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Add CS, PRL, LDC and RDC access patterns with supporting config (#118)
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* Add CS, PRL, RDC, and LDC patterns and supporting config
* Remove extra whitespace
* Add Readme for the new patterns
* Bugfix: Checks on parameter values separated for different access patterns
* Add and modify code documentation
* Remove unused parameters to functions
* Committing clang-format changes
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@aniket-modi
aniket-modi authored Nov 9, 2023
1 parent 2da97cd commit 9f2b68d
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Showing 12 changed files with 603 additions and 22 deletions.
159 changes: 139 additions & 20 deletions commons/h5bench_util.c
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Original file line number Diff line number Diff line change
Expand Up @@ -587,23 +587,77 @@ _set_io_pattern(bench_params *params_in_out)
(params_in_out->io_op == IO_APPEND)) { // file --> mem
if (params_in_out->mem_pattern == PATTERN_CONTIG) {
if (params_in_out->file_pattern == PATTERN_CONTIG) {
switch (params_in_out->num_dims) {
case 1:
(*params_in_out).access_pattern.pattern_read = CONTIG_1D;
ret = 0;
break;
case 2:
(*params_in_out).access_pattern.pattern_read = CONTIG_2D;
ret = 0;
break;
case 3:
(*params_in_out).access_pattern.pattern_read = CONTIG_3D;
ret = 0;
break;
default:
ret = -1;
printf("%s() failed on line %d\n", __func__, __LINE__);
break;
if (params_in_out->read_option == LDC) {
switch (params_in_out->num_dims) {
case 2:
(*params_in_out).access_pattern.pattern_read = LDC_2D;
ret = 0;
break;
default:
ret = -1;
printf("%s(). Unexpected Dimensions for LDC. failed on line %d\n", __func__,
__LINE__);
break;
}
}
else if (params_in_out->read_option == RDC) {
switch (params_in_out->num_dims) {
case 2:
(*params_in_out).access_pattern.pattern_read = RDC_2D;
ret = 0;
break;
default:
ret = -1;
printf("%s(). Unexpected Dimensions for RDC. failed on line %d\n", __func__,
__LINE__);
break;
}
}
else if (params_in_out->read_option == PRL) {
switch (params_in_out->num_dims) {
case 2:
(*params_in_out).access_pattern.pattern_read = PRL_2D;
ret = 0;
break;
default:
ret = -1;
printf("%s(). Unexpected Dimensions for PRL. failed on line %d\n", __func__,
__LINE__);
break;
}
}
else if (params_in_out->read_option == CS) {
switch (params_in_out->num_dims) {
case 2:
(*params_in_out).access_pattern.pattern_read = CS_2D;
ret = 0;
break;
default:
ret = -1;
printf("%s(). Unexpected Dimensions for CS. failed on line %d\n", __func__,
__LINE__);
break;
}
}
else {
switch (params_in_out->num_dims) {
case 1:
(*params_in_out).access_pattern.pattern_read = CONTIG_1D;
ret = 0;
break;
case 2:
(*params_in_out).access_pattern.pattern_read = CONTIG_2D;
ret = 0;
break;
case 3:
(*params_in_out).access_pattern.pattern_read = CONTIG_3D;
ret = 0;
break;
default:
ret = -1;
printf("%s() failed on line %d\n", __func__, __LINE__);
break;
}
}
}
else if (params_in_out->file_pattern == PATTERN_STRIDED) {
Expand Down Expand Up @@ -772,15 +826,28 @@ _set_params(char *key, char *val_in, bench_params *params_in_out, int do_write)
}
}
else if (strcmp(key, "READ_OPTION") == 0) {
if (val_in[0] == 'F') { // FULL
if (strcmp(val_in, "FULL") == 0) { // FULL
(*params_in_out).read_option = READ_FULL;
}
else if (val_in[0] == 'P') { // PARTIAL
else if (strcmp(val_in, "PARTIAL") == 0) { // PARTIAL
(*params_in_out).read_option = READ_PARTIAL;
}
else if (val_in[0] == 'S') { // STRIDED
else if (strcmp(val_in, "STRIDED") == 0) { // STRIDED
(*params_in_out).read_option = READ_STRIDED;
}
else if (strcmp(val_in, "LDC") == 0) {
(*params_in_out).read_option = LDC;
}
else if (strcmp(val_in, "RDC") == 0) {
(*params_in_out).read_option = RDC;
}
else if (strcmp(val_in, "PRL") == 0) {
(*params_in_out).read_option = PRL;
}
else if (strcmp(val_in, "CS") == 0) {
(*params_in_out).read_option = CS;
}

else
(*params_in_out).read_option = READ_OPTION_INVALID;
}
Expand Down Expand Up @@ -873,12 +940,36 @@ _set_params(char *key, char *val_in, bench_params *params_in_out, int do_write)
return -1;
(*params_in_out).stride = num;
}
else if (strcmp(key, "STRIDE_SIZE_2") == 0) {
unsigned long long num = 0;
if (str_to_ull(val, &num) < 0)
return -1;
(*params_in_out).stride_2 = num;
}
else if (strcmp(key, "STRIDE_SIZE_3") == 0) {
unsigned long long num = 0;
if (str_to_ull(val, &num) < 0)
return -1;
(*params_in_out).stride_3 = num;
}
else if (strcmp(key, "BLOCK_SIZE") == 0) {
unsigned long long num = 0;
if (str_to_ull(val, &num) < 0)
return -1;
(*params_in_out).block_size = num;
}
else if (strcmp(key, "BLOCK_SIZE_2") == 0) {
unsigned long long num = 0;
if (str_to_ull(val, &num) < 0)
return -1;
(*params_in_out).block_size_2 = num;
}
else if (strcmp(key, "BLOCK_SIZE_3") == 0) {
unsigned long long num = 0;
if (str_to_ull(val, &num) < 0)
return -1;
(*params_in_out).block_size_3 = num;
}
else if (strcmp(key, "BLOCK_CNT") == 0) {
unsigned long long num = 0;
if (str_to_ull(val, &num) < 0)
Expand Down Expand Up @@ -985,7 +1076,11 @@ bench_params_init(bench_params *params_out)
(*params_out).num_dims = 1;

(*params_out).stride = 0;
(*params_out).stride_2 = 0;
(*params_out).stride_3 = 0;
(*params_out).block_size = 0;
(*params_out).block_size_2 = 0;
(*params_out).block_size_3 = 0;
(*params_out).block_cnt = 0;
(*params_out).dim_1 = 1;
(*params_out).dim_2 = 1;
Expand Down Expand Up @@ -1109,6 +1204,30 @@ read_config(const char *file_path, bench_params *params_out, int do_write)
return -1;
}
}
if (params_out->access_pattern.pattern_read == LDC_2D) {
if (params_out->block_size < 1 || params_out->block_size_2 < 1) {
printf("LDC read requires BLOCK_SIZE/BLOCK_SIZE_2 no less than 1.\n");
return -1;
}
}
if (params_out->access_pattern.pattern_read == RDC_2D) {
if (params_out->block_size < 1 || params_out->block_size_2 < 1) {
printf("RDC read requires BLOCK_SIZE/BLOCK_SIZE_2 no less than 1.\n");
return -1;
}
}
if (params_out->access_pattern.pattern_read == PRL_2D) {
if (params_out->block_size < 1 || params_out->block_size_2 < 1) {
printf("PRL read requires BLOCK_SIZE/BLOCK_SIZE_2 no less than 1.\n");
return -1;
}
}
if (params_out->access_pattern.pattern_read == CS_2D) {
if (params_out->stride < 1 || params_out->stride_2 < 1) {
printf("CS read requires STRIDE_SIZE/STRIDE_SIZE_2 no less than 1.\n");
return -1;
}
}
}
if (params_out->subfiling > 0 && params_out->data_coll == 1) {
printf("Subfiling does not support collective data buffering for data.\n");
Expand Down
19 changes: 18 additions & 1 deletion commons/h5bench_util.h
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Original file line number Diff line number Diff line change
Expand Up @@ -68,6 +68,10 @@ typedef enum read_pattern {
STRIDED_1D,
CONTIG_2D,
CONTIG_3D,
LDC_2D,
RDC_2D,
CS_2D,
PRL_2D,
} read_pattern;

