Segmentation Fault when using MPI_Isend - c

Question

The aim of my program is calculate the electrostatic potential between an inner conductor and an outer conductor by splitting it up into a grid and then into grid slices. Each processor gets a slice and runs the calculations on each slice. I send data between processors using MPI_Isend and MPI_Irecv. When testing the code I get a segmentation fault:
[physnode5:81440] *** Process received signal ***
[physnode5:81440] Signal: Segmentation fault (11)
[physnode5:81440] Signal code: Address not mapped (1)
[physnode5:81440] Failing at address: 0x58
[physnode5:81440] [ 0] /lib64/libpthread.so.0(+0xf5d0)[0x2ab8069df5d0]
[physnode5:81440] [ 1] /opt/yarcc/libraries/openmpi/2.1.0/1/default/lib/libmpi.so.20(ompi_request_default_wait+0xd)[0x2ab8066495ed]
[physnode5:81440] [ 2] /opt/yarcc/libraries/openmpi/2.1.0/1/default/lib/libmpi.so.20(MPI_Wait+0x5d)[0x2ab80667a00d]
[physnode5:81440] [ 3] ./mpi_tezt.exe[0x400ffc]
[physnode5:81440] [ 4] /lib64/libc.so.6(__libc_start_main+0xf5)[0x2ab806c0e3d5]
[physnode5:81440] [ 5] ./mpi_tezt.exe[0x4009b9]
[physnode5:81440] *** End of error message ***
when this bit of code is executed. please not i have ssh'ed into a cluster. The file name is mpi_tezt.exe (yes i mispelled it).
I have checked the arrays I want to send are correctly allocated and the send and recv are not sending or receiving data that isn't there (i.e sending data outside range of array.
My code for the MPI_Isend and MPI_Irecv is as follows:
#include <stdio.h>
#include <stdlib.h>
#include <math.h>
#include <time.h>
#include <mpi.h>
int main(int argc, char *argv[])
{
/*MPI Specific Variables*/
int my_size, my_rank, up, down;
MPI_Request reqU, reqD, sreqU, sreqD;
MPI_Status rUstatus, rDstatus, sUstatus, sDstatus;
/*Physical Dimensions*/
double Linner = 5.0;/*mm*/
double Rinner = 1.0;/*mm*/
double phi_0 = 1000.0;/*V*/
/*Other Variables*/
int grid_size = 100;
int slice;
int x,y;
double grid_res_y = 0.2;
double grid_res_x = 0.1;
int xboundary, yboundary;
MPI_Init(&argc, &argv);
MPI_Comm_rank(MPI_COMM_WORLD, &my_rank);
MPI_Comm_size(MPI_COMM_WORLD, &my_size);
/*Determining neighbours*/
if (my_rank != 0) /*if statemets used to stop highest and lowest rank neighbours arent outside 0 - my_size-1 range of ranks*/
{
up = my_rank-1;
}
else
{
up = 0;
}
if(my_rank != my_size-1)
{
down = my_rank+1;
}
else
{
down = my_size-1;
}
/*cross-check: presumed my_size is a factor of gridsize else there are odd sized slices and this is not coded for*/
if (grid_size%my_size != 0)
{
printf("ERROR - number of procs = %d, this is not a factor of grid_size %d\n", my_size, grid_size);
exit(0);
}
/*Set Up Distributed Data Approach*/
slice = grid_size/my_size;
yboundary = Linner/grid_res_y; /*y grid index of inner conductor wall*/
xboundary = Rinner/grid_res_x; /*x grid and individual array index of inner conductor wall*/
double phi[slice+2][grid_size]; /*extra 2 rows to allow for halo data*/
for (y=0; y < slice+2; y++)
{
for (x=0; x < grid_size; x++)
{
phi[y][x] = 0.0;
}
}
if(my_rank == 0) /*Boundary Containing rank does 2 loops. One over part with inner conductor and one over part without inner conductor*/
{
for(y=0; y < slice+1; y++)
{
for(x=xboundary; x < grid_size; x++)
{
phi[y][x] = phi_0;
}
}
}
if (my_rank < my_size-1)
{
/*send top most strip up one node to be recieved as bottom halo*/
MPI_Isend(&phi[1][0], grid_size , MPI_DOUBLE, down, 1, MPI_COMM_WORLD, &sreqU);
/*recv top halo from up one node*/
MPI_Irecv(&phi[slice+1][0], grid_size, MPI_DOUBLE, down, 2, MPI_COMM_WORLD, &reqU);
}
if (my_rank > 0)
{
/*recv top halo from down one node*/
MPI_Irecv(&phi[0][0], grid_size , MPI_DOUBLE, up, 2, MPI_COMM_WORLD, &reqD);
/*send bottom most strip down one node to be recieved as top halo*/
MPI_Isend(&phi[slice][0], grid_size , MPI_DOUBLE, up, 1, MPI_COMM_WORLD, &sreqD);
}
if (my_rank<my_size-1)
{
/*Wait for send to down one rank to complete*/
MPI_Wait(&sreqD, &sDstatus);
/*Wait for recieve from up one rank to complete*/
MPI_Wait(&reqD, &rDstatus);
}
if (my_rank>0)
{
/*Wait for send to up down one rank to complete*/
MPI_Wait(&sreqU, &sUstatus);
/*Wait for recieve from down one rank to complete*/
MPI_Wait(&reqU, &rUstatus);
}
MPI_Finalize();
return 0;
}
I have been testing on 2 processors (ranks 0 and 1) with the hope of extending it to more.
