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simple_dedisperse_block_threaded_memtest.c
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simple_dedisperse_block_threaded_memtest.c
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// Copyright Jonathan Sievers, 2015. All rights reserved. This code may only be used with permission of the owner.
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <omp.h>
#include "nt_memcpy.h"
#include <emmintrin.h>
float **matrix(int n, int m)
{
float *vec=(float *)malloc(sizeof(float)*n*m);
float **mat=(float **)malloc(sizeof(float *)*n);
memset(vec,0,n*m*sizeof(float));
for (int i=0;i<n;i++)
mat[i]=vec+i*m;
return mat;
}
/*--------------------------------------------------------------------------------*/
void dedisperse_kernel(float **in, float **out, int n, int m)
{
int npair=n/2;
for (int jj=0;jj<npair;jj++) {
for (int i=0;i<m;i++)
out[jj][i]=in[2*jj][i]+in[2*jj+1][i];
for (int i=0;i<m-jj-1;i++)
out[jj+npair][i]=in[2*jj][i+jj]+in[2*jj+1][i+jj+1];
}
}
/*--------------------------------------------------------------------------------*/
void dedisperse_kernel_v2(float **in, float **out, int n, int m)
{
int npair=n/2;
for (int jj=0;jj<npair;jj++) {
for (int i=0;i<jj;i++)
out[jj][i]=in[2*jj][i]+in[2*jj+1][i];
for (int i=jj;i<m-1;i++) {
out[jj][i]=in[2*jj][i]+in[2*jj+1][i];
out[jj+npair][i-jj]=in[2*jj][i]+in[2*jj+1][i+1];
}
}
}
/*--------------------------------------------------------------------------------*/
int get_npass(int n)
{
int nn=0;
while (n>1) {
nn++;
n/=2;
}
return nn;
}
/*--------------------------------------------------------------------------------*/
void dedisperse(float **inin, float **outout, int nchan,int ndat)
{
//return;
int npass=get_npass(nchan);
//printf("need %d passes.\n",npass);
//npass=2;
int bs=nchan;
float **in=inin;
float **out=outout;
for (int i=0;i<npass;i++) {
//#pragma omp parallel for
for (int j=0;j<nchan;j+=bs) {
dedisperse_kernel(in+j,out+j,bs,ndat);
}
bs/=2;
float **tmp=in;
in=out;
out=tmp;
}
memcpy(out[0],in[0],nchan*ndat*sizeof(float));
}
/*--------------------------------------------------------------------------------*/
void dedisperse_2pass(float **dat, float **dat2, int nchan, int ndat)
{
dedisperse_kernel(dat,dat2,nchan,ndat);
dedisperse_kernel(dat2,dat,nchan/2,ndat);
dedisperse_kernel(dat2+nchan/2,dat+nchan/2,nchan/2,ndat);
}
/*--------------------------------------------------------------------------------*/
void write_mat(float **dat, int n, int m, char *fname)
{
FILE *outfile=fopen(fname,"w");
fwrite(&n,sizeof(int),1,outfile);
fwrite(&m,sizeof(int),1,outfile);
fwrite(dat[0],sizeof(float),n*m,outfile);
fclose(outfile);
}
/*--------------------------------------------------------------------------------*/
void find_peak(float **dat, int nchan, int ndat, int *best_chan, int *best_dat)
{
float max=0;
int ichan=0;
int idat=0;
for (int i=0;i<nchan;i++)
for (int j=0;j<ndat;j++) {
if (dat[i][j]>max) {
max=dat[i][j];
ichan=i;
idat=j;
}
}
float slope=(float)ichan/(float)nchan;
float flux=dat[ichan][idat]+dat[ichan][idat-1]+dat[ichan][idat+1];
printf("I found a peak at slope %8.4f at time %d with average flux %8.4f\n",slope,idat,flux/(float)nchan);
if (best_chan)
*best_chan=ichan;
if (best_dat)
*best_dat=idat;
}
/*--------------------------------------------------------------------------------*/
void dedisperse_blocked(float **dat, float **dat2, int nchan, int ndat)
{
int nchan1=64;
int npass1=get_npass(nchan1);
int npass=get_npass(nchan);
int npass2=npass-npass1;
int nchan2=nchan/nchan1;
int nblock=nchan/nchan1;
int nblock2=nchan/nchan2;
for (int i=0;i<nblock;i++)
dedisperse(dat+i*nchan1,dat2+i*nchan1,nchan1,ndat);
for (int i=0;i<nblock;i++)
for (int j=0;j<nchan1;j++)
memcpy(dat2[j*nblock+i],dat[i*nchan1+j]+i*j,ndat-i*j);
for (int i=0;i<nblock2;i++)
dedisperse(dat2+i*nchan2,dat+i*nchan2,nchan2,ndat);
}
/*--------------------------------------------------------------------------------*/
void dedisperse_blocked_cached(float **dat, float **dat2, int nchan, int ndat)
