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

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.hpp (modified) (3 diffs)

src/Fragmentation/Automation/Jobs/FragmentJob.hpp

@@ -43 +43 @@
   typedef boost::shared_ptr<FragmentJob> ptr;
 
-  FragmentJob();
-  FragmentJob(const std::string &_command, const std::string &_outputfile, const JobId_t _JobId);
+  FragmentJob(const JobId_t _JobId);
   ~FragmentJob();
 
-  FragmentResult::ptr Work();
+  virtual FragmentResult::ptr Work() = 0;
 
   bool operator==(const FragmentJob &other) const;
@@ -55 +54 @@
   }
 
-  //!> string containing the command to launch the solver
-  std::string command;
+private:
+  /** private default cstor for serialization only
+   *
+   * Use normal cstor with JobId::IllegalJob if you want to instantiate
+   * a job without id.
+   */
+  FragmentJob();
 
-  //!> string containing the configuration file for the solver
-  std::string outputfile;
-
-private:
   friend class boost::serialization::access;
   // serialization
@@ -68 +68 @@
   {
     ar & boost::serialization::base_object<JobId>(*this);
-    ar & command;
-    ar & outputfile;
   }
 };