void
pcl::pcl_2d::morphology<PointT>::closingGray (pcl::PointCloud<PointT> &output){
PointCloudInPtr intermediate_output (new PointCloudIn);
dilationGray (*intermediate_output);
setInputCloud (intermediate_output);
erosionGray (output);
}
template <typename PointT> void
pcl::Morphology<PointT>::closingGray (pcl::PointCloud<PointT> &output)
{
PointCloudInPtr intermediate_output (new PointCloudIn);
dilationGray (*intermediate_output);
this->setInputCloud (intermediate_output);
erosionGray (output);
}
// Main function
int main(int argc, char **argv) {
int i, ts, thisbody, otherbody;
int bn;
double vavgx, vavgy, vavgz, ax, ay, az, deltaf[3];
// Serial Timing Functions: See the timer.h include file in this directory
double etime, etime0, etime1, cptime;
int send_counts[8], recv_counts[8], send_offsets[8], recv_offsets[8];
int rank, size, type=99;
MPI_Init(&argc, &argv);
MPI_Comm_size(MPI_COMM_WORLD, &size); // Get no. of processes
MPI_Comm_rank(MPI_COMM_WORLD, &rank); // Which process am I?
if(rank == 0){
// Read basic inputs
scanf("%d\n",&N);
scanf("%d\n",&K);
scanf("%le\n",&dt);
}
// broadcast N, K, dt to all processes
MPI_Bcast(&N, 1, MPI_INT, 0, MPI_COMM_WORLD);
MPI_Bcast(&K, 1, MPI_INT, 0, MPI_COMM_WORLD);
MPI_Bcast(&dt, 1, MPI_DOUBLE, 0, MPI_COMM_WORLD);
dt2 = dt/2.;
// Allocate arrays
// times 8 to make sure it won't excced the boundary use.
// since one body may be boundary body for 7 processes
mass = calloc(N * 8, sizeof(double)); // mass[i] is mass of body i
x = calloc(N * 8, sizeof(double)); // x[i] is x position of body i
y = calloc(N * 8, sizeof(double)); // y[i] is y position of body i
z = calloc(N * 8, sizeof(double)); // z[i] is z position of body i
vx = calloc(N * 8, sizeof(double)); // vx[i] is x velocity of body i
vy = calloc(N * 8, sizeof(double)); // vy[i] is y velocity of body i
vz = calloc(N * 8, sizeof(double)); // vz[i] is z velocity of body i
fx = calloc(N * 8, sizeof(double)); // fx[i] is x force on body i
fy = calloc(N * 8, sizeof(double)); // fy[i] is y force on body i
fz = calloc(N * 8, sizeof(double)); // fz[i] is z force on body i
bmass = calloc(N * 8, sizeof(double)); // boundary body mass
bx = calloc(N * 8, sizeof(double)); // boundary body x
by = calloc(N * 8, sizeof(double)); // boundary body y
bz = calloc(N * 8, sizeof(double)); // boundary body z
buf = calloc(N * 8, sizeof(double)); // boundary body z
if(rank == 0){
// Read initial conditions
for (i=0; i<N; i++) scanf("%le\n",&mass[i]);
for (i=0; i<N; i++) scanf("%le %le %le\n",&x[i],&y[i],&z[i]);
for (i=0; i<N; i++) scanf("%le %le %le\n",&vx[i],&vy[i],&vz[i]);
n = N;
}else{
n = 0;
}
MPI_Barrier(MPI_COMM_WORLD);
// Start Timer
timing(&etime0,&cptime);
// Timestamp Loop
// loop phase
for (ts=0; ts<K; ts++) {
if (ts%128 == 0) intermediate_output(ts, rank); // Print output if necessary
// partition bodies into 8 groups based on its coordination
partition(n, send_offsets);
for(i = 0; i < size - 1; i++){
send_counts[i] = send_offsets[i + 1] - send_offsets[i];
}
send_counts[size - 1] = n - send_offsets[size - 1];
// alltoall number of bodies
MPI_Alltoall(send_counts, 1, MPI_INT, recv_counts, 1, MPI_INT, MPI_COMM_WORLD);
recv_offsets[0] = 0;
for(i = 1; i < size; i++){
recv_offsets[i] = recv_offsets[i - 1] + recv_counts[i - 1];
}
// n is not correct
// update n
n = recv_offsets[size - 1] + recv_counts[size - 1];
// alltoallv bodies
MPI_Alltoallv(mass, send_counts, send_offsets, MPI_DOUBLE,
buf, recv_counts, recv_offsets, MPI_DOUBLE, MPI_COMM_WORLD);
swap(&mass, &buf);
MPI_Alltoallv(x, send_counts, send_offsets, MPI_DOUBLE,
buf, recv_counts, recv_offsets, MPI_DOUBLE, MPI_COMM_WORLD);
swap(&x, &buf);
MPI_Alltoallv(y, send_counts, send_offsets, MPI_DOUBLE,
buf, recv_counts, recv_offsets, MPI_DOUBLE, MPI_COMM_WORLD);
swap(&y, &buf);
MPI_Alltoallv(z, send_counts, send_offsets, MPI_DOUBLE,
buf, recv_counts, recv_offsets, MPI_DOUBLE, MPI_COMM_WORLD);
swap(&z, &buf);
MPI_Alltoallv(vx, send_counts, send_offsets, MPI_DOUBLE,
buf, recv_counts, recv_offsets, MPI_DOUBLE, MPI_COMM_WORLD);
swap(&vx, &buf);
MPI_Alltoallv(vy, send_counts, send_offsets, MPI_DOUBLE,
buf, recv_counts, recv_offsets, MPI_DOUBLE, MPI_COMM_WORLD);
swap(&vy, &buf);
MPI_Alltoallv(vz, send_counts, send_offsets, MPI_DOUBLE,
buf, recv_counts, recv_offsets, MPI_DOUBLE, MPI_COMM_WORLD);
swap(&vz, &buf);
// extract boundary points
extract(n, send_offsets, &bn);
// alltoall number of boundary points
for(i = 0; i < size - 1; i++){
send_counts[i] = send_offsets[i + 1] - send_offsets[i];
}
send_counts[size - 1] = bn - send_offsets[size - 1];
// alltoall number of bodies
MPI_Alltoall(send_counts, 1, MPI_INT, recv_counts, 1, MPI_INT, MPI_COMM_WORLD);
recv_offsets[0] = 0;
for(i = 1; i < size; i++){
recv_offsets[i] = recv_offsets[i - 1] + recv_counts[i - 1];
}
bn = recv_offsets[size - 1] + recv_counts[size - 1];
// alltoallv boundary points mass
MPI_Alltoallv(bmass, send_counts, send_offsets, MPI_DOUBLE,
buf, recv_counts, recv_offsets, MPI_DOUBLE, MPI_COMM_WORLD);
swap(&bmass, &buf);
// alltoallv boundary points x
MPI_Alltoallv(bx, send_counts, send_offsets, MPI_DOUBLE,
buf, recv_counts, recv_offsets, MPI_DOUBLE, MPI_COMM_WORLD);
swap(&bx, &buf);
// alltoallv boundary points y
MPI_Alltoallv(by, send_counts, send_offsets, MPI_DOUBLE,
buf, recv_counts, recv_offsets, MPI_DOUBLE, MPI_COMM_WORLD);
swap(&by, &buf);
// alltoallv boundary points z
MPI_Alltoallv(bz, send_counts, send_offsets, MPI_DOUBLE,
buf, recv_counts, recv_offsets, MPI_DOUBLE, MPI_COMM_WORLD);
swap(&bz, &buf);
// Initialize forces on bodies
for (thisbody=0; thisbody<n; thisbody++) {
fx[thisbody] = 0.;
fy[thisbody] = 0.;
fz[thisbody] = 0.;
}
// Compute all pairwise interbody forces (Note that we take advantage of symmetry.)
for (thisbody=0; thisbody<n; thisbody++) {
for (otherbody=thisbody+1; otherbody<n; otherbody++) {
force(thisbody, otherbody, deltaf); // This function computes the pairwise force of otherbody on thisbody
fx[thisbody] += deltaf[0]; // Add x component of force to thisbody
fy[thisbody] += deltaf[1]; // Add y component of force to thisbody
fz[thisbody] += deltaf[2]; // Add z component of force to thisbody
fx[otherbody] -= deltaf[0]; // Subtract x component of force from otherbody
fy[otherbody] -= deltaf[1]; // Subtract y component of force from otherbody
fz[otherbody] -= deltaf[2]; // Subtract z component of force from otherbody
}
}
// Compute all pairwise boundary body forces (Note that we take advantage of symmetry.)
