Commit ca3c7632 authored by Francois Tessier's avatar Francois Tessier

Split HACC-IO SoA in two files for read and write. Fix HACC-IO AoS.

parent 7ddb837c
......@@ -44,7 +44,7 @@ int main (int argc, char * argv[])
file_id = atoi ( argv[2] );
#ifdef BGQ
snprintf (output, 100, "/projects/visualization/ftessier/debug/HACC-SOA-%08d-%d.dat", mycolor, file_id);
snprintf (output, 100, "/projects/visualization/ftessier/debug/HACC-AOS-%08d-%d.dat", mycolor, file_id);
#elif XC40
snprintf (output, 100, "/lus/theta-fs0/projects/Performance/ftessier/HACC/HACC-AOS-%08d-%d.dat", mycolor, file_id);
#else
......
......@@ -44,7 +44,7 @@ int main (int argc, char * argv[])
file_id = atoi ( argv[2] );
#ifdef BGQ
snprintf (output, 100, "/projects/visualization/ftessier/debug/HACC-SOA-%08d-%d.dat", mycolor, file_id);
snprintf (output, 100, "/projects/visualization/ftessier/debug/HACC-AOS-%08d-%d.dat", mycolor, file_id);
#elif XC40
snprintf (output, 100, "/lus/theta-fs0/projects/Performance/ftessier/HACC/HACC-AOS-%08d-%d.dat", mycolor, file_id);
#else
......
#include <stdio.h>
#include <stdlib.h>
#include <assert.h>
#include <stdint.h>
#include <mpi.h>
#include "tapioca.hpp"
#define RED "\x1b[31m"
#define GREEN "\x1b[32m"
#define BLUE "\x1b[34m"
#define RESET "\x1b[0m"
int main (int argc, char * argv[])
{
int world_numtasks, world_myrank, mycolor, mykey, sub_numtasks, sub_myrank, i, file_id;
int64_t num_particles;
int64_t sub_particles, tot_particles, particle_size, file_size, tot_size;
int64_t scan_size = 0, offset, hdr = 0;
double start_time, end_time, tot_time, max_time;
double io_bw;
MPI_Comm sub_comm;
MPI_Status status;
char output[100];
Tapioca tp;
int64_t chunkCount[9], chunkOffset[9];
int chunkSize[9];
MPI_Init(&argc, &argv);
MPI_Comm_size(MPI_COMM_WORLD, &world_numtasks);
MPI_Comm_rank(MPI_COMM_WORLD, &world_myrank);
mycolor = tp.topology.BridgeNodeId ();
mykey = world_myrank;
MPI_Comm_split (MPI_COMM_WORLD, mycolor, mykey, &sub_comm);
MPI_Comm_size(sub_comm, &sub_numtasks);
MPI_Comm_rank(sub_comm, &sub_myrank);
num_particles = atoi ( argv[1] );
file_id = 0;
if ( argv[2] != NULL )
file_id = atoi ( argv[2] );
#ifdef BGQ
snprintf (output, 100, "/projects/visualization/ftessier/debug/HACC-SOA-%08d-%d.dat", mycolor, file_id);
#elif XC40
snprintf (output, 100, "/lus/theta-fs0/projects/Performance/ftessier/HACC/HACC-AOS-%08d-%d.dat", mycolor, file_id);
#else
snprintf (output, 100, "./HACC-SOA-%08d-%d.dat", mycolor, file_id);
#endif
/*****************/
/* WRITE */
/*****************/
float *xx, *yy, *zz, *vx, *vy, *vz, *phi;
int64_t* pid;
uint16_t* mask;
xx = new float[num_particles];
yy = new float[num_particles];
zz = new float[num_particles];
vx = new float[num_particles];
vy = new float[num_particles];
vz = new float[num_particles];
phi = new float[num_particles];
pid = new int64_t[num_particles];
mask = new uint16_t[num_particles];
for (uint64_t i = 0; i< num_particles; i++)
{
xx[i] = (float)i;
yy[i] = (float)i;
zz[i] = (float)i;
vx[i] = (float)i;
vy[i] = (float)i;
vz[i] = (float)i;
phi[i] = (float)i;
pid[i] = (int64_t)i;
mask[i] = (uint16_t)world_myrank;
}
MPI_Allreduce(&num_particles, &sub_particles, 1, MPI_LONG_LONG, MPI_SUM, sub_comm);
MPI_Allreduce(&num_particles, &tot_particles, 1, MPI_LONG_LONG, MPI_SUM, MPI_COMM_WORLD);
particle_size = (7 * sizeof(float)) + sizeof(int64_t) + sizeof(uint16_t);
file_size = particle_size * sub_particles;
tot_size = particle_size * tot_particles;
MPI_Exscan (&num_particles, &scan_size, 1, MPI_LONG_LONG, MPI_SUM, sub_comm);
if (0 == sub_myrank) {
fprintf (stdout, GREEN "[INFO]" RESET " [%08d] miniHACC-SoA\n", mycolor);
fprintf (stdout, GREEN "[INFO]" RESET " [%08d] Read output file (SoA data layout)\n", mycolor);
fprintf (stdout, GREEN "[INFO]" RESET " [%08d] --> %lld particles per rank\n", mycolor, num_particles);
fprintf (stdout, GREEN "[INFO]" RESET " [%08d] --> File size: %.2f MB (%lld particles)\n",
mycolor, (double)file_size/(1024*1024), sub_particles);
}
/*****************/
/* READ */
/*****************/
float *xx_r, *yy_r, *zz_r, *vx_r, *vy_r, *vz_r, *phi_r;
int64_t* pid_r;
uint16_t* mask_r;
xx_r = new float[num_particles];
yy_r = new float[num_particles];
zz_r = new float[num_particles];
vx_r = new float[num_particles];
vy_r = new float[num_particles];
vz_r = new float[num_particles];
phi_r = new float[num_particles];
pid_r = new int64_t[num_particles];
mask_r = new uint16_t[num_particles];
/*****************/
/* INIT TAPIOCA */
/*****************/
for ( i = 0; i < 9; i++ ) {
chunkCount[i] = num_particles;
}
chunkSize[0] = sizeof(float);
chunkSize[1] = sizeof(float);
chunkSize[2] = sizeof(float);
chunkSize[3] = sizeof(float);
chunkSize[4] = sizeof(float);
chunkSize[5] = sizeof(float);
chunkSize[6] = sizeof(float);
chunkSize[7] = sizeof(int64_t);
chunkSize[8] = sizeof(uint16_t);
chunkOffset[0] = hdr + scan_size * chunkSize[0];
for ( i = 1; i < 9; i++ ) {
chunkOffset[i] = chunkOffset[i - 1];
chunkOffset[i] += (sub_particles - scan_size) * chunkSize[i - 1];
chunkOffset[i] += scan_size * chunkSize[i];
}
tp.Init (chunkCount, chunkSize, chunkOffset, 9, hdr, sub_comm);
tp.setAggregationTier (NVR, "/scratch/tmp");
tp.setTargetTier (HDD, file_size, output);
/*****************/
start_time = MPI_Wtime();
if (0 == sub_myrank)
fprintf (stdout, GREEN "[INFO]" RESET " [%08d] Read output file\n", mycolor);
offset = scan_size * sizeof(float);
tp.Read (offset, xx_r, num_particles, MPI_FLOAT, &status);
offset += (sub_particles - scan_size) * sizeof(float) + scan_size * sizeof(float);
tp.Read (offset, yy_r, num_particles, MPI_FLOAT, &status);
offset += (sub_particles - scan_size) * sizeof(float) + scan_size * sizeof(float);
tp.Read (offset, zz_r, num_particles, MPI_FLOAT, &status);
offset += (sub_particles - scan_size) * sizeof(float) + scan_size * sizeof(float);
tp.Read (offset, vx_r, num_particles, MPI_FLOAT, &status);
offset += (sub_particles - scan_size) * sizeof(float) + scan_size * sizeof(float);
tp.Read (offset, vy_r, num_particles, MPI_FLOAT, &status);
offset += (sub_particles - scan_size) * sizeof(float) + scan_size * sizeof(float);
tp.Read (offset, vz_r, num_particles, MPI_FLOAT, &status);
offset += (sub_particles - scan_size) * sizeof(float) + scan_size * sizeof(float);
tp.Read (offset, phi_r, num_particles, MPI_FLOAT, &status);
offset += (sub_particles - scan_size) * sizeof(float) + scan_size * sizeof(int64_t);
tp.Read (offset, pid_r, num_particles, MPI_LONG_LONG, &status);
offset += (sub_particles - scan_size) * sizeof(int64_t) + scan_size * sizeof(uint16_t);
tp.Read (offset, mask_r, num_particles, MPI_UNSIGNED_SHORT, &status);
end_time = MPI_Wtime();
tot_time = end_time - start_time;
MPI_Reduce (&tot_time, &max_time, 1, MPI_DOUBLE, MPI_MAX, 0, MPI_COMM_WORLD);
if (0 == world_myrank) {
io_bw = (double)tot_size / max_time / (1024 * 1024);
fprintf (stdout, BLUE "[TIMING]" RESET " Read I/O bandwidth: %.2f MBps (%.2f MB in %.2f ms)\n",
io_bw, (double)tot_size/(1024*1024), max_time * 1000);
}
tp.Finalize ();
/*****************/
/* VERIFICATION */
/*****************/
for (uint64_t i = 0; i< num_particles; i++) {
if ((xx[i] != xx_r[i]) || (yy[i] != yy_r[i]) || (zz[i] != zz_r[i])
|| (vx[i] != vx_r[i]) || (vy[i] != vy_r[i]) || (vz[i] != vz_r[i])
|| (phi[i] != phi_r[i])|| (pid[i] != pid_r[i]) || (mask[i] != mask_r[i]))
{
fprintf (stdout, RED "[ERROR]" RESET " Wrong value for particle %d\n", i);
MPI_Abort (MPI_COMM_WORLD, -1);
}
}
if (0 == sub_myrank)
fprintf (stdout, GREEN "[INFO]" RESET " [%08d] Content verified and consistent\n", mycolor);
/*****************/
/* FREE */
/*****************/
delete [] xx;
delete [] xx_r;
delete [] yy;
delete [] yy_r;
delete [] zz;
delete [] zz_r;
delete [] vx;
delete [] vx_r;
delete [] vy;
delete [] vy_r;
delete [] vz;
delete [] vz_r;
delete [] phi;
delete [] phi_r;
delete [] pid;
delete [] pid_r;
delete [] mask;
delete [] mask_r;
MPI_Finalize ();
}
#include <stdio.h>
#include <stdlib.h>
#include <assert.h>
#include <stdint.h>
#include <mpi.h>
#include "tapioca.hpp"
#define RED "\x1b[31m"
#define GREEN "\x1b[32m"
#define BLUE "\x1b[34m"
#define RESET "\x1b[0m"
int main (int argc, char * argv[])
{
int world_numtasks, world_myrank, mycolor, mykey, sub_numtasks, sub_myrank, i, file_id;
int64_t num_particles;
int64_t sub_particles, tot_particles, particle_size, file_size, tot_size;
int64_t scan_size = 0, offset, hdr = 0;
double start_time, end_time, tot_time, max_time;
double io_bw;
MPI_Comm sub_comm;
MPI_Status status;
char output[100];
Tapioca tp;
int64_t chunkCount[9], chunkOffset[9];
int chunkSize[9];
MPI_Init(&argc, &argv);
MPI_Comm_size(MPI_COMM_WORLD, &world_numtasks);
MPI_Comm_rank(MPI_COMM_WORLD, &world_myrank);
mycolor = tp.topology.BridgeNodeId ();
mykey = world_myrank;
MPI_Comm_split (MPI_COMM_WORLD, mycolor, mykey, &sub_comm);
MPI_Comm_size(sub_comm, &sub_numtasks);
MPI_Comm_rank(sub_comm, &sub_myrank);
num_particles = atoi ( argv[1] );
file_id = 0;
if ( argv[2] != NULL )
file_id = atoi ( argv[2] );
#ifdef BGQ
snprintf (output, 100, "/projects/visualization/ftessier/debug/HACC-SOA-%08d-%d.dat", mycolor, file_id);
#elif XC40
snprintf (output, 100, "/lus/theta-fs0/projects/Performance/ftessier/HACC/HACC-AOS-%08d-%d.dat", mycolor, file_id);
#else
snprintf (output, 100, "./HACC-SOA-%08d-%d.dat", mycolor, file_id);
#endif
/*****************/
/* WRITE */
/*****************/
float *xx, *yy, *zz, *vx, *vy, *vz, *phi;
int64_t* pid;
uint16_t* mask;
xx = new float[num_particles];
yy = new float[num_particles];
zz = new float[num_particles];
vx = new float[num_particles];
vy = new float[num_particles];
vz = new float[num_particles];
phi = new float[num_particles];
pid = new int64_t[num_particles];
mask = new uint16_t[num_particles];
for (uint64_t i = 0; i< num_particles; i++)
{
xx[i] = (float)i;
yy[i] = (float)i;
zz[i] = (float)i;
vx[i] = (float)i;
vy[i] = (float)i;
vz[i] = (float)i;
phi[i] = (float)i;
pid[i] = (int64_t)i;
mask[i] = (uint16_t)world_myrank;
}
MPI_Allreduce(&num_particles, &sub_particles, 1, MPI_LONG_LONG, MPI_SUM, sub_comm);
MPI_Allreduce(&num_particles, &tot_particles, 1, MPI_LONG_LONG, MPI_SUM, MPI_COMM_WORLD);
particle_size = (7 * sizeof(float)) + sizeof(int64_t) + sizeof(uint16_t);
file_size = particle_size * sub_particles;
tot_size = particle_size * tot_particles;
MPI_Exscan (&num_particles, &scan_size, 1, MPI_LONG_LONG, MPI_SUM, sub_comm);
if (0 == sub_myrank) {
fprintf (stdout, GREEN "[INFO]" RESET " [%08d] miniHACC-SoA\n", mycolor);
fprintf (stdout, GREEN "[INFO]" RESET " [%08d] Write output file (SoA data layout)\n", mycolor);
fprintf (stdout, GREEN "[INFO]" RESET " [%08d] --> %lld particles per rank\n", mycolor, num_particles);
fprintf (stdout, GREEN "[INFO]" RESET " [%08d] --> File size: %.2f MB (%lld particles)\n",
mycolor, (double)file_size/(1024*1024), sub_particles);
}
/*****************/
/* INIT TAPIOCA */
/*****************/
for ( i = 0; i < 9; i++ ) {
chunkCount[i] = num_particles;
}
chunkSize[0] = sizeof(float);
chunkSize[1] = sizeof(float);
chunkSize[2] = sizeof(float);
chunkSize[3] = sizeof(float);
chunkSize[4] = sizeof(float);
chunkSize[5] = sizeof(float);
chunkSize[6] = sizeof(float);
chunkSize[7] = sizeof(int64_t);
chunkSize[8] = sizeof(uint16_t);
chunkOffset[0] = hdr + scan_size * chunkSize[0];
for ( i = 1; i < 9; i++ ) {
chunkOffset[i] = chunkOffset[i - 1];
chunkOffset[i] += (sub_particles - scan_size) * chunkSize[i - 1];
chunkOffset[i] += scan_size * chunkSize[i];
}
tp.Init (chunkCount, chunkSize, chunkOffset, 9, hdr, sub_comm);
tp.setAggregationTier (NVR, "/scratch/tmp");
