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MooseUtils.C
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1 //* This file is part of the MOOSE framework
2 //* https://www.mooseframework.org
3 //*
4 //* All rights reserved, see COPYRIGHT for full restrictions
5 //* https://github.com/idaholab/moose/blob/master/COPYRIGHT
6 //*
7 //* Licensed under LGPL 2.1, please see LICENSE for details
8 //* https://www.gnu.org/licenses/lgpl-2.1.html
9 
10 // MOOSE includes
11 #include "MooseUtils.h"
12 #include "MooseError.h"
13 #include "MaterialProperty.h"
14 #include "MultiMooseEnum.h"
15 #include "InputParameters.h"
16 #include "ExecFlagEnum.h"
17 #include "InfixIterator.h"
18 #include "Registry.h"
19 #include "MortarConstraintBase.h"
20 #include "MortarNodalAuxKernel.h"
21 #include "ExecFlagRegistry.h"
22 #include "RestartableDataReader.h"
23 
24 #include "libmesh/utility.h"
25 #include "libmesh/elem.h"
26 
27 // External includes
28 #include "pcrecpp.h"
29 #include "tinydir.h"
30 
31 // C++ includes
32 #include <iostream>
33 #include <fstream>
34 #include <istream>
35 #include <iterator>
36 #include <filesystem>
37 #include <ctime>
38 #include <cstdlib>
39 
40 // System includes
41 #include <sys/stat.h>
42 #include <numeric>
43 #include <unistd.h>
44 
45 #include "petscsys.h"
46 
47 #ifdef __WIN32__
48 #include <windows.h>
49 #include <winbase.h>
50 #include <fileapi.h>
51 #else
52 #include <sys/ioctl.h>
53 #endif
54 
55 namespace MooseUtils
56 {
57 std::filesystem::path
58 pathjoin(const std::filesystem::path & p)
59 {
60  return p;
61 }
62 
63 std::string
65 {
66  auto build_loc = pathjoin(Moose::getExecutablePath(), "run_tests");
67  if (pathExists(build_loc) && checkFileReadable(build_loc))
68  return build_loc;
69  // TODO: maybe no path prefix - just moose_test_runner here?
70  return pathjoin(Moose::getExecutablePath(), "moose_test_runner");
71 }
72 
73 std::string
75 {
76  std::string path = ".";
77  for (int i = 0; i < 5; i++)
78  {
79  auto testroot = pathjoin(path, "testroot");
80  if (pathExists(testroot) && checkFileReadable(testroot))
81  return testroot;
82  path += "/..";
83  }
84  return "";
85 }
86 
87 bool
88 parsesToReal(const std::string & input)
89 {
90  std::istringstream ss(input);
91  Real real_value;
92  if (ss >> real_value && ss.eof())
93  return true;
94  return false;
95 }
96 
97 std::string
98 installedInputsDir(const std::string & app_name,
99  const std::string & dir_name,
100  const std::string & extra_error_msg)
101 {
102  // See moose.mk for a detailed explanation of the assumed installed application
103  // layout. Installed inputs are expected to be installed in "share/<app_name>/<folder>".
104  // The binary, which has a defined location will be in "bin", a peer directory to "share".
105  std::string installed_path =
106  pathjoin(Moose::getExecutablePath(), "..", "share", app_name, dir_name);
107 
108  auto test_root = pathjoin(installed_path, "testroot");
109  if (!pathExists(installed_path))
110  mooseError("Couldn't locate any installed inputs to copy in path: ",
111  installed_path,
112  '\n',
113  extra_error_msg);
114 
115  checkFileReadable(test_root);
116  return installed_path;
117 }
118 
119 std::string
120 docsDir(const std::string & app_name)
121 {
122  // See moose.mk for a detailed explanation of the assumed installed application
123  // layout. Installed docs are expected to be installed in "share/<app_name>/doc".
124  // The binary, which has a defined location will be in "bin", a peer directory to "share".
125  std::string installed_path = pathjoin(Moose::getExecutablePath(), "..", "share", app_name, "doc");
126 
127  auto docfile = pathjoin(installed_path, "css", "moose.css");
128  if (pathExists(docfile) && checkFileReadable(docfile))
129  return installed_path;
130  return "";
131 }
132 
133 std::string
134 replaceAll(std::string str, const std::string & from, const std::string & to)
135 {
136  size_t start_pos = 0;
137  while ((start_pos = str.find(from, start_pos)) != std::string::npos)
138  {
139  str.replace(start_pos, from.length(), to);
140  start_pos += to.length(); // Handles case where 'to' is a substring of 'from'
141  }
142  return str;
143 }
144 
145 std::string
146 convertLatestCheckpoint(std::string orig)
147 {
148  auto slash_pos = orig.find_last_of("/");
149  auto path = orig.substr(0, slash_pos);
150  auto file = orig.substr(slash_pos + 1);
151  if (file != "LATEST")
152  return orig;
153 
155 
156  if (converted.empty())
157  mooseError("Unable to find suitable recovery file!");
158 
159  return converted;
160 }
161 
162 // this implementation is copied from
163 // https://en.wikibooks.org/wiki/Algorithm_Implementation/Strings/Levenshtein_distance#C.2B.2B
164 int
165 levenshteinDist(const std::string & s1, const std::string & s2)
166 {
167  // To change the type this function manipulates and returns, change
168  // the return type and the types of the two variables below.
169  auto s1len = s1.size();
170  auto s2len = s2.size();
171 
172  auto column_start = (decltype(s1len))1;
173 
174  auto column = new decltype(s1len)[s1len + 1];
175  std::iota(column + column_start, column + s1len + 1, column_start);
176 
177  for (auto x = column_start; x <= s2len; x++)
178  {
179  column[0] = x;
180  auto last_diagonal = x - column_start;
181  for (auto y = column_start; y <= s1len; y++)
182  {
183  auto old_diagonal = column[y];
184  auto possibilities = {
185  column[y] + 1, column[y - 1] + 1, last_diagonal + (s1[y - 1] == s2[x - 1] ? 0 : 1)};
186  column[y] = std::min(possibilities);
187  last_diagonal = old_diagonal;
188  }
189  }
190  auto result = column[s1len];
191  delete[] column;
192  return result;
193 }
194 
195 void
196 escape(std::string & str)
197 {
198  std::map<char, std::string> escapes;
199  escapes['\a'] = "\\a";
200  escapes['\b'] = "\\b";
201  escapes['\f'] = "\\f";
202  escapes['\n'] = "\\n";
203  escapes['\t'] = "\\t";
204  escapes['\v'] = "\\v";
205  escapes['\r'] = "\\r";
206 
207  for (const auto & it : escapes)
208  for (size_t pos = 0; (pos = str.find(it.first, pos)) != std::string::npos;
209  pos += it.second.size())
210  str.replace(pos, 1, it.second);
211 }
212 
213 std::string
214 trim(const std::string & str, const std::string & white_space)
215 {
216  const auto begin = str.find_first_not_of(white_space);
217  if (begin == std::string::npos)
218  return ""; // no content
219  const auto end = str.find_last_not_of(white_space);
220  return str.substr(begin, end - begin + 1);
221 }
222 
223 bool
224 pathContains(const std::string & expression,
225  const std::string & string_to_find,
226  const std::string & delims)
227 {
228  std::vector<std::string> elements;
229  tokenize(expression, elements, 0, delims);
230 
231  std::vector<std::string>::iterator found_it =
232  std::find(elements.begin(), elements.end(), string_to_find);
233  if (found_it != elements.end())
234  return true;
235  else
236  return false;
237 }
238 
239 bool
240 pathExists(const std::string & path)
241 {
242  struct stat buffer;
243  return (stat(path.c_str(), &buffer) == 0);
244 }
245 
246 bool
247 pathIsDirectory(const std::string & path)
248 {
249  return std::filesystem::is_directory(path);
250 }
251 
252 bool
253 checkFileReadable(const std::string & filename,
254  bool check_line_endings,
255  bool throw_on_unreadable,
256  bool check_for_git_lfs_pointer)
257 {
258  std::ifstream in(filename.c_str(), std::ifstream::in);
259  if (in.fail())
260  {
261  if (throw_on_unreadable)
262  mooseError(
263  (std::string("Unable to open file \"") + filename +
264  std::string("\". Check to make sure that it exists and that you have read permission."))
265  .c_str());
266  else
267  return false;
268  }
269 
270  if (check_line_endings)
271  {
272  std::istream_iterator<char> iter(in);
273  std::istream_iterator<char> eos;
274  in >> std::noskipws;
275  while (iter != eos)
276  if (*iter++ == '\r')
277  mooseError(filename + " contains Windows(DOS) line endings which are not supported.");
278  }
279 
280  if (check_for_git_lfs_pointer && checkForGitLFSPointer(in))
281  mooseError(filename + " appears to be a Git-LFS pointer. Make sure you have \"git-lfs\" "
282  "installed so that you may pull this file.");
283  in.close();
284 
285  return true;
286 }
287 
288 bool
289 checkForGitLFSPointer(std::ifstream & file)
290 {
291  mooseAssert(file.is_open(), "Passed in file handle is not open");
292 
293  std::string line;
294 
295  // git-lfs pointer files contain several name value pairs. The specification states that the
296  // first name/value pair must be "version {url}". We'll do a simplified check for that.
297  file.seekg(0);
298  std::getline(file, line);
299  if (line.find("version https://") != std::string::npos)
300  return true;
301  else
302  return false;
303 }
304 
305 bool
306 checkFileWriteable(const std::string & filename, bool throw_on_unwritable)
307 {
308  std::ofstream out(filename.c_str(), std::ios_base::app);
309  if (out.fail())
310  {
311  if (throw_on_unwritable)
312  mooseError(
313  (std::string("Unable to open file \"") + filename +
314  std::string("\". Check to make sure that it exists and that you have write permission."))
315  .c_str());
316  else
317  return false;
318  }
319 
320  out.close();
321 
322  return true;
323 }
324 
325 void
326 parallelBarrierNotify(const Parallel::Communicator & comm, bool messaging)
327 {
328  processor_id_type secondary_processor_id;
329 
330  if (messaging)
331  Moose::out << "Waiting For Other Processors To Finish" << std::endl;
332  if (comm.rank() == 0)
333  {
334  // The primary process is already through, so report it
335  if (messaging)
336  Moose::out << "Jobs complete: 1/" << comm.size() << (1 == comm.size() ? "\n" : "\r")
337  << std::flush;
338  for (unsigned int i = 2; i <= comm.size(); ++i)
339  {
340  comm.receive(MPI_ANY_SOURCE, secondary_processor_id);
341  if (messaging)
342  Moose::out << "Jobs complete: " << i << "/" << comm.size()
343  << (i == comm.size() ? "\n" : "\r") << std::flush;
344  }
345  }
346  else
347  {
348  secondary_processor_id = comm.rank();
349  comm.send(0, secondary_processor_id);
350  }
351 
352  comm.barrier();
353 }
354 
355 void
357 {
358  // unless we are the first processor...
359  if (comm.rank() > 0)
360  {
361  // ...wait for the previous processor to finish
362  int dummy = 0;
363  comm.receive(comm.rank() - 1, dummy);
364  }
365  else if (warn)
366  mooseWarning("Entering serial execution block (use only for debugging)");
367 }
368 
369 void
371 {
372  // unless we are the last processor...
373  if (comm.rank() + 1 < comm.size())
374  {
375  // ...notify the next processor of its turn
376  int dummy = 0;
377  comm.send(comm.rank() + 1, dummy);
378  }
379 
380  comm.barrier();
381  if (comm.rank() == 0 && warn)
382  mooseWarning("Leaving serial execution block (use only for debugging)");
383 }
384 
385 bool
386 hasExtension(const std::string & filename, std::string ext, bool strip_exodus_ext)
387 {
388  // Extract the extension, w/o the '.'
389  std::string file_ext;
390  if (strip_exodus_ext)
391  {
392  pcrecpp::RE re(
393  ".*\\.([^\\.]*?)(?:-s\\d+)?\\s*$"); // capture the complete extension, ignoring -s*
394  re.FullMatch(filename, &file_ext);
395  }
396  else
397  {
398  pcrecpp::RE re(".*\\.([^\\.]*?)\\s*$"); // capture the complete extension
399  re.FullMatch(filename, &file_ext);
400  }
401 
402  // Perform the comparision
403  if (file_ext == ext)
404  return true;
405  else
406  return false;
407 }
408 
409 std::string
410 stripExtension(const std::string & s)
411 {
412  auto pos = s.rfind(".");
413  if (pos != std::string::npos)
414  return s.substr(0, pos);
415  return s;
416 }
417 
418 std::string
420 {
421  // Note: At the time of creating this method, our minimum compiler still
422  // does not support <filesystem>. Additionally, the inclusion of that header
423  // requires an additional library to be linked so for now, we'll just
424  // use the Unix standard library to get us the cwd().
425  constexpr unsigned int BUF_SIZE = 1024;
426  char buffer[BUF_SIZE];
427 
428  return getcwd(buffer, BUF_SIZE) != nullptr ? buffer : "";
429 }
430 
431 void
432 makedirs(const std::string & dir_name, bool throw_on_failure)
433 {
434  // split path into directories with delimiter '/'
435  std::vector<std::string> split_dir_names;
436  MooseUtils::tokenize(dir_name, split_dir_names);
437 
438  auto n = split_dir_names.size();
439 
440  // remove '.' and '..' when possible
441  auto i = n;
442  i = 0;
443  while (i != n)
444  {
445  if (split_dir_names[i] == ".")
446  {
447  for (auto j = i + 1; j < n; ++j)
448  split_dir_names[j - 1] = split_dir_names[j];
449  --n;
450  }
451  else if (i > 0 && split_dir_names[i] == ".." && split_dir_names[i - 1] != "..")
452  {
453  for (auto j = i + 1; j < n; ++j)
454  split_dir_names[j - 2] = split_dir_names[j];
455  n -= 2;
456  --i;
457  }
458  else
459  ++i;
460  }
461  if (n == 0)
462  return;
463 
464  split_dir_names.resize(n);
465 
466  // start creating directories recursively
467  std::string cur_dir = dir_name[0] == '/' ? "" : ".";
468  for (auto & dir : split_dir_names)
469  {
470  cur_dir += "/" + dir;
471 
472  if (!pathExists(cur_dir))
473  {
474  auto code = Utility::mkdir(cur_dir.c_str());
475  if (code != 0)
476  {
477  std::string msg = "Failed creating directory " + dir_name;
478  if (throw_on_failure)
479  throw std::invalid_argument(msg);
480  else
481  mooseError(msg);
482  }
483  }
484  }
485 }
486 
487 void
488 removedirs(const std::string & dir_name, bool throw_on_failure)
489 {
490  // split path into directories with delimiter '/'
491  std::vector<std::string> split_dir_names;
492  MooseUtils::tokenize(dir_name, split_dir_names);
493 
494  auto n = split_dir_names.size();
495 
496  // remove '.' and '..' when possible
497  auto i = n;
498  i = 0;
499  while (i != n)
500  {
501  if (split_dir_names[i] == ".")
502  {
503  for (auto j = i + 1; j < n; ++j)
504  split_dir_names[j - 1] = split_dir_names[j];
505  --n;
506  }
507  else if (i > 0 && split_dir_names[i] == ".." && split_dir_names[i - 1] != "..")
508  {
509  for (auto j = i + 1; j < n; ++j)
510  split_dir_names[j - 2] = split_dir_names[j];
511  n -= 2;
512  --i;
513  }
514  else
515  ++i;
516  }
517  if (n == 0)
518  return;
519 
520  split_dir_names.resize(n);
521 
522  // start removing directories recursively
523  std::string base_dir = dir_name[0] == '/' ? "" : ".";
524  for (i = n; i > 0; --i)
525  {
526  std::string cur_dir = base_dir;
527  auto j = i;
528  for (j = 0; j < i; ++j)
529  cur_dir += "/" + split_dir_names[j];
530 
531  // listDir should return at least '.' and '..'
532  if (pathExists(cur_dir) && listDir(cur_dir).size() == 2)
533  {
534  auto code = rmdir(cur_dir.c_str());
535  if (code != 0)
536  {
537  std::string msg = "Failed removing directory " + dir_name;
538  if (throw_on_failure)
539  throw std::invalid_argument(msg);
540  else
541  mooseError(msg);
542  }
543  }
544  else
545  // stop removing
546  break;
547  }
548 }
549 
550 std::string
551 camelCaseToUnderscore(const std::string & camel_case_name)
552 {
553  std::string replaced = camel_case_name;
554  // Put underscores in front of each contiguous set of capital letters
555  pcrecpp::RE("(?!^)(?<![A-Z_])([A-Z]+)").GlobalReplace("_\\1", &replaced);
556 
557  // Convert all capital letters to lower case
558  std::transform(replaced.begin(), replaced.end(), replaced.begin(), ::tolower);
559  return replaced;
560 }
561 
562 std::string
563 underscoreToCamelCase(const std::string & underscore_name, bool leading_upper_case)
564 {
565  pcrecpp::StringPiece input(underscore_name);
566  pcrecpp::RE re("([^_]*)(_|$)");
567 
568  std::string result;
569  std::string us, not_us;
570  bool make_upper = leading_upper_case;
571  while (re.Consume(&input, &not_us, &us))
572  {
573  if (not_us.length() > 0)
574  {
575  if (make_upper)
576  {
577  result += std::toupper(not_us[0]);
578  if (not_us.length() > 1)
579  result += not_us.substr(1);
580  }
581  else
582  result += not_us;
583  }
584  if (us == "")
585  break;
586 
587  // Toggle flag so next match is upper cased
588  make_upper = true;
589  }
590 
591  return result;
592 }
593 
594 std::string
595 shortName(const std::string & name)
596 {
597  return name.substr(name.find_last_of('/') != std::string::npos ? name.find_last_of('/') + 1 : 0);
598 }
599 
600 std::string
601 baseName(const std::string & name)
602 {
603  return name.substr(0, name.find_last_of('/') != std::string::npos ? name.find_last_of('/') : 0);
604 }
605 
606 std::string
608 {
609  char hostname[1024];
610  hostname[1023] = '\0';
611 #ifndef __WIN32__
612  if (gethostname(hostname, 1023))
613  mooseError("Failed to retrieve hostname!");
614 #else
615  DWORD dwSize = sizeof(hostname);
616  if (!GetComputerNameEx(ComputerNamePhysicalDnsHostname, hostname, &dwSize))
617  mooseError("Failed to retrieve hostname!");
618 #endif
619  return hostname;
620 }
621 
622 unsigned short
623 getTermWidth(bool use_environment)
624 {
625 #ifndef __WIN32__
626  struct winsize w;
627 #else
628  struct
629  {
630  unsigned short ws_col;
631  } w;
632 #endif
633 
638 
639  if (use_environment)
640  {
641  char * pps_width = std::getenv("MOOSE_PPS_WIDTH");
642  if (pps_width != NULL)
643  {
644  std::stringstream ss(pps_width);
645  ss >> w.ws_col;
646  }
647  }
648  // Default to AUTO if no environment variable was set
650  {
651 #ifndef __WIN32__
652  try
653  {
654  ioctl(0, TIOCGWINSZ, &w);
655  }
656  catch (...)
