Nektar++
BasicUtils/SessionReader.cpp
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1///////////////////////////////////////////////////////////////////////////////
2//
3// File: SessionReader.cpp
4//
5// For more information, please see: http://www.nektar.info
6//
7// The MIT License
8//
9// Copyright (c) 2006 Division of Applied Mathematics, Brown University (USA),
10// Department of Aeronautics, Imperial College London (UK), and Scientific
11// Computing and Imaging Institute, University of Utah (USA).
12//
13// Permission is hereby granted, free of charge, to any person obtaining a
14// copy of this software and associated documentation files (the "Software"),
15// to deal in the Software without restriction, including without limitation
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24// OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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29// DEALINGS IN THE SOFTWARE.
30//
31// Description: Session reader
32//
33///////////////////////////////////////////////////////////////////////////////
34
35#ifndef TIXML_USE_STL
36#define TIXML_USE_STL
37#endif
38
41
42#include <fstream>
43#include <iostream>
44#include <string>
45
46#include <boost/algorithm/string.hpp>
47#include <boost/iostreams/copy.hpp>
48#include <boost/iostreams/filter/gzip.hpp>
49#include <boost/iostreams/filtering_streambuf.hpp>
50
51#include <tinyxml.h>
52
60
61#include <boost/format.hpp>
62#include <boost/program_options.hpp>
63
64#ifndef NEKTAR_VERSION
65#define NEKTAR_VERSION "Unknown"
66#endif
67
68using namespace std;
69
70namespace po = boost::program_options;
71namespace io = boost::iostreams;
72
74{
75/**
76 * @class SessionReader
77 *
78 * This class provides an interface to Nektar++-specific content in a
79 * supplied XML document. It also initialises a Nektar++ session
80 * including setting up communication for parallel execution and where
81 * necessary partitioning the supplied mesh for running across multiple
82 * processes.
83 *
84 * A session should be initialised at the beginning of a user's
85 * application by passing the command-line arguments. This not only
86 * allows the SessionReader to extract the name of the XML document to
87 * load containing Nektar++ session information, but also supplies the
88 * MPI arguments necessary for setting up parallel communication. The
89 * SessionReader should be initialised using the #CreateInstance
90 * function:
91 * @code
92 * LibUtilities::SessionReaderSharedPtr vSession
93 * = LibUtilities::SessionReader::CreateInstance(argc, argv);
94 * @endcode
95 * The instance \c vSession can now be passed to other key Nektar++
96 * components during their construction.
97 * @note At the end of the user application, it is important to call the
98 * #Finalise routine in order to finalise any MPI communication and
99 * correctly free resources.
100 *
101 * The SessionReader class provides streamlined, validated access to
102 * session parameters, solver information and functions defined within a
103 * Nektar++ XML document. The available routines and their usage is
104 * documented below.
105 *
106 * In the case of solver information properties, the classes to which
107 * these parameters are pertinent may register with the SessionReader
108 * class the set of valid values for a given property. Such values may
109 * also be associated with an enumeration value for more transparent use
110 * of the property values in code.
111 */
112
113/**
114 * This map of maps stores the list of valid string values for a number
115 * of solver information parameters. The top level map connects
116 * different parameter names to their list of possible values. The list
117 * of possible values is also a map, mapping a valid string to a
118 * corresponding enum value.
119 *
120 * This list is populated through the #RegisterEnumValue static member
121 * function which is called statically from various classes to register
122 * the valid values for solver info parameters associated with them. The
123 * map is therefore fully populated before the SessionReader class is
124 * instantiated and a file is read in and parsed.
125 */
127{
128 static EnumMapList solverInfoEnums;
129 return solverInfoEnums;
130}
131
132/**
133 * List of default values for solver information parameters to be used
134 * in the case of them not being provided.
135 *
136 * This list is populated through the #RegisterDefaultSolverInfo static
137 * member variable which is called statically from various classes to
138 * register the default value for a given parameter.
139 */
141{
142 static SolverInfoMap solverInfoMap;
143 return solverInfoMap;
144}
145
146/**
147 * List of values for GlobalSysSoln parameters to be used to override
148 * details given in SolverInfo
149 *
150 * This list is populated by ReadGlobalSysSolnInfo if the
151 * GLOBALSYSSOLNINFO section is defined in the input file.
152 * This List allows for details to define for the Global Sys
153 * solver for each variable.
154 */
156{
157 static GloSysSolnInfoList gloSysSolnInfoList;
158 return gloSysSolnInfoList;
159}
160
161/**
162 * Lists the possible command-line argument which can be specified for
163 * this executable.
164 *
165 * This list is populated through the #RegisterCmdLineArgument static
166 * member function which is called statically from various classes to
167 * register command-line arguments they need.
168 */
170{
171 static CmdLineArgMap cmdLineArguments;
172 return cmdLineArguments;
173}
174
175/**
176 * This constructor parses the command-line arguments given to the user
177 * application to set up any MPI communication, read supplied XML
178 * session files, and partition meshes where necessary.
179 *
180 * @param argc Number of command-line arguments
181 * @param argv Array of command-line arguments
182 */
183SessionReader::SessionReader(int argc, char *argv[])
184{
185 m_xmlDoc = nullptr;
187
188 ASSERTL0(m_filenames.size() > 0, "No session file(s) given.");
189
191
192 // Create communicator
193 CreateComm(argc, argv);
194
196
197 // Split up the communicator
199
200 // If running in parallel change the default global sys solution
201 // type.
202 if (m_comm->GetSpaceComm()->GetSize() > 1)
203 {
204 GetSolverInfoDefaults()["GLOBALSYSSOLN"] = "IterativeStaticCond";
205 }
206
208 m_interpreter->SetRandomSeed((m_comm->GetSpaceComm()->GetRank() + 1) *
209 (unsigned int)time(nullptr));
210}
211
212/**
213 *
214 */
215SessionReader::SessionReader(int argc, char *argv[],
216 const std::vector<std::string> &pFilenames,
217 const CommSharedPtr &pComm, const int &timelevel)
218{
219 ASSERTL0(pFilenames.size() > 0, "No filenames specified.");
220
221 ParseCommandLineArguments(argc, argv);
222 m_xmlDoc = nullptr;
223 m_filenames = pFilenames;
224
226
227 // Create communicator
228 if (!pComm.get())
229 {
230 CreateComm(argc, argv);
231 }
232 else
233 {
234 m_comm = pComm;
235 }
236
238
239 // Split up the communicator
241
242 // If running in parallel change the default global sys solution
243 // type.
244 if (m_comm->GetSpaceComm()->GetSize() > 1)
245 {
246 GetSolverInfoDefaults()["GLOBALSYSSOLN"] = "IterativeStaticCond";
247 }
248
250 m_interpreter->SetRandomSeed((m_comm->GetSpaceComm()->GetRank() + 1) *
251 (unsigned int)time(nullptr));
252
253 // Set time level (Parallel-in-Time)
254 m_timeLevel = timelevel;
255}
256
257/**
258 *
259 */
261{
262 if (m_xmlDoc)
263 {
264 delete m_xmlDoc;
265 }
266}
267
268/**
269 * Performs the main initialisation of the object. The XML file provided
270 * on the command-line is loaded and any mesh partitioning is done. The
271 * resulting process-specific XML file (containing the process's
272 * geometry partition) is then reloaded and parsed.
273 */
274void SessionReader::InitSession(const std::vector<std::string> &filenames)
275{
276 // Re-load filenames for session if required.
277 if (filenames.size() > 0)
278 {
279 m_filenames = filenames;
280 }
281
282 // check specified opt file
283 std::string optfile;
284 int exists;
285
286 if (DefinesCmdLineArgument("use-opt-file"))
287 {
288 optfile =
289 m_cmdLineOptions.find("use-opt-file")->second.as<std::string>();
290 exists = fs::exists(optfile.c_str());
291 ASSERTL0(exists, "A valid .opt file was not specified "
292 "with the --use-opt-file command line option");
293
294 m_filenames.push_back(optfile);
295
296 // put opt file at beginning
297 std::rotate(m_filenames.rbegin(), m_filenames.rbegin() + 1,
298 m_filenames.rend());
299 }
300 else // check for write-opt-file
301 {
302 // check for opt file
303 optfile = m_sessionName.substr(0, m_sessionName.find("_xml/")) + ".opt";
304 exists = fs::exists(optfile.c_str());
305
306 // For Paralell-in-Time
307 if (exists && m_comm->IsParallelInTime())
308 {
309 TiXmlDocument doc;
310 doc.LoadFile(optfile);
311 TiXmlElement *xmlTag = doc.FirstChildElement("NEKTAR")
312 ->FirstChildElement("COLLECTIONS")
313 ->FirstChildElement("TIMELEVEL");
314 if (xmlTag)
315 {
316 // if there is a TIMELEVEL tag, then turn existing flag to false
317 // and check if the required time level is specified in the
318 // optfile.
319 exists = false;
320 while (xmlTag)
321 {
322 if (m_timeLevel == stoi(xmlTag->Attribute("VALUE")))
323 {
324 exists = true;
325 break;
326 }
327 xmlTag = xmlTag->NextSiblingElement();
328 }
329 }
330 }
331
332 if (exists)
333 {
334 m_filenames.push_back(optfile);
335 // rotate order so opt file can be overwritten by
336 // direct choice in xml file
337 std::rotate(m_filenames.rbegin(), m_filenames.rbegin() + 1,
338 m_filenames.rend());
339 }
340 else
341 {
342 m_updateOptFile = true;
343 }
344 }
345
346 // Merge document if required.
347 if (m_xmlDoc)
348 {
349 delete m_xmlDoc;
350 }
351
353
354 // Parse the XML data in #m_xmlDoc
356
357 // Override SOLVERINFO and parameters with any specified on the
358 // command line.
360
361 // Verify SOLVERINFO values
363
364 // Disable backups if NEKTAR_DISABLE_BACKUPS is set.
365 if (std::getenv("NEKTAR_DISABLE_BACKUPS") != nullptr)
366 {
367 m_backups = false;
368 }
369
370 // In verbose mode, print out parameters and solver info sections
371 if (m_verbose && m_comm)
372 {
373 if (m_comm->TreatAsRankZero() && m_parameters.size() > 0)
374 {
375 cout << "Parameters:" << endl;
376 for (auto &x : m_parameters)
377 {
378 cout << "\t" << x.first << " = " << x.second << endl;
379 }
380 cout << endl;
381 }
382
383 if (m_comm->TreatAsRankZero() && m_solverInfo.size() > 0)
384 {
385 cout << "Solver Info:" << endl;
386 for (auto &x : m_solverInfo)
387 {
388 cout << "\t" << x.first << " = " << x.second << endl;
389 }
390 cout << endl;
391 }
392 }
393}
394
395/**
396 *
397 */
399{
400 m_sharedFilesystem = false;
401
402 if (m_comm->GetSize() > 1)
403 {
404 if (m_comm->GetRank() == 0)
405 {
406 std::ofstream testfile("shared-fs-testfile");
407 testfile << "" << std::endl;
408 ASSERTL1(!testfile.fail(), "Test file creation failed");
409 testfile.close();
410 }
411 m_comm->Block();
412
413 int exists = fs::exists("shared-fs-testfile");
414 m_comm->AllReduce(exists, LibUtilities::ReduceSum);
415
416 m_sharedFilesystem = (exists == m_comm->GetSize());
417
418 if ((m_sharedFilesystem && m_comm->GetRank() == 0) ||
420 {
421 std::remove("shared-fs-testfile");
422 }
423 }
424 else
425 {
426 m_sharedFilesystem = false;
427 }
428
429 if (m_verbose && m_comm->GetRank() == 0 && m_sharedFilesystem)
430 {
431 cout << "Shared filesystem detected" << endl;
432 }
433}
434
435/**
436 * @brief Parses the command-line arguments for known options and
437 * filenames.
