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
        Candidate_v1.7.0
        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
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        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
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        Switchable_LogView
        ThirdParty_MPQC_rebuilt_buildsystem
        TrajectoryDependenant_MaxOrder
        TremoloParser_IncreasedPrecision
        TremoloParser_MultipleTimesteps
        TremoloParser_setsAtomName
        Ubuntu_1604_changes
        stable
      
      
        
          | Last change
 on this file since 86a1e8 was             d920b9, checked in by Frederik Heber <heber@…>, 13 years ago | 
        
          | 
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.
 | 
        
          | 
              
Property                 mode
 set to                 100644 | 
        
          | File size:
            1.6 KB | 
      
      
| Rev | Line |  | 
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| [31ca5f] | 1 | /* | 
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|  | 2 | * FragmentJob.hpp | 
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|  | 3 | * | 
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|  | 4 | *  Created on: Oct 19, 2011 | 
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|  | 5 | *      Author: heber | 
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|  | 6 | */ | 
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|  | 7 |  | 
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|  | 8 | #ifndef FRAGMENTJOB_HPP_ | 
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|  | 9 | #define FRAGMENTJOB_HPP_ | 
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|  | 10 |  | 
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|  | 11 | // include config.h | 
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|  | 12 | #ifdef HAVE_CONFIG_H | 
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|  | 13 | #include <config.h> | 
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|  | 14 | #endif | 
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|  | 15 |  | 
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|  | 16 | #include <string> | 
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|  | 17 |  | 
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| [78ad7d] | 18 | #include "boost/shared_ptr.hpp" | 
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|  | 19 | #include "boost/serialization/access.hpp" | 
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|  | 20 | #include "boost/serialization/shared_ptr.hpp" | 
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| [31ca5f] | 21 |  | 
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| [7670865] | 22 | #include "Results/FragmentResult.hpp" | 
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| [b05673] | 23 | #include "JobId.hpp" | 
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| [4b58cc] | 24 | #include "types.hpp" | 
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|  | 25 |  | 
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| [57876b] | 26 | class FragmentJobTest; | 
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|  | 27 | class FragmentQueueTest; | 
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| [8c9596] | 28 | class FragmentWorker; | 
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| [31ca5f] | 29 |  | 
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|  | 30 | /** FragmentJob contains all information for the Worker to start the job and | 
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|  | 31 | * deliver a FragmentResult. | 
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|  | 32 | * | 
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|  | 33 | * Important is that this class is fully serializable such that it can be | 
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|  | 34 | * transfered to a scheduler (server) and be deserialized by the Worker. | 
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|  | 35 | */ | 
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| [b05673] | 36 | class FragmentJob : public JobId | 
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| [31ca5f] | 37 | { | 
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| [57876b] | 38 | //!> allow FragmentQueue unit test access | 
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| [02f346] | 39 | friend class FragmentQueueTest; | 
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| [57876b] | 40 | //!> allow own unit test access | 
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|  | 41 | friend class FragmentJobTest; | 
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| [31ca5f] | 42 | public: | 
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| [78ad7d] | 43 | typedef boost::shared_ptr<FragmentJob> ptr; | 
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|  | 44 |  | 
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| [d920b9] | 45 | FragmentJob(const JobId_t _JobId); | 
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| [31ca5f] | 46 | ~FragmentJob(); | 
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|  | 47 |  | 
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| [d920b9] | 48 | virtual FragmentResult::ptr Work() = 0; | 
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| [7b22e9] | 49 |  | 
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| [31ca5f] | 50 | bool operator==(const FragmentJob &other) const; | 
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|  | 51 |  | 
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|  | 52 | bool operator!=(const FragmentJob &other) const { | 
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|  | 53 | return !(*this == other); | 
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|  | 54 | } | 
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|  | 55 |  | 
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|  | 56 | private: | 
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| [d920b9] | 57 | /** private default cstor for serialization only | 
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|  | 58 | * | 
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|  | 59 | * Use normal cstor with JobId::IllegalJob if you want to instantiate | 
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|  | 60 | * a job without id. | 
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|  | 61 | */ | 
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|  | 62 | FragmentJob(); | 
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|  | 63 |  | 
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| [31ca5f] | 64 | friend class boost::serialization::access; | 
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|  | 65 | // serialization | 
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|  | 66 | template <typename Archive> | 
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|  | 67 | void serialize(Archive& ar, const unsigned int version) | 
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|  | 68 | { | 
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| [b05673] | 69 | ar & boost::serialization::base_object<JobId>(*this); | 
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| [31ca5f] | 70 | } | 
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|  | 71 | }; | 
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|  | 72 |  | 
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|  | 73 |  | 
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|  | 74 | #endif /* FRAGMENTJOB_HPP_ */ | 
|---|
       
      
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