Changeset d920b9 for src/Fragmentation/Automation/Jobs/FragmentJob.cpp

Timestamp:

Jun 27, 2012, 4:07:18 PM (13 years ago)

Author:

Frederik Heber <heber@…>

Branches:

Action_Thermostats, Add_AtomRandomPerturbation, Add_FitFragmentPartialChargesAction, Add_RotateAroundBondAction, Add_SelectAtomByNameAction, Added_ParseSaveFragmentResults, AddingActions_SaveParseParticleParameters, Adding_Graph_to_ChangeBondActions, Adding_MD_integration_tests, Adding_ParticleName_to_Atom, Adding_StructOpt_integration_tests, AtomFragments, Automaking_mpqc_open, AutomationFragmentation_failures, Candidate_v1.5.4, Candidate_v1.6.0, Candidate_v1.6.1, ChangeBugEmailaddress, ChangingTestPorts, ChemicalSpaceEvaluator, CombiningParticlePotentialParsing, Combining_Subpackages, Debian_Package_split, Debian_package_split_molecuildergui_only, Disabling_MemDebug, Docu_Python_wait, EmpiricalPotential_contain_HomologyGraph, EmpiricalPotential_contain_HomologyGraph_documentation, Enable_parallel_make_install, Enhance_userguide, Enhanced_StructuralOptimization, Enhanced_StructuralOptimization_continued, Example_ManyWaysToTranslateAtom, Exclude_Hydrogens_annealWithBondGraph, FitPartialCharges_GlobalError, Fix_BoundInBox_CenterInBox_MoleculeActions, Fix_ChargeSampling_PBC, Fix_ChronosMutex, Fix_FitPartialCharges, Fix_FitPotential_needs_atomicnumbers, Fix_ForceAnnealing, Fix_IndependentFragmentGrids, Fix_ParseParticles, Fix_ParseParticles_split_forward_backward_Actions, Fix_PopActions, Fix_QtFragmentList_sorted_selection, Fix_Restrictedkeyset_FragmentMolecule, Fix_StatusMsg, Fix_StepWorldTime_single_argument, Fix_Verbose_Codepatterns, Fix_fitting_potentials, Fixes, ForceAnnealing_goodresults, ForceAnnealing_oldresults, ForceAnnealing_tocheck, ForceAnnealing_with_BondGraph, ForceAnnealing_with_BondGraph_continued, ForceAnnealing_with_BondGraph_continued_betteresults, ForceAnnealing_with_BondGraph_contraction-expansion, FragmentAction_writes_AtomFragments, FragmentMolecule_checks_bonddegrees, GeometryObjects, Gui_Fixes, Gui_displays_atomic_force_velocity, ImplicitCharges, IndependentFragmentGrids, IndependentFragmentGrids_IndividualZeroInstances, IndependentFragmentGrids_IntegrationTest, IndependentFragmentGrids_Sole_NN_Calculation, JobMarket_RobustOnKillsSegFaults, JobMarket_StableWorkerPool, JobMarket_unresolvable_hostname_fix, MoreRobust_FragmentAutomation, ODR_violation_mpqc_open, PartialCharges_OrthogonalSummation, PdbParser_setsAtomName, PythonUI_with_named_parameters, QtGui_reactivate_TimeChanged_changes, Recreated_GuiChecks, Rewrite_FitPartialCharges, RotateToPrincipalAxisSystem_UndoRedo, SaturateAtoms_findBestMatching, SaturateAtoms_singleDegree, StoppableMakroAction, Subpackage_CodePatterns, Subpackage_JobMarket, Subpackage_LinearAlgebra, Subpackage_levmar, Subpackage_mpqc_open, Subpackage_vmg, Switchable_LogView, ThirdParty_MPQC_rebuilt_buildsystem, TrajectoryDependenant_MaxOrder, TremoloParser_IncreasedPrecision, TremoloParser_MultipleTimesteps, TremoloParser_setsAtomName, Ubuntu_1604_changes, stable

Children:

cc276e

Parents:

7670865

git-author:

Frederik Heber <heber@…> (02/06/12 09:57:56)

git-committer:

Frederik Heber <heber@…> (06/27/12 16:07:18)

Message:

Abstracted FragmentJob and introduced SystemCommandJob which has its former functionality.

