Changeset ac9ca4 for src/Actions/FragmentationAction/FragmentationAutomationAction.cpp

Timestamp:

Apr 15, 2013, 10:28:22 AM (12 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:

4f44ae

Parents:

dd0c8f

git-author:

Frederik Heber <heber@…> (03/04/13 13:54:11)

git-committer:

Frederik Heber <heber@…> (04/15/13 10:28:22)

Message:

FragmentAction creates FragmentJobs if no output-types are given.

• ExportGraph_ToJobs now creates jobs for a FragmentJobQueue.
• new singleton FragmentJobQueue to contain FragmentJobs.
• MPQCFragmentController rewritten to use FragmentJobQueue, too.
• FragmentationAutomationAction just fills FragmentJobQueue with given fragment-jobs.
• added KeySetsContainer::clear().
• removed ExportGraph::operator().
• Smaller fixes to Fragmentation(Automation)Action w.r.t. optional parameters.
• We now require JobMarket 1.1.3, as we need FragmentController::changeId().

File:

• src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) (3 diffs)

src/Actions/FragmentationAction/FragmentationAutomationAction.cpp

@@ -57 +57 @@
 #include "Fragmentation/Automation/extractJobIds.hpp"
 #include "Fragmentation/Automation/FragmentationChargeDensity.hpp"
+#include "Fragmentation/Automation/FragmentJobQueue.hpp"
 #include "Fragmentation/Automation/FragmentationResults.hpp"
 #include "Fragmentation/Automation/MPQCFragmentController.hpp"
@@ -478 +479 @@
   // TODO: Have io_service run in second thread and merge with current again eventually
 
+  // check some things prior to work
+  enum OutputType_t {
+    ToFiles,
+    ToJobs,
+    ToNone
+  };
+  enum OutputType_t outputtype = ToNone;
+  if (params.jobfiles.get().size() != 0) {
+    // we got no job files, hence we use FragmentJobQueue
+    if (params.path.get().size() == 0) {
+      ELOG(1, "Missing path to fragment files.");
+      return Action::failure;
+    }
+    outputtype = ToFiles;
+
+    // parse in fragment-jobs if given
+    if(!FragmentJobQueue::getInstance().addJobsFromFiles(
+        params.jobfiles.get(),
+        params.level.get()))
+      return Action::failure;
+  } else {
+    if (params.path.get().size() != 0) {
+      ELOG(2, "Path to fragment given although we use FragmentJobQueue.");
+    }
+    outputtype = ToJobs;
+  }
+
   size_t Exitflag = 0;
   std::map<JobId_t, MPQCData> fragmentData;
   {
+    const size_t NumberJobs = FragmentJobQueue::getInstance().size();
     MPQCFragmentController mpqccontroller(io_service);
     mpqccontroller.setHost(params.host.get());
     mpqccontroller.setPort(params.port.get());
-    mpqccontroller.setLevel(params.level.get());
     // Phase One: obtain ids
-    std::vector< boost::filesystem::path > jobfiles = params.jobfiles.get();
-    mpqccontroller.requestIds(jobfiles.size());
-
-    // Phase Two: create and add MPQCJobs
-    if (!mpqccontroller.addJobsFromFiles(params.executable.get().string(), jobfiles))
-      return Action::failure;
+    mpqccontroller.requestIds(NumberJobs);
+
+    // Phase Two: add MPQCJobs and send
+    mpqccontroller.addJobsFromQueue();
+    mpqccontroller.run();
 
     // Phase Three: calculate result
-    mpqccontroller.waitforResults(jobfiles.size());
+    mpqccontroller.waitforResults(NumberJobs);
     mpqccontroller.getResults(fragmentