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Commit abb09095 authored by Francois Tessier's avatar Francois Tessier
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Update HACC-IO to use the new TAPIOCA API

parent b58ff105
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Showing with 43 additions and 48 deletions
examples/HACC-IO/Makefile
View file @ abb09095
include ../make.inc/Makefile.$(ARCHI)
all: miniHACC-AoS miniHACC-SoA miniHACC-AoS-MPIIO miniHACC-SoA-MPIIO
all: miniHACC-AoS #miniHACC-SoA miniHACC-AoS-MPIIO miniHACC-SoA-MPIIO
miniHACC-AoS:miniHACC-AoS.cpp
$(MPICXX) $(MPI_CFLAGS) $? -o $@ $(MPI_LDFLAGS)
......
examples/HACC-IO/miniHACC-AoS.cpp
View file @ abb09095
......@@ -20,7 +20,6 @@ int main (int argc, char * argv[])
double start_time, end_time, tot_time, max_time;
double io_bw;
MPI_Comm sub_comm;
MPI_File file_handle;
MPI_Status status;
char output[100];
Tapioca tp;
......@@ -91,12 +90,12 @@ int main (int argc, char * argv[])
file_size = particle_size * sub_particles;
tot_size = particle_size * tot_particles;
if (sub_myrank == 0) {
MPI_File_open(MPI_COMM_SELF, output,
MPI_MODE_WRONLY | MPI_MODE_CREATE, MPI_INFO_NULL, &file_handle);
MPI_File_set_size(file_handle, file_size);
MPI_File_close (&file_handle);
}
// if (sub_myrank == 0) {
// MPI_File_open(MPI_COMM_SELF, output,
// MPI_MODE_WRONLY | MPI_MODE_CREATE, MPI_INFO_NULL, &file_handle);
// MPI_File_set_size(file_handle, file_size);
// MPI_File_close (&file_handle);
// }
MPI_Exscan (&num_particles, &scan_size, 1, MPI_LONG_LONG, MPI_SUM, sub_comm);
......@@ -130,44 +129,43 @@ int main (int argc, char * argv[])
chunkOffset[i] = chunkOffset[i - 1] + chunkCount[i - 1] * chunkSize[i - 1];
}
tp.WriteInitialize (output, chunkCount, chunkSize, chunkOffset, 9, hdr, ARRAY_OF_STRUCTURES, sub_comm);
tp.Init (chunkCount, chunkSize, chunkOffset, 9, hdr, sub_comm);
tp.setAggregationTier (DDR, "");
tp.setTargetTier (HDD, file_size, output);
/*****************/
start_time = MPI_Wtime();
MPI_File_open(sub_comm, output,
MPI_MODE_WRONLY, MPI_INFO_NULL, &file_handle);
offset = scan_size * particle_size;
tp.Write (file_handle, offset, xx, num_particles, MPI_FLOAT, &status);
tp.Write (offset, xx, num_particles, MPI_FLOAT, &status);
offset += num_particles * sizeof(float);
tp.Write (file_handle, offset, yy, num_particles, MPI_FLOAT, &status);
tp.Write (offset, yy, num_particles, MPI_FLOAT, &status);
offset += num_particles * sizeof(float);
tp.Write (file_handle, offset, zz, num_particles, MPI_FLOAT, &status);
tp.Write (offset, zz, num_particles, MPI_FLOAT, &status);
offset += num_particles * sizeof(float);
tp.Write (file_handle, offset, vx, num_particles, MPI_FLOAT, &status);
tp.Write (offset, vx, num_particles, MPI_FLOAT, &status);
offset += num_particles * sizeof(float);
tp.Write (file_handle, offset, vy, num_particles, MPI_FLOAT, &status);
tp.Write (offset, vy, num_particles, MPI_FLOAT, &status);
offset += num_particles * sizeof(float);
tp.Write (file_handle, offset, vz, num_particles, MPI_FLOAT, &status);
tp.Write (offset, vz, num_particles, MPI_FLOAT, &status);
offset += num_particles * sizeof(float);
tp.Write (file_handle, offset, phi, num_particles, MPI_FLOAT, &status);
tp.Write (offset, phi, num_particles, MPI_FLOAT, &status);
offset += num_particles * sizeof(float);
tp.Write (file_handle, offset, pid, num_particles, MPI_LONG_LONG, &status);
tp.Write (offset, pid, num_particles, MPI_LONG_LONG, &status);
offset += num_particles * sizeof(int64_t);
tp.Write (file_handle, offset, mask, num_particles, MPI_UNSIGNED_SHORT, &status);
MPI_File_close (&file_handle);
tp.Write (offset, mask, num_particles, MPI_UNSIGNED_SHORT, &status);
tp.Finalize ();
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);
......@@ -180,8 +178,6 @@ int main (int argc, char * argv[])
MPI_Barrier (MPI_COMM_WORLD);
tp.Finalize ();
/*****************/
/* READ */
/*****************/
......@@ -202,47 +198,46 @@ int main (int argc, char * argv[])
/*****************/
/* INIT TAPIOCA */
/*****************/
tp.ReadInitialize (output, chunkCount, chunkSize, chunkOffset, 9, hdr, ARRAY_OF_STRUCTURES, sub_comm);
tp.Init (chunkCount, chunkSize, chunkOffset, 9, hdr, sub_comm);
tp.setAggregationTier (DDR, "");
tp.setTargetTier (HDD, file_size, output);
/*****************/
start_time = MPI_Wtime();
MPI_File_open(sub_comm, output,
MPI_MODE_RDONLY, MPI_INFO_NULL, &file_handle);
if (0 == sub_myrank)
if (0 == sub_myrank)
fprintf (stdout, GREEN "[INFO]" RESET " [%08d] Read output file\n", mycolor);
offset = scan_size * particle_size;
tp.Read (file_handle, offset, xx_r, num_particles, MPI_FLOAT, &status);
tp.Read (offset, xx_r, num_particles, MPI_FLOAT, &status);
offset += num_particles * sizeof(float);
tp.Read (file_handle, offset, yy_r, num_particles, MPI_FLOAT, &status);
tp.Read (offset, yy_r, num_particles, MPI_FLOAT, &status);
offset += num_particles * sizeof(float);
tp.Read (file_handle, offset, zz_r, num_particles, MPI_FLOAT, &status);
tp.Read (offset, zz_r, num_particles, MPI_FLOAT, &status);
offset += num_particles * sizeof(float);
tp.Read (file_handle, offset, vx_r, num_particles, MPI_FLOAT, &status);
tp.Read (offset, vx_r, num_particles, MPI_FLOAT, &status);
offset += num_particles * sizeof(float);
tp.Read (file_handle, offset, vy_r, num_particles, MPI_FLOAT, &status);
tp.Read (offset, vy_r, num_particles, MPI_FLOAT, &status);
offset += num_particles * sizeof(float);
tp.Read (file_handle, offset, vz_r, num_particles, MPI_FLOAT, &status);
tp.Read (offset, vz_r, num_particles, MPI_FLOAT, &status);
offset += num_particles * sizeof(float);
tp.Read (file_handle, offset, phi_r, num_particles, MPI_FLOAT, &status);
tp.Read (offset, phi_r, num_particles, MPI_FLOAT, &status);
offset += num_particles * sizeof(float);
tp.Read (file_handle, offset, pid_r, num_particles, MPI_LONG_LONG, &status);
tp.Read (offset, pid_r, num_particles, MPI_LONG_LONG, &status);
offset += num_particles * sizeof(int64_t);
tp.Read (file_handle, offset, mask_r, num_particles, MPI_UNSIGNED_SHORT, &status);
MPI_File_close (&file_handle);
tp.Read (offset, mask_r, num_particles, MPI_UNSIGNED_SHORT, &status);
tp.Finalize ();
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);
......
examples/HACC-IO/miniHACC-SoA.cpp
View file @ abb09095
......@@ -131,7 +131,7 @@ int main (int argc, char * argv[])
chunkOffset[i] += scan_size * chunkSize[i];
}
tp.WriteInitialize (output, chunkCount, chunkSize, chunkOffset, 9, hdr, STRUCTURE_OF_ARRAYS, sub_comm);
tp.Initialize (chunkCount, chunkSize, chunkOffset, 9, hdr, STRUCTURE_OF_ARRAYS, sub_comm);
/*****************/
start_time = MPI_Wtime();
......@@ -203,7 +203,7 @@ int main (int argc, char * argv[])
/*****************/
/* INIT TAPIOCA */
/*****************/
tp.ReadInitialize (output, chunkCount, chunkSize, chunkOffset, 9, hdr, ARRAY_OF_STRUCTURES, sub_comm);
tp.Initialize (chunkCount, chunkSize, chunkOffset, 9, hdr, ARRAY_OF_STRUCTURES, sub_comm);
/*****************/
start_time = MPI_Wtime();
......
examples/HACC-IO/run_debug_xc40.sh
View file @ abb09095
#!/bin/bash
NODES=8
NODES=64
PPN=16
NPROCS=$((NODES*PPN))
TARGET="/lus/theta-fs0/projects/Performance/ftessier/HACC"
DDT="/soft/debuggers/forge/bin/ddt --connect"
STRIPE_COUNT=2
STRIPE_COUNT=8
STRIPE_SIZE=8388608
AGGR_MULT=1
......@@ -14,7 +14,7 @@ cd $HOME/install/$ARCHI/bin/
export TAPIOCA_DEVNULL=false
export TAPIOCA_COMMSPLIT=true
export TAPIOCA_STRATEGY=TOPOLOGY_AWARE
export TAPIOCA_NBAGGR=2
export TAPIOCA_NBAGGR=8
export TAPIOCA_BUFFERSIZE=16777216
function setLustreFS ()
......@@ -50,5 +50,5 @@ PARTICLES=25000
BIN=miniHACC-AoS
updateSettings
setLustreFS >> $OUTPUT
$DDT aprun $SETTINGS -n $NPROCS -N $PPN ./$BIN $PARTICLES
setLustreFS
aprun $SETTINGS -n $NPROCS -N $PPN ./$BIN $PARTICLES
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