IOSS 2.0

Ioss_Utils.h
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32
33 #ifndef IOSS_Ioss_Utils_h
34 #define IOSS_Ioss_Utils_h
35
36 #include <Ioss_CodeTypes.h>
37 #include <Ioss_Field.h>
38 #include <algorithm> // for sort, lower_bound, copy, etc
39 #include <cassert>
40 #include <cmath>
41 #include <cstddef> // for size_t
42 #include <cstdint> // for int64_t
43 #include <cstdlib> // for nullptrr
44 #include <iostream> // for ostringstream, etcstream, etc
45 #include <stdexcept> // for runtime_error
46 #include <string> // for string
47 #include <vector> // for vector
48 namespace Ioss {
49 class Field;
50 } // namespace Ioss
51 namespace Ioss {
52 class GroupingEntity;
53 class Region;
54 class SideBlock;
55 class PropertyManager;
56 struct MeshCopyOptions;
57 } // namespace Ioss
58
59 #if __cplusplus > 199711L
60 #define TOPTR(x) x.data()
61 #else
62 #define TOPTR(x) (x.empty() ? nullptr : &x[0])
63 #endif
64
65 #define IOSS_ERROR(errmsg) throw std::runtime_error(errmsg.str())
66 #define IOSS_WARNING std::cerr
67
68 namespace {
69 // SEE: http://lemire.me/blog/2017/04/10/removing-duplicates-from-lists-quickly
70 template <typename T> size_t unique(std::vector<T> &out, bool skip_first)
71 {
72 if (out.empty())
73 return 0;
74 size_t i = 1;
75 size_t pos = 1;
76 T oldv = out[0];
77 if (skip_first) {
78 i = 2;
79 pos = 2;
80 oldv = out[1];
81 }
82 for (; i < out.size(); ++i) {
83 T newv = out[i];
84 out[pos] = newv;
85 pos += (newv != oldv);
86 oldv = newv;
87 }
88 return pos;
89 }
90 } // namespace
91
92 namespace Ioss {
93
94 /* \brief Utility methods.
95 */
96 class Utils
97 {
98 public:
99 Utils() = default;
100 ~Utils() = default;
101
102 static void check_dynamic_cast(const void *ptr)
103 {
104 if (ptr == nullptr) {
105 std::cerr << "INTERNAL ERROR: Invalid dynamic cast returned nullptr\n";
106 exit(EXIT_FAILURE);
107 }
108 }
109
110 template <typename T> static void uniquify(std::vector<T> &vec, bool skip_first = false)
111 {
112 auto it = vec.begin();
113 if (skip_first) {
114 it++;
115 }
116 std::sort(it, vec.end());
117 vec.resize(unique(vec, skip_first));
118 vec.shrink_to_fit();
119 }
120
121 template <typename T> static void generate_index(std::vector<T> &index)
122 {
123 T sum = 0;
124 for (size_t i = 0; i < index.size() - 1; i++) {
125 T cnt = index[i];
126 index[i] = sum;
127 sum += cnt;
128 }
129 index.back() = sum;
130 }
131
132 template <typename T> static T find_index_location(T node, const std::vector<T> &index)
133 {
134 // 0-based node numbering
135 // index[p] = first node (0-based) on processor p
136
137 #if 1
138 // Assume data coherence. I.e., a new search will be close to the
139 // previous search.
140 static size_t prev = 1;
141
142 size_t nproc = index.size();
143 if (prev < nproc && index[prev - 1] <= node && index[prev] > node) {
144 return prev - 1;
145 }
146
147 for (size_t p = 1; p < nproc; p++) {
148 if (index[p] > node) {
149 prev = p;
150 return p - 1;
151 }
152 }
153 std::cerr << "FATAL ERROR: find_index_location. Searching for " << node << " in:\n";
154 for (auto idx : index) {
155 std::cerr << idx << ", ";
156 }
157 std::cerr << "\n";
158 assert(1 == 0); // Cannot happen...
159 return 0;
160 #else
161 return std::distance(index.begin(), std::upper_bound(index.begin(), index.end(), node)) - 1;
162 #endif
163 }
164
165 static void copy_string(char *dest, char const *source, size_t elements);
166
167 static void copy_string(char *dest, const std::string &source, size_t elements)
168 {
169 copy_string(dest, source.c_str(), elements);
170 }
171
172 template <size_t size> static void copy_string(char (&output)[size], const std::string &source)
173 {
174 copy_string(output, source.c_str(), size);
175 }
176
177 template <size_t size> static void copy_string(char (&output)[size], const char *source)
178 {
179 // Copy the string — don’t copy too many bytes.
180 copy_string(output, source, size);
181 }
182
183 template <typename T> static void clear(std::vector<T> &vec)
184 {
185 vec.clear();
186 vec.shrink_to_fit();
187 assert(vec.capacity() == 0);
188 }
189
190 /**
191 * Returns the number of digits required to print the number.
192 * If `use_commas` is specified, then the width will be adjusted
193 * to account for the comma used every 3 digits.
194 * (1,234,567,890 would return 13)
195 * Typically used with the `fmt::print()` functions as:
196 * ```
197 * fmt::print("{:{}n}", number, number_width(number,true))
198 * fmt::print("{:{}d}", number, number_width(number,false))
199 * ```
200 */
201 inline static int number_width(const size_t number, bool use_commas = false)
202 {
203 if (number == 0) {
204 return 1;
205 }
206 int width = int(std::floor(std::log10(number))) + 1;
207 if (use_commas) {
208 width += ((width - 1) / 3);
209 }
210 return width;
211 }
212
213 inline static int power_2(int count)
214 {
215 // Return the power of two which is equal to or greater than `count`
216 // count = 15 -> returns 16
217 // count = 16 -> returns 16
218 // count = 17 -> returns 32
219
220 // Use brute force...
221 int pow2 = 1;
222 while (pow2 < count) {
223 pow2 *= 2;
224 }
225 return pow2;
226 }
227
228 template <typename T> static bool check_block_order(const std::vector<T *> &blocks)
229 {
230 #ifndef NDEBUG
231 // Verify that element blocks are defined in sorted offset order...
232 typename std::vector<T *>::const_iterator I;
233
234 int64_t eb_offset = -1;
235 for (I = blocks.begin(); I != blocks.end(); ++I) {
236 int64_t this_off = (*I)->get_offset();
237 if (this_off < eb_offset) {
238 {
239 {
240 return false;
241 }
242 }
243 }
244 eb_offset = this_off;
245 }
246 #endif
247 return true;
248 }
249
250 static int term_width();
251
252 static int log_power_2(uint64_t value);
253
254 static char **get_name_array(size_t count, int size);
255 static void delete_name_array(char **names, int count);
256
257 /** \brief Get formatted time and date strings.
258 *
259 * Fill time_string and date_string with current time and date
260 * formatted as "HH:MM:SS" for time and "yy/mm/dd" or "yyyy/mm/dd"
261 * for date.
262 *
263 * \param[out] time_string The formatted time string.
264 * \param[out] date_string The formatted date string.
265 * \param[in] length Use 8 for short-year date format, or 10 for long-year date format.
266 */
267 static void time_and_date(char *time_string, char *date_string, size_t length);
268
269 static std::string decode_filename(const std::string &filename, int processor,
270 int num_processors);
271 static size_t get_number(const std::string &suffix);
272 static int64_t extract_id(const std::string &name_id);
273 static std::string encode_entity_name(const std::string &entity_type, int64_t id);
274
275 /** \brief create a string that describes the list of input `ids` collapsing ranges if possible.
276 *
277 * Traverse the sorted input vector `ids` and return a string that has all sequential ranges
278 * collapsed and separated by `rng_sep` and all individual ids or ranges separated by `seq_sep`.
279 * Will throw an exception if `ids` is not sorted. An empty list returns an empty string.
280 * The sequence of ids `1, 2, 3, 5, 6, 7` with `rng_sep=".."` will return the default
281 * string `1..3, 5..8`
282 */
283 static std::string format_id_list(const std::vector<size_t> &ids,
284 const std::string & rng_sep = " to ",
285 const std::string & seq_sep = ", ");
286
287 /** \brief Convert a string to lower case, and convert spaces to `_`.
288 *
289 * The conversion is performed in place.