657 #endif
658  {
659  }
660  }
661 
662  // Something bad happened, make sure we have a sane value
663  // 132 seems good for medium sized screens, and is available as a GNOME preset
665  w.ws_col = 132;
666 
667  return w.ws_col;
668 }
669 
670 void
673 {
674  // Loop through the elements
675  for (const auto & elem_it : props)
676  {
677  Moose::out << "Element " << elem_it.first->id() << '\n';
678 
679  // Loop through the sides
680  for (const auto & side_it : elem_it.second)
681  {
682  Moose::out << " Side " << side_it.first << '\n';
683 
684  // Loop over properties
685  unsigned int cnt = 0;
686  for (const auto & mat_prop : side_it.second)
687  {
688  if (auto mp = dynamic_cast<const MaterialProperty<Real> *>(&mat_prop))
689  {
690  Moose::out << " Property " << cnt << '\n';
691  cnt++;
692 
693  // Loop over quadrature points
694  for (unsigned int qp = 0; qp < mp->size(); ++qp)
695  Moose::out << " prop[" << qp << "] = " << (*mp)[qp] << '\n';
696  }
697  }
698  }
699  }
700 
701  Moose::out << std::flush;
702 }
703 
704 std::string &
705 removeColor(std::string & msg)
706 {
707  pcrecpp::RE re("(\\33\\[3[0-7]m))", pcrecpp::DOTALL());
708  re.GlobalReplace(std::string(""), &msg);
709  return msg;
710 }
711 
712 void
713 addLineBreaks(std::string & message,
714  unsigned int line_width /*= ConsoleUtils::console_line_length*/)
715 {
716  for (auto i : make_range(int(message.length() / line_width)))
717  message.insert((i + 1) * (line_width + 2) - 2, "\n");
718 }
719 
720 void
721 indentMessage(const std::string & prefix,
722  std::string & message,
723  const char * color /*= COLOR_CYAN*/,
724  bool indent_first_line,
725  const std::string & post_prefix)
726 {
727  // First we need to see if the message we need to indent (with color) also contains color codes
728  // that span lines.
729  // The code matches all of the XTERM constants (see XTermConstants.h). If it does, then we'll work
730  // on formatting
731  // each colored multiline chunk one at a time with the right codes.
732  std::string colored_message;
733  std::string curr_color = COLOR_DEFAULT; // tracks last color code before newline
734  std::string line, color_code;
735 
736  bool ends_in_newline = message.empty() ? true : message.back() == '\n';
737 
738  bool first = true;
739 
740  std::istringstream iss(message);
741  for (std::string line; std::getline(iss, line);) // loop over each line
742  {
743  const static pcrecpp::RE match_color(".*(\\33\\[3\\dm)((?!\\33\\[3\\d)[^\n])*");
744  pcrecpp::StringPiece line_piece(line);
745  match_color.FindAndConsume(&line_piece, &color_code);
746 
747  if (!first || indent_first_line)
748  colored_message += color + prefix + post_prefix + curr_color;
749 
750  colored_message += line;
751 
752  // Only add a newline to the last line if it had one to begin with!
753  if (!iss.eof() || ends_in_newline)
754  colored_message += "\n";
755 
756  if (!color_code.empty())
757  curr_color = color_code; // remember last color of this line
758 
759  first = false;
760  }
761  message = colored_message;
762 }
763 
764 std::list<std::string>
765 listDir(const std::string path, bool files_only)
766 {
767  std::list<std::string> files;
768 
769  tinydir_dir dir;
770  dir.has_next = 0; // Avoid a garbage value in has_next (clang StaticAnalysis)
771  tinydir_open(&dir, path.c_str());
772 
773  while (dir.has_next)
774  {
775  tinydir_file file;
776  file.is_dir = 0; // Avoid a garbage value in is_dir (clang StaticAnalysis)
777  tinydir_readfile(&dir, &file);
778 
779  if (!files_only || !file.is_dir)
780  files.push_back(path + "/" + file.name);
781 
782  tinydir_next(&dir);
783  }
784 
785  tinydir_close(&dir);
786 
787  return files;
788 }
789 
790 std::list<std::string>
791 getFilesInDirs(const std::list<std::string> & directory_list, const bool files_only /* = true */)
792 {
793  std::list<std::string> files;
794 
795  for (const auto & dir_name : directory_list)
796  files.splice(files.end(), listDir(dir_name, files_only));
797 
798  return files;
799 }
800 
801 std::string
802 getLatestCheckpointFilePrefix(const std::list<std::string> & checkpoint_files)
803 {
804  // Create storage for newest restart files
805  // Note that these might have the same modification time if the simulation was fast.
806  // In that case we're going to save all of the "newest" files and sort it out momentarily
807  std::time_t newest_time = 0;
808  std::list<std::string> newest_restart_files;
809 
810  // Loop through all possible files and store the newest
811  for (const auto & cp_file : checkpoint_files)
812  {
813  if (MooseUtils::hasExtension(cp_file, "rd"))
814  {
815  struct stat stats;
816  stat(cp_file.c_str(), &stats);
817 
818  std::time_t mod_time = stats.st_mtime;
819  if (mod_time > newest_time)
820  {
821  newest_restart_files.clear(); // If the modification time is greater, clear the list
822  newest_time = mod_time;
823  }
824 
825  if (mod_time == newest_time)
826  newest_restart_files.push_back(cp_file);
827  }
828  }
829 
830  // Loop through all of the newest files according the number in the file name
831  int max_file_num = -1;
832  std::string max_file;
833  std::string max_prefix;
834 
835  // Pull out the path including the number and the number itself
836  // This takes something_blah_out_cp/0024-restart-1.rd
837  // and returns "something_blah_out_cp/0024" as the "prefix"
838  // and then "24" as the number itself
839  pcrecpp::RE re_file_num("(.*?(\\d+))-restart-\\d+.rd$");
840 
841  // Now, out of the newest files find the one with the largest number in it
842  for (const auto & res_file : newest_restart_files)
843  {
844  int file_num = 0;
845 
846  // All of the file up to and including the digits
847  std::string file_prefix;
848 
849  re_file_num.FullMatch(res_file, &file_prefix, &file_num);
850 
851  if (file_num > max_file_num)
852  {
853  // Need both the header and the data
854  if (!RestartableDataReader::isAvailable(res_file))
855  continue;
856 
857  max_file_num = file_num;
858  max_file = res_file;
859  max_prefix = file_prefix;
860  }
861  }
862 
863  // Error if nothing was located
864  if (max_file_num == -1)
865  mooseError("No checkpoint file found!");
866 
867  return max_prefix;
868 }
869 
870 bool
871 wildCardMatch(std::string name, std::string search_string)
872 {
873  // Assume that an empty string matches anything
874  if (search_string == "")
875  return true;
876 
877  // transform to lower for case insenstive matching
878  std::transform(name.begin(), name.end(), name.begin(), (int (*)(int))std::toupper);
879  std::transform(search_string.begin(),
880  search_string.end(),
881  search_string.begin(),
882  (int (*)(int))std::toupper);
883 
884  // exact match!
885  if (search_string.find("*") == std::string::npos)
886  return search_string == name;
887 
888  // wildcard
889  std::vector<std::string> tokens;
890  MooseUtils::tokenize(search_string, tokens, 1, "*");
891 
892  size_t pos = 0;
893  for (unsigned int i = 0; i < tokens.size() && pos != std::string::npos; ++i)
894  {
895  pos = name.find(tokens[i], pos);
896  // See if we have a leading wildcard
897  if (search_string[0] != '*' && i == 0 && pos != 0)
898  return false;
899  }
900 
901  if (pos != std::string::npos && tokens.size() > 0)
902  {
903  // Now see if we have a trailing wildcard
904  size_t last_token_length = tokens.back().length();
905  if (*search_string.rbegin() == '*' || pos == name.size() - last_token_length)
906  return true;
907  else
908  return false;
909  }
910  else
911  return false;
912 }
913 
914 bool
915 globCompare(const std::string & candidate,
916  const std::string & pattern,
917  std::size_t c,
918  std::size_t p)
919 {
920  if (p == pattern.size())
921  return c == candidate.size();
922 
923  if (pattern[p] == '*')
924  {
925  for (; c < candidate.size(); ++c)
926  if (globCompare(candidate, pattern, c, p + 1))
927  return true;
928  return globCompare(candidate, pattern, c, p + 1);
929  }
930 
931  if (pattern[p] != '?' && pattern[p] != candidate[c])
932  return false;
933 
934  return globCompare(candidate, pattern, c + 1, p + 1);
935 }
936 
937 template <typename T>
938 T
939 convertStringToInt(const std::string & str, bool throw_on_failure)
940 {
941  T val;
942 
943  // Let's try to read a double and see if we can cast it to an int
944  // This would be the case for scientific notation
945  long double double_val;
946  std::stringstream double_ss(str);
947  double_ss >> double_val;
948 
949  // on arm64 the long double does not have sufficient precission
950  bool use_int = false;
951  std::stringstream int_ss(str);
952  if (!(int_ss >> val).fail() && int_ss.eof())
953  use_int = true;
954 
955  if (double_ss.fail() || !double_ss.eof())
956  {
957  std::string msg =
958  std::string("Unable to convert '") + str + "' to type " + demangle(typeid(T).name());
959 
960  if (throw_on_failure)
961  throw std::invalid_argument(msg);
962  else
963  mooseError(msg);
964  }
965 
966  // Check to see if it's an integer (and within range of an integer)
967  if (double_val == static_cast<T>(double_val))
968  return use_int ? val : static_cast<T>(double_val);
969 
970  // Still failure
971  std::string msg =
972  std::string("Unable to convert '") + str + "' to type " + demangle(typeid(T).name());
973 
974  if (throw_on_failure)
975  throw std::invalid_argument(msg);
976  else
977  mooseError(msg);
978 }
979 
980 template <>
981 short int
982 convert<short int>(const std::string & str, bool throw_on_failure)
983 {
984  return convertStringToInt<short int>(str, throw_on_failure);
985 }
986 
987 template <>
988 unsigned short int
989 convert<unsigned short int>(const std::string & str, bool throw_on_failure)
990 {
991  return convertStringToInt<unsigned short int>(str, throw_on_failure);
992 }
993 
994 template <>
995 int
996 convert<int>(const std::string & str, bool throw_on_failure)
997 {
998  return convertStringToInt<int>(str, throw_on_failure);
999 }
1000 
1001 template <>
1002 unsigned int
1003 convert<unsigned int>(const std::string & str, bool throw_on_failure)
1004 {
1005  return convertStringToInt<unsigned int>(str, throw_on_failure);
1006 }
1007 
1008 template <>
1009 long int
1010 convert<long int>(const std::string & str, bool throw_on_failure)
1011 {
1012  return convertStringToInt<long int>(str, throw_on_failure);
1013 }
1014 
1015 template <>
1016 unsigned long int
1017 convert<unsigned long int>(const std::string & str, bool throw_on_failure)
1018 {
1019  return convertStringToInt<unsigned long int>(str, throw_on_failure);
1020 }
1021 
1022 template <>
1023 long long int
1024 convert<long long int>(const std::string & str, bool throw_on_failure)
1025 {
1026  return convertStringToInt<long long int>(str, throw_on_failure);
1027 }
1028 
1029 template <>
1030 unsigned long long int
1031 convert<unsigned long long int>(const std::string & str, bool throw_on_failure)
1032 {
1033  return convertStringToInt<unsigned long long int>(str, throw_on_failure);
1034 }
1035 
1036 std::string
1037 toUpper(const std::string & name)
1038 {
1039  std::string upper(name);
1040  std::transform(upper.begin(), upper.end(), upper.begin(), ::toupper);
1041  return upper;
1042 }
1043 
1044 std::string
1045 toLower(const std::string & name)
1046 {
1047  std::string lower(name);
1048  std::transform(lower.begin(), lower.end(), lower.begin(), ::tolower);
1049  return lower;
1050 }
1051 
1054 {
1056 }
1057 
1058 int
1059 stringToInteger(const std::string & input, bool throw_on_failure)
1060 {
1061  return convert<int>(input, throw_on_failure);
1062 }
1063 
1064 void
1066  dof_id_type num_chunks,
1067  dof_id_type chunk_id,
1068  dof_id_type & num_local_items,
1069  dof_id_type & local_items_begin,
1070  dof_id_type & local_items_end)
1071 {
1072  auto global_num_local_items = num_items / num_chunks;
1073 
1074  num_local_items = global_num_local_items;
1075 
1076  auto leftovers = num_items % num_chunks;
1077 
1078  if (chunk_id < leftovers)
1079  {
1080  num_local_items++;
1081  local_items_begin = num_local_items * chunk_id;
1082  }
1083  else
1084  local_items_begin =
1085  (global_num_local_items + 1) * leftovers + global_num_local_items * (chunk_id - leftovers);
1086 
1087  local_items_end = local_items_begin + num_local_items;
1088 }
1089 
1092 {
1093  auto global_num_local_items = num_items / num_chunks;
1094 
1095  auto leftovers = num_items % num_chunks;
1096 
1097  auto first_item_past_first_part = leftovers * (global_num_local_items + 1);
1098 
1099  // Is it in the first section (that gets an extra item)
1100  if (item_id < first_item_past_first_part)
1101  return item_id / (global_num_local_items + 1);
1102  else
1103  {
1104  auto new_item_id = item_id - first_item_past_first_part;
1105 
1106  // First chunk after the first section + the number of chunks after that
1107  return leftovers + (new_item_id / global_num_local_items);
1108  }
1109 }
1110 
1111 std::vector<std::string>
1112 split(const std::string & str, const std::string & delimiter, std::size_t max_count)
1113 {
1114  std::vector<std::string> output;
1115  std::size_t count = 0;
1116  size_t prev = 0, pos = 0;
1117  do
1118  {
1119  pos = str.find(delimiter, prev);
1120  output.push_back(str.substr(prev, pos - prev));
1121  prev = pos + delimiter.length();
1122  count += 1;
1123  } while (pos != std::string::npos && count < max_count);
1124 
1125  if (pos != std::string::npos)
1126  output.push_back(str.substr(prev));
1127 
1128  return output;
1129 }
1130 
1131 std::vector<std::string>
1132 rsplit(const std::string & str, const std::string & delimiter, std::size_t max_count)
1133 {
1134  std::vector<std::string> output;
1135  std::size_t count = 0;
1136  size_t prev = str.length(), pos = str.length();
1137  do
1138  {
1139  pos = str.rfind(delimiter, prev);
1140  output.insert(output.begin(), str.substr(pos + delimiter.length(), prev - pos));
1141  prev = pos - delimiter.length();
1142  count += 1;
1143  } while (pos != std::string::npos && pos > 0 && count < max_count);
1144 
1145  if (pos != std::string::npos)
1146  output.insert(output.begin(), str.substr(0, pos));
1147 
1148  return output;
1149 }
1150 
1151 void
1152 createSymlink(const std::string & target, const std::string & link)
1153 {
1154  clearSymlink(link);
1155 #ifndef __WIN32__
1156  auto err = symlink(target.c_str(), link.c_str());
1157 #else
1158  auto err = CreateSymbolicLink(target.c_str(), link.c_str(), 0);
1159 #endif
1160  if (err)
1161  mooseError("Failed to create symbolic link (via 'symlink') from ", target, " to ", link);
1162 }
1163 
1164 void
1165 clearSymlink(const std::string & link)
1166 {
1167 #ifndef __WIN32__
1168  struct stat sbuf;
1169  if (lstat(link.c_str(), &sbuf) == 0)
1170  {
1171  auto err = unlink(link.c_str());
1172  if (err != 0)
1173  mooseError("Failed to remove symbolic link (via 'unlink') to ", link);
1174  }
1175 #else
1176  auto attr = GetFileAttributesA(link.c_str());
1177  if (attr != INVALID_FILE_ATTRIBUTES)
1178  {
1179  auto err = _unlink(link.c_str());
1180  if (err != 0)
1181  mooseError("Failed to remove link/file (via '_unlink') to ", link);
1182  }
1183 #endif
1184 }
1185 
1186 std::size_t
1187 fileSize(const std::string & filename)
1188 {
1189 #ifndef __WIN32__
1190  struct stat buffer;
1191  if (!stat(filename.c_str(), &buffer))
1192  return buffer.st_size;
1193 #else
1194  HANDLE hFile = CreateFile(filename.c_str(),
1195  GENERIC_READ,
1196  FILE_SHARE_READ | FILE_SHARE_WRITE,
1197  NULL,
1198  OPEN_EXISTING,
1199  FILE_ATTRIBUTE_NORMAL,
1200  NULL);
1201  if (hFile == INVALID_HANDLE_VALUE)
1202  return 0;
1203 
1204  LARGE_INTEGER size;
1205  if (GetFileSizeEx(hFile, &size))
1206  {
1207  CloseHandle(hFile);
1208  return size.QuadPart;
1209  }
1210 
1211  CloseHandle(hFile);
1212 #endif
1213  return 0;
1214 }
1215 
1216 std::string
1217 realpath(const std::string & path)
1218 {
1219  return std::filesystem::absolute(path);
1220 }
1221 
1222 BoundingBox
1223 buildBoundingBox(const Point & p1, const Point & p2)
1224 {
1225  BoundingBox bb;
1226  bb.union_with(p1);
1227  bb.union_with(p2);
1228  return bb;
1229 }
1230 
1231 std::string
1232 prettyCppType(const std::string & cpp_type)
1233 {
1234  // On mac many of the std:: classes are inline namespaced with __1
1235  // On linux std::string can be inline namespaced with __cxx11
1236  std::string s = cpp_type;
1237  // Remove all spaces surrounding a >
1238  pcrecpp::RE("\\s(?=>)").GlobalReplace("", &s);
1239  pcrecpp::RE("std::__\\w+::").GlobalReplace("std::", &s);
1240  // It would be nice if std::string actually looked normal
1241  pcrecpp::RE("\\s*std::basic_string<char, std::char_traits<char>, std::allocator<char>>\\s*")
1242  .GlobalReplace("std::string", &s);
1243  // It would be nice if std::vector looked normal
1244  pcrecpp::RE r("std::vector<([[:print:]]+),\\s?std::allocator<\\s?\\1\\s?>\\s?>");
1245  r.GlobalReplace("std::vector<\\1>", &s);
1246  // Do it again for nested vectors
1247  r.GlobalReplace("std::vector<\\1>", &s);
1248  return s;
1249 }
1250 } // MooseUtils namespace
1251 
1252 void
1253 removeSubstring(std::string & main, const std::string & sub)
1254 {
1255  std::string::size_type n = sub.length();
1256  for (std::string::size_type i = main.find(sub); i != std::string::npos; i = main.find(sub))
1257  main.erase(i, n);
1258 }
1259 
1260 std::string
1261 removeSubstring(const std::string & main, const std::string & sub)
1262 {
1263  std::string copy_main = main;
1264  std::string::size_type n = sub.length();
1265  for (std::string::size_type i = copy_main.find(sub); i != std::string::npos;
1266  i = copy_main.find(sub))
1267  copy_main.erase(i, n);
1268  return copy_main;
1269 }
std::string name(const ElemQuality q)
OStreamProxy err
bool parsesToReal(const std::string &input)
Check if the input string can be parsed into a Real.
