank == 3)
..
if (my_rank == 4)
..
}
//INITIAL CONDITIONS ALSO VARY BASED ON NODE
for (Columns = 0; Columns<48; i++) // Normal Direction
{
for (Rows = 0; Rows<48; y++) //Transverse Direction
{
if (Flag =1 )
{
if (my_rank == 0)
{
Initial conditions for elements
}
if (my_rank == 1) //MPI
{
}
..
..
..
//SIMULATION START
while(t[0][0] < TOTAL TIME)
{
for (Columns=0; Columns ++) //Normal Direction
{
for (Rows=0; Rows++) //Transverse Direction
{
//SOME MORE PROPERTIES BASED ON NODE
if (my_rank == 0)
{
if (FLAG = 1)
{
Condition 1
}
else
{
Condition 2
}
}
if (my_rank = 1)
....
....
...
//Evaluate functions (differential equations)
Function 1 ();
Function 2 ();
...
...
//Based on output of differential equations, different nodes estimate variable values. Since
the problem is of nearest neighbor, corners and edges have different neighbors/ boundary
conditions
if (my_rank == 0)
{
If (Row/Column at bottom_left)
{
Variables =
}
if (Row/Column at Bottom Right)
{
Variables =
}
}
...
...
//Keeping track of time for each element in Row and Column. Time is updated for a certain
element.
t[Column][Row] = t[Column][Row]+dt;
}
}//END OF ROWS AND COLUMNS
// MPI IMPLEMENTATION. AT END OF EVERY TIME STEP, Nodes communicate with nearest neighbor
//First step is to populate arrays with values estimated above
for (Columns, ++)
{
for (Rows, ++)
{
if (my_rank == 0)
{
//Loading the Edges of the (Row x Column) to variables. This One dimensional Array data
is shared with its nearest neighbor for computation at next time step.
if (Column == 47)
{
A[i] = V[Column][Row];
…
}
if (Row == 47)
{
B[i] = V[Column][Row];
}
}
...
...
//NON BLOCKING MPI SEND RECV TO SHARE DATA WITH NEAREST NEIGHBOR
if ((my_rank) == 0)
{
MPI_Isend(A, Rows, MPI_DOUBLE, my_rank+1, 0, MPI_COMM_WORLD, &request[1]);
MPI_Irecv(AA, Rows, MPI_DOUBLE, my_rank+1, MPI_ANY_TAG, MPI_COMM_WORLD, &request[3]);
MPI_Wait(&request[3], &status[3]);
MPI_Isend(B, Rows, MPI_DOUBLE, my_rank+2, 0, MPI_COMM_WORLD, &request[5]);
MPI_Irecv(BB, Rows, MPI_DOUBLE, my_rank+2, MPI_ANY_TAG, MPI_COMM_WORLD, &request[7]);
MPI_Wait(&request[7], &status[7]);
}
if ((my_rank) == 1)
{
MPI_Irecv(CC, Rows, MPI_DOUBLE, my_rank-1, MPI_ANY_TAG, MPI_COMM_WORLD, &request[1]);
MPI_Wait(&request[1], &status[1]);
MPI_Isend(Cmpi, Rows, MPI_DOUBLE, my_rank-1, 0, MPI_COMM_WORLD, &request[3]);
MPI_Isend(D, Rows, MPI_DOUBLE, my_rank+2, 0, MPI_COMM_WORLD, &request[6]);
MPI_Irecv(DD, Rows, MPI_DOUBLE, my_rank+2, MPI_ANY_TAG, MPI_COMM_WORLD, &request[8]);
MPI_Wait(&request[8], &status[8]);
}
if ((my_rank) == 2)
{
MPI_Isend(E, Rows, MPI_DOUBLE, my_rank+1, 0, MPI_COMM_WORLD, &request[2]);
MPI_Irecv(EE, Rows, MPI_DOUBLE, my_rank+1, MPI_ANY_TAG, MPI_COMM_WORLD, &request[4]);
MPI_Wait(&request[4], &status[4]);
MPI_Irecv(FF, Rows, MPI_DOUBLE, my_rank-2, MPI_ANY_TAG, MPI_COMM_WORLD, &request[5]);
MPI_Wait(&request[5], &status[5]);
MPI_Isend(Fmpi, Rows, MPI_DOUBLE, my_rank-2, 0, MPI_COMM_WORLD, &request[7]);
}
if ((my_rank) == 3)
{
MPI_Irecv(GG, Rows, MPI_DOUBLE, my_rank-1, MPI_ANY_TAG, MPI_COMM_WORLD, &request[2]);
MPI_Wait(&request[2], &status[2]);
MPI_Isend(G, Rows, MPI_DOUBLE, my_rank-1, 0, MPI_COMM_WORLD, &request[4]);
MPI_Irecv(HH, Rows, MPI_DOUBLE, my_rank-2, MPI_ANY_TAG, MPI_COMM_WORLD, &request[6]);
MPI_Wait(&request[6], &status[6]);
MPI_Isend(H, Rows, MPI_DOUBLE, my_rank-2, 0, MPI_COMM_WORLD, &request[8]);
}
//RELOADING Data (from MPI_IRecv array to array used to compute at next time step)
for (Columns, ++)
{
for (Rows, ++)
{
if (my_rank == 0)
{
if (Column == 47)
{
V[Column][Row]= A[i];
}
if (Row == 47)
{
V[Column][Row]=B[i];
}
}
….
//PRINT TO OUTPUT FILE AT CERTAIN POINT
printval = 100;
if ((printdata>=printval))
{
prttofile ();
printdata = 0;
}
printdata = printdata+1;
compute_dt ();
}//CLOSE ALL TIME STEPS
MPI_Finalize ();
}//CLOSE MAIN