• FragmentJob now has just virtual function Work(), not implemented.
• former command and outputfile is taken over by SystemCommandJob.
• a FragmentJob or derived class is default cstor'ed always with JobId::IllegalJob.
• so far SystemCommandJob captures command's stdout and parses it back from file. We use mkstemps() for creating a random file and popen() to pipe stdout directly. For this we require boost::iostreams and ::filesystem.
• SystemCommandJob has virtual method extractString() to be adaptable to the output of various system commands.
• changes almost everywhere due to SystemCommandJob taking place of FragmentJob and FragmentJob::ptr and FragmentResult::ptr requirements.
• added FragmentWorker::dummyInit() to enforce binding of the executable to all possible derived FragmentJob's.
• added unit test for SystemCommandJob.
• added FragmentJobStub that implements a no-brainer job for testing.
• NOTE: boost::iostreams is incompatible with MemDebug due to placement new.

File:

• src/Fragmentation/Automation/Jobs/FragmentJob.cpp (modified) (4 diffs)

src/Fragmentation/Automation/Jobs/FragmentJob.cpp

@@ -20 +20 @@
 #include "CodePatterns/MemDebug.hpp"
 
-#include <cstdlib>
-#include <fstream>
-#include <string>
-
-#include "CodePatterns/Info.hpp"
-#include "CodePatterns/Log.hpp"
-#include "CodePatterns/toString.hpp"
 #include "FragmentJob.hpp"
 #include "Results/FragmentResult.hpp"
@@ -34 +27 @@
  */
 FragmentJob::FragmentJob() :
-  JobId(-1),
-  outputfile("")
+  JobId(JobId::IllegalJob)
 {}
 
 /** Constructor for class FragmentJob.
  *
- * \param _command command to execute
- * \param _outputfile configuration file for solver
  * \param _JobId unique id of this job
  */
-FragmentJob::FragmentJob(const std::string &_command, const std::string &_outputfile, const JobId_t _JobId) :
-  JobId(_JobId),
-  command(_command),
-  outputfile(_outputfile)
+FragmentJob::FragmentJob(const JobId_t _JobId) :
+  JobId(_JobId)
 {}
 
@@ -56 +44 @@
 {}
 
-/** Work routine of this FragmentJob.
- *
- * This function encapsulates all the work that has to be done to generate
- * a FragmentResult. Hence, the FragmentWorker does not need to know anything
- * about the operation: it just receives it and executes this function.
- *
- * \return result of this job
- */
-FragmentResult::ptr FragmentJob::Work()
-{
-  Info info((std::string(__FUNCTION__)+std::string(", id #")+toString(getId())).c_str());
-  FragmentResult::ptr s( new FragmentResult(getId()) );
-
-  // write outputfile to file
-  std::string inputfilename =
-      std::string("/tmp/dummy_")
-      +toString(getId());
-  std::string outputfilename = inputfilename+std::string(".out");
-  inputfilename += std::string(".dat");
-  std::ofstream output(outputfilename.c_str());
-  output << outputfile << std::endl;
-  output.close();
-
-  // fork into subprocess and launch command
-  s->exitflag = std::system((command+std::string(" ")+inputfilename
-                        +std::string(" >")+outputfilename).c_str());
-  std::ifstream resultfile;
-  resultfile.open(outputfilename.c_str(), ifstream::in);
-  char line[1024];
-  while (resultfile.good()) {
-    resultfile.getline(line, 1023);
-    s->result += line;
-  }
-  resultfile.close();
-
-  return s;
-}
-
 /** Comparator for class FragmentJob.
  * \param other instance to compare to
@@ -100 +50 @@
 bool FragmentJob::operator==(const FragmentJob &other) const
 {
-  return (command == other.command)
-      && (outputfile == other.outputfile)
-      && (getId() == other.getId());
+  return (getId() == other.getId());
 }