Definition: MooseUtils.C:88
std::string docsDir(const std::string &app_name)
Returns the directory of any installed docs/site.
Definition: MooseUtils.C:120
bool globCompare(const std::string &candidate, const std::string &pattern, std::size_t c=0, std::size_t p=0)
Definition: MooseUtils.C:915
A MultiMooseEnum object to hold "execute_on" flags.
Definition: ExecFlagEnum.h:21
void serialEnd(const libMesh::Parallel::Communicator &comm, bool warn=true)
Closes a section of code that is executed in serial rank by rank, and that was opened with a call to ...
Definition: MooseUtils.C:370
std::string toLower(const std::string &name)
Convert supplied string to lower case.
Definition: MooseUtils.C:1045
void tokenize(const std::string &str, std::vector< T > &elements, unsigned int min_len=1, const std::string &delims="/")
This function will split the passed in string on a set of delimiters appending the substrings to the ...
Definition: MooseUtils.h:779
HashMap is an abstraction for dictionary data type, we make it thread-safe by locking inserts...
Definition: HashMap.h:18
int stringToInteger(const std::string &input, bool throw_on_failure=false)
Robust string to integer conversion that fails for cases such at "1foo".
Definition: MooseUtils.C:1059
std::string toUpper(const std::string &name)
Convert supplied string to upper case.
Definition: MooseUtils.C:1037
void mooseError(Args &&... args)
Emit an error message with the given stringified, concatenated args and terminate the application...
Definition: MooseError.h:284
void MaterialPropertyStorageDump(const HashMap< const libMesh::Elem *, HashMap< unsigned int, MaterialProperties >> &props)
Function to dump the contents of MaterialPropertyStorage for debugging purposes.
Definition: MooseUtils.C:671
std::string installedInputsDir(const std::string &app_name, const std::string &dir_name, const std::string &extra_error_msg="")
Returns the directory of any installed inputs or the empty string if none are found.
Definition: MooseUtils.C:98
std::string getExecutablePath()
This function returns the PATH of the running executable.
void mooseWarning(Args &&... args)
Emit a warning message with the given stringified, concatenated args.
Definition: MooseError.h:296
bool pathIsDirectory(const std::string &path)
Definition: MooseUtils.C:247
std::list< std::string > getFilesInDirs(const std::list< std::string > &directory_list, const bool files_only=true)
Retrieves the names of all of the files contained within the list of directories passed into the rout...
Definition: MooseUtils.C:791
processor_id_type rank() const
std::string stripExtension(const std::string &s)
Removes any file extension from the given string s (i.e.
Definition: MooseUtils.C:410
void removedirs(const std::string &dir_name, bool throw_on_failure=false)
Recursively remove directories from inner-most when the directories are empty.
Definition: MooseUtils.C:488
void main(int argc, char *argv[])
Initialize, create and run a MooseApp.
Definition: MooseMain.h:37
void linearPartitionItems(dof_id_type num_items, dof_id_type num_chunks, dof_id_type chunk_id, dof_id_type &num_local_items, dof_id_type &local_items_begin, dof_id_type &local_items_end)
Linearly partition a number of items.
Definition: MooseUtils.C:1065
bool checkForGitLFSPointer(std::ifstream &file)
Check if the file is a Git-LFS pointer.
Definition: MooseUtils.C:289
std::string realpath(const std::string &path)
Wrapper around PetscGetRealPath, which is a cross-platform replacement for realpath.
Definition: MooseUtils.C:1217
static ExecFlagRegistry & getExecFlagRegistry()
Return Singleton instance.
std::string convertLatestCheckpoint(std::string orig)
Replaces "LATEST" placeholders with the latest checkpoint file name.
Definition: MooseUtils.C:146
std::string hostname()
Get the hostname the current process is running on.
Definition: MooseUtils.C:607
auto max(const L &left, const R &right)
std::string camelCaseToUnderscore(const std::string &camel_case_name)
Function for converting a camel case name to a name containing underscores.
Definition: MooseUtils.C:551
std::string shortName(const std::string &name)
Function for stripping name after the file / in parser block.
Definition: MooseUtils.C:595
void removeSubstring(std::string &main, const std::string &sub)
find, erase, length algorithm for removing a substring from a string
Definition: MooseUtils.C:1253
std::vector< std::string > split(const std::string &str, const std::string &delimiter, std::size_t max_count=std::numeric_limits< std::size_t >::max())
Python like split functions for strings.
Definition: MooseUtils.C:1112
ExecFlagEnum getDefaultExecFlagEnum()
Return the default ExecFlagEnum for MOOSE.
Definition: MooseUtils.C:1053
T convertStringToInt(const std::string &str, bool throw_on_failure)
Definition: MooseUtils.C:939
processor_id_type size() const
std::vector< std::string > rsplit(const std::string &str, const std::string &delimiter, std::size_t max_count=std::numeric_limits< std::size_t >::max())
Definition: MooseUtils.C:1132
uint8_t processor_id_type
Status receive(const unsigned int dest_processor_id, T &buf, const MessageTag &tag=any_tag) const
int convert< int >(const std::string &str, bool throw_on_failure)
Definition: MooseUtils.C:996
void indentMessage(const std::string &prefix, std::string &message, const char *color=COLOR_CYAN, bool dont_indent_first_line=true, const std::string &post_prefix=": ")
Indents the supplied message given the prefix and color.
Definition: MooseUtils.C:721
void parallelBarrierNotify(const libMesh::Parallel::Communicator &comm, bool messaging=true)
This function implements a parallel barrier function but writes progress to stdout.
std::string getLatestCheckpointFilePrefix(const std::list< std::string > &checkpoint_files)
Returns the most recent checkpoint prefix (the four numbers at the begining) If a suitable file isn&#39;t...
Definition: MooseUtils.C:802
void serialBegin(const libMesh::Parallel::Communicator &comm, bool warn=true)
This function marks the begin of a section of code that is executed in serial rank by rank...
Definition: MooseUtils.C:356
bool checkFileReadable(const std::string &filename, bool check_line_endings=false, bool throw_on_unreadable=true, bool check_for_git_lfs_pointer=true)
Checks to see if a file is readable (exists and permissions)
Definition: MooseUtils.C:253
std::string trim(const std::string &str, const std::string &white_space=" \\\)
Standard scripting language trim function.
Definition: MooseUtils.C:214
std::string runTestsExecutable()
Returns the location of either a local repo run_tests script - or an installed test executor script i...
Definition: MooseUtils.C:64
std::size_t fileSize(const std::string &filename)
Check the file size.
Definition: MooseUtils.C:1187
unsigned int convert< unsigned int >(const std::string &str, bool throw_on_failure)
Definition: MooseUtils.C:1003
std::string underscoreToCamelCase(const std::string &underscore_name, bool leading_upper_case)
Function for converting an underscore name to a camel case name.
Definition: MooseUtils.C:563
bool hasExtension(const std::string &filename, std::string ext, bool strip_exodus_ext=false)
Function tests if the supplied filename as the desired extension.
Definition: MooseUtils.C:386
std::string & removeColor(std::string &msg)
remove ANSI escape sequences for terminal color from msg
Definition: MooseUtils.C:705
std::string demangle(const char *name)
bool checkFileWriteable(const std::string &filename, bool throw_on_unwritable=true)
Check if the file is writable (path exists and permissions)
Definition: MooseUtils.C:306
void addLineBreaks(std::string &message, unsigned int line_width)
Definition: MooseUtils.C:713
charT const * delimiter
Definition: InfixIterator.h:34
void clearSymlink(const std::string &link)
Remove a symbolic link, if the given filename is a link.
Definition: MooseUtils.C:1165
long long int convert< long long int >(const std::string &str, bool throw_on_failure)
Definition: MooseUtils.C:1024
processor_id_type linearPartitionChunk(dof_id_type num_items, dof_id_type num_chunks, dof_id_type item_id)
Return the chunk_id that is assigned to handle item_id.
Definition: MooseUtils.C:1091
void createSymlink(const std::string &target, const std::string &link)
Create a symbolic link, if the link already exists it is replaced.
Definition: MooseUtils.C:1152
short int convert< short int >(const std::string &str, bool throw_on_failure)
Definition: MooseUtils.C:982
std::filesystem::path pathjoin(const std::filesystem::path &p)
Definition: MooseUtils.C:58
unsigned long int convert< unsigned long int >(const std::string &str, bool throw_on_failure)
Definition: MooseUtils.C:1017
std::string baseName(const std::string &name)
Function for string the information before the final / in a parser block.
Definition: MooseUtils.C:601
DIE A HORRIBLE DEATH HERE typedef LIBMESH_DEFAULT_SCALAR_TYPE Real
bool wildCardMatch(std::string name, std::string search_string)
Definition: MooseUtils.C:871
void send(const unsigned int dest_processor_id, const T &buf, const MessageTag &tag=no_tag) const
OStreamProxy out
IntRange< T > make_range(T beg, T end)
const ExecFlagEnum & getDefaultFlags() const
std::list< std::string > listDir(const std::string path, bool files_only=false)
Definition: MooseUtils.C:765
BoundingBox buildBoundingBox(const Point &p1, const Point &p2)
Construct a valid bounding box from 2 arbitrary points.
Definition: MooseUtils.C:1223
int levenshteinDist(const std::string &s1, const std::string &s2)
Computes and returns the Levenshtein distance between strings s1 and s2.
Definition: MooseUtils.C:165
std::string getCurrentWorkingDir()
Returns the current working directory as a string.
Definition: MooseUtils.C:419
void makedirs(const std::string &dir_name, bool throw_on_failure=false)
Recursively make directories.
Definition: MooseUtils.C:432
long int convert< long int >(const std::string &str, bool throw_on_failure)
Definition: MooseUtils.C:1010
unsigned short int convert< unsigned short int >(const std::string &str, bool throw_on_failure)
Definition: MooseUtils.C:989
bool pathContains(const std::string &expression, const std::string &string_to_find, const std::string &delims="/")
This function tokenizes a path and checks to see if it contains the string to look for...
Definition: MooseUtils.C:224
bool pathExists(const std::string &path)
Definition: MooseUtils.C:240
std::string replaceAll(std::string str, const std::string &from, const std::string &to)
Replaces all occurences of from in str with to and returns the result.
Definition: MooseUtils.C:134
auto min(const L &left, const R &right)
unsigned long long int convert< unsigned long long int >(const std::string &str, bool throw_on_failure)
Definition: MooseUtils.C:1031
void ErrorVector unsigned int
void escape(std::string &str)
This function will escape all of the standard C++ escape characters so that they can be printed...
Definition: MooseUtils.C:196
std::string prettyCppType(const std::string &cpp_type)
Definition: MooseUtils.C:1232
uint8_t dof_id_type
std::string findTestRoot()
Searches in the current working directory and then recursively up in each parent directory looking fo...
Definition: MooseUtils.C:74
unsigned short getTermWidth(bool use_environment)
Returns the width of the terminal using sys/ioctl.
Definition: MooseUtils.C:623
static bool isAvailable(const std::filesystem::path &folder_base)