for (thisbody=0; thisbody<n; thisbody++) {
for (otherbody=0; otherbody<bn; otherbody++) {
bforce(thisbody, otherbody, deltaf); // This function computes the pairwise force of otherbody on thisbody
fx[thisbody] += deltaf[0]; // Add x component of force to thisbody
fy[thisbody] += deltaf[1]; // Add y component of force to thisbody
fz[thisbody] += deltaf[2]; // Add z component of force to thisbody
}
}
// Now move the bodies (assumes constant acceleration during the timestep)
for (thisbody=0; thisbody<n; thisbody++) {
ax = fx[thisbody]/mass[thisbody]; // Compute x-direction acceleration of thisbody
ay = fy[thisbody]/mass[thisbody]; // Compute y-direction acceleration of thisbody
az = fz[thisbody]/mass[thisbody]; // Compute z-direction acceleration of thisbody
vavgx = vx[thisbody] + dt2*ax; // Compute average x velocity of thisbody
vavgy = vy[thisbody] + dt2*ay; // Compute average y velocity of thisbody
vavgz = vz[thisbody] + dt2*az; // Compute average z velocity of thisbody
x[thisbody] = x[thisbody] + dt*vavgx; // Compute new x position of thisbody
y[thisbody] = y[thisbody] + dt*vavgy; // Compute new y position of thisbody
z[thisbody] = z[thisbody] + dt*vavgz; // Compute new z position of thisbody
vx[thisbody] += dt*ax; // Compute x velocity of thisbody at end of timestep
vy[thisbody] += dt*ay; // Compute y velocity of thisbody at end of timestep
vz[thisbody] += dt*az; // Compute z velocity of thisbody at end of timestep
}
}
// gather results
// gather numbers
MPI_Gather(&n, 1, MPI_INT, recv_counts, 1, MPI_INT, 0, MPI_COMM_WORLD);
recv_offsets[0] = 0;
for(i = 1; i < size; i++){
recv_offsets[i] = recv_offsets[i - 1] + recv_counts[i - 1];
}
// gatherv x
MPI_Gatherv(x, n, MPI_DOUBLE, buf, recv_counts, recv_offsets, MPI_DOUBLE, 0, MPI_COMM_WORLD);
swap(&x, &buf);
// gatherv y
MPI_Gatherv(y, n, MPI_DOUBLE, buf, recv_counts, recv_offsets, MPI_DOUBLE, 0, MPI_COMM_WORLD);
swap(&y, &buf);
// gatherv z
MPI_Gatherv(z, n, MPI_DOUBLE, buf, recv_counts, recv_offsets, MPI_DOUBLE, 0, MPI_COMM_WORLD);
swap(&z, &buf);
// gatherv mass
MPI_Gatherv(mass, n, MPI_DOUBLE, buf, recv_counts, recv_offsets, MPI_DOUBLE, 0, MPI_COMM_WORLD);
swap(&mass, &buf);
// gatherv vx
MPI_Gatherv(vx, n, MPI_DOUBLE, buf, recv_counts, recv_offsets, MPI_DOUBLE, 0, MPI_COMM_WORLD);
swap(&vx, &buf);
// gatherv vy
MPI_Gatherv(vy, n, MPI_DOUBLE, buf, recv_counts, recv_offsets, MPI_DOUBLE, 0, MPI_COMM_WORLD);
swap(&vy, &buf);
// gatherv vz
MPI_Gatherv(vz, n, MPI_DOUBLE, buf, recv_counts, recv_offsets, MPI_DOUBLE, 0, MPI_COMM_WORLD);
swap(&vz, &buf);
if(rank == 0){
n = N;
output(K); // Final output
timing(&etime1, &cptime);
etime = etime1 - etime0;
printf ("\nTime for %d timesteps with %d bodies: %9.4f seconds\n", K, N, etime);
}
// Free arrays
free(mass);
free(x);
free(y);
free(z);
free(vx);
free(vy);
free(vz);
free(fx);
free(fy);
free(fz);
free(bx);
free(by);
free(bz);
free(bmass);
free(buf);
MPI_Finalize();
}