290 *
291 * \param[in,out] name On input, the string to convert. On output, the converted string.
292 *
293 */
294 static void fixup_name(char *name);
295
296 /** \brief Convert a string to lower case, and convert spaces to `_`.
297 *
298 * The conversion is performed in place.
299 *
300 * \param[in,out] name On input, the string to convert. On output, the converted string.
301 *
302 */
303 static void fixup_name(std::string &name);
304
305 /** \brief Check whether property `prop_name` exists and if so, set `prop_value`
306 *
307 * based on the property value. Either "TRUE", "YES", "ON", or nonzero for true;
308 * or "FALSE", "NO", "OFF", or 0 for false.
309 * \param[in] properties the Ioss::PropertyManager containing the properties to be checked.
310 * \param[in] prop_name the name of the property to check whether it exists and if so, set its
311 * value.
312 * \param[out] prop_value if `prop_name` exists and has a valid value, set prop_value
313 * accordingly. Does not modify if `prop_name` does not exist. \returns true/false depending on
314 * whether property found and value set.
315 */
316
317 static bool check_set_bool_property(const Ioss::PropertyManager &properties,
318 const std::string &prop_name, bool &prop_value);
319
320 /** \brief Determine whether an entity has the property `omitted`.
321 *
322 * \param[in] block The entity.
323 * \returns True if the entity has the property `omitted`.
324 */
325 static bool block_is_omitted(Ioss::GroupingEntity *block);
326
327 /** \brief Process the base element type `base` which has
328 * `nodes_per_element` nodes and a spatial dimension of `spatial`
329 * into a form that the IO system can (hopefully) recognize.
330 *
331 * Lowercases the name; converts spaces to `_`, adds
332 * nodes_per_element at end of name (if not already there), and
333 * does some other transformations to remove some exodusII ambiguity.
334 *
335 * \param[in] base The element base name.
336 * \param[in] nodes_per_element The number of nodes per element.
337 * \param[in] spatial The spatial dimension of the element.
338 * \returns The Ioss-formatted element name.
339 */
340 static std::string fixup_type(const std::string &base, int nodes_per_element, int spatial);
341
342 /** \brief Convert a string to upper case.
343 *
344 * \param[in] name The string to convert.
345 * \returns The converted string.
346 */
347 static std::string uppercase(std::string name);
348
349 /** \brief Convert a string to lower case.
350 *
351 * \param[in] name The string to convert.
352 * \returns The converted string.
353 */
354 static std::string lowercase(std::string name);
355
356 static void check_non_null(void *ptr, const char *type, const std::string &name,
357 const std::string &func);
358
359 /** \brief Case-insensitive string comparison.
360 *
361 * \param[in] s1 First string
362 * \param[in] s2 Second string
363 * \returns 0 if strings are equal, nonzero otherwise.
364 */
365 static int case_strcmp(const std::string &s1, const std::string &s2);
366
367 /** \brief Get a string containing `uname` output.
368 *
369 * This output contains information about the current computing platform.
370 * This is used as information data in the created results file to help
371 * in tracking when/where/... the file was created.
372 *
373 * \returns The platform information string.
374 */
375 static std::string platform_information();
376
377 /** \brief Return amount of memory being used on this processor */
378 static size_t get_memory_info();
379 static size_t get_hwm_memory_info();
380
381 /** \brief Get a filename relative to the specified working directory (if any)
382 * of the current execution.
383 *
384 * Working_directory must end with `/` or be empty.
385 *
386 * \param[in] relative_filename The file path to be appended to the working directory path.
387 * \param[in] type The file type. "generated" file types are treated differently.
388 * \param[in] working_directory the path to which the relative_filename path is appended.
389 * \returns The full path (working_directory + relative_filename)
390 */
391 static std::string local_filename(const std::string &relative_filename, const std::string &type,
392 const std::string &working_directory);
393
394 static void get_fields(int64_t entity_count, char **names, size_t num_names,
395 Ioss::Field::RoleType fld_role, bool enable_field_recognition,
396 char suffix_separator, int *local_truth,
397 std::vector<Ioss::Field> &fields);
398
399 static int field_warning(const Ioss::GroupingEntity *ge, const Ioss::Field &field,
400 const std::string &inout);
401
402 static void calculate_sideblock_membership(IntVector &face_is_member, const SideBlock *ef_blk,
403 size_t int_byte_size, const void *element,
404 const void *sides, int64_t number_sides,
405 const Region *region);
406
407 /** \brief Get the appropriate index offset for the sides of elements in a SideBlock.
408 *
409 * And yet another idiosyncrasy of sidesets...
410 * The side of an element (especially shells) can be
411 * either a face or an edge in the same sideset. The
412 * ordinal of an edge is (local_edge_number+numfaces) on the
413 * database, but needs to be (local_edge_number) for Sierra...
414 *
415 * If the sideblock has a "parent_element_topology" and a
416 * "topology", then we can determine whether to offset the
417 * side ordinals...
418 *
419 * \param[in] sb Compute the offset for element sides in this SideBlock
420 * \returns The offset.
421 */
422 static int64_t get_side_offset(const Ioss::SideBlock *sb);
423
424 static unsigned int hash(const std::string &name);
425
426 static double timer();
427
428 /** \brief Convert an input file to a vector of strings containing one string for each line of
429 * the file.
430 *
431 * Should only be called by a single processor or each processor will be accessing the file
432 * at the same time...
433 *
434 * \param[in] file_name The name of the file.
435 * \param[out] lines The vector of strings containing the lines of the file
436 * \param[in] max_line_length The maximum number of characters in any line of the file.
437 */
438 static void input_file(const std::string &file_name, std::vector<std::string> *lines,
439 size_t max_line_length = 0);
440
441 template <class T> static std::string to_string(const T &t) { return std::to_string(t); }
442
443 //! \brief Tries to shorten long variable names to an acceptable
444 //! length, and converts to lowercase and spaces to `_`
445 //!
446 //! Many databases have a maximum length for variable names which can
447 //! cause a problem with variable name length.
448 //!
449
450 //! This routine tries to shorten long variable names to an
451 //! acceptable length (`max_var_len` characters max). If the name
452 //! is already less than this length, it is returned unchanged...
453 //!
454 //! Since there is a (good) chance that two shortened names will match,
455 //! a 2-letter `hash` code is appended to the end of the variable name.
456 //!
457 //! So, we shorten the name to a maximum of `max_var_len`-3
458 //! characters and append a 2 character hash+separator.
459 //!
460 //! It also converts name to lowercase and converts spaces to `_`
461 static std::string variable_name_kluge(const std::string &name, size_t component_count,
462 size_t copies, size_t max_var_len);
463
464 /** \brief Create a nominal mesh for use in history databases.
465 *
466 * The model for a history file is a single sphere element (1 node, 1 element).
467 * This is needed for some applications that read this file that require a
468 * "mesh" even though a history file is just a collection of global variables
469 * with no real mesh. This routine will add the mesh portion to a history file.
470 *
471 * \param[in,out] region The region on which the nominal mesh is to be defined.
472 */
473 static void generate_history_mesh(Ioss::Region *region);
474
475 //! Copy the mesh in `region` to `output_region`. Behavior can be controlled
476 //! via options in `options`
477 static void copy_database(Ioss::Region &region, Ioss::Region &output_region,
478 Ioss::MeshCopyOptions &options);
479 };
480 } // namespace Ioss
481 #endif
Ioss::Utils::copy_string
static void copy_string(char(&output)[size], const std::string &source)
Definition: Ioss_Utils.h:172
Ioss::Field
Holds metadata for bulk data associated with a GroupingEntity.
Definition: Ioss_Field.h:47
Ioss::Utils::field_warning
static int field_warning(const Ioss::GroupingEntity *ge, const Ioss::Field &field, const std::string &inout)
Definition: Ioss_Utils.C:471
Ioss::Utils::hash
static unsigned int hash(const std::string &name)
Definition: Ioss_Utils.C:1110
Ioss::Utils::uniquify
static void uniquify(std::vector< T > &vec, bool skip_first=false)
Definition: Ioss_Utils.h:110
Ioss::Utils::fixup_type
static std::string fixup_type(const std::string &base, int nodes_per_element, int spatial)
Process the base element type base which has nodes_per_element nodes and a spatial dimension of spati...
Definition: Ioss_Utils.C:390
Ioss::Utils::copy_string
static void copy_string(char *dest, char const *source, size_t elements)
Definition: Ioss_Utils.C:1372
Ioss::Utils::find_index_location
static T find_index_location(T node, const std::vector< T > &index)
Definition: Ioss_Utils.h:132
anonymous_namespace{Iofx_DatabaseIO.C}::max_line_length
const size_t max_line_length
Definition: Iofx_DatabaseIO.C:96
Ioss::Utils::get_number
static size_t get_number(const std::string &suffix)
Definition: Ioss_Utils.C:304
Ioss::IntVector
std::vector< int > IntVector
Definition: Ioss_CodeTypes.h:51
Ioss::Utils::term_width
static int term_width()
Definition: Ioss_Utils.C:1401
Ioss::Utils::~Utils
~Utils()=default
Ioss::Utils::case_strcmp
static int case_strcmp(const std::string &s1, const std::string &s2)
Case-insensitive string comparison.
Definition: Ioss_Utils.C:1169
Ioss::Utils::platform_information
static std::string platform_information()
Get a string containing uname output.
Definition: Ioss_Utils.C:877
Ioss::Utils::get_hwm_memory_info
static size_t get_hwm_memory_info()
Definition: Ioss_Utils.C:957
Ioss::MeshCopyOptions
Definition: Ioss_MeshCopyOptions.h:35
Ioss
The main namespace for the Ioss library.
Definition: Ioad_DatabaseIO.C:66
Ioss::Utils::to_string
static std::string to_string(const T &t)
Definition: Ioss_Utils.h:441
Ioss::Utils::clear
static void clear(std::vector< T > &vec)
Definition: Ioss_Utils.h:183
Ioss::Utils::extract_id
static int64_t extract_id(const std::string &name_id)
Definition: Ioss_Utils.C:314
anonymous_namespace{Iovs_DatabaseIO.C}::entity_type
entity_type
Definition: Iovs_DatabaseIO.C:81
Ioss::Utils::number_width
static int number_width(const size_t number, bool use_commas=false)
Definition: Ioss_Utils.h:201
Ioss::Utils::encode_entity_name
static std::string encode_entity_name(const std::string &entity_type, int64_t id)
Definition: Ioss_Utils.C:363
Ioss::Region
A grouping entity that contains other grouping entities.
Definition: Ioss_Region.h:98
anonymous_namespace{Ioss_Utils.h}::unique
size_t unique(std::vector< T > &out, bool skip_first)
Definition: Ioss_Utils.h:70
Ioss::Utils::get_fields
static void get_fields(int64_t entity_count, char **names, size_t num_names, Ioss::Field::RoleType fld_role, bool enable_field_recognition, char suffix_separator, int *local_truth, std::vector< Ioss::Field > &fields)
Definition: Ioss_Utils.C:759
Ioss::PropertyManager
A collection of Ioss::Property objects.
Definition: Ioss_PropertyManager.h:49
Ioss::Utils::get_name_array
static char ** get_name_array(size_t count, int size)
Definition: Ioss_Utils.C:372
Ioss::Utils::get_memory_info
static size_t get_memory_info()
Return amount of memory being used on this processor.
Definition: Ioss_Utils.C:893
Ioss::Utils::calculate_sideblock_membership
static void calculate_sideblock_membership(IntVector &face_is_member, const SideBlock *ef_blk, size_t int_byte_size, const void *element, const void *sides, int64_t number_sides, const Region *region)
Definition: Ioss_Utils.C:1003
Ioss::Utils::local_filename
static std::string local_filename(const std::string &relative_filename, const std::string &type, const std::string &working_directory)
Get a filename relative to the specified working directory (if any) of the current execution.
Definition: Ioss_Utils.C:459
Ioss::Utils::uppercase
static std::string uppercase(std::string name)
Convert a string to upper case.
Definition: Ioss_Utils.C:1183
Ioss::Utils::check_set_bool_property
static bool check_set_bool_property(const Ioss::PropertyManager &properties, const std::string &prop_name, bool &prop_value)
Check whether property prop_name exists and if so, set prop_value
Definition: Ioss_Utils.C:1195
Ioss::Utils::copy_string
static void copy_string(char *dest, const std::string &source, size_t elements)
Definition: Ioss_Utils.h:167
Ioss::Utils::fixup_name
static void fixup_name(char *name)
Convert a string to lower case, and convert spaces to _.
Definition: Ioss_Utils.C:1225
Ioss::Utils::timer
static double timer()
Definition: Ioss_Utils.C:1129
Ioss::SideBlock
A collection of element sides having the same topology.
Definition: Ioss_SideBlock.h:59
Ioss_Field.h
Ioss::Utils::power_2
static int power_2(int count)
Definition: Ioss_Utils.h:213
Ioss::Utils::block_is_omitted
static bool block_is_omitted(Ioss::GroupingEntity *block)
Determine whether an entity has the property omitted.
Definition: Ioss_Utils.C:994
Ioss::Utils::check_dynamic_cast
static void check_dynamic_cast(const void *ptr)
Definition: Ioss_Utils.h:102
Ioss::Utils::copy_database
static void copy_database(Ioss::Region &region, Ioss::Region &output_region, Ioss::MeshCopyOptions &options)
Definition: Ioss_Utils.C:1418
Ioss::Utils::variable_name_kluge
static std::string variable_name_kluge(const std::string &name, size_t component_count, size_t copies, size_t max_var_len)
Tries to shorten long variable names to an acceptable length, and converts to lowercase and spaces to...
Definition: Ioss_Utils.C:1275
Ioss::Utils::decode_filename
static std::string decode_filename(const std::string &filename, int processor, int num_processors)
Definition: Ioss_Utils.C:287
Ioss::Utils::generate_index
static void generate_index(std::vector< T > &index)
Definition: Ioss_Utils.h:121
Ioss::Utils::copy_string
static void copy_string(char(&output)[size], const char *source)
Definition: Ioss_Utils.h:177
Ioss::Utils::log_power_2
static int log_power_2(uint64_t value)
Definition: Ioss_Utils.C:1388
Ioss::Utils::Utils
Utils()=default
Ioss::Utils::check_non_null
static void check_non_null(void *ptr, const char *type, const std::string &name, const std::string &func)
Definition: Ioss_Utils.C:275
Ioss::Utils::delete_name_array
static void delete_name_array(char **names, int count)
Definition: Ioss_Utils.C:382
Ioss::Utils::input_file
static void input_file(const std::string &file_name, std::vector< std::string > *lines, size_t max_line_length=0)
Convert an input file to a vector of strings containing one string for each line of the file.
Definition: Ioss_Utils.C:1135
Ioss::Utils::format_id_list
static std::string format_id_list(const std::vector< size_t > &ids, const std::string &rng_sep=" to ", const std::string &seq_sep=", ")
create a string that describes the list of input ids collapsing ranges if possible.
Definition: Ioss_Utils.C:327
Ioss::Field::RoleType
RoleType
Definition: Ioss_Field.h:75
anonymous_namespace{io_info.C}::name
std::string name(const Ioss::GroupingEntity *entity)
Definition: io_info.C:89
Ioss::Utils::generate_history_mesh
static void generate_history_mesh(Ioss::Region *region)
Create a nominal mesh for use in history databases.
Definition: Ioss_Utils.C:1340
Ioss::Utils::get_side_offset
static int64_t get_side_offset(const Ioss::SideBlock *sb)
Get the appropriate index offset for the sides of elements in a SideBlock.
Definition: Ioss_Utils.C:1092
Ioss::GroupingEntity
Base class for all 'grouping' entities. The following derived classes are typical:
Definition: Ioss_GroupingEntity.h:93
Ioss_CodeTypes.h
Ioss::Utils
Definition: Ioss_Utils.h:96
Ioss::Utils::time_and_date
static void time_and_date(char *time_string, char *date_string, size_t length)
Get formatted time and date strings.
Definition: Ioss_Utils.C:259
Ioss::Utils::check_block_order
static bool check_block_order(const std::vector< T * > &blocks)
Definition: Ioss_Utils.h:228
Ioss::Utils::lowercase
static std::string lowercase(std::string name)
Convert a string to lower case.
Definition: Ioss_Utils.C:1189