{
//int nchan1=128;
//int chunk_size=768;
int nchan1=128;
int chunk_size=1024;
int nchunk=ndat/chunk_size;
int npass1=get_npass(nchan1);
int npass=get_npass(nchan);
int npass2=npass-npass1;
int nchan2=nchan/nchan1;
int nblock=nchan/nchan1;
int nblock2=nchan/nchan2;
#pragma omp parallel
{
float **tmp1=matrix(nchan1,chunk_size+nchan1);
float **tmp2=matrix(nchan1,chunk_size+nchan1);
#pragma omp for collapse(2) schedule(dynamic,2)
for (int i=0;i<nblock;i++) {
//printf("i is %d\n",i);
for (int j=0;j<nchunk;j++) {
int istart=j*chunk_size;
int istop=(j+1)*chunk_size+nchan1;
if (istop>ndat) {
istop=ndat;
for (int k=0;k<nchan1;k++)
memset(tmp1[k]+chunk_size,0,sizeof(float)*nchan1);
}
for (int k=0;k<nchan1;k++) {
memcpy(tmp1[k],&(dat[i*nchan1+k][istart]),(istop-istart)*sizeof(float));
//t_memcpy(tmp1[k],&(dat[i*nchan1+k][istart]),(istop-istart)*sizeof(float));
}
#ifndef NO_DEDISPERSE
dedisperse(tmp1,tmp2,nchan1,chunk_size+nchan1);
#endif
for (int k=0;k<nchan1;k++) {
memcpy(&(dat2[i*nchan1+k][istart]),tmp1[k],chunk_size*sizeof(float));
//nt_memcpy(&(dat2[i*nchan1+k][istart]),tmp1[k],chunk_size*sizeof(float));
}
}
}
#if 1
free(tmp1[0]);
free(tmp1);
free(tmp2[0]);
free(tmp2);
#endif
}
float **dat_shift=(float **)malloc(sizeof(float *)*nchan);
for (int i=0;i<nblock;i++)
for (int j=0;j<nchan1;j++)
dat_shift[j*nblock+i]=dat2[i*nchan1+j]+i*j;
//recalculate block sizes to keep amount in cache about the same
int nelem=nchan1*chunk_size;
chunk_size=nelem/nchan2;
nchunk=ndat/chunk_size;
#pragma omp parallel
{
float **tmp1=matrix(nchan2,chunk_size+nchan2);
float **tmp2=matrix(nchan2,chunk_size+nchan2);
#pragma omp for collapse(2) schedule(dynamic,4)
for (int i=0;i<nblock2;i++) {
//printf("i is now %d\n",i);
for (int j=0;j<nchunk;j++) {
int istart=j*chunk_size;
int istop=(j+1)*chunk_size+nchan2;
if (istop>ndat) {
istop=ndat;
for (int k=0;k<nchan2;k++)
memset(tmp1[k]+chunk_size,0,sizeof(float)*nchan2);
}
for (int k=0;k<nchan2;k++) {
memcpy(tmp1[k],dat_shift[i*nchan2+k]+istart,(istop-istart)*sizeof(float));
//t_memcpy(tmp1[k],dat_shift[i*nchan2+k]+istart,(istop-istart)*sizeof(float));
}
#ifndef NO_DEDISPERSE
dedisperse(tmp1,tmp2,nchan2,chunk_size+nchan2);
#endif
for (int k=0;k<nchan2;k++) {
memcpy(dat[i*nchan2+k]+istart,tmp2[k],chunk_size*sizeof(float));
//nt_memcpy(dat[i*nchan2+k]+istart,tmp2[k],chunk_size*sizeof(float));
}
}
}
free(tmp1[0]);
free(tmp1);
free(tmp2[0]);
free(tmp2);
}
//printf("Finished dedispersion.\n");
}
/*================================================================================*/
int main(int argc, char *argv[])
{
//int nchan=4096;
//int ndat=12000;
int nchan=1024;
int ndat=327680;
int nrep=1;
if (argc>1)
nchan=atoi(argv[1]);
if (argc>2)
ndat=atoi(argv[2]);
if (argc>3)
nrep=atoi(argv[3]);
float **dat=matrix(nchan,ndat+nchan);
float **dat2=matrix(nchan,ndat+nchan);
if (1)
for (int i=0;i<nchan;i++)
dat[i][(int)(0.8317*i+160.2)]=1;
else
for (int i=0;i<nchan;i++)
dat[i][ndat/2]=1;
#if 0
write_mat(dat,nchan,ndat,"dat_starting.dat");
dedisperse_kernel(dat,dat2,nchan,ndat);
write_mat(dat2,nchan,ndat,"dat_1pass.dat");
dedisperse_2pass(dat,dat2,nchan,ndat);
write_mat(dat,nchan,ndat,"dat_2pass.dat");
#endif
double t1=omp_get_wtime();
//dedisperse(dat,dat2,nchan,ndat);
//dedisperse_blocked(dat,dat2,nchan,ndat);
dedisperse_blocked_cached(dat,dat2,nchan,ndat);
double t2=omp_get_wtime();
printf("took %12.4f seconds.\n",t2-t1);
int ichan,idat;
find_peak(dat,nchan,ndat,&ichan,&idat);
t1=omp_get_wtime();
printf("took %12.4f seconds to find peak.\n",t1-t2);
for (int i=0;i<10;i++) {
t1=omp_get_wtime();
for (int j=0;j<nrep;j++) {
dedisperse_blocked_cached(dat,dat2,nchan,ndat);
//dedisperse(dat,dat2,nchan,ndat);
}
t2=omp_get_wtime();
double nops=get_npass(nchan)*(nchan+0.0)*(ndat+0.0)*(nrep+0.0);
printf("took %12.6f seconds at rate %12.6f.\n",t2-t1,nops/(t2-t1)/1024/1024);
//printf("took %12.4f seconds.\n",t2-t1);
}
//write_mat(dat,nchan,ndat,"dat_final1.dat");
//write_mat(dat2,nchan,ndat,"dat_final2.dat");
}