Any ideas where the fault may lie?

Answer 1

You're faulting in the first MPI_Wait (for rank 0). This is step 7 in the example code below.
Using mpirun -np 2 ./whatever:
It appears that sReqD is not being set correctly. This is set at step 5 by rank 1.
But, step 7 is being executed by rank 0, which does not set sReqD.
So, you need to adjust your if statements to match up correctly for which rank does which MPI_Wait, etc.
Here is your code with some debug printf statements:
#include <stdio.h>
#include <stdlib.h>
#include <math.h>
#include <time.h>
#include <mpi.h>
int
main(int argc, char *argv[])
{
/* MPI Specific Variables */
int my_size,
my_rank,
up,
down;
MPI_Request reqU,
reqD,
sreqU,
sreqD;
MPI_Status rUstatus,
rDstatus,
sUstatus,
sDstatus;
/* Physical Dimensions */
double Linner = 5.0; /* mm */
double Rinner = 1.0; /* mm */
double phi_0 = 1000.0;
/*V*/
/* Other Variables */
int grid_size = 100;
int slice;
int x,
y;
double grid_res_y = 0.2;
double grid_res_x = 0.1;
int xboundary,
yboundary;
MPI_Init(&argc, &argv);
MPI_Comm_rank(MPI_COMM_WORLD, &my_rank);
MPI_Comm_size(MPI_COMM_WORLD, &my_size);
/* Determining neighbours */
/* if statemets used to stop highest and lowest rank neighbours arent
outside 0 - my_size-1 range of ranks */
if (my_rank != 0) {
up = my_rank - 1;
}
else {
up = 0;
}
if (my_rank != my_size - 1) {
down = my_rank + 1;
}
else {
down = my_size - 1;
}
printf("my_rank=%d my_size=%d up=%d down=%d\n",my_rank,my_size,up,down);
/* cross-check: presumed my_size is a factor of gridsize else there are
odd sized slices and this is not coded for */
if (grid_size % my_size != 0) {
printf("ERROR - number of procs = %d, this is not a factor of grid_size %d\n", my_size, grid_size);
exit(0);
}
/* Set Up Distributed Data Approach */
slice = grid_size / my_size;
/* y grid index of inner conductor wall */
yboundary = Linner / grid_res_y;
/* x grid and individual array index of inner conductor wall */
xboundary = Rinner / grid_res_x;
if (my_rank == 0) {
printf("Linner=%g grid_res_y=%g yboundary=%d\n",
Linner,grid_res_y,yboundary);
printf("Rinner=%g grid_res_x=%g xboundary=%d\n",
Rinner,grid_res_x,xboundary);
printf("slice=%d grid_size=%d phi=%ld\n",
slice,grid_size,sizeof(double) * (slice + 2) * grid_size);
}
/* extra 2 rows to allow for halo data */
double phi[slice + 2][grid_size];
for (y = 0; y < slice + 2; y++) {
for (x = 0; x < grid_size; x++) {
phi[y][x] = 0.0;
}
}
/* Boundary Containing rank does 2 loops. One over part with inner
conductor and one over part without inner conductor */
if (my_rank == 0) {
for (y = 0; y < slice + 1; y++) {
for (x = xboundary; x < grid_size; x++) {
phi[y][x] = phi_0;
}
}
}
if (my_rank < my_size - 1) {
/* send top most strip up one node to be recieved as bottom halo */
printf("1: my_rank=%d MPI_Isend\n",my_rank);
MPI_Isend(&phi[1][0], grid_size, MPI_DOUBLE, down, 1, MPI_COMM_WORLD,
&sreqU);
/* recv top halo from up one node */
printf("2: my_rank=%d MPI_Irecv\n",my_rank);
MPI_Irecv(&phi[slice + 1][0], grid_size, MPI_DOUBLE, down, 2,
MPI_COMM_WORLD, &reqU);
printf("3: my_rank=%d\n",my_rank);
}
if (my_rank > 0) {
/* recv top halo from down one node */
printf("4: my_rank=%d MPI_Irecv\n",my_rank);
MPI_Irecv(&phi[0][0], grid_size, MPI_DOUBLE, up, 2, MPI_COMM_WORLD,
&reqD);
/* send bottom most strip down one node to be recieved as top halo */
printf("5: my_rank=%d MPI_Isend\n",my_rank);
MPI_Isend(&phi[slice][0], grid_size, MPI_DOUBLE, up, 1, MPI_COMM_WORLD,
&sreqD);
printf("6: my_rank=%d\n",my_rank);
}
if (my_rank < my_size - 1) {
/* Wait for send to down one rank to complete */
printf("7: my_rank=%d\n",my_rank);
MPI_Wait(&sreqD, &sDstatus);
printf("8: my_rank=%d\n",my_rank);
/* Wait for recieve from up one rank to complete */
printf("9: my_rank=%d\n",my_rank);
MPI_Wait(&reqD, &rDstatus);
printf("10: my_rank=%d\n",my_rank);
}
if (my_rank > 0) {
/* Wait for send to up down one rank to complete */
printf("11: my_rank=%d\n",my_rank);
MPI_Wait(&sreqU, &sUstatus);
printf("12: my_rank=%d\n",my_rank);
/* Wait for recieve from down one rank to complete */
printf("12: my_rank=%d\n",my_rank);
MPI_Wait(&reqU, &rUstatus);
printf("13: my_rank=%d\n",my_rank);
}
MPI_Finalize();
return 0;
}
Here is the output. Notice that step 7 prints (which is before the first MPI_Wait for rank 0). But, rank 0 never gets to step 8 (the printf after that call)
my_rank=0 my_size=2 up=0 down=1
Linner=5 grid_res_y=0.2 yboundary=25
Rinner=1 grid_res_x=0.1 xboundary=10
slice=50 grid_size=100 phi=41600
1: my_rank=0 MPI_Isend
2: my_rank=0 MPI_Irecv
3: my_rank=0
7: my_rank=0
my_rank=1 my_size=2 up=0 down=1
4: my_rank=1 MPI_Irecv
5: my_rank=1 MPI_Isend
6: my_rank=1
11: my_rank=1
[manderly:230404] *** Process received signal ***
[manderly:230403] *** Process received signal ***
[manderly:230403] Signal: Segmentation fault (11)
[manderly:230403] Signal code: Address not mapped (1)
[manderly:230403] Failing at address: 0x58
[manderly:230404] Signal: Segmentation fault (11)
[manderly:230404] Signal code: Address not mapped (1)
[manderly:230404] Failing at address: 0x58
[manderly:230403] [ 0] [manderly:230404] [ 0] /lib64/libpthread.so.0(+0x121c0)/lib64/libpthread.so.0(+0x121c0)[0x7fa5478341c0]
[0x7fa0ebe951c0]
[manderly:230404] [ 1] [manderly:230403] [ 1] /usr/lib64/openmpi/lib/libmpi.so.20(ompi_request_default_wait+0x31)[0x7fa0ec0e9a81]
[manderly:230404] [ 2] /usr/lib64/openmpi/lib/libmpi.so.20(ompi_request_default_wait+0x31)[0x7fa547a88a81]
[manderly:230403] [ 2] /usr/lib64/openmpi/lib/libmpi.so.20(PMPI_Wait+0x60)[0x7fa0ec12c350]
[manderly:230404] [ 3] ./fix2[0x400f93]
[manderly:230404] [ 4] /usr/lib64/openmpi/lib/libmpi.so.20(PMPI_Wait+0x60)[0x7fa547acb350]
[manderly:230403] [ 3] ./fix2[0x400ef7]
/lib64/libc.so.6(__libc_start_main+0xea)[0x7fa0ebaedfea]
[manderly:230404] [ 5] ./fix2[0x40081a[manderly:230403] [ 4] ]
[manderly:230404] *** End of error message ***
/lib64/libc.so.6(__libc_start_main+0xea)[0x7fa54748cfea]
[manderly:230403] [ 5] ./fix2[0x40081a]
[manderly:230403] *** End of error message ***
--------------------------------------------------------------------------
mpirun noticed that process rank 0 with PID 0 on node manderly exited on signal 11 (Segmentation fault).
--------------------------------------------------------------------------