tp.setTargetTier (HDD, file_size, output);
/*****************/
start_time = MPI_Wtime();
offset = scan_size * sizeof(float);
tp.Write (offset, xx, num_particles, MPI_FLOAT, &status);
offset += (sub_particles - scan_size) * sizeof(float) + scan_size * sizeof(float);
tp.Write (offset, yy, num_particles, MPI_FLOAT, &status);
offset += (sub_particles - scan_size) * sizeof(float) + scan_size * sizeof(float);
tp.Write (offset, zz, num_particles, MPI_FLOAT, &status);
offset += (sub_particles - scan_size) * sizeof(float) + scan_size * sizeof(float);
tp.Write (offset, vx, num_particles, MPI_FLOAT, &status);
offset += (sub_particles - scan_size) * sizeof(float) + scan_size * sizeof(float);
tp.Write (offset, vy, num_particles, MPI_FLOAT, &status);
offset += (sub_particles - scan_size) * sizeof(float) + scan_size * sizeof(float);
tp.Write (offset, vz, num_particles, MPI_FLOAT, &status);
offset += (sub_particles - scan_size) * sizeof(float) + scan_size * sizeof(float);
tp.Write (offset, phi, num_particles, MPI_FLOAT, &status);
offset += (sub_particles - scan_size) * sizeof(float) + scan_size * sizeof(int64_t);
tp.Write (offset, pid, num_particles, MPI_LONG_LONG, &status);
offset += (sub_particles - scan_size) * sizeof(int64_t) + scan_size * sizeof(uint16_t);
tp.Write (offset, mask, num_particles, MPI_UNSIGNED_SHORT, &status);
end_time = MPI_Wtime();
tot_time = end_time - start_time;
MPI_Reduce (&tot_time, &max_time, 1, MPI_DOUBLE, MPI_MAX, 0, MPI_COMM_WORLD);
if (0 == world_myrank) {
io_bw = (double)tot_size / max_time / (1024 * 1024);
fprintf (stdout, BLUE "[TIMING]" RESET " Write I/O bandwidth: %.2f MBps (%.2f MB in %.2f ms)\n",
io_bw, (double)tot_size/(1024*1024), max_time * 1000);
}
MPI_Barrier (MPI_COMM_WORLD);
tp.Finalize ();
/*****************/
/* READ */
/*****************/
float *xx_r, *yy_r, *zz_r, *vx_r, *vy_r, *vz_r, *phi_r;
int64_t* pid_r;
uint16_t* mask_r;
xx_r = new float[num_particles];
yy_r = new float[num_particles];
zz_r = new float[num_particles];
vx_r = new float[num_particles];
vy_r = new float[num_particles];
vz_r = new float[num_particles];
phi_r = new float[num_particles];
pid_r = new int64_t[num_particles];
mask_r = new uint16_t[num_particles];
/*****************/
/* INIT TAPIOCA */
/*****************/
tp.Init (chunkCount, chunkSize, chunkOffset, 9, hdr, sub_comm);
tp.setAggregationTier (NVR, "/scratch/tmp");
tp.setTargetTier (HDD, file_size, output);
/*****************/
start_time = MPI_Wtime();
if (0 == sub_myrank)
fprintf (stdout, GREEN "[INFO]" RESET " [%08d] Read output file\n", mycolor);
offset = scan_size * sizeof(float);
tp.Read (offset, xx_r, num_particles, MPI_FLOAT, &status);
offset += (sub_particles - scan_size) * sizeof(float) + scan_size * sizeof(float);
tp.Read (offset, yy_r, num_particles, MPI_FLOAT, &status);
offset += (sub_particles - scan_size) * sizeof(float) + scan_size * sizeof(float);
tp.Read (offset, zz_r, num_particles, MPI_FLOAT, &status);
offset += (sub_particles - scan_size) * sizeof(float) + scan_size * sizeof(float);
tp.Read (offset, vx_r, num_particles, MPI_FLOAT, &status);
offset += (sub_particles - scan_size) * sizeof(float) + scan_size * sizeof(float);
tp.Read (offset, vy_r, num_particles, MPI_FLOAT, &status);
offset += (sub_particles - scan_size) * sizeof(float) + scan_size * sizeof(float);
tp.Read (offset, vz_r, num_particles, MPI_FLOAT, &status);
offset += (sub_particles - scan_size) * sizeof(float) + scan_size * sizeof(float);
tp.Read (offset, phi_r, num_particles, MPI_FLOAT, &status);
offset += (sub_particles - scan_size) * sizeof(float) + scan_size * sizeof(int64_t);
tp.Read (offset, pid_r, num_particles, MPI_LONG_LONG, &status);
offset += (sub_particles - scan_size) * sizeof(int64_t) + scan_size * sizeof(uint16_t);
tp.Read (offset, mask_r, num_particles, MPI_UNSIGNED_SHORT, &status);
end_time = MPI_Wtime();
tot_time = end_time - start_time;
MPI_Reduce (&tot_time, &max_time, 1, MPI_DOUBLE, MPI_MAX, 0, MPI_COMM_WORLD);
if (0 == world_myrank) {
io_bw = (double)tot_size / max_time / (1024 * 1024);
fprintf (stdout, BLUE "[TIMING]" RESET " Read I/O bandwidth: %.2f MBps (%.2f MB in %.2f ms)\n",
io_bw, (double)tot_size/(1024*1024), max_time * 1000);
}
tp.Finalize ();
/*****************/
/* VERIFICATION */
/*****************/
for (uint64_t i = 0; i< num_particles; i++) {
if ((xx[i] != xx_r[i]) || (yy[i] != yy_r[i]) || (zz[i] != zz_r[i])
|| (vx[i] != vx_r[i]) || (vy[i] != vy_r[i]) || (vz[i] != vz_r[i])
|| (phi[i] != phi_r[i])|| (pid[i] != pid_r[i]) || (mask[i] != mask_r[i]))
{
fprintf (stdout, RED "[ERROR]" RESET " Wrong value for particle %d\n", i);
MPI_Abort (MPI_COMM_WORLD, -1);
}
}
if (0 == sub_myrank)
fprintf (stdout, GREEN "[INFO]" RESET " [%08d] Content verified and consistent\n", mycolor);
/*****************/
/* FREE */
/*****************/
delete [] xx;
delete [] xx_r;
delete [] yy;
delete [] yy_r;
delete [] zz;
delete [] zz_r;
delete [] vx;
delete [] vx_r;
delete [] vy;
delete [] vy_r;
delete [] vz;
delete [] vz_r;
delete [] phi;
delete [] phi_r;
delete [] pid;
delete [] pid_r;
delete [] mask;
delete [] mask_r;
MPI_Finalize ();
}
......@@ -28,13 +28,14 @@ function outputFile ()
printenv | egrep "TAPIOCA_"
rm $TARGET/*
mpirun -f $COBALT_NODEFILE -n $NPROCS ./miniHACC-AoS 15000
#rm $TARGET/*
#mpirun -f $COBALT_NODEFILE -n $NPROCS ./miniHACC-AoS 15000
# ls -l $TARGET/
sleep 5
# sleep 5
rm $TARGET/*
mpirun -f $COBALT_NODEFILE -n $NPROCS ./miniHACC-SoA 15000
# mpirun -f $COBALT_NODEFILE -n $NPROCS ./miniHACC-AoS-R 15000
mpirun -f $COBALT_NODEFILE -n $NPROCS ./miniHACC-SoA-MPIIO 15000
sleep 30
mpirun -f $COBALT_NODEFILE -n $NPROCS ./miniHACC-SoA-R 15000
# sleep 5
echo
echo "---------------------------------------------"
......
Markdown is supported
0% or
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment