1 #define PETSC_DESIRE_FEATURE_TEST_MACROS /* for strdup() */ 2 #include <petsc/private/petscimpl.h> /*I "petscsys.h" I*/ 3 4 #if defined(PETSC_HAVE_YAML) 5 #include <yaml.h> /* use external LibYAML */ 6 #else 7 #include <../src/sys/yaml/include/yaml.h> 8 #endif 9 10 static MPI_Comm petsc_yaml_comm = MPI_COMM_NULL; /* only used for parallel error handling */ 11 12 PETSC_STATIC_INLINE MPI_Comm PetscYAMLGetComm(void) 13 { 14 return PetscLikely(petsc_yaml_comm != MPI_COMM_NULL) ? petsc_yaml_comm : (petsc_yaml_comm = PETSC_COMM_SELF); 15 } 16 17 PETSC_STATIC_INLINE MPI_Comm PetscYAMLSetComm(MPI_Comm comm) 18 { 19 MPI_Comm prev = PetscYAMLGetComm(); petsc_yaml_comm = comm; return prev; 20 } 21 22 #define TAG(node) ((const char *)((node)->tag)) 23 #define STR(node) ((const char *)((node)->data.scalar.value)) 24 #define SEQ(node) ((node)->data.sequence.items) 25 #define MAP(node) ((node)->data.mapping.pairs) 26 27 static PetscErrorCode PetscParseLayerYAML(PetscOptions options, yaml_document_t *doc, yaml_node_t *node) 28 { 29 MPI_Comm comm = PetscYAMLGetComm(); 30 char name[PETSC_MAX_OPTION_NAME] = "", prefix[PETSC_MAX_OPTION_NAME] = ""; 31 PetscErrorCode ierr; 32 33 PetscFunctionBegin; 34 if (node->type != YAML_MAPPING_NODE) SETERRQ(comm, PETSC_ERR_SUP, "Unsupported YAML node type: expected mapping"); 35 for (yaml_node_pair_t *pair = MAP(node).start; pair < MAP(node).top; pair++) { 36 yaml_node_t *keynode = yaml_document_get_node(doc, pair->key); 37 yaml_node_t *valnode = yaml_document_get_node(doc, pair->value); 38 PetscBool isMergeKey,isDummyKey,isIncludeTag; 39 40 if (!keynode) SETERRQ(comm, PETSC_ERR_LIB, "Corrupt YAML document"); 41 if (!valnode) SETERRQ(comm, PETSC_ERR_LIB, "Corrupt YAML document"); 42 if (keynode->type != YAML_SCALAR_NODE) SETERRQ(comm, PETSC_ERR_SUP, "Unsupported YAML node type: expected scalar"); 43 44 /* "<<" is the merge key: don't increment the prefix */ 45 ierr = PetscStrcmp(STR(keynode), "<<", &isMergeKey);CHKERRQ(ierr); 46 if (isMergeKey) { 47 if (valnode->type == YAML_SEQUENCE_NODE) { 48 for (yaml_node_item_t *item = SEQ(valnode).start; item < SEQ(valnode).top; item++) { 49 yaml_node_t *itemnode = yaml_document_get_node(doc, *item); 50 if (!itemnode) SETERRQ(comm, PETSC_ERR_LIB, "Corrupt YAML document"); 51 if (itemnode->type != YAML_MAPPING_NODE) SETERRQ(comm, PETSC_ERR_SUP, "Unsupported YAML node type: expected mapping"); 52 ierr = PetscParseLayerYAML(options, doc, itemnode);CHKERRQ(ierr); 53 } 54 } else if (valnode->type == YAML_MAPPING_NODE) { 55 ierr = PetscParseLayerYAML(options, doc, valnode);CHKERRQ(ierr); 56 } else SETERRQ(comm, PETSC_ERR_SUP, "Unsupported YAML node type: expected sequence or mapping"); 57 continue; /* to next pair */ 58 } 59 60 /* "$$*" are treated as dummy keys, we use them for !include tags and to define anchors */ 61 ierr = PetscStrbeginswith(STR(keynode), "$$", &isDummyKey);CHKERRQ(ierr); 62 if (isDummyKey) { 63 ierr = PetscStrendswith(TAG(valnode), "!include", &isIncludeTag);CHKERRQ(ierr);CHKERRQ(ierr); 64 if (isIncludeTag) { /* TODO: add proper support relative paths */ 65 ierr = PetscOptionsInsertFileYAML(comm, options, STR(valnode), PETSC_TRUE);CHKERRQ(ierr); 66 } 67 continue; /* to next pair */ 68 } 69 70 if (valnode->type == YAML_SCALAR_NODE) { 71 ierr = PetscSNPrintf(name, sizeof(name), "-%s", STR(keynode));CHKERRQ(ierr); 72 ierr = PetscOptionsSetValue(options, name, STR(valnode));CHKERRQ(ierr); 73 74 } else if (valnode->type == YAML_SEQUENCE_NODE) { 75 PetscSegBuffer seg; 76 char *buf, *strlist; 77 PetscBool addSep = PETSC_FALSE; 78 79 ierr = PetscSegBufferCreate(sizeof(char), PETSC_MAX_PATH_LEN, &seg);CHKERRQ(ierr); 80 for (yaml_node_item_t *item = SEQ(valnode).start; item < SEQ(valnode).top; item++) { 81 yaml_node_t *itemnode = yaml_document_get_node(doc, *item); 82 const char *itemstr = NULL; 83 size_t itemlen; 84 85 if (!itemnode) SETERRQ(comm, PETSC_ERR_LIB, "Corrupt YAML document"); 86 87 if (itemnode->type == YAML_SCALAR_NODE) { 88 itemstr = STR(itemnode); 89 90 } else if (itemnode->type == YAML_MAPPING_NODE) { 91 yaml_node_pair_t *kvn = itemnode->data.mapping.pairs.start; 92 yaml_node_pair_t *top = itemnode->data.mapping.pairs.top; 93 94 if (top - kvn > 1) SETERRQ(comm, PETSC_ERR_SUP, "Unsupported YAML node value: expected a single key:value pair"); 95 if (top - kvn > 0) { 96 yaml_node_t *kn = yaml_document_get_node(doc, kvn->key); 97 yaml_node_t *vn = yaml_document_get_node(doc, kvn->value); 98 99 if (!kn) SETERRQ(comm, PETSC_ERR_LIB, "Corrupt YAML document"); 100 if (!vn) SETERRQ(comm, PETSC_ERR_LIB, "Corrupt YAML document"); 101 if (kn->type != YAML_SCALAR_NODE) SETERRQ(comm, PETSC_ERR_SUP, "Unsupported YAML node type: expected scalar"); 102 103 ierr = PetscStrcmp(STR(kn), "<<", &isMergeKey);CHKERRQ(ierr); 104 if (isMergeKey) SETERRQ(comm, PETSC_ERR_SUP, "Unsupported YAML node value: merge key '<<' not supported here"); 105 106 ierr = PetscStrbeginswith(STR(kn), "$$", &isDummyKey);CHKERRQ(ierr); 107 if (isDummyKey) continue; 108 itemstr = STR(kn); 109 } 110 111 ierr = PetscSNPrintf(prefix,sizeof(prefix), "%s_", STR(keynode));CHKERRQ(ierr); 112 ierr = PetscOptionsPrefixPush(options, prefix);CHKERRQ(ierr); 113 ierr = PetscParseLayerYAML(options, doc, itemnode);CHKERRQ(ierr); 114 ierr = PetscOptionsPrefixPop(options);CHKERRQ(ierr); 115 116 } else SETERRQ(comm, PETSC_ERR_SUP, "Unsupported YAML node type: expected scalar or mapping"); 117 118 ierr = PetscStrlen(itemstr, &itemlen);CHKERRQ(ierr); 119 if (itemlen) { 120 if (addSep) { 121 ierr = PetscSegBufferGet(seg, 1, &buf);CHKERRQ(ierr); 122 ierr = PetscArraycpy(buf, ",", 1);CHKERRQ(ierr); 123 } 124 ierr = PetscSegBufferGet(seg, itemlen, &buf);CHKERRQ(ierr); 125 ierr = PetscArraycpy(buf, itemstr, itemlen);CHKERRQ(ierr); 126 addSep = PETSC_TRUE; 127 } 128 } 129 ierr = PetscSegBufferGet(seg, 1, &buf);CHKERRQ(ierr); 130 ierr = PetscArrayzero(buf, 1);CHKERRQ(ierr); 131 ierr = PetscSegBufferExtractAlloc(seg, &strlist);CHKERRQ(ierr); 132 ierr = PetscSegBufferDestroy(&seg);CHKERRQ(ierr); 133 134 ierr = PetscSNPrintf(name, sizeof(name), "-%s", STR(keynode));CHKERRQ(ierr); 135 ierr = PetscOptionsSetValue(options, name, strlist);CHKERRQ(ierr); 136 ierr = PetscFree(strlist);CHKERRQ(ierr); 137 138 } else if (valnode->type == YAML_MAPPING_NODE) { 139 ierr = PetscSNPrintf(prefix,sizeof(prefix), "%s_", STR(keynode));CHKERRQ(ierr); 140 ierr = PetscOptionsPrefixPush(options, prefix);CHKERRQ(ierr); 141 ierr = PetscParseLayerYAML(options, doc, valnode);CHKERRQ(ierr); 142 ierr = PetscOptionsPrefixPop(options);CHKERRQ(ierr); 143 144 } else SETERRQ(comm, PETSC_ERR_SUP, "Unsupported YAML node type: expected scalar, sequence or mapping"); 145 } 146 PetscFunctionReturn(0); 147 } 148 149 /*@C 150 PetscOptionsInsertStringYAML - Inserts YAML-formatted options into the database from a string 151 152 Logically Collective 153 154 Input Parameter: 155 + options - options database, use NULL for default global database 156 - in_str - YAML-formatted string options 157 158 Level: intermediate 159 160 .seealso: PetscOptionsSetValue(), PetscOptionsView(), PetscOptionsHasName(), PetscOptionsGetInt(), 161 PetscOptionsGetReal(), PetscOptionsGetString(), PetscOptionsGetIntArray(), PetscOptionsBool(), 162 PetscOptionsName(), PetscOptionsBegin(), PetscOptionsEnd(), PetscOptionsHead(), 163 PetscOptionsStringArray(),PetscOptionsRealArray(), PetscOptionsScalar(), 164 PetscOptionsBoolGroupBegin(), PetscOptionsBoolGroup(), PetscOptionsBoolGroupEnd(), 165 PetscOptionsFList(), PetscOptionsEList(), PetscOptionsInsertFile(), PetscOptionsInsertFileYAML() 166 @*/ 167 PetscErrorCode PetscOptionsInsertStringYAML(PetscOptions options,const char in_str[]) 168 { 169 MPI_Comm comm = PetscYAMLGetComm(); 170 yaml_parser_t parser; 171 yaml_document_t doc; 172 yaml_node_t *root; 173 PetscErrorCode ierr; 174 175 PetscFunctionBegin; 176 if (!in_str) in_str = ""; 177 ierr = !yaml_parser_initialize(&parser); if (ierr) SETERRQ(comm, PETSC_ERR_LIB, "YAML parser initialization error"); 178 yaml_parser_set_input_string(&parser, (const unsigned char *)in_str, strlen(in_str)); 179 do { 180 ierr = !yaml_parser_load(&parser, &doc); if (ierr) SETERRQ(comm, PETSC_ERR_LIB, "YAML parser loading error"); 181 root = yaml_document_get_root_node(&doc); 182 if (root) { 183 ierr = PetscParseLayerYAML(options, &doc, root);CHKERRQ(ierr); 184 } 185 yaml_document_delete(&doc); 186 } while (root); 187 yaml_parser_delete(&parser); 188 PetscFunctionReturn(0); 189 } 190 191 /*@C 192 PetscOptionsInsertFileYAML - Insert a YAML-formatted file in the option database 193 194 Collective 195 196 Input Parameter: 197 + comm - the processes that will share the options (usually PETSC_COMM_WORLD) 198 . options - options database, use NULL for default global database 199 . file - name of file 200 - require - if PETSC_TRUE will generate an error if the file does not exist 201 202 Only a small subset of the YAML standard is implemented. Non-scalar keys are NOT supported; 203 aliases and the merge key "<<" are. 204 The algorithm recursively parses the yaml file, pushing and popping prefixes 205 and inserting key + values pairs using PetscOptionsSetValue(). 206 207 PETSc will generate an error condition that stops the program if a YAML error 208 is detected, hence the user should check that the YAML file is valid before 209 supplying it, for instance at http://www.yamllint.com/ . 210 211 Inspired by https://stackoverflow.com/a/621451 212 213 Level: intermediate 214 215 .seealso: PetscOptionsSetValue(), PetscOptionsView(), PetscOptionsHasName(), PetscOptionsGetInt(), 216 PetscOptionsGetReal(), PetscOptionsGetString(), PetscOptionsGetIntArray(), PetscOptionsBool(), 217 PetscOptionsName(), PetscOptionsBegin(), PetscOptionsEnd(), PetscOptionsHead(), 218 PetscOptionsStringArray(),PetscOptionsRealArray(), PetscOptionsScalar(), 219 PetscOptionsBoolGroupBegin(), PetscOptionsBoolGroup(), PetscOptionsBoolGroupEnd(), 220 PetscOptionsFList(), PetscOptionsEList(), PetscOptionsInsertFile(), PetscOptionsInsertStringYAML() 221 @*/ 222 PetscErrorCode PetscOptionsInsertFileYAML(MPI_Comm comm,PetscOptions options,const char file[],PetscBool require) 223 { 224 int yamlLength = -1; 225 char *yamlString = NULL; 226 MPI_Comm prev; 227 PetscMPIInt rank; 228 PetscErrorCode ierr; 229 230 PetscFunctionBegin; 231 ierr = MPI_Comm_rank(comm, &rank);CHKERRMPI(ierr); 232 if (!rank) { 233 char fpath[PETSC_MAX_PATH_LEN]; 234 char fname[PETSC_MAX_PATH_LEN]; 235 FILE *fd; 236 size_t rd; 237 238 ierr = PetscStrreplace(PETSC_COMM_SELF, file, fpath, sizeof(fpath));CHKERRQ(ierr); 239 ierr = PetscFixFilename(fpath, fname);CHKERRQ(ierr); 240 241 fd = fopen(fname, "r"); 242 if (fd) { 243 fseek(fd, 0, SEEK_END); 244 yamlLength = (int)ftell(fd); 245 fseek(fd, 0, SEEK_SET); 246 if (yamlLength < 0) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_FILE_OPEN, "Unable to query size of YAML file: %s", fname); 247 ierr = PetscMalloc1(yamlLength+1, &yamlString);CHKERRQ(ierr); 248 rd = fread(yamlString, 1, (size_t)yamlLength, fd); 249 if (rd != (size_t)yamlLength) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_FILE_READ, "Unable to read entire YAML file: %s", fname); 250 yamlString[yamlLength] = 0; 251 fclose(fd); 252 } 253 } 254 255 ierr = MPI_Bcast(&yamlLength, 1, MPI_INT, 0, comm);CHKERRMPI(ierr); 256 if (require && yamlLength < 0) SETERRQ1(comm, PETSC_ERR_FILE_OPEN, "Unable to open YAML option file: %s\n", file); 257 if (yamlLength < 0) PetscFunctionReturn(0); 258 259 if (rank) {ierr = PetscMalloc1(yamlLength+1, &yamlString);CHKERRQ(ierr);} 260 ierr = MPI_Bcast(yamlString, yamlLength+1, MPI_CHAR, 0, comm);CHKERRMPI(ierr); 261 262 prev = PetscYAMLSetComm(comm); 263 ierr = PetscOptionsInsertStringYAML(options, yamlString);CHKERRQ(ierr); 264 (void) PetscYAMLSetComm(prev); 265 266 ierr = PetscFree(yamlString);CHKERRQ(ierr); 267 PetscFunctionReturn(0); 268 } 269 270 271 #if !defined(PETSC_HAVE_YAML) 272 273 /* 274 #if !defined(PETSC_HAVE_STRDUP) 275 #define strdup(s) (char*)memcpy(malloc(strlen(s)+1),s,strlen(s)+1) 276 #endif 277 */ 278 279 /* Embed LibYAML in this compilation unit */ 280 #include <../src/sys/yaml/src/api.c> 281 #include <../src/sys/yaml/src/loader.c> 282 #include <../src/sys/yaml/src/parser.c> 283 #include <../src/sys/yaml/src/reader.c> 284 #include <../src/sys/yaml/src/scanner.c> 285 286 /* Silence a few unused-function warnings */ 287 static PETSC_UNUSED void petsc_yaml_unused(void) 288 { 289 (void)yaml_parser_scan; 290 (void)yaml_document_get_node; 291 (void)yaml_parser_set_encoding; 292 (void)yaml_parser_set_input; 293 (void)yaml_parser_set_input_file; 294 } 295 296 #endif 297