438 */
439std::vector<std::string> SessionReader::ParseCommandLineArguments(int argc,
440 char *argv[])
441{
442 // List the publically visible options (listed using --help).
443 po::options_description desc("Allowed options");
444 po::options_description dep("Deprecated options");
445
446 // clang-format off
447 desc.add_options()
448 ("force-output,f","disables backups files and forces output to be "
449 "written without any checks")
450 ("help,h", "print this help message")
451 ("solverinfo,I", po::value<vector<std::string>>(),
452 "override a SOLVERINFO property")
453 ("parameter,P", po::value<vector<std::string>>(),
454 "override a parameter")
455 ("verbose,v", "be verbose")
456 ("version,V", "print version information")
457 ("no-exp-opt", "Do not use expansion optimisation for collections")
458 ("npx", po::value<int>(),
459 "number of procs in X-dir")
460 ("npy", po::value<int>(),
461 "number of procs in Y-dir")
462 ("npz", po::value<int>(),
463 "number of procs in Z-dir")
464 ("nsz", po::value<int>(),
465 "number of slices in Z-dir")
466 ("npt", po::value<int>(),
467 "number of procs in T-dir (parareal)")
468 ("part-only", po::value<int>(),
469 "only partition mesh into N partitions.")
470 ("part-only-overlapping", po::value<int>(),
471 "only partition mesh into N overlapping partitions.")
472 ("part-info", "output partition information")
473 ("write-opt-file","write an optimisation file")
474 ("use-opt-file", po::value<std::string>(),
475 "use an optimisation file");
476 // clang-format on
477
478#ifdef NEKTAR_USE_CWIPI
479 desc.add_options()("cwipi", po::value<std::string>(), "set CWIPI name");
480#endif
481
482 for (auto &cmdIt : GetCmdLineArgMap())
483 {
484 std::string names = cmdIt.first;
485 if (cmdIt.second.shortName != "")
486 {
487 names += "," + cmdIt.second.shortName;
488 }
489 if (cmdIt.second.isFlag)
490 {
491 desc.add_options()(names.c_str(), cmdIt.second.description.c_str());
492 }
493 else
494 {
495 desc.add_options()(names.c_str(), po::value<std::string>(),
496 cmdIt.second.description.c_str());
497 }
498 }
499
500 // Deprecated options: introduced in 5.4.0 to homogenise command-line
501 // options to use '-' instead of camelCase or no spaces.
502 std::map<std::string, std::string> deprecated = {
503 {"forceoutput", "force-output"},
504 {"writeoptfile", "write-opt-file"},
505 {"useoptfile", "use-opt-file"}};
506
507 for (auto &d : deprecated)
508 {
509 std::string description = "Deprecated: use --" + d.second;
510 dep.add_options()(d.first.c_str(), description.c_str());
511 }
512
513 // List hidden options (e.g. session file arguments are not actually
514 // specified using the input-file option by the user).
515 po::options_description hidden("Hidden options");
516
517 hidden.add_options()("input-file", po::value<vector<string>>(),
518 "input filename");
519
520 // Combine all options for the parser
521 po::options_description all("All options");
522 all.add(desc).add(dep).add(hidden);
523
524 // Session file is a positional option
525 po::positional_options_description p;
526 p.add("input-file", -1);
527
528 // Parse the command-line options
529 po::parsed_options parsed = po::command_line_parser(argc, argv)
530 .options(all)
531 .positional(p)
532 .allow_unregistered()
533 .run();
534
535 // Extract known options to map and update
536 po::store(parsed, m_cmdLineOptions);
537 po::notify(m_cmdLineOptions);
538
539 // Help message
540 if (m_cmdLineOptions.count("help"))
541 {
542 cout << desc;
543 exit(0);
544 }
545
546 // Version information
547 if (m_cmdLineOptions.count("version"))
548 {
549 cout << "Nektar++ version " << NEKTAR_VERSION;
550
551 if (NekConstants::kGitSha1 != "GITDIR-NOTFOUND")
552 {
554 string branch(NekConstants::kGitBranch);
555 boost::replace_all(branch, "refs/heads/", "");
556
557 cout << " (git changeset " << sha1.substr(0, 8) << ", ";
558
559 if (branch == "")
560 {
561 cout << "detached head";
562 }
563 else
564 {
565 cout << "head " << branch;
566 }
567
568 cout << ")";
569 }
570
571 cout << endl;
572 exit(0);
573 }
574
575 // Deal with deprecated options.
576 for (auto &d : deprecated)
577 {
578 if (m_cmdLineOptions.count(d.first))
579 {
580 std::cerr << "Warning: --" << d.first << " deprecated: use --"
581 << d.second << std::endl;
582 m_cmdLineOptions.emplace(
583 d.second, po::variable_value(m_cmdLineOptions[d.first]));
584 }
585 }
586
587 // Enable verbose mode
588 if (m_cmdLineOptions.count("verbose"))
589 {
590 m_verbose = true;
591 }
592 else
593 {
594 m_verbose = false;
595 }
596
597 // Disable backups
598 if (m_cmdLineOptions.count("force-output"))
599 {
600 m_backups = false;
601 }
602 else
603 {
604 m_backups = true;
605 }
606
607 // Enable update optimisation file
608 if (m_cmdLineOptions.count("write-opt-file"))
609 {
610 m_updateOptFile = true;
611 }
612 else
613 {
614 m_updateOptFile = false;
615 }
616
617 // Print a warning for unknown options
618 for (auto &x : parsed.options)
619 {
620 if (x.unregistered)
621 {
622 cout << "Warning: Unknown option: " << x.string_key << endl;
623 }
624 }
625
626 // Return the vector of filename(s) given as positional options
627 if (m_cmdLineOptions.count("input-file"))
628 {
629 return m_cmdLineOptions["input-file"].as<std::vector<std::string>>();
630 }
631 else
632 {
633 return std::vector<std::string>();
634 }
635}
636
637/**
638 *
639 */
640std::string SessionReader::ParseSessionName(std::vector<std::string> &filenames)
641{
642 ASSERTL0(!filenames.empty(), "At least one filename expected.");
643
644 std::string retval = "";
645
646 // First input file defines the session name
647 std::string fname = filenames[0];
648
649 // If loading a pre-partitioned mesh, remove _xml extension
650 if (fname.size() > 4 && fname.substr(fname.size() - 4, 4) == "_xml")
651 {
652 retval = fname.substr(0, fname.find_last_of("_"));
653 }
654 // otherwise remove the .xml extension
655 else if (fname.size() > 4 && fname.substr(fname.size() - 4, 4) == ".xml")
656 {
657 retval = fname.substr(0, fname.find_last_of("."));
658 }
659 // If compressed .xml.gz, remove both extensions
660 else if (fname.size() > 7 && fname.substr(fname.size() - 7, 7) == ".xml.gz")
661 {
662 retval = fname.substr(0, fname.find_last_of("."));
663 retval = retval.substr(0, retval.find_last_of("."));
664 }
665
666 return retval;
667}
668
669/**
670 *
671 */
673{
674 ASSERTL1(m_xmlDoc, "XML Document not defined.");
675 return *m_xmlDoc;
676}
677
678/**
679 * The single parameter specifies a path to the requested element in a
680 * similar format to the filesystem path. Given the following XML:
681 * @code
682 * <NEKTAR>
683 * <CONDITIONS>
684 * <PARAMETERS>
685 * ...
686 * </PARAMETERS>
687 * </CONDITIONS>
688 * </NEKTAR>
689 * @endcode
690 * the PARAMETERS element would be retrieved by requesting the path:
691 * @code
692 * Nektar/Conditions/Parameters
693 * @endcode
694 * @note Paths are case-insensitive.
695 *
696 * @param pPath Path to requested element.
697 *
698 * @return Direct pointer to requested XML Element.
699 */
700TiXmlElement *SessionReader::GetElement(const string &pPath)
701{
702 std::string vPath = boost::to_upper_copy(pPath);
703 std::vector<std::string> st;
704 boost::split(st, vPath, boost::is_any_of("\\/ "));
705 ASSERTL0(st.size() > 0, "No path given in XML element request.");
706
707 TiXmlElement *vReturn = m_xmlDoc->FirstChildElement(st[0].c_str());
708 ASSERTL0(vReturn,
709 std::string("Cannot find element '") + st[0] + std::string("'."));
710 for (int i = 1; i < st.size(); ++i)
711 {
712 vReturn = vReturn->FirstChildElement(st[i].c_str());
713 ASSERTL0(vReturn, std::string("Cannot find element '") + st[i] +
714 std::string("'."));
715 }
716 return vReturn;
717}
718
719/**
720 *
721 */
722bool SessionReader::DefinesElement(const std::string &pPath) const
723{
724 std::string vPath = boost::to_upper_copy(pPath);
725 std::vector<std::string> st;
726 boost::split(st, vPath, boost::is_any_of("\\/ "));
727 ASSERTL0(st.size() > 0, "No path given in XML element request.");
728
729 TiXmlElement *vReturn = m_xmlDoc->FirstChildElement(st[0].c_str());
730 ASSERTL0(vReturn,
731 std::string("Cannot find element '") + st[0] + std::string("'."));
732 for (int i = 1; i < st.size(); ++i)
733 {
734 vReturn = vReturn->FirstChildElement(st[i].c_str());
735 if (!vReturn)
736 {
737 return false;
738 }
739 }
740 return true;
741}
742
743/**
744 *
745 */
746const std::vector<std::string> &SessionReader::GetFilenames() const
747{
748 return m_filenames;
749}
750
751/**
752 *
753 */
754const std::string &SessionReader::GetSessionName() const
755{
756 return m_sessionName;
757}
758
759/**
760 *
761 */
763{
764 return m_comm;
765}
766
768{
769 return m_sharedFilesystem;
770}
771
772/**
773 * This routine finalises any parallel communication.
774 *
775 * @note This routine should be called at the very end of a users
776 * application.
777 */
779{
780 m_comm->Finalise();
781}
782
783/**
784 *
785 */
786bool SessionReader::DefinesParameter(const std::string &pName) const
787{
788 std::string vName = boost::to_upper_copy(pName);
789 return m_parameters.find(vName) != m_parameters.end();
790}
791
792/**
793 * If the parameter is not defined, termination occurs. Therefore, the
794 * parameters existence should be tested for using #DefinesParameter
795 * before calling this function.
796 *
797 * @param pName The name of a floating-point parameter.
798 * @returns The value of the floating-point parameter.
799 */
800const NekDouble &SessionReader::GetParameter(const std::string &pName) const
801{
802 std::string vName = boost::to_upper_copy(pName);
803 auto paramIter = m_parameters.find(vName);
804
805 ASSERTL0(paramIter != m_parameters.end(),
806 "Unable to find requested parameter: " + pName);
807
808 return paramIter->second;
809}
810
811/**
812 * Getter for the session's parameters
813 * @returns A reference to the parameter map
814 */
816{
817 return m_parameters;
818}
819
820/**
821 *
822 */
823void SessionReader::LoadParameter(const std::string &pName, int &pVar) const
824{
825 std::string vName = boost::to_upper_copy(pName);
826 auto paramIter = m_parameters.find(vName);
827 ASSERTL0(paramIter != m_parameters.end(),
828 "Required parameter '" + pName + "' not specified in session.");
829 NekDouble param = round(paramIter->second);
830 pVar = checked_cast<int>(param);
831}
832
833/**
834 *
835 */
836void SessionReader::LoadParameter(const std::string &pName, int &pVar,
837 const int &pDefault) const
838{
839 std::string vName = boost::to_upper_copy(pName);
840 auto paramIter = m_parameters.find(vName);
841 if (paramIter != m_parameters.end())
842 {
843 NekDouble param = round(paramIter->second);
844 pVar = checked_cast<int>(param);
845 }
846 else
847 {
848 pVar = pDefault;
849 }
850}
851
852/**
853 *
854 */
855void SessionReader::LoadParameter(const std::string &pName, size_t &pVar) const
856{
857 std::string vName = boost::to_upper_copy(pName);
858 auto paramIter = m_parameters.find(vName);
859 ASSERTL0(paramIter != m_parameters.end(),
860 "Required parameter '" + pName + "' not specified in session.");
861 NekDouble param = round(paramIter->second);
862 pVar = checked_cast<int>(param);
863}
864
865/**
866 *
867 */
868void SessionReader::LoadParameter(const std::string &pName, size_t &pVar,
869 const size_t &pDefault) const
870{
871 std::string vName = boost::to_upper_copy(pName);
872 auto paramIter = m_parameters.find(vName);
873 if (paramIter != m_parameters.end())
874 {
875 NekDouble param = round(paramIter->second);
876 pVar = checked_cast<int>(param);
877 }
878 else
879 {
880 pVar = pDefault;
881 }
882}
883
884/**
885 *
886 */
887void SessionReader::LoadParameter(const std::string &pName,
888 NekDouble &pVar) const
889{
890 std::string vName = boost::to_upper_copy(pName);
891 auto paramIter = m_parameters.find(vName);
892 ASSERTL0(paramIter != m_parameters.end(),
893 "Required parameter '" + pName + "' not specified in session.");
894 pVar = paramIter->second;
895}
896
897/**
898 *
899 */
900void SessionReader::LoadParameter(const std::string &pName, NekDouble &pVar,
901 const NekDouble &pDefault) const
902{
903 std::string vName = boost::to_upper_copy(pName);
904 auto paramIter = m_parameters.find(vName);
905 if (paramIter != m_parameters.end())
906 {
907 pVar = paramIter->second;
908 }
909 else
910 {
911 pVar = pDefault;
912 }
913}
914
915/**
916 *
917 */
918void SessionReader::SetParameter(const std::string &pName, int &pVar)
919{
920 std::string vName = boost::to_upper_copy(pName);
921 m_parameters[vName] = pVar;
922}
923
924/**
925 *
926 */
927void SessionReader::SetParameter(const std::string &pName, size_t &pVar)
928{
929 std::string vName = boost::to_upper_copy(pName);
930 m_parameters[vName] = pVar;
931}
932
933/**
934 *
935 */
936void SessionReader::SetParameter(const std::string &pName, NekDouble &pVar)
937{
938 std::string vName = boost::to_upper_copy(pName);
939 m_parameters[vName] = pVar;
940}
941
942/**
943 *
944 */
945bool SessionReader::DefinesSolverInfo(const std::string &pName) const
946{
947 std::string vName = boost::to_upper_copy(pName);
948 auto infoIter = m_solverInfo.find(vName);
949 return (infoIter != m_solverInfo.end());
950}
951
952/**
953 *
954 */
956 const std::string &pProperty) const
957{
958 std::string vProperty = boost::to_upper_copy(pProperty);
959 auto iter = m_solverInfo.find(vProperty);
960
961 ASSERTL1(iter != m_solverInfo.end(),
962 "Unable to find requested property: " + pProperty);
963
964 return iter->second;
965}
966
967/**
968 *
969 */
970void SessionReader::SetSolverInfo(const std::string &pProperty,
971 const std::string &pValue)
972{
973 std::string vProperty = boost::to_upper_copy(pProperty);
974 auto iter = m_solverInfo.find(vProperty);
975
976 ASSERTL1(iter != m_solverInfo.end(),
977 "Unable to find requested property: " + pProperty);
978
979 iter->second = pValue;
980}
981
982/**
983 *
984 */
985void SessionReader::LoadSolverInfo(const std::string &pName, std::string &pVar,
986 const std::string &pDefault) const
987{
988 std::string vName = boost::to_upper_copy(pName);
989 auto infoIter = m_solverInfo.find(vName);
990 if (infoIter != m_solverInfo.end())
991 {
992 pVar = infoIter->second;
993 }
994 else
995 {
996 pVar = pDefault;
997 }
998}
999
1000/**
1001 *
1002 */
1003void SessionReader::MatchSolverInfo(const std::string &pName,
1004 const std::string &pTrueVal, bool &pVar,
1005 const bool &pDefault) const
1006{
1007 std::string vName = boost::to_upper_copy(pName);
1008 auto infoIter = m_solverInfo.find(vName);
1009 if (infoIter != m_solverInfo.end())
1010 {
1011 pVar = boost::iequals(infoIter->second, pTrueVal);
1012 }
1013 else
1014 {
1015 pVar = pDefault;
1016 }
1017}
1018
1019/**
1020 *
1021 */
1022bool SessionReader::MatchSolverInfo(const std::string &pName,
1023 const std::string &pTrueVal) const
1024{
1025 if (DefinesSolverInfo(pName))
1026 {
1027 std::string vName = boost::to_upper_copy(pName);
1028 auto iter = m_solverInfo.find(vName);
1029 if (iter != m_solverInfo.end())
1030 {
1031 return boost::iequals(iter->second, pTrueVal);
1032 }
1033 }
1034 return false;
1035}
1036
1037/**
1038 *
1039 */
1040bool SessionReader::DefinesGlobalSysSolnInfo(const std::string &pVariable,
1041 const std::string &pProperty) const
1042{
1043 auto iter = GetGloSysSolnList().find(pVariable);
1044 if (iter == GetGloSysSolnList().end())
1045 {
1046 return false;
1047 }
1048
1049 std::string vProperty = boost::to_upper_copy(pProperty);
1050
1051 auto iter1 = iter->second.find(vProperty);
1052 if (iter1 == iter->second.end())
1053 {
1054 return false;
1055 }
1056
1057 return true;
1058}
1059
1060/**
1061 *
1062 */
1064 const std::string &pVariable, const std::string &pProperty) const
1065{
1066 auto iter = GetGloSysSolnList().find(pVariable);
1067 ASSERTL0(iter != GetGloSysSolnList().end(),
1068 "Failed to find variable in GlobalSysSolnInfoList");
1069
1070 std::string vProperty = boost::to_upper_copy(pProperty);
1071 auto iter1 = iter->second.find(vProperty);
1072
1073 ASSERTL0(iter1 != iter->second.end(),
1074 "Failed to find property: " + vProperty +
1075 " in GlobalSysSolnInfoList");
1076
1077 return iter1->second;
1078}
1079
1080/**
1081 * @brief Returns true if the TIMEINTEGRATIONSCHEME section is defined
1082 * in the session file.
1083 */
1085{
1086 return m_timeIntScheme.method != "";
1087}
1088
1089/**
1090 * @brief Returns the time integration scheme structure #m_timeIntScheme
1091 * from the session file.
1092 */
1094{
1095 return m_timeIntScheme;
1096}
1097
1098/**
1099 *
1100 */
1102{
1103 TiXmlElement *xmlGeom =
1104 m_xmlDoc->FirstChildElement("NEKTAR")->FirstChildElement("GEOMETRY");
1105 ASSERTL1(xmlGeom, "Failed to find a GEOMETRY section in m_xmlDoc");
1106
1107 TiXmlAttribute *attr = xmlGeom->FirstAttribute();
1108 while (attr)
1109 {
1110 std::string attrName(attr->Name());
1111 if (attrName == "HDF5FILE")
1112 {
1113 // there is a file pointer, therefore is HDF5
1114 return "HDF5";
1115 }
1116 // Get the next attribute.
1117 attr = attr->Next();
1118 }
1119
1120 // Check the VERTEX block. If this is compressed, assume the file is
1121 // compressed, otherwise assume uncompressed.
1122 TiXmlElement *element = xmlGeom->FirstChildElement("VERTEX");
1123 string IsCompressed;
1124 element->QueryStringAttribute("COMPRESSED", &IsCompressed);
1125
1126 if (IsCompressed.size() > 0)
1127 {
1128 return "XmlCompressed";
1129 }
1130
1131 // no file pointer or compressed, just standard xml
1132 return "Xml";
1133}
1134
1135/**
1136 *
1137 */
1138const std::string &SessionReader::GetVariable(const unsigned int &idx) const
1139{
1140 ASSERTL0(idx < m_variables.size(), "Variable index out of range.");
1141 return m_variables[idx];
1142}
1143
1144/**
1145 *
1146 */
1147void SessionReader::SetVariable(const unsigned int &idx, std::string newname)
1148{
1149 ASSERTL0(idx < m_variables.size(), "Variable index out of range.");
1150 m_variables[idx] = newname;
1151}
1152
1153/**
1154 *
1155 */
1156std::vector<std::string> SessionReader::GetVariables() const
1157{
1158 return m_variables;
1159}
1160
1161/**
1162 *
1163 */
1165{
1166 return m_backups;
1167}
1168
1169/**
1170 *
1171 */
1172bool SessionReader::DefinesFunction(const std::string &pName) const
1173{
1174 std::string vName = boost::to_upper_copy(pName);
1175 return m_functions.find(vName) != m_functions.end();
1176}
1177
1178/**
1179 *
1180 */
1181bool SessionReader::DefinesFunction(const std::string &pName,
1182 const std::string &pVariable,
1183 const int pDomain) const
1184{
1185 std::string vName = boost::to_upper_copy(pName);
1186
1187 // Check function exists
1188 auto it1 = m_functions.find(vName);
1189 if (it1 != m_functions.end())
1190 {
1191 pair<std::string, int> key(pVariable, pDomain);
1192 pair<std::string, int> defkey("*", pDomain);
1193 bool varExists = it1->second.find(key) != it1->second.end() ||
1194 it1->second.find(defkey) != it1->second.end();
1195 return varExists;
1196 }
1197 return false;
1198}
1199
1200/**
1201 *
1202 */
1204 const std::string &pVariable,
1205 const int pDomain) const
1206{
1207 std::string vName = boost::to_upper_copy(pName);
1208 auto it1 = m_functions.find(vName);
1209
1210 ASSERTL0(it1 != m_functions.end(),
1211 std::string("No such function '") + pName +
1212 std::string("' has been defined in the session file."));
1213
1214 // Check for specific and wildcard definitions
1215 pair<std::string, int> key(pVariable, pDomain);
1216 pair<std::string, int> defkey("*", pDomain);
1217
1218 auto it2 = it1->second.find(key);
1219 auto it3 = it1->second.find(defkey);
1220 bool specific = it2 != it1->second.end();
1221 bool wildcard = it3 != it1->second.end();
1222
1223 // Check function is defined somewhere
1224 ASSERTL0(specific || wildcard,
1225 "No such variable " + pVariable + " in domain " +
1226 boost::lexical_cast<string>(pDomain) +
1227 " defined for function " + pName + " in session file.");
1228
1229 // If not specific, must be wildcard
1230 if (!specific)
1231 {
1232 it2 = it3;
1233 }
1234
1235 ASSERTL0((it2->second.m_type == eFunctionTypeExpression),
1236 std::string("Function is defined by a file."));
1237 return it2->second.m_expression;
1238}
1239
1240/**
1241 *
1242 */
1244 const unsigned int &pVar,
1245 const int pDomain) const
1246{
1247 ASSERTL0(pVar < m_variables.size(), "Variable index out of range.");
1248 return GetFunction(pName, m_variables[pVar], pDomain);
1249}
1250
1251/**
1252 *
1253 */
1254enum FunctionType SessionReader::GetFunctionType(const std::string &pName,
1255 const std::string &pVariable,
1256 const int pDomain) const
1257{
1258 std::string vName = boost::to_upper_copy(pName);
1259 auto it1 = m_functions.find(vName);
1260
1261 ASSERTL0(it1 != m_functions.end(),
1262 std::string("Function '") + pName + std::string("' not found."));
1263
1264 // Check for specific and wildcard definitions
1265 pair<std::string, int> key(pVariable, pDomain);
1266 pair<std::string, int> defkey("*", pDomain);
1267
1268 auto it2 = it1->second.find(key);
1269 auto it3 = it1->second.find(defkey);
1270 bool specific = it2 != it1->second.end();
1271 bool wildcard = it3 != it1->second.end();
1272
1273 // Check function is defined somewhere
1274 ASSERTL0(specific || wildcard,
1275 "No such variable " + pVariable + " in domain " +
1276 boost::lexical_cast<string>(pDomain) +
1277 " defined for function " + pName + " in session file.");
1278
1279 // If not specific, must be wildcard
1280 if (!specific)
1281 {
1282 it2 = it3;
1283 }
1284
1285 return it2->second.m_type;
1286}
1287
1288/**
1289 *
1290 */
1291enum FunctionType SessionReader::GetFunctionType(const std::string &pName,
1292 const unsigned int &pVar,
1293 const int pDomain) const
1294{
1295 ASSERTL0(pVar < m_variables.size(), "Variable index out of range.");
1296 return GetFunctionType(pName, m_variables[pVar], pDomain);
1297}
1298
1299/**
1300 *
1301 */
1302std::string SessionReader::GetFunctionFilename(const std::string &pName,
1303 const std::string &pVariable,
1304 const int pDomain) const
1305{
1306 std::string vName = boost::to_upper_copy(pName);
1307 auto it1 = m_functions.find(vName);
1308
1309 ASSERTL0(it1 != m_functions.end(),
1310 std::string("Function '") + pName + std::string("' not found."));
1311
1312 // Check for specific and wildcard definitions
1313 pair<std::string, int> key(pVariable, pDomain);
1314 pair<std::string, int> defkey("*", pDomain);
1315
1316 auto it2 = it1->second.find(key);
1317 auto it3 = it1->second.find(defkey);
1318 bool specific = it2 != it1->second.end();
1319 bool wildcard = it3 != it1->second.end();
1320
1321 // Check function is defined somewhere
1322 ASSERTL0(specific || wildcard,
1323 "No such variable " + pVariable + " in domain " +
1324 boost::lexical_cast<string>(pDomain) +
1325 " defined for function " + pName + " in session file.");
1326
1327 // If not specific, must be wildcard
1328 if (!specific)
1329 {
1330 it2 = it3;
1331 }
1332
1333 return it2->second.m_filename;
1334}
1335
1336/**
1337 *
1338 */
1339std::string SessionReader::GetFunctionFilename(const std::string &pName,
1340 const unsigned int &pVar,
1341 const int pDomain) const
1342{
1343 ASSERTL0(pVar < m_variables.size(), "Variable index out of range.");
1344 return GetFunctionFilename(pName, m_variables[pVar], pDomain);
1345}
1346
1347/**
1348 *
1349 */
1351 const std::string &pName, const std::string &pVariable,
1352 const int pDomain) const
1353{
1354 std::string vName = boost::to_upper_copy(pName);
1355 auto it1 = m_functions.find(vName);
1356
1357 ASSERTL0(it1 != m_functions.end(),
1358 std::string("Function '") + pName + std::string("' not found."));
1359
1360 // Check for specific and wildcard definitions
1361 pair<std::string, int> key(pVariable, pDomain);
1362 pair<std::string, int> defkey("*", pDomain);
1363
1364 auto it2 = it1->second.find(key);
1365 auto it3 = it1->second.find(defkey);
1366 bool specific = it2 != it1->second.end();
1367 bool wildcard = it3 != it1->second.end();
1368
1369 // Check function is defined somewhere
1370 ASSERTL0(specific || wildcard,
1371 "No such variable " + pVariable + " in domain " +
1372 boost::lexical_cast<string>(pDomain) +
1373 " defined for function " + pName + " in session file.");
1374
1375 // If not specific, must be wildcard
1376 if (!specific)
1377 {
1378 it2 = it3;
1379 }
1380
1381 return it2->second.m_fileVariable;
1382}
1383
1384/**
1385 *
1386 */
1387bool SessionReader::DefinesTag(const std::string &pName) const
1388{
1389 std::string vName = boost::to_upper_copy(pName);
1390 return m_tags.find(vName) != m_tags.end();
1391}
1392
1393/**
1394 *
1395 */
1396void SessionReader::SetTag(const std::string &pName, const std::string &pValue)
1397{
1398 std::string vName = boost::to_upper_copy(pName);
1399 m_tags[vName] = pValue;
1400}
1401
1402/**
1403 *
1404 */
1405const std::string &SessionReader::GetTag(const std::string &pName) const
1406{
1407 std::string vName = boost::to_upper_copy(pName);
1408 auto vTagIterator = m_tags.find(vName);
1409 ASSERTL0(vTagIterator != m_tags.end(), "Requested tag does not exist.");
1410 return vTagIterator->second;
1411}
1412
1413/**
1414 *
1415 */
1417{
1418 return m_filters;
1419}
1420
1421/**
1422 *
1423 */
1424bool SessionReader::DefinesCmdLineArgument(const std::string &pName) const
1425{
1426 return (m_cmdLineOptions.find(pName) != m_cmdLineOptions.end());
1427}
1428
1429/**
1430 *
1431 */
1432void SessionReader::GetXMLElementTimeLevel(TiXmlElement *&Element,
1433 const size_t timeLevel,
1434 const bool enableCheck)
1435{
1436 if (Element && Element->FirstChildElement("TIMELEVEL"))
1437 {
1438 Element = Element->FirstChildElement("TIMELEVEL");
1439 std::string timeLevelStr;
1440 while (Element)
1441 {
1442 std::stringstream tagcontent;
1443 tagcontent << *Element;
1444 ASSERTL0(Element->Attribute("VALUE"),
1445 "Missing LEVEL attribute in solver info "
1446 "XML element: \n\t'" +
1447 tagcontent.str() + "'");
1448 timeLevelStr = Element->Attribute("VALUE");
1449 ASSERTL0(!timeLevelStr.empty(),
1450 "LEVEL attribute must be non-empty in XML "
1451 "element: \n\t'" +
1452 tagcontent.str() + "'");
1453 if (stoi(timeLevelStr) == timeLevel)
1454 {
1455 break;
1456 }
1457 Element = Element->NextSiblingElement("TIMELEVEL");
1458 }
1459 if (enableCheck)
1460 {
1461 ASSERTL0(stoi(timeLevelStr) == timeLevel,
1462 "TIMELEVEL value " + std::to_string(timeLevel) +
1463 " not found in solver info "
1464 "XML element: \n\t'");
1465 }
1466 }
1467}
1468
1469/**
1470 *
1471 */
1472void SessionReader::LoadDoc(const std::string &pFilename,
1473 TiXmlDocument *pDoc) const
1474{
1475 if (pFilename.size() > 3 &&
1476 pFilename.substr(pFilename.size() - 3, 3) == ".gz")
1477 {
1478 ifstream file(pFilename.c_str(), ios_base::in | ios_base::binary);
1479 ASSERTL0(file.good(), "Unable to open file: " + pFilename);
1480 stringstream ss;
1481 io::filtering_streambuf<io::input> in;
1482 in.push(io::gzip_decompressor());
1483 in.push(file);
1484 try
1485 {
1486 io::copy(in, ss);
1487 ss >> (*pDoc);
1488 }
1489 catch (io::gzip_error &)
1490 {
1492 "Error: File '" + pFilename + "' is corrupt.");
1493 }
1494 }
1495 else if (pFilename.size() > 4 &&
1496 pFilename.substr(pFilename.size() - 4, 4) == "_xml")
1497 {
1498 fs::path pdirname(pFilename);
1499 boost::format pad("P%1$07d.xml");
1500 pad % m_comm->GetSpaceComm()->GetRank();
1501 fs::path pRankFilename(pad.str());
1502 fs::path fullpath = pdirname / pRankFilename;
1503
1504 ifstream file(PortablePath(fullpath).c_str());
1505 ASSERTL0(file.good(), "Unable to open file: " + fullpath.string());
1506 file >> (*pDoc);
1507 }
1508 else
1509 {
1510 ifstream file(pFilename.c_str());
1511 ASSERTL0(file.good(), "Unable to open file: " + pFilename);
1512 file >> (*pDoc);
1513 }
1514}
1515
1516/**
1517 *
1518 */
1520 const std::vector<std::string> &pFilenames) const
1521{
1522 ASSERTL0(pFilenames.size() > 0, "No filenames for merging.");
1523
1524 // Read the first document
1525 TiXmlDocument *vMainDoc = new TiXmlDocument;
1526 LoadDoc(pFilenames[0], vMainDoc);
1527
1528 TiXmlHandle vMainHandle(vMainDoc);
1529 TiXmlElement *vMainNektar =
1530 GetChildElementOrThrow(pFilenames[0], "NEKTAR", vMainHandle);
1531
1532 // Read all subsequent XML documents.
1533 // For each element within the NEKTAR tag, use it to replace the
1534 // version already present in the loaded XML data.
1535 for (int i = 1; i < pFilenames.size(); ++i)
1536 {
1537 if ((pFilenames[i].compare(pFilenames[i].size() - 3, 3, "xml") == 0) ||
1538 (pFilenames[i].compare(pFilenames[i].size() - 6, 6, "xml.gz") ==
1539 0) ||
1540 (pFilenames[i].compare(pFilenames[i].size() - 3, 3, "opt") == 0))
1541 {
1542 TiXmlDocument *vTempDoc = new TiXmlDocument;
1543 LoadDoc(pFilenames[i], vTempDoc);
1544
1545 TiXmlHandle docHandle(vTempDoc);
1546 TiXmlElement *vTempNektar =
1547 GetChildElementOrThrow(pFilenames[i], "NEKTAR", docHandle);
1548 TiXmlElement *p = vTempNektar->FirstChildElement();
1549
1550 while (p)
1551 {
1552 TiXmlElement *vMainEntry =
1553 vMainNektar->FirstChildElement(p->Value());
1554
1555 // First check if the new item is in fact blank
1556 // replace if it is a COLLECTIONS section however.
1557 if (!p->FirstChild() && vMainEntry &&
1558 !boost::iequals(p->Value(), "COLLECTIONS"))
1559 {
1560 std::string warningmsg =
1561 "File " + pFilenames[i] + " contains " +
1562 "an empty XML element " + std::string(p->Value()) +
1563 " which will be ignored.";
1564 NEKERROR(ErrorUtil::ewarning, warningmsg.c_str());
1565 }
1566 else
1567 {
1568 if (vMainEntry)
1569 {
1570 vMainNektar->RemoveChild(vMainEntry);
1571 }
1572 TiXmlElement *q = new TiXmlElement(*p);
1573 vMainNektar->LinkEndChild(q);
1574 }
1575 p = p->NextSiblingElement();
1576 }
1577 delete vTempDoc;
1578 }
1579 }
1580 return vMainDoc;
1581}
1582
1583/**
1584 *
1585 */
1587{
1588 // Check we actually have a document loaded.
1589 ASSERTL0(m_xmlDoc, "No XML document loaded.");
1590
1591 TiXmlHandle docHandle(m_xmlDoc);
1592 TiXmlElement *e;
1593
1594 // Look for all data in CONDITIONS block.
1595 e = docHandle.FirstChildElement("NEKTAR")
1596 .FirstChildElement("CONDITIONS")
1597 .Element();
1598
1599 // Read the various sections of the CONDITIONS block
1600 ReadParameters(e);
1601 ReadSolverInfo(e);
1604 ReadVariables(e);
1605 ReadFunctions(e);
1606
1607 // Look for all data in FILTERS block.
1608 e = docHandle.FirstChildElement("NEKTAR")
1609 .FirstChildElement("FILTERS")
1610 .Element();
1611
1612 // Read the various sections of the FILTERS block
1613 ReadFilters(e);
1614}
1615
1616/**
1617 *
1618 */
1619void SessionReader::CreateComm(int &argc, char *argv[])
1620{
1621 if (argc == 0)
1622 {
1623 m_comm = GetCommFactory().CreateInstance("Serial", 0, 0);
1624 }
1625 else
1626 {
1627 string vCommModule("Serial");
1628 if (GetCommFactory().ModuleExists("ParallelMPI"))
1629 {
1630 vCommModule = "ParallelMPI";
1631 }
1632 if (m_cmdLineOptions.count("cwipi") &&
1633 GetCommFactory().ModuleExists("CWIPI"))
1634 {
1635 vCommModule = "CWIPI";
1636 }
1637
1638 m_comm = GetCommFactory().CreateInstance(vCommModule, argc, argv);
1639 }
1640}
1641
1642/**
1643 * Splits the processes into a cartesian grid and creates communicators
1644 * for each row and column of the grid.
1645 */
1647{
1648 if (m_comm->GetSize() > 1)
1649 {
1650 int nProcZ = 1;
1651 int nProcY = 1;
1652 int nProcX = 1;
1653 int nStripZ = 1;
1654 int nTime = 1;
1655 if (DefinesCmdLineArgument("npx"))
1656 {
1657 nProcX = GetCmdLineArgument<int>("npx");
1658 }
1659 if (DefinesCmdLineArgument("npy"))
1660 {
1661 nProcY = GetCmdLineArgument<int>("npy");
1662 }
1663 if (DefinesCmdLineArgument("npz"))
1664 {
1665 nProcZ = GetCmdLineArgument<int>("npz");
1666 }
1667 if (DefinesCmdLineArgument("nsz"))
1668 {
1669 nStripZ = GetCmdLineArgument<int>("nsz");
1670 }
1671 if (DefinesCmdLineArgument("npt"))
1672 {
1673 nTime = GetCmdLineArgument<int>("npt");
1674 }
1675 ASSERTL0(m_comm->GetSize() % nTime == 0,
1676 "Cannot exactly partition time using npt value.");
1677 ASSERTL0((m_comm->GetSize() / nTime) % (nProcZ * nProcY * nProcX) == 0,
1678 "Cannot exactly partition using PROC_Z value.");
1679 ASSERTL0(nProcZ % nProcY == 0,
1680 "Cannot exactly partition using PROC_Y value.");
1681 ASSERTL0(nProcY % nProcX == 0,
1682 "Cannot exactly partition using PROC_X value.");
1683
1684 // Number of processes associated with the spectral method
1685 int nProcSm = nProcZ * nProcY * nProcX;
1686
1687 // Number of processes associated with the spectral element
1688 // method.
1689 int nProcSem = m_comm->GetSize() / nTime / nProcSm;
1690
1691 m_comm->SplitComm(nProcSm, nProcSem, nTime);
1692 m_comm->GetColumnComm()->SplitComm(nProcZ / nStripZ, nStripZ);
1693 m_comm->GetColumnComm()->GetColumnComm()->SplitComm((nProcY * nProcX),
1694 nProcZ / nStripZ);
1695 m_comm->GetColumnComm()->GetColumnComm()->GetColumnComm()->SplitComm(
1696 nProcX, nProcY);
1697 }
1698}
1699
1700/**
1701 *
1702 */
1703void SessionReader::ReadParameters(TiXmlElement *conditions)
1704{
1705 m_parameters.clear();
1706
1707 if (!conditions)
1708 {
1709 return;
1710 }
1711
1712 TiXmlElement *parametersElement =
1713 conditions->FirstChildElement("PARAMETERS");
1714 GetXMLElementTimeLevel(parametersElement, m_timeLevel);
1715
1716 // See if we have parameters defined. They are optional so we go on
1717 // if not.
1718 if (parametersElement)
1719 {
1720 TiXmlElement *parameter = parametersElement->FirstChildElement("P");
1721
1722 ParameterMap caseSensitiveParameters;
1723
1724 // Multiple nodes will only occur if there is a comment in
1725 // between definitions.
1726 while (parameter)
1727 {
1728 stringstream tagcontent;
1729 tagcontent << *parameter;
1730 TiXmlNode *node = parameter->FirstChild();
1731
1732 while (node && node->Type() != TiXmlNode::TINYXML_TEXT)
1733 {
1734 node = node->NextSibling();
1735 }
1736
1737 if (node)
1738 {
1739 // Format is "paramName = value"
1740 std::string line = node->ToText()->Value(), lhs, rhs;
1741
1742 try
1743 {
1744 ParseEquals(line, lhs, rhs);
1745 }
1746 catch (...)
1747 {
1749 "Syntax error in parameter expression '" + line +
1750 "' in XML element: \n\t'" + tagcontent.str() +
1751 "'");
1752 }
1753
1754 // We want the list of parameters to have their RHS
1755 // evaluated, so we use the expression evaluator to do
1756 // the dirty work.
1757 if (!lhs.empty() && !rhs.empty())
1758 {
1759 NekDouble value = 0.0;
1760 try
1761 {
1762 LibUtilities::Equation expession(m_interpreter, rhs);
1763 value = expession.Evaluate();
1764 }
1765 catch (const std::runtime_error &)
1766 {
1768 "Error evaluating parameter expression"
1769 " '" +
1770 rhs + "' in XML element: \n\t'" +
1771 tagcontent.str() + "'");
1772 }
1773 m_interpreter->SetParameter(lhs, value);
1774 caseSensitiveParameters[lhs] = value;
1775 boost::to_upper(lhs);
1776 m_parameters[lhs] = value;
1777 }
1778 }
1779 parameter = parameter->NextSiblingElement();
1780 }
1781 }
1782}
1783
1784/**
1785 *
1786 */
1787void SessionReader::ReadSolverInfo(TiXmlElement *conditions)
1788{
1789 m_solverInfo.clear();
1791
1792 if (!conditions)
1793 {
1794 return;
1795 }
1796
1797 TiXmlElement *solverInfoElement =
1798 conditions->FirstChildElement("SOLVERINFO");
1799 GetXMLElementTimeLevel(solverInfoElement, m_timeLevel);
1800
1801 if (solverInfoElement)
1802 {
1803 TiXmlElement *solverInfo = solverInfoElement->FirstChildElement("I");
1804
1805 while (solverInfo)
1806 {
1807 std::stringstream tagcontent;
1808 tagcontent << *solverInfo;
1809 // read the property name
1810 ASSERTL0(solverInfo->Attribute("PROPERTY"),
1811 "Missing PROPERTY attribute in solver info "
1812 "XML element: \n\t'" +
1813 tagcontent.str() + "'");
1814 std::string solverProperty = solverInfo->Attribute("PROPERTY");
1815 ASSERTL0(!solverProperty.empty(),
1816 "PROPERTY attribute must be non-empty in XML "
1817 "element: \n\t'" +
1818 tagcontent.str() + "'");
1819
1820 // make sure that solver property is capitalised
1821 std::string solverPropertyUpper =
1822 boost::to_upper_copy(solverProperty);
1823
1824 // read the value
1825 ASSERTL0(solverInfo->Attribute("VALUE"),
1826 "Missing VALUE attribute in solver info "
1827 "XML element: \n\t'" +
1828 tagcontent.str() + "'");
1829 std::string solverValue = solverInfo->Attribute("VALUE");
1830 ASSERTL0(!solverValue.empty(),
1831 "VALUE attribute must be non-empty in XML "
1832 "element: \n\t'" +
1833 tagcontent.str() + "'");
1834
1835 // Set Variable
1836 m_solverInfo[solverPropertyUpper] = solverValue;
1837 solverInfo = solverInfo->NextSiblingElement("I");
1838 }
1839 }
1840
1841 if (m_comm && m_comm->GetRowComm()->GetSize() > 1)
1842 {
1843 ASSERTL0(
1844 m_solverInfo["GLOBALSYSSOLN"] == "IterativeFull" ||
1845 m_solverInfo["GLOBALSYSSOLN"] == "IterativeStaticCond" ||
1846 m_solverInfo["GLOBALSYSSOLN"] ==
1847 "IterativeMultiLevelStaticCond" ||
1848 m_solverInfo["GLOBALSYSSOLN"] == "XxtFull" ||
1849 m_solverInfo["GLOBALSYSSOLN"] == "XxtStaticCond" ||
1850 m_solverInfo["GLOBALSYSSOLN"] == "XxtMultiLevelStaticCond" ||
1851 m_solverInfo["GLOBALSYSSOLN"] == "PETScFull" ||
1852 m_solverInfo["GLOBALSYSSOLN"] == "PETScStaticCond" ||
1853 m_solverInfo["GLOBALSYSSOLN"] == "PETScMultiLevelStaticCond",
1854 "A parallel solver must be used when run in parallel.");
1855 }
1856}
1857
1858/**
1859 *
1860 */
1861void SessionReader::ReadGlobalSysSolnInfo(TiXmlElement *conditions)
1862{
1863 GetGloSysSolnList().clear();
1864
1865 if (!conditions)
1866 {
1867 return;
1868 }
1869
1870 TiXmlElement *GlobalSys =
1871 conditions->FirstChildElement("GLOBALSYSSOLNINFO");
1873
1874 if (!GlobalSys)
1875 {
1876 return;
1877 }
1878
1879 TiXmlElement *VarInfo = GlobalSys->FirstChildElement("V");
1880
1881 while (VarInfo)
1882 {
1883 std::stringstream tagcontent;
1884 tagcontent << *VarInfo;
1885
1886 ASSERTL0(VarInfo->Attribute("VAR"),
1887 "Missing VAR attribute in GobalSysSolnInfo XML "
1888 "element: \n\t'" +
1889 tagcontent.str() + "'");
1890 std::string VarList = VarInfo->Attribute("VAR");
1891 ASSERTL0(!VarList.empty(),
1892 "VAR attribute must be non-empty in XML element:\n\t'" +
1893 tagcontent.str() + "'");
1894
1895 // generate a list of variables.
1896 std::vector<std::string> varStrings;
1897 bool valid = ParseUtils::GenerateVector(VarList, varStrings);
1898
1899 ASSERTL0(valid, "Unable to process list of variable in XML "
1900 "element \n\t'" +
1901 tagcontent.str() + "'");
1902
1903 if (varStrings.size())
1904 {
1905 TiXmlElement *SysSolnInfo = VarInfo->FirstChildElement("I");
1906
1907 while (SysSolnInfo)
1908 {
1909 tagcontent.clear();
1910 tagcontent << *SysSolnInfo;
1911 // read the property name
1912 ASSERTL0(SysSolnInfo->Attribute("PROPERTY"),
1913 "Missing PROPERTY attribute in "
1914 "GlobalSysSolnInfo for variable(s) '" +
1915 VarList + "' in XML element: \n\t'" +
1916 tagcontent.str() + "'");
1917 std::string SysSolnProperty =
1918 SysSolnInfo->Attribute("PROPERTY");
1919 ASSERTL0(!SysSolnProperty.empty(),
1920 "GlobalSysSolnIno properties must have a "
1921 "non-empty name for variable(s) : '" +
1922 VarList + "' in XML element: \n\t'" +
1923 tagcontent.str() + "'");
1924
1925 // make sure that solver property is capitalised
1926 std::string SysSolnPropertyUpper =
1927 boost::to_upper_copy(SysSolnProperty);
1928
1929 // read the value
1930 ASSERTL0(SysSolnInfo->Attribute("VALUE"),
1931 "Missing VALUE attribute in GlobalSysSolnInfo "
1932 "for variable(s) '" +
1933 VarList + "' in XML element: \n\t" +
1934 tagcontent.str() + "'");
1935 std::string SysSolnValue = SysSolnInfo->Attribute("VALUE");
1936 ASSERTL0(!SysSolnValue.empty(),
1937 "GlobalSysSolnInfo properties must have a "
1938 "non-empty value for variable(s) '" +
1939 VarList + "' in XML element: \n\t'" +
1940 tagcontent.str() + "'");
1941
1942 // Store values under variable map.
1943 for (int i = 0; i < varStrings.size(); ++i)
1944 {
1945 auto x = GetGloSysSolnList().find(varStrings[i]);
1946 if (x == GetGloSysSolnList().end())
1947 {
1948 (GetGloSysSolnList()[varStrings[i]])
1949 [SysSolnPropertyUpper] = SysSolnValue;
1950 }
1951 else
1952 {
1953 x->second[SysSolnPropertyUpper] = SysSolnValue;
1954 }
1955 }
1956 SysSolnInfo = SysSolnInfo->NextSiblingElement("I");
1957 }
1958 VarInfo = VarInfo->NextSiblingElement("V");
1959 }
1960 }
1961
1962 if (m_verbose && GetGloSysSolnList().size() > 0 && m_comm)
1963 {
1964 if (m_comm->GetRank() == 0)
1965 {
1966 cout << "GlobalSysSoln Info:" << endl;
1967
1968 for (auto &x : GetGloSysSolnList())
1969 {
1970 cout << "\t Variable: " << x.first << endl;
1971
1972 for (auto &y : x.second)
1973 {
1974 cout << "\t\t " << y.first << " = " << y.second << endl;
1975 }
1976 }
1977 cout << endl;
1978 }
1979 }
1980}
1981
1982/**
1983 * @brief Read the time-integration scheme structure, if present.
1984 */
1985void SessionReader::ReadTimeIntScheme(TiXmlElement *conditions)
1986{
1987 if (!conditions)
1988 {
1989 return;
1990 }
1991
1992 TiXmlElement *timeInt =
1993 conditions->FirstChildElement("TIMEINTEGRATIONSCHEME");
1995
1996 if (!timeInt)
1997 {
1998 return;
1999 }
2000
2001 TiXmlElement *method = timeInt->FirstChildElement("METHOD");
2002 TiXmlElement *variant = timeInt->FirstChildElement("VARIANT");
2003 TiXmlElement *order = timeInt->FirstChildElement("ORDER");
2004 TiXmlElement *params = timeInt->FirstChildElement("FREEPARAMETERS");
2005
2006 // Only the method and order are required.
2007 ASSERTL0(method, "Missing METHOD tag inside "
2008 "TIMEINTEGRATIONSCHEME.");
2009 ASSERTL0(order, "Missing ORDER tag inside "
2010 "TIMEINTEGRATIONSCHEME.");
2011
2012 m_timeIntScheme.method = method->GetText();
2013
2014 std::string orderStr = order->GetText();
2015
2016 // Only the method and order are required.
2017 ASSERTL0(m_timeIntScheme.method.size() > 0,
2018 "Empty text inside METHOD tag in TIMEINTEGRATIONSCHEME.");
2019 ASSERTL0(orderStr.size() > 0,
2020 "Empty text inside ORDER tag in TIMEINTEGRATIONSCHEME.");
2021 try
2022 {
2023 m_timeIntScheme.order = boost::lexical_cast<unsigned int>(orderStr);
2024 }
2025 catch (...)
2026 {
2027 NEKERROR(ErrorUtil::efatal, "In ORDER tag, unable to convert "
2028 "string '" +
2029 orderStr + "' to an unsigned integer.");
2030 }
2031
2032 if (variant)
2033 {
2034 m_timeIntScheme.variant = variant->GetText();
2035 }
2036
2037 if (params)
2038 {
2039 std::string paramsStr = params->GetText();
2040 ASSERTL0(paramsStr.size() > 0,
2041 "Empty text inside FREEPARAMETERS tag in "
2042 "TIMEINTEGRATIONSCHEME.");
2043
2044 std::vector<std::string> pSplit;
2045 boost::split(pSplit, paramsStr, boost::is_any_of(" "));
2046
2047 m_timeIntScheme.freeParams.resize(pSplit.size());
2048 for (size_t i = 0; i < pSplit.size(); ++i)
2049 {
2050 try
2051 {
2053 boost::lexical_cast<NekDouble>(pSplit[i]);
2054 }
2055 catch (...)
2056 {
2057 NEKERROR(ErrorUtil::efatal, "In FREEPARAMETERS tag, "
2058 "unable to convert string '" +
2059 pSplit[i] +
2060 "' "
2061 "to a floating-point value.");
2062 }
2063 }
2064 }
2065
2066 if (m_verbose && m_comm)
2067 {
2068 if (m_comm->GetRank() == 0)
2069 {
2070 cout << "Trying to use time integration scheme:" << endl;
2071 cout << "\t Method : " << m_timeIntScheme.method << endl;
2072 cout << "\t Variant: " << m_timeIntScheme.variant << endl;
2073 cout << "\t Order : " << m_timeIntScheme.order << endl;
2074
2075 if (m_timeIntScheme.freeParams.size() > 0)
2076 {
2077 cout << "\t Params :";
2078 for (auto &x : m_timeIntScheme.freeParams)
2079 {
2080 cout << " " << x;
2081 }
2082 cout << endl;
2083 }
2084 }
2085 }
2086}
2087
2088/**
2089 *
2090 */
2091void SessionReader::ReadVariables(TiXmlElement *conditions)
2092{
2093 m_variables.clear();
2094
2095 if (!conditions)
2096 {
2097 return;
2098 }
2099
2100 TiXmlElement *variablesElement = conditions->FirstChildElement("VARIABLES");
2101 GetXMLElementTimeLevel(variablesElement, m_timeLevel);
2102
2103 // See if we have parameters defined. They are optional so we go on
2104 // if not.
2105 if (variablesElement)
2106 {
2107 TiXmlElement *varElement = variablesElement->FirstChildElement("V");
2108
2109 // Sequential counter for the composite numbers.
2110 int nextVariableNumber = -1;
2111
2112 while (varElement)
2113 {
2114 stringstream tagcontent;
2115 tagcontent << *varElement;
2116
2117 /// All elements are of the form: "<V ID="#"> name = value
2118 /// </V>", with ? being the element type.
2119 nextVariableNumber++;
2120
2121 int i;
2122 int err = varElement->QueryIntAttribute("ID", &i);
2123 ASSERTL0(err == TIXML_SUCCESS,
2124 "Variables must have a unique ID number attribute "
2125 "in XML element: \n\t'" +
2126 tagcontent.str() + "'");
2127 ASSERTL0(i == nextVariableNumber,
2128 "ID numbers for variables must begin with zero and"
2129 " be sequential in XML element: \n\t'" +
2130 tagcontent.str() + "'");
2131
2132 TiXmlNode *varChild = varElement->FirstChild();
2133 // This is primarily to skip comments that may be present.
2134 // Comments appear as nodes just like elements. We are
2135 // specifically looking for text in the body of the
2136 // definition.
2137 while (varChild && varChild->Type() != TiXmlNode::TINYXML_TEXT)
2138 {
2139 varChild = varChild->NextSibling();
2140 }
2141
2142 ASSERTL0(varChild, "Unable to read variable definition body for "
2143 "variable with ID " +
2144 boost::lexical_cast<string>(i) +
2145 " in XML element: \n\t'" + tagcontent.str() +
2146 "'");
2147 std::string variableName = varChild->ToText()->ValueStr();
2148
2149 std::istringstream variableStrm(variableName);
2150 variableStrm >> variableName;
2151
2153 variableName) == m_variables.end(),
2154 "Variable with ID " + boost::lexical_cast<string>(i) +
2155 " in XML element \n\t'" + tagcontent.str() +
2156 "'\nhas already been defined.");
2157
2158 m_variables.push_back(variableName);
2159
2160 varElement = varElement->NextSiblingElement("V");
2161 }
2162
2163 ASSERTL0(nextVariableNumber > -1,
2164 "Number of variables must be greater than zero.");
2165 }
2166}
2167
2168/**
2169 *
2170 */
2171void SessionReader::ReadFunctions(TiXmlElement *conditions)
2172{
2173 m_functions.clear();
2174
2175 if (!conditions)
2176 {
2177 return;
2178 }
2179
2180 // Scan through conditions section looking for functions.
2181 TiXmlElement *function = conditions->FirstChildElement("FUNCTION");
2182
2183 while (function)
2184 {
2185 stringstream tagcontent;
2186 tagcontent << *function;
2187
2188 // Every function must have a NAME attribute
2189 ASSERTL0(function->Attribute("NAME"),
2190 "Functions must have a NAME attribute defined in XML "
2191 "element: \n\t'" +
2192 tagcontent.str() + "'");
2193 std::string functionStr = function->Attribute("NAME");
2194 ASSERTL0(!functionStr.empty(),
2195 "Functions must have a non-empty name in XML "
2196 "element: \n\t'" +
2197 tagcontent.str() + "'");
2198
2199 // Store function names in uppercase to remain case-insensitive.
2200 boost::to_upper(functionStr);
2201
2202 // Retrieve first entry (variable, or file)
2203 TiXmlElement *element = function;
2204 GetXMLElementTimeLevel(element, m_timeLevel, false);
2205 TiXmlElement *variable = element->FirstChildElement();
2206
2207 // Create new function structure with default type of none.
2208 FunctionVariableMap functionVarMap;
2209
2210 // Process all entries in the function block
2211 while (variable)
2212 {
2214 std::string conditionType = variable->Value();
2215
2216 // If no var is specified, assume wildcard
2217 std::string variableStr;
2218 if (!variable->Attribute("VAR"))
2219 {
2220 variableStr = "*";
2221 }
2222 else
2223 {
2224 variableStr = variable->Attribute("VAR");
2225 }
2226
2227 // Parse list of variables
2228 std::vector<std::string> variableList;
2229 ParseUtils::GenerateVector(variableStr, variableList);
2230
2231 // If no domain is specified, put to 0
2232 std::string domainStr;
2233 if (!variable->Attribute("DOMAIN"))
2234 {
2235 domainStr = "0";
2236 }
2237 else
2238 {
2239 domainStr = variable->Attribute("DOMAIN");
2240 }
2241
2242 // Parse list of domains
2243 std::vector<std::string> varSplit;
2244 std::vector<unsigned int> domainList;
2245 ParseUtils::GenerateSeqVector(domainStr, domainList);
2246
2247 // if no evars is specified, put "x y z t"
2248 std::string evarsStr = "x y z t";
2249 if (variable->Attribute("EVARS"))
2250 {
2251 evarsStr =
2252 evarsStr + std::string(" ") + variable->Attribute("EVARS");
2253 }
2254
2255 // Expressions are denoted by E
2256 if (conditionType == "E")
2257 {
2259
2260 // Expression must have a VALUE.
2261 ASSERTL0(variable->Attribute("VALUE"),
2262 "Attribute VALUE expected for function '" +
2263 functionStr + "'.");
2264 std::string fcnStr = variable->Attribute("VALUE");
2265 ASSERTL0(!fcnStr.empty(),
2266 (std::string("Expression for var: ") + variableStr +
2267 std::string(" must be specified."))
2268 .c_str());
2269
2270 // set expression
2271 funcDef.m_expression =
2273 m_interpreter, fcnStr, evarsStr);
2274 }
2275
2276 // Files are denoted by F
2277 else if (conditionType == "F")
2278 {
2279 // Check if transient or not
2280 if (variable->Attribute("TIMEDEPENDENT") &&
2281 boost::lexical_cast<bool>(
2282 variable->Attribute("TIMEDEPENDENT")))
2283 {
2285 }
2286 else
2287 {
2288 funcDef.m_type = eFunctionTypeFile;
2289 }
2290
2291 // File must have a FILE.
2292 ASSERTL0(variable->Attribute("FILE"),
2293 "Attribute FILE expected for function '" +
2294 functionStr + "'.");
2295 std::string filenameStr = variable->Attribute("FILE");
2296 ASSERTL0(!filenameStr.empty(),
2297 "A filename must be specified for the FILE "
2298 "attribute of function '" +
2299 functionStr + "'.");
2300
2301 std::vector<std::string> fSplit;
2302 boost::split(fSplit, filenameStr, boost::is_any_of(":"));
2303 ASSERTL0(fSplit.size() == 1 || fSplit.size() == 2,
2304 "Incorrect filename specification in function " +
2305 functionStr +
2306 "'. "
2307 "Specify variables inside file as: "
2308 "filename:var1,var2");
2309
2310 // set the filename
2311 fs::path fullpath = fSplit[0];
2312 fs::path ftype = fullpath.extension();
2313 if (fullpath.parent_path().extension() == ".pit")
2314 {
2315 string filename = fullpath.stem().string();
2316 fullpath = fullpath.parent_path();
2317 size_t start = filename.find_last_of("_") + 1;
2318 int index =
2319 atoi(filename.substr(start, filename.size()).c_str());
2320 fullpath /= filename.substr(0, start) +
2321 std::to_string(
2322 index + m_comm->GetTimeComm()->GetRank()) +
2323 ftype.string();
2324 }
2325 funcDef.m_filename = fullpath.string();
2326
2327 if (fSplit.size() == 2)
2328 {
2329 ASSERTL0(variableList[0] != "*",
2330 "Filename variable mapping not valid "
2331 "when using * as a variable inside "
2332 "function '" +
2333 functionStr + "'.");
2334
2335 boost::split(varSplit, fSplit[1], boost::is_any_of(","));
2336 ASSERTL0(varSplit.size() == variableList.size(),
2337 "Filename variables should contain the "
2338 "same number of variables defined in "
2339 "VAR in function " +
2340 functionStr + "'.");
2341 }
2342 }
2343
2344 // Nothing else supported so throw an error
2345 else
2346 {
2347 stringstream tagcontent;
2348 tagcontent << *variable;
2349
2351 "Identifier " + conditionType + " in function " +
2352 std::string(function->Attribute("NAME")) +
2353 " is not recognised in XML element: \n\t'" +
2354 tagcontent.str() + "'");
2355 }
2356
2357 // Add variables to function
2358 for (unsigned int i = 0; i < variableList.size(); ++i)
2359 {
2360 for (unsigned int j = 0; j < domainList.size(); ++j)
2361 {
2362 // Check it has not already been defined
2363 pair<std::string, int> key(variableList[i], domainList[j]);
2364 auto fcnsIter = functionVarMap.find(key);
2365 ASSERTL0(fcnsIter == functionVarMap.end(),
2366 "Error setting expression '" + variableList[i] +
2367 " in domain " + std::to_string(domainList[j]) +
2368 "' in function '" + functionStr +
2369 "'. "
2370 "Expression has already been defined.");
2371
2372 if (varSplit.size() > 0)
2373 {
2374 FunctionVariableDefinition funcDef2 = funcDef;
2375 funcDef2.m_fileVariable = varSplit[i];
2376 functionVarMap[key] = funcDef2;
2377 }
2378 else
2379 {
2380 functionVarMap[key] = funcDef;
2381 }
2382 }
2383 }
2384 variable = variable->NextSiblingElement();
2385 }
2386
2387 // Add function definition to map
2388 m_functions[functionStr] = functionVarMap;
2389 function = function->NextSiblingElement("FUNCTION");
2390 }
2391}
2392
2393/**
2394 *
2395 */
2396void SessionReader::ReadFilters(TiXmlElement *filters)
2397{
2398 if (!filters)
2399 {
2400 return;
2401 }
2402
2403 m_filters.clear();
2404
2405 TiXmlElement *filter = filters->FirstChildElement("FILTER");
2406
2407 while (filter)
2408 {
2409 ASSERTL0(filter->Attribute("TYPE"),
2410 "Missing attribute 'TYPE' for filter.");
2411 std::string typeStr = filter->Attribute("TYPE");
2412
2413 std::map<std::string, std::string> vParams;
2414
2415 TiXmlElement *element = filter;
2416 GetXMLElementTimeLevel(element, m_timeLevel, false);
2417 TiXmlElement *param = element->FirstChildElement("PARAM");
2418 while (param)
2419 {
2420 ASSERTL0(param->Attribute("NAME"),
2421 "Missing attribute 'NAME' for parameter in filter " +
2422 typeStr + "'.");
2423 std::string nameStr = param->Attribute("NAME");
2424
2425 ASSERTL0(param->GetText(), "Empty value string for param.");
2426 std::string valueStr = param->GetText();
2427
2428 vParams[nameStr] = valueStr;
2429
2430 param = param->NextSiblingElement("PARAM");
2431 }
2432
2433 m_filters.push_back(
2434 std::pair<std::string, FilterParams>(typeStr, vParams));
2435
2436 filter = filter->NextSiblingElement("FILTER");
2437 }
2438}
2439
2440/**
2441 *
2442 */
2443void SessionReader::ParseEquals(const std::string &line, std::string &lhs,
2444 std::string &rhs)
2445{
2446 /// Pull out lhs and rhs and eliminate any spaces.
2447 size_t beg = line.find_first_not_of(" ");
2448 size_t end = line.find_first_of("=");
2449 // Check for no parameter name
2450 if (beg == end)
2451 {
2452 throw 1;
2453 }
2454 // Check for no parameter value
2455 if (end != line.find_last_of("="))
2456 {
2457 throw 1;
2458 }
2459 // Check for no equals sign
2460 if (end == std::string::npos)
2461 {
2462 throw 1;
2463 }
2464
2465 lhs = line.substr(line.find_first_not_of(" "), end - beg);
2466 lhs = lhs.substr(0, lhs.find_last_not_of(" ") + 1);
2467 rhs = line.substr(line.find_last_of("=") + 1);
2468 rhs = rhs.substr(rhs.find_first_not_of(" "));
2469 rhs = rhs.substr(0, rhs.find_last_not_of(" ") + 1);
2470}
2471
2472/**
2473 *
2474 */
2476{
2477 // Parse solver info overrides
2478 if (m_cmdLineOptions.count("solverinfo"))
2479 {
2480 std::vector<std::string> solverInfoList =
2481 m_cmdLineOptions["solverinfo"].as<std::vector<std::string>>();
2482
2483 for (size_t i = 0; i < solverInfoList.size(); ++i)
2484 {
2485 std::string lhs, rhs;
2486
2487 try
2488 {
2489 ParseEquals(solverInfoList[i], lhs, rhs);
2490 }
2491 catch (...)
2492 {
2493 NEKERROR(ErrorUtil::efatal, "Parse error with command line "
2494 "option: " +
2495 solverInfoList[i]);
2496 }
2497
2498 std::string lhsUpper = boost::to_upper_copy(lhs);
2499 m_solverInfo[lhsUpper] = rhs;
2500 }
2501 }
2502
2503 if (m_cmdLineOptions.count("parameter"))
2504 {
2505 std::vector<std::string> parametersList =
2506 m_cmdLineOptions["parameter"].as<std::vector<std::string>>();
2507
2508 for (size_t i = 0; i < parametersList.size(); ++i)
2509 {
2510 std::string lhs, rhs;
2511
2512 try
2513 {
2514 ParseEquals(parametersList[i], lhs, rhs);
2515 }
2516 catch (...)
2517 {
2518 NEKERROR(ErrorUtil::efatal, "Parse error with command line "
2519 "option: " +
2520 parametersList[i]);
2521 }
2522
2523 std::string lhsUpper = boost::to_upper_copy(lhs);
2524
2525 try
2526 {
2527 m_parameters[lhsUpper] = boost::lexical_cast<NekDouble>(rhs);
2528 }
2529 catch (...)
2530 {
2531 NEKERROR(ErrorUtil::efatal, "Unable to convert string: " + rhs +
2532 "to double value.");
2533 }
2534 }
2535 }
2536}
2537
2538/**
2539 *
2540 */
2542{
2543 for (auto &x : m_solverInfo)
2544 {
2545 std::string solverProperty = x.first;
2546 std::string solverValue = x.second;
2547
2548 auto propIt = GetSolverInfoEnums().find(solverProperty);
2549 if (propIt != GetSolverInfoEnums().end())
2550 {
2551 auto valIt = propIt->second.find(solverValue);
2552 ASSERTL0(valIt != propIt->second.end(), "Value '" + solverValue +
2553 "' is not valid for "
2554 "property '" +
2555 solverProperty + "'");
2556 }
2557 }
2558}
2559
2560/**
2561 *
2562 */
2564{
2565 return m_interpreter;
2566}
2567
2568/**
2569 * Helper function that gets a pointer to a child element, or throws an
2570 * exception if no such element exists
2571 */
2572TiXmlElement *GetChildElementOrThrow(const std::string &filename,
2573 std::string elementName,
2574 const TiXmlHandle &docHandle)
2575{
2576 TiXmlElement *element = docHandle.FirstChildElement(elementName).Element();
2577
2578 if (!element)
2579 {
2580 NEKERROR(ErrorUtil::efatal, "Unable to find '" + elementName +
2581 "' XML node in " + filename);
2582 }
2583
2584 return element;
2585}
2586
2587} // namespace Nektar::LibUtilities
#define NEKTAR_VERSION
#define ASSERTL0(condition, msg)
Definition: ErrorUtil.hpp:208
#define NEKERROR(type, msg)
Assert Level 0 – Fundamental assert which is used whether in FULLDEBUG, DEBUG or OPT compilation mode...
Definition: ErrorUtil.hpp:202
#define ASSERTL1(condition, msg)
Assert Level 1 – Debugging which is used whether in FULLDEBUG or DEBUG compilation mode....
Definition: ErrorUtil.hpp:242
tBaseSharedPtr CreateInstance(tKey idKey, tParam... args)
Create an instance of the class referred to by idKey.
const std::string & GetGlobalSysSolnInfo(const std::string &variable, const std::string &property) const
void ReadSolverInfo(TiXmlElement *conditions)
Reads the SOLVERINFO section of the XML document.
bool DefinesFunction(const std::string &name) const
Checks if a specified function is defined in the XML document.
std::string GetFunctionFilenameVariable(const std::string &name, const std::string &variable, const int pDomain=0) const
Returns the filename variable to be loaded for a given variable index.
std::vector< std::string > ParseCommandLineArguments(int argc, char *argv[])
Parse the program arguments and fill m_cmdLineOptions.
static SolverInfoMap & GetSolverInfoDefaults()
Default solver info options.
TimeIntScheme m_timeIntScheme
Time integration scheme information.
InterpreterSharedPtr GetInterpreter()
Returns the instance of the Interpreter specific to this session.
TiXmlElement * GetElement(const std::string &pPath)
Provides direct access to the TiXmlElement specified.
void ReadVariables(TiXmlElement *conditions)
Reads the VARIABLES section of the XML document.
bool DefinesSolverInfo(const std::string &name) const
Checks if a solver info property is specified.
const std::string & GetSessionName() const
Returns the session name of the loaded XML document.
void ReadTimeIntScheme(TiXmlElement *conditions)
Reads the TIMEINTEGRATIONSCHEME section of the XML document.
void ReadFilters(TiXmlElement *filters)
Reads the FILTERS section of the XML document.
void ReadGlobalSysSolnInfo(TiXmlElement *conditions)
Reads the GLOBALSYSSOLNINFO section of the XML document.
bool GetBackups() const
Returns the backups.
void InitSession(const std::vector< std::string > &filenames=std::vector< std::string >())
VariableList m_variables
Variables.
SolverInfoMap m_solverInfo
Solver information properties.
std::vector< std::string > GetVariables() const
Returns the names of all variables.
static CmdLineArgMap & GetCmdLineArgMap()
CmdLine argument map.
TiXmlDocument * MergeDoc(const std::vector< std::string > &pFilenames) const
Creates an XML document from a list of input files.
void SetVariable(const unsigned int &idx, std::string newname)
void CmdLineOverride()
Enforce parameters from command line arguments.
void ParseDocument()
Loads and parses the specified file.
bool m_sharedFilesystem
Running on a shared filesystem.
static void GetXMLElementTimeLevel(TiXmlElement *&element, const size_t timeLevel, const bool enableCheck=true)
Get XML elment time level (Parallel-in-Time)
std::string ParseSessionName(std::vector< std::string > &filenames)
Parse the session name.
std::string GetFunctionFilename(const std::string &name, const std::string &variable, const int pDomain=0) const
Returns the filename to be loaded for a given variable.
enum FunctionType GetFunctionType(const std::string &name, const std::string &variable, const int pDomain=0) const
Returns the type of a given function variable.
bool DefinesTag(const std::string &pName) const
Checks if a specified tag is defined.
bool m_updateOptFile
Update optimisation file.
void LoadParameter(const std::string &name, int &var) const
Load an integer parameter.
CommSharedPtr GetComm()
Returns the communication object.
const NekDouble & GetParameter(const std::string &pName) const
Returns the value of the specified parameter.
ParameterMap m_parameters
Parameters.
void SetParameter(const std::string &name, int &var)
Set an integer parameter.
InterpreterSharedPtr m_interpreter
Interpreter instance.
static EnumMapList & GetSolverInfoEnums()
String to enumeration map for Solver Info parameters.
void VerifySolverInfo()
Check values of solver info options are valid.
SessionReader(int argc, char *argv[], const std::vector< std::string > &pFilenames, const CommSharedPtr &pComm, const int &timelevel)
void SetSolverInfo(const std::string &pProperty, const std::string &pValue)
Sets the value of the specified solver info property.
const std::string & GetVariable(const unsigned int &idx) const
Returns the name of the variable specified by the given index.
EquationSharedPtr GetFunction(const std::string &name, const std::string &variable, const int pDomain=0) const
Returns an EquationSharedPtr to a given function variable.
const std::string & GetTag(const std::string &pName) const
Returns the value of a specified tag.
FunctionMap m_functions
Functions.
TiXmlDocument & GetDocument()
Provides direct access to the TiXmlDocument object.
bool DefinesElement(const std::string &pPath) const
Tests if a specified element is defined in the XML document.
std::vector< std::string > m_filenames
Filenames.
bool DefinesGlobalSysSolnInfo(const std::string &variable, const std::string &property) const
void ReadFunctions(TiXmlElement *conditions)
Reads the FUNCTIONS section of the XML document.
void LoadDoc(const std::string &pFilename, TiXmlDocument *pDoc) const
Loads an xml file into a tinyxml doc and decompresses if needed.
bool DefinesParameter(const std::string &name) const
Checks if a parameter is specified in the XML document.
const TimeIntScheme & GetTimeIntScheme() const
Returns the time integration scheme structure m_timeIntScheme from the session file.
void SetTag(const std::string &pName, const std::string &pValue)
Sets a specified tag.
boost::program_options::variables_map m_cmdLineOptions
std::string m_sessionName
Session name of the loaded XML document (filename minus ext).
CommSharedPtr m_comm
Communication object.
void MatchSolverInfo(const std::string &name, const std::string &trueval, bool &var, const bool &def=false) const
Check if the value of a solver info property matches.
void CreateComm(int &argc, char *argv[])
Loads the given XML document and instantiates an appropriate communication object.
const std::string & GetSolverInfo(const std::string &pProperty) const
Returns the value of the specified solver info property.
void ParseEquals(const std::string &line, std::string &lhs, std::string &rhs)
Parse a string in the form lhs = rhs.
bool DefinesTimeIntScheme() const
Returns true if the TIMEINTEGRATIONSCHEME section is defined in the session file.
const std::vector< std::string > & GetFilenames() const
Returns the filename of the loaded XML document.
bool GetSharedFilesystem()
Returns if file system shared.
static GloSysSolnInfoList & GetGloSysSolnList()
GlobalSysSoln Info map.
void PartitionComm()
Partitions the comm object based on session parameters.
bool DefinesCmdLineArgument(const std::string &pName) const
Checks if a specified cmdline argument has been given.
TiXmlDocument * m_xmlDoc
Pointer to the loaded XML document.
void ReadParameters(TiXmlElement *conditions)
Reads the PARAMETERS section of the XML document.
void LoadSolverInfo(const std::string &name, std::string &var, const std::string &def="") const
Check for and load a solver info property.
static std::shared_ptr< DataType > AllocateSharedPtr(const Args &...args)
Allocate a shared pointer from the memory pool.
static bool GenerateVector(const std::string &str, std::vector< T > &out)
Takes a comma-separated string and converts it to entries in a vector.
Definition: ParseUtils.cpp:130
static bool GenerateSeqVector(const std::string &str, std::vector< unsigned int > &out)
Takes a comma-separated compressed string and converts it to entries in a vector.
Definition: ParseUtils.cpp:104
def copy(self)
Definition: pycml.py:2663
def description(self, force=False, cellml=False)
Definition: pycml.py:2670
std::shared_ptr< Interpreter > InterpreterSharedPtr
Definition: Interpreter.h:322
std::map< std::string, std::string > SolverInfoMap
Definition: SessionReader.h:56
std::map< std::string, GloSysInfoMap > GloSysSolnInfoList
Definition: SessionReader.h:77
std::map< std::pair< std::string, int >, FunctionVariableDefinition > FunctionVariableMap
std::map< std::string, NekDouble > ParameterMap
Definition: SessionReader.h:57
static std::string PortablePath(const fs::path &path)
create portable path on different platforms for std::filesystem path.
Definition: Filesystem.hpp:56
std::shared_ptr< Equation > EquationSharedPtr
Definition: Equation.h:125
TiXmlElement * GetChildElementOrThrow(const std::string &filename, std::string elementName, const TiXmlHandle &docHandle)
std::map< std::string, EnumMap > EnumMapList
Definition: SessionReader.h:74
std::vector< std::pair< std::string, FilterParams > > FilterMap
Definition: SessionReader.h:62
CommFactory & GetCommFactory()
std::map< std::string, CmdLineArg > CmdLineArgMap
Definition: SessionReader.h:71
std::shared_ptr< Comm > CommSharedPtr
Pointer to a Communicator object.
Definition: Comm.h:55
const std::string kGitBranch
Definition: GitRevision.h:46
const std::string kGitSha1
Definition: GitRevision.h:45
InputIterator find(InputIterator first, InputIterator last, InputIterator startingpoint, const EqualityComparable &value)
Definition: StdRegions.hpp:475
std::vector< double > d(NPUPPER *NPUPPER)
std::vector< double > q(NPUPPER *NPUPPER)
double NekDouble
Definition: sha1.cpp:72
STL namespace.
std::vector< NekDouble > freeParams
Definition: SessionReader.h:87