typedef enum pattern {
Expand All @@ -85,7 +89,16 @@ typedef enum io_operation {
IO_APPEND,
} io_operation;

typedef enum read_option { READ_OPTION_INVALID, READ_FULL, READ_PARTIAL, READ_STRIDED } read_option;
typedef enum read_option {
READ_OPTION_INVALID,
READ_FULL,
READ_PARTIAL,
READ_STRIDED,
LDC,
RDC,
PRL,
CS
} read_option;

typedef struct bench_params {
io_operation io_op;
Expand Down Expand Up @@ -115,7 +128,11 @@ typedef struct bench_params {
duration compute_time;
int num_dims;
unsigned long stride;
unsigned long stride_2;
unsigned long stride_3;
unsigned long block_size;
unsigned long block_size_2;
unsigned long block_size_3;
unsigned long block_cnt;
unsigned long dim_1;
unsigned long dim_2;
Expand Down
37 changes: 37 additions & 0 deletions h5bench_patterns/README.md
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Original file line number Diff line number Diff line change
@@ -0,0 +1,37 @@
## Additions to H5Bench_read
4 new patterns are added to the h5bench read benchmark:
1. CS: Refers to the Cross Stencil data access pattern. A block of fixed sides is used to read data from HDF5. This block is given a fixed stride in each dimension and data till end of file is read.
2. LDC: Refers to the Left Diagonal Corner data access pattern. Data is read from two identical blocks of fixed sides, one in the top left corner and the other in the bottom right corner in the 2D HDF5 file
3. RDC: Refers to the Right Diagonal Corner data access pattern. Data is read from two identical blocks of fixed sides, one in the top right corner and the other in the bottom left corner in the 2D HDF5 file
4. PRL: Refers to the Peripheral data access pattern. Data is read from the periphery of the file, which is a frame of fixed width and height around the file.

These patterns work with a single MPI process. In case multiple processes are used, only the root performs the read operations and all other processes skip the reads. Illustrations of the patterns are given in the table below:

| Pattern -> | CS | LDC | RDC | PRL |
| ---------- | ---------- | ---------- | ---------- | ---------- |
|Illustration | ![CS Pattern](./images/CS.png) | ![LDC Pattern](./images/LDC.png) | ![RDC Pattern](./images/RDC.png) | ![PRL Pattern](./images/PRL.png) |



Steps for running these benchmarks are the same as the other benchmarks. All parameter and requirements and running instructions remain same, except for the following parameters which are additionally required to be provided in the configuration:
1. CS
| Parameter | Description |
| --------- | ----------- |
| `BLOCK_SIZE` | Size of the block of data along `dim_1` |
| `BLOCK_SIZE_2` | Size of the block of data along `dim_2` |
| `STRIDE_SIZE` | Size of the block of data along `dim_1` |
| `STRIDE_SIZE_2` | Size of the block of data along `dim_2` |

2. LDC/RDC
| Parameter | Description |
| --------- | ----------- |
| `BLOCK_SIZE` | Size of the block of data along `dim_1` |
| `BLOCK_SIZE_2` | Size of the block of data along `dim_2` |

3. PRL
| Parameter | Description |
| --------- | ----------- |
| `BLOCK_SIZE` | Size of the frame along `dim_1` |
| `BLOCK_SIZE_2` | Size of the frame along `dim_2` |

Exmaples of some configurations are provided in `h5bench/samples/sync-write-1d-contig-contig-read-<pattern>.json`
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