IOSS 2.0

Ioss_Utils.h
Go to the documentation of this file.
1 // Copyright(C) 1999-2017 National Technology & Engineering Solutions
2 // of Sandia, LLC (NTESS). Under the terms of Contract DE-NA0003525 with
3 // NTESS, the U.S. Government retains certain rights in this software.
4 //
5 // Redistribution and use in source and binary forms, with or without
6 // modification, are permitted provided that the following conditions are
7 // met:
8 //
9 // * Redistributions of source code must retain the above copyright
10 // notice, this list of conditions and the following disclaimer.
11 //
12 // * Redistributions in binary form must reproduce the above
13 // copyright notice, this list of conditions and the following
14 // disclaimer in the documentation and/or other materials provided
15 // with the distribution.
16 //
17 // * Neither the name of NTESS nor the names of its
18 // contributors may be used to endorse or promote products derived
19 // from this software without specific prior written permission.
20 //
21 // THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
22 // "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
23 // LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
24 // A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
25 // OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
26 // SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
27 // LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
28 // DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
29 // THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
30 // (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
31 // OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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 // Assignment operator
103 // Copy constructor
104
105 static void check_dynamic_cast(const void *ptr)
106 {
107 if (ptr == nullptr) {
108 std::cerr << "INTERNAL ERROR: Invalid dynamic cast returned nullptr\n";
109 exit(EXIT_FAILURE);
110 }
111 }
112
113 template <typename T> static void uniquify(std::vector<T> &vec, bool skip_first = false)
114 {
115 auto it = vec.begin();
116 if (skip_first) {
117 it++;
118 }
119 std::sort(it, vec.end());
120 vec.resize(unique(vec, skip_first));
121 vec.shrink_to_fit();
122 }
123
124 template <typename T> static void generate_index(std::vector<T> &index)
125 {
126 T sum = 0;
127 for (size_t i = 0; i < index.size() - 1; i++) {
128 T cnt = index[i];
129 index[i] = sum;
130 sum += cnt;
131 }
132 index.back() = sum;
133 }
134
135 template <typename T> static T find_index_location(T node, const std::vector<T> &index)
136 {
137 // 0-based node numbering
138 // index[p] = first node (0-based) on processor p
139
140 #if 1
141 // Assume data coherence. I.e., a new search will be close to the
142 // previous search.
143 static size_t prev = 1;
144
145 size_t nproc = index.size();
146 if (prev < nproc && index[prev - 1] <= node && index[prev] > node) {
147 return prev - 1;
148 }
149
150 for (size_t p = 1; p < nproc; p++) {
151 if (index[p] > node) {
152 prev = p;
153 return p - 1;
154 }
155 }
156 std::cerr << "FATAL ERROR: find_index_location. Searching for " << node << " in:\n";
157 for (auto idx : index) {
158 std::cerr << idx << ", ";
159 }
160 std::cerr << "\n";
161 assert(1 == 0); // Cannot happen...
162 return 0;
163 #else
164 return std::distance(index.begin(), std::upper_bound(index.begin(), index.end(), node)) - 1;
165 #endif
166 }
167
168 static void copy_string(char *dest, char const *source, size_t elements);
169
170 static void copy_string(char *dest, const std::string &source, size_t elements)
171 {
172 copy_string(dest, source.c_str(), elements);
173 }
174
175 template <size_t size> static void copy_string(char (&output)[size], const std::string &source)
176 {
177 copy_string(output, source.c_str(), size);
178 }
179
180 template <size_t size> static void copy_string(char (&output)[size], const char *source)
181 {
182 // Copy the string — don’t copy too many bytes.
183 copy_string(output, source, size);
184 }
185
186 template <typename T> static void clear(std::vector<T> &vec)
187 {
188 vec.clear();
189 vec.shrink_to_fit();
190 assert(vec.capacity() == 0);
191 }
192
193 /**
194 * Returns the number of digits required to print the number.
195 * If `use_commas` is specified, then the width will be adjusted
196 * to account for the comma used every 3 digits.
197 * (1,234,567,890 would return 13)
198 * Typically used with the `fmt::print()` functions as:
199 * `fmt::print("{:{}n}", number, number_width(number,true))`
200 * `fmt::print("{:{}d}", number, number_width(number,false))`
201 */
202 inline static int number_width(const size_t number, bool use_commas = false)
203 {
204 int width = std::floor(std::log10(number)) + 1;
205 if (use_commas) {
206 width += (width / 3);
207 }
208 return width;
209 }
210
211 inline static int power_2(int count)
212 {
213 // Return the power of two which is equal to or greater than 'count'
214 // count = 15 -> returns 16
215 // count = 16 -> returns 16
216 // count = 17 -> returns 32
217
218 // Use brute force...
219 int pow2 = 1;
220 while (pow2 < count) {
221 pow2 *= 2;
222 }
223 return pow2;
224 }
225
226 template <typename T> static bool check_block_order(const std::vector<T *> &blocks)
227 {
228 #ifndef NDEBUG
229 // Verify that element blocks are defined in sorted offset order...
230 typename std::vector<T *>::const_iterator I;
231
232 int64_t eb_offset = -1;
233 for (I = blocks.begin(); I != blocks.end(); ++I) {
234 int64_t this_off = (*I)->get_offset();
235 if (this_off < eb_offset) {
236 {
237 {
238 return false;
239 }
240 }
241 }
242 eb_offset = this_off;
243 }
244 #endif
245 return true;
246 }
247
248 static int log_power_2(uint64_t value);
249
250 static char **get_name_array(size_t count, int size);
251 static void delete_name_array(char **names, int count);
252
253 // Fill time_string and date_string with current time and date
254 // formatted as "HH:MM:SS" for time and "yy/mm/dd" or "yyyy/mm/dd"
255 // for date
256 static void time_and_date(char *time_string, char *date_string, size_t length);
257
258 static std::string decode_filename(const std::string &filename, int processor,
259 int num_processors);
260 static size_t get_number(const std::string &suffix);
261 static int64_t extract_id(const std::string &name_id);
262 static std::string encode_entity_name(const std::string &entity_type, int64_t id);
263
264 // Convert 'name' to lowercase and convert spaces to '_'
265 static void fixup_name(char *name);
266 static void fixup_name(std::string &name);
267
268 // Check whether property 'prop_name' exists and if so, set 'prop_value'
269 // based on the property value. Either "TRUE", "YES", "ON", or 1 for true;
270 // or "FALSE", "NO", "OFF", or not equal to 1 for false.
271 // Returns true/false depending on whether property found and value set.
272 // Does not set 'prop_val' if 'prop_name' does not exist.
273 static bool check_set_bool_property(const Ioss::PropertyManager &properties,
274 const std::string &prop_name, bool &prop_value);
275
276 // Returns true if the property "omitted" exists on "block"
277 static bool block_is_omitted(Ioss::GroupingEntity *block);
278
279 // Process the base element type 'base' which has
280 // 'nodes_per_element' nodes and a spatial dimension of 'spatial'
281 // into a form that the IO system can (hopefully) recognize.
282 // Lowercases the name; converts spaces to '_', adds
283 // nodes_per_element at end of name (if not already there), and
284 // does some other transformations to remove some exodusII ambiguity.
285 static std::string fixup_type(const std::string &base, int nodes_per_element, int spatial);
286
287 static std::string uppercase(std::string name);
288 static std::string lowercase(std::string name);
289
290 static void check_non_null(void *ptr, const char *type, const std::string &name,
291 const std::string &func);
292
293 static int case_strcmp(const std::string &s1, const std::string &s2);
294
295 // Return a string containing information about the current :
296 // computing platform. This is used as information data in the
297 // created results file to help in tracking when/where/... the file
298 // was created.
299 static std::string platform_information();
300
301 // Return amount of memory being used on this processor
302 static size_t get_memory_info();
303 static size_t get_hwm_memory_info();
304
305 // Return a filename relative to the specified working directory (if any)
306 // of the current execution. Working_directory must end with '/' or be empty.
307 static std::string local_filename(const std::string &relative_filename, const std::string &type,
308 const std::string &working_directory);
309
310 static void get_fields(int64_t entity_count, char **names, size_t num_names,
311 Ioss::Field::RoleType fld_role, bool enable_field_recognition,
312 char suffix_separator, int *local_truth,
313 std::vector<Ioss::Field> &fields);
314
315 static int field_warning(const Ioss::GroupingEntity *ge, const Ioss::Field &field,
316 const std::string &inout);
317
318 static void calculate_sideblock_membership(IntVector &face_is_member, const SideBlock *ef_blk,
319 size_t int_byte_size, const void *element,
320 const void *sides, int64_t number_sides,
321 const Region *region);
322
323 // And yet another idiosyncrasy of sidesets...
324 // The side of an element (especially shells) can be
325 // either a face or an edge in the same sideset. The
326 // ordinal of an edge is (local_edge_number+#faces) on the
327 // database, but needs to be (local_edge_number) for
328 // Sierra...
329 //
330 // If the sideblock has a "parent_element_topology" and a
331 // "topology", then we can determine whether to offset the
332 // side ordinals...
333 static int64_t get_side_offset(const Ioss::SideBlock *sb);
334
335 static unsigned int hash(const std::string &name);
336
337 static double timer();
338
339 // Return a vector of strings containing the lines of the input file.
340 // Should only be called by a single processor or each processor will
341 // be accessing the file at the same time...
342 static void input_file(const std::string &file_name, std::vector<std::string> *lines,
343 size_t max_line_length = 0);
344
345 template <class T> static std::string to_string(const T &t) { return std::to_string(t); }
346
347 // Many databases have a maximum length for variable names which can
348 // cause a problem with variable name length.
349 //
350 // This routine tries to shorten long variable names to an acceptable
351 // length ('max_var_len' characters max). If the name is already less than this
352 // length, it is returned unchanged...
353 //
354 // Since there is a (good) chance that two shortened names will match,
355 // a 2-letter 'hash' code is appended to the end of the variable name.
356 //
357 // So, we shorten the name to a maximum of 'max_var_len'-3 characters and append a
358 // 2 character hash+separator.
359 //
360 // It also converts name to lowercase and converts spaces to '_'
361 static std::string variable_name_kluge(const std::string &name, size_t component_count,
362 size_t copies, size_t max_var_len);
363
364 // The model for a history file is a single sphere element (1 node, 1 element)
365 // This is needed for some applications that read this file that require a "mesh"
366 // even though a history file is just a collection of global variables with no
367 // real mesh. This routine will add the mesh portion to a history file.
368 static void generate_history_mesh(Ioss::Region *region);
369
370 // Copy the mesh in 'region' to 'output_region'. Behavior can be controlled
371 // via options in 'options'
372 static void copy_database(Ioss::Region &region, Ioss::Region &output_region,
373 Ioss::MeshCopyOptions &options);
374 };
375 } // namespace Ioss
376 #endif
Ioss_CodeTypes.h
Ioss::Utils::Utils
Utils()=default
Ioss::Utils::number_width
static int number_width(const size_t number, bool use_commas=false)
Definition: Ioss_Utils.h:202
Ioss::Utils::uppercase
static std::string uppercase(std::string name)
Convert a string to upper case.
Definition: Ioss_Utils.C:1198
Ioss::Utils::power_2
static int power_2(int count)
Definition: Ioss_Utils.h:211
Ioss::Utils::get_memory_info
static size_t get_memory_info()
Return amount of memory being used on this processor.
Definition: Ioss_Utils.C:873
Ioss
The main namespace for the Ioss library.
Definition: Ioad_DatabaseIO.C:66
Ioss::Utils::check_dynamic_cast
static void check_dynamic_cast(const void *ptr)
Definition: Ioss_Utils.h:105
Ioss::Utils::~Utils
~Utils()=default
Ioss::Utils
Definition: Ioss_Utils.h:96
Ioss::GroupingEntity
Base class for all 'grouping' entities. The following derived classes are typical:
Definition: Ioss_GroupingEntity.h:93
Ioss::Field::RoleType
RoleType
Definition: Ioss_Field.h:75
Ioss::MeshCopyOptions
Definition: Ioss_MeshCopyOptions.h:35
Ioss::Utils::encode_entity_name
static std::string encode_entity_name(const std::string &entity_type, int64_t id)
Definition: Ioss_Utils.C:309
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:1139
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:1226
Ioss::Utils::copy_string
static void copy_string(char(&output)[size], const char *source)
Definition: Ioss_Utils.h:180
Ioss::SideBlock
A collection of element sides having the same topology.
Definition: Ioss_SideBlock.h:61
Ioss::IntVector
std::vector< int > IntVector
Definition: Ioss_CodeTypes.h:43
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:967
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:1350
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:1080
Ioss::Utils::case_strcmp
static int case_strcmp(const std::string &s1, const std::string &s2)
Case-insensitive string comparison.
Definition: Ioss_Utils.C:1179
Ioss::Utils::lowercase
static std::string lowercase(std::string name)
Convert a string to lower case.
Definition: Ioss_Utils.C:1209
Ioss::Utils::hash
static unsigned int hash(const std::string &name)
Definition: Ioss_Utils.C:1098
Ioss::Utils::copy_string
static void copy_string(char *dest, const std::string &source, size_t elements)
Definition: Ioss_Utils.h:170
anonymous_namespace{Ioss_Utils.h}::unique
size_t unique(std::vector< T > &out, bool skip_first)
Definition: Ioss_Utils.h:70
Ioss::Utils::to_string
static std::string to_string(const T &t)
Definition: Ioss_Utils.h:345
Ioss::Utils::fixup_name
static void fixup_name(char *name)
Convert a string to lower case, and convert spaces to '_'.
Definition: Ioss_Utils.C:1263
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:730
Ioss::Utils::find_index_location
static T find_index_location(T node, const std::vector< T > &index)
Definition: Ioss_Utils.h:135
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 '...
Definition: Ioss_Utils.C:349
Ioss::Utils::check_block_order
static bool check_block_order(const std::vector< T * > &blocks)
Definition: Ioss_Utils.h:226
Ioss::Utils::platform_information
static std::string platform_information()
Get a string containing 'uname' output.
Definition: Ioss_Utils.C:856
Ioss::Utils::get_number
static size_t get_number(const std::string &suffix)
Definition: Ioss_Utils.C:286
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:257
Ioss::Utils::delete_name_array
static void delete_name_array(char **names, int count)
Definition: Ioss_Utils.C:328
Ioss::Utils::copy_string
static void copy_string(char *dest, char const *source, size_t elements)
Definition: Ioss_Utils.C:1493
anonymous_namespace{Iofx_DatabaseIO.C}::max_line_length
const size_t max_line_length
Definition: Iofx_DatabaseIO.C:97
Ioss_Field.h
Ioss::Utils::copy_database
static void copy_database(Ioss::Region &region, Ioss::Region &output_region, Ioss::MeshCopyOptions &options)
Definition: Ioss_Utils.C:1522
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:241
Ioss::Region
A grouping entity that contains other grouping entities.
Definition: Ioss_Region.h:98
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:976
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:428
anonymous_namespace{io_info.C}::name
std::string name(Ioss::GroupingEntity *entity)
Definition: io_info.C:89
Ioss::Utils::timer
static double timer()
Definition: Ioss_Utils.C:1117
Ioss::Utils::extract_id
static int64_t extract_id(const std::string &name_id)
Definition: Ioss_Utils.C:296
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:440
Ioss::Utils::uniquify
static void uniquify(std::vector< T > &vec, bool skip_first=false)
Definition: Ioss_Utils.h:113
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:1461
Ioss::Utils::get_name_array
static char ** get_name_array(size_t count, int size)
Definition: Ioss_Utils.C:318
Ioss::PropertyManager
A collection of Ioss::Property objects.
Definition: Ioss_PropertyManager.h:49
anonymous_namespace{Iovs_DatabaseIO.C}::entity_type
entity_type
Definition: Iovs_DatabaseIO.C:81
Ioss::Utils::get_hwm_memory_info
static size_t get_hwm_memory_info()
Definition: Ioss_Utils.C:928
Ioss::Utils::copy_string
static void copy_string(char(&output)[size], const std::string &source)
Definition: Ioss_Utils.h:175
Ioss::Utils::decode_filename
static std::string decode_filename(const std::string &filename, int processor, int num_processors)
Definition: Ioss_Utils.C:269
Ioss::Utils::generate_index
static void generate_index(std::vector< T > &index)
Definition: Ioss_Utils.h:124
Ioss::Utils::log_power_2
static int log_power_2(uint64_t value)
Definition: Ioss_Utils.C:1509
Ioss::Utils::clear
static void clear(std::vector< T > &vec)
Definition: Ioss_Utils.h:186