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Read write per timestep timing #141

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26 changes: 19 additions & 7 deletions commons/h5bench_util.c
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Original file line number Diff line number Diff line change
Expand Up @@ -175,7 +175,7 @@ ts_delayed_close(mem_monitor *mon, unsigned long *metadata_time_total, int dset_
if (!mon || !metadata_time_total)
return -1;

time_step * ts_run;
time_step *ts_run;
size_t num_in_progress;
H5ES_status_t op_failed;
unsigned long t1, t2;
Expand Down Expand Up @@ -212,7 +212,7 @@ mem_monitor_check_run(mem_monitor *mon, unsigned long *metadata_time_total, unsi
return -1;
if (!has_vol_async)
return 0;
time_step * ts_run;
time_step *ts_run;
size_t num_in_progress;
hbool_t op_failed;
unsigned long t1, t2, t3, t4;
Expand Down Expand Up @@ -248,14 +248,23 @@ mem_monitor_check_run(mem_monitor *mon, unsigned long *metadata_time_total, unsi
return 0;
}

/**
* data_wait_time_per_step, metadata_wait_time_per_step can
* safely but set to NULL if info is not needed.
*/
int
mem_monitor_final_run(mem_monitor *mon, unsigned long *metadata_time_total, unsigned long *data_time_total)
mem_monitor_final_run(mem_monitor *mon, unsigned long *metadata_time_total, unsigned long *data_time_total,
unsigned long *data_wait_time_per_step, unsigned long *metadata_wait_time_per_step)
{
if (metadata_wait_time_per_step != NULL)
memset(metadata_wait_time_per_step, 0, mon->time_step_cnt * sizeof(unsigned long));
if (data_wait_time_per_step)
memset(data_wait_time_per_step, 0, mon->time_step_cnt * sizeof(unsigned long));
*metadata_time_total = 0;
*data_time_total = 0;
size_t num_in_progress;
hbool_t op_failed;
time_step * ts_run;
time_step *ts_run;
unsigned long t1, t2, t3, t4, t5, t6;
unsigned long meta_time = 0, data_time = 0;
int dset_cnt = 8;
Expand Down Expand Up @@ -292,7 +301,6 @@ mem_monitor_final_run(mem_monitor *mon, unsigned long *metadata_time_total, unsi
ts_run->status = TS_READY;
}
}

t2 = get_time_usec();
meta_time += (t2 - t1);

Expand All @@ -317,6 +325,10 @@ mem_monitor_final_run(mem_monitor *mon, unsigned long *metadata_time_total, unsi

t6 = get_time_usec();

if (metadata_wait_time_per_step != NULL)
metadata_wait_time_per_step[i] = ((t2 - t1) + (t4 - t3));
if (data_wait_time_per_step != NULL)
data_wait_time_per_step[i] = (t3 - t2);
meta_time += ((t2 - t1) + (t4 - t3));
data_time += (t3 - t2);
ts_run->status = TS_DONE;
Expand Down Expand Up @@ -439,7 +451,7 @@ parse_time(char *str_in, duration *time)
if (!time)
time = calloc(1, sizeof(duration));
unsigned long long num = 0;
char * unit_str;
char *unit_str;
parse_unit(str_in, &num, &unit_str);

if (!unit_str)
Expand Down Expand Up @@ -470,7 +482,7 @@ str_to_ull(char *str_in, unsigned long long *num_out)
return -1;
}
unsigned long long num = 0;
char * unit_str;
char *unit_str;
int ret = parse_unit(str_in, &num, &unit_str);
if (ret < 0)
return -1;
Expand Down
23 changes: 12 additions & 11 deletions commons/h5bench_util.h
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Original file line number Diff line number Diff line change
Expand Up @@ -102,8 +102,8 @@ typedef struct bench_params {
} access_pattern;

