Merge branch 'master' into jeanbez-patch-8

hpc-io · Dec 11, 2023 · 75c96af · 75c96af
2 parents 6c7bcf8 + 7b2a7d8
commit 75c96af
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diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
@@ -133,7 +133,7 @@ metrics-perlmutter:
         - export RESULTS="/global/homes/j/jeanbez/h5bench-ci-metrics/perlmutter/$(date +%s)"
         - mkdir -p $RESULTS
         - echo "Fetching Darshan log file"
-        - cp /pscratch/darshanlogs/$(date +%Y)/$(date +%-m)/$(date +%d | sed 's/^0*//')/jeanbez_h5bench* ${RESULTS}
+        - cp /pscratch/darshanlogs/$(date +%Y)/$(date +%-m)/$(date +%d | sed 's/^0*//')/jeanbez_h5bench* ${RESULTS} 2> /dev/null || true
         - echo "Fetching runtime files"
         - cp h5bench-suite-sync.err ${RESULTS}
         - cp h5bench-suite-sync.out ${RESULTS}

diff --git a/CITATION.cff b/CITATION.cff
@@ -0,0 +1,61 @@
+# This CITATION.cff file was generated with cffinit.
+# Visit https://bit.ly/cffinit to generate yours today!
+
+cff-version: 1.2.0
+title: h5bench
+message: >-
+  If you use this software, please cite it using the
+  metadata from this file.
+type: software
+authors:
+  - given-names: Suren
+    family-names: Byna
+    email: [email protected]
+    affiliation: Lawrence Berkeley National Laboratory
+    orcid: 'https://orcid.org/0000-0003-3048-3448'
+  - given-names: Jean Luca
+    family-names: Bez
+    email: [email protected]
+    affiliation: Lawrence Berkeley National Laboratory
+    orcid: 'https://orcid.org/0000-0002-3915-1135'
+  - given-names: Tonglin
+    family-names: Li
+    affiliation: Lawrence Berkeley National Laboratory
+  - given-names: Quincey
+    family-names: Koziol
+    affiliation: National Energy Research Scientific Computing Center
+  - given-names: Houjun
+    family-names: Tang
+    email: [email protected]
+    affiliation: Lawrence Berkeley National Laboratory
+    orcid: 'https://orcid.org/0000-0001-7038-8360'
+  - given-names: Qiao
+    family-names: Kang
+    affiliation: Lawrence Berkeley National Laboratory
+identifiers:
+  - type: url
+    value: >-
+      https://sdm.lbl.gov/~sbyna/research/papers/2021/202106-CUG_2021_h5bench.pdf
+    description: CUG Paper
+  - type: url
+    value: 'https://github.com/hpc-io/h5bench'
+    description: Github Repository
+  - type: url
+    value: 'https://h5bench.readthedocs.io'
+    description: h5bench Documentation
+repository-code: 'https://github.com/hpc-io/h5bench'
+abstract: >-
+  h5bench is a suite of parallel I/O benchmarks or kernels
+  representing I/O patterns that are commonly used in HDF5
+  applications on high performance computing systems.
+  h5bench measures I/O performance from various aspects,
+  including the I/O overhead, observed I/O rate, etc. 
+keywords:
+  - HDF5
+  - I/O
+  - HPC
+  - I/O benchmark
+  - I/O kernel
+commit: ' 67a3e6d91508e5ab77db79c6187b2eb3c96119e0'
+version: v.1.4
+date-released: '2023-05-31'
diff --git a/commons/h5bench_util.c b/commons/h5bench_util.c
@@ -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) {
@@ -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;
     }
@@ -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)
@@ -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;
@@ -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");

diff --git a/commons/h5bench_util.h b/commons/h5bench_util.h
@@ -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 {
@@ -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;
@@ -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;

diff --git a/docs/requirements.txt b/docs/requirements.txt
@@ -1,2 +1,4 @@
+sphinx==6.2.1
+sphinx-rtd-theme==1.2.2
 sphinxemoji
 urllib3==1.26.15
diff --git a/h5bench_patterns/README.md b/h5bench_patterns/README.md
@@ -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`