// write_pattern bench_pattern;
char * data_file_path;
char * pattern_name;
char *data_file_path;
char *pattern_name;
int meta_coll; // for write only, metadata collective
int data_coll; // data collective
int cnt_time_step;
Expand All @@ -123,9 +123,9 @@ typedef struct bench_params {
unsigned long chunk_dim_1;
unsigned long chunk_dim_2;
unsigned long chunk_dim_3;
char * csv_path;
char * env_meta_path;
FILE * csv_fs;
char *csv_path;
char *env_meta_path;
FILE *csv_fs;
int file_per_proc;
int align;
unsigned long align_threshold;
Expand All @@ -136,10 +136,10 @@ typedef struct bench_params {
typedef struct data_md {
unsigned long long particle_cnt;
unsigned long long dim_1, dim_2, dim_3;
float * x, *y, *z;
float * px, *py, *pz;
int * id_1;
float * id_2;
float *x, *y, *z;
float *px, *py, *pz;
int *id_1;
float *id_2;
} data_contig_md;

typedef struct csv_hanle {
Expand All @@ -166,7 +166,7 @@ typedef struct mem_monitor {
unsigned long long mem_used;
unsigned long long mem_threshold;
async_mode mode;
time_step * time_steps;
time_step *time_steps;
} mem_monitor;

unsigned long long read_time_val(duration time, time_unit unit);
Expand All @@ -183,7 +183,8 @@ int ts_delayed_close(mem_monitor *mon, unsigned long *metadata_time_tot
int mem_monitor_check_run(mem_monitor *mon, unsigned long *metadata_time_total,
unsigned long *data_time_total);
int mem_monitor_final_run(mem_monitor *mon, unsigned long *metadata_time_total,
unsigned long *data_time_total);
unsigned long *data_time_total, unsigned long *data_wait_time_per_step,
unsigned long *metadata_wait_time_per_step);
// Uniform random number
float uniform_random_number();

Expand Down
8 changes: 4 additions & 4 deletions h5bench_patterns/h5bench_append.c
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Original file line number Diff line number Diff line change
Expand Up @@ -33,7 +33,7 @@ hid_t PARTICLE_COMPOUND_TYPE_SEPARATES[8];

herr_t ierr;
data_contig_md *BUF_STRUCT;
mem_monitor * MEM_MONITOR;
mem_monitor *MEM_MONITOR;

void
print_data(int n)
Expand Down Expand Up @@ -71,7 +71,7 @@ append_h5_data(bench_params params, time_step *ts, hid_t loc, hid_t *dset_ids, h

dapl = H5Pcreate(H5P_DATASET_ACCESS);

int * data_1D_INT, **data_2D_INT, ***data_3D_INT;
int *data_1D_INT, **data_2D_INT, ***data_3D_INT;
float *data_1D_FLOAT, **data_2D_FLOAT, ***data_3D_FLOAT;

if (params.num_dims == 1) {
Expand Down Expand Up @@ -473,7 +473,7 @@ _run_benchmark_modify(hid_t file_id, hid_t fapl, hid_t gapl, hid_t filespace, be
*inner_metadata_time += (meta_time1 + meta_time2 + meta_time3 + meta_time4 + meta_time5);
}

mem_monitor_final_run(MEM_MONITOR, &metadata_time_imp, &read_time_imp);
mem_monitor_final_run(MEM_MONITOR, &metadata_time_imp, &read_time_imp, NULL, NULL);
*raw_read_time_out += read_time_imp;
*inner_metadata_time += metadata_time_imp;
*total_data_size_out = nts * actual_read_cnt * (6 * sizeof(float) + 2 * sizeof(int));
Expand Down Expand Up @@ -657,7 +657,7 @@ main(int argc, char *argv[])

if (MY_RANK == 0) {
human_readable value;
char * mode_str = NULL;
char *mode_str = NULL;

if (has_vol_async) {
mode_str = "ASYNC";
Expand Down
8 changes: 4 additions & 4 deletions h5bench_patterns/h5bench_overwrite.c
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Original file line number Diff line number Diff line change
Expand Up @@ -32,7 +32,7 @@ hid_t PARTICLE_COMPOUND_TYPE_SEPARATES[8];

herr_t ierr;
data_contig_md *BUF_STRUCT;
mem_monitor * MEM_MONITOR;
mem_monitor *MEM_MONITOR;

void
print_data(int n)
Expand Down Expand Up @@ -67,7 +67,7 @@ overwrite_h5_data(bench_params params, time_step *ts, hid_t loc, hid_t *dset_ids

dapl = H5Pcreate(H5P_DATASET_ACCESS);

int * data_1D_INT, **data_2D_INT, ***data_3D_INT;
int *data_1D_INT, **data_2D_INT, ***data_3D_INT;
float *data_1D_FLOAT, **data_2D_FLOAT, ***data_3D_FLOAT;

if (params.num_dims == 1) {
Expand Down Expand Up @@ -449,7 +449,7 @@ _run_benchmark_modify(hid_t file_id, hid_t fapl, hid_t gapl, hid_t filespace, be
*inner_metadata_time += (meta_time1 + meta_time2 + meta_time3 + meta_time4 + meta_time5);
}

mem_monitor_final_run(MEM_MONITOR, &metadata_time_imp, &read_time_imp);
mem_monitor_final_run(MEM_MONITOR, &metadata_time_imp, &read_time_imp, NULL, NULL);
*raw_read_time_out += read_time_imp;
*inner_metadata_time += metadata_time_imp;
*total_data_size_out = nts * actual_read_cnt * (6 * sizeof(float) + 2 * sizeof(int));
Expand Down Expand Up @@ -633,7 +633,7 @@ main(int argc, char *argv[])

if (MY_RANK == 0) {
human_readable value;
char * mode_str = NULL;
char *mode_str = NULL;

if (has_vol_async) {
mode_str = "ASYNC";
Expand Down
77 changes: 61 additions & 16 deletions h5bench_patterns/h5bench_read.c
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Original file line number Diff line number Diff line change
Expand Up @@ -63,7 +63,7 @@ int subfiling = 0;

herr_t ierr;
data_contig_md *BUF_STRUCT;
mem_monitor * MEM_MONITOR;
mem_monitor *MEM_MONITOR;

void
print_data(int n)
Expand Down Expand Up @@ -278,10 +278,14 @@ set_dataspace(bench_params params, unsigned long long try_read_elem_cnt, hid_t *
int
_run_benchmark_read(hid_t file_id, hid_t fapl, hid_t gapl, hid_t filespace, bench_params params,
unsigned long *total_data_size_out, unsigned long *raw_read_time_out,
unsigned long *inner_metadata_time)
unsigned long *inner_metadata_time, unsigned long *data_time_per_step,
unsigned long *metadata_time_per_step, unsigned long *data_wait_time_per_step,
unsigned long *metadata_wait_time_per_step)
{
*raw_read_time_out = 0;
*inner_metadata_time = 0;
*raw_read_time_out = 0;
*inner_metadata_time = 0;
memset(metadata_time_per_step, 0, params.cnt_time_step * sizeof(unsigned long));
memset(data_time_per_step, 0, params.cnt_time_step * sizeof(unsigned long));
int nts = params.cnt_time_step;
unsigned long long read_elem_cnt = params.try_num_particles;
hid_t grp;
Expand Down Expand Up @@ -370,11 +374,14 @@ _run_benchmark_read(hid_t file_id, hid_t fapl, hid_t gapl, hid_t filespace, benc
}
}

*raw_read_time_out += (read_time_exp + read_time_imp);
*inner_metadata_time += (meta_time1 + meta_time2 + meta_time3 + meta_time4 + meta_time5);
metadata_time_per_step[ts_index] = (meta_time1 + meta_time2 + meta_time3 + meta_time4 + meta_time5);
data_time_per_step[ts_index] = (read_time_exp + read_time_imp);
*raw_read_time_out += data_time_per_step[ts_index];
*inner_metadata_time += metadata_time_per_step[ts_index];
}

mem_monitor_final_run(MEM_MONITOR, &metadata_time_imp, &read_time_imp);
mem_monitor_final_run(MEM_MONITOR, &metadata_time_imp, &read_time_imp, data_wait_time_per_step,
metadata_wait_time_per_step);
*raw_read_time_out += read_time_imp;
*inner_metadata_time += metadata_time_imp;
*total_data_size_out = nts * actual_read_cnt * (6 * sizeof(float) + 2 * sizeof(int));
Expand Down Expand Up @@ -416,13 +423,12 @@ main(int argc, char *argv[])
assert(MPI_THREAD_MULTIPLE == mpi_thread_lvl_provided);
MPI_Comm_rank(MPI_COMM_WORLD, &MY_RANK);
MPI_Comm_size(MPI_COMM_WORLD, &NUM_RANKS);

int sleep_time = 0;

bench_params params;

char *cfg_file_path = argv[1];
char *file_name = argv[2]; // data file to read
int sleep_time = 0;
bench_params params;
char *cfg_file_path = argv[1];
char *file_name = argv[2]; // data file to read
unsigned long *data_time_per_step = NULL, *metadata_time_per_step = NULL;
unsigned long *data_wait_time_per_step = NULL, *metadata_wait_time_per_step = NULL;

if (MY_RANK == 0) {
printf("Configuration file: %s\n", argv[1]);
Expand Down Expand Up @@ -516,6 +522,11 @@ main(int argc, char *argv[])
printf("Number of particles available per rank: %llu \n", NUM_PARTICLES);
}

data_time_per_step = malloc(NUM_TIMESTEPS * sizeof(unsigned long));
metadata_time_per_step = malloc(NUM_TIMESTEPS * sizeof(unsigned long));
data_wait_time_per_step = malloc(NUM_TIMESTEPS * sizeof(unsigned long));
metadata_wait_time_per_step = malloc(NUM_TIMESTEPS * sizeof(unsigned long));

MPI_Barrier(MPI_COMM_WORLD);

MPI_Allreduce(&NUM_PARTICLES, &TOTAL_PARTICLES, 1, MPI_LONG_LONG, MPI_SUM, MPI_COMM_WORLD);
Expand All @@ -537,7 +548,8 @@ main(int argc, char *argv[])
unsigned long raw_read_time, metadata_time, local_data_size;

int ret = _run_benchmark_read(file_id, fapl, gapl, filespace, params, &local_data_size, &raw_read_time,
&metadata_time);
&metadata_time, data_time_per_step, metadata_time_per_step,
data_wait_time_per_step, metadata_wait_time_per_step);

if (ret < 0) {
if (MY_RANK == 0)
Expand All @@ -558,7 +570,7 @@ main(int argc, char *argv[])

if (MY_RANK == 0) {
human_readable value;
char * mode_str = NULL;
char *mode_str = NULL;

if (has_vol_async) {
mode_str = "ASYNC";
Expand Down Expand Up @@ -617,6 +629,29 @@ main(int argc, char *argv[])
value = format_human_readable(or_bs);
fprintf(params.csv_fs, "observed rate, %.3f, %cB/s\n", value.value, value.unit);
fprintf(params.csv_fs, "observed time, %.3f, %s\n", oct_s, "seconds");
// Per timestep data time
for (int i = 0; i < NUM_TIMESTEPS; i++) {
float t = (float)data_time_per_step[i] / (1000.0 * 1000.0);
fprintf(params.csv_fs, "timestep %d data time, %.3f, %s\n", i, t, "seconds");
}
// Per timestep inner metadata time
for (int i = 0; i < NUM_TIMESTEPS; i++) {
float t = (float)metadata_time_per_step[i] / (1000.0 * 1000.0);
fprintf(params.csv_fs, "timestep %d metadata time, %.3f, %s\n", i, t, "seconds");
}
// Print wait time if async is enabled
if (has_vol_async) {
// Per timestep data wait time
for (int i = 0; i < NUM_TIMESTEPS; i++) {
float t = (float)data_wait_time_per_step[i] / (1000.0 * 1000.0);
fprintf(params.csv_fs, "timestep %d data wait time, %.3f, %s\n", i, t, "seconds");
}
// Per timestep metadata wait time
for (int i = 0; i < NUM_TIMESTEPS; i++) {
float t = (float)metadata_wait_time_per_step[i] / (1000.0 * 1000.0);
fprintf(params.csv_fs, "timestep %d metadata wait time, %.3f, %s\n", i, t, "seconds");
}
}
fclose(params.csv_fs);
}
}
Expand All @@ -631,6 +666,16 @@ main(int argc, char *argv[])

done:
H5close();

if (data_time_per_step)
free(data_time_per_step);
if (metadata_time_per_step)
free(metadata_time_per_step);
if (data_wait_time_per_step)
free(data_wait_time_per_step);
if (metadata_wait_time_per_step)
free(metadata_wait_time_per_step);

MPI_Finalize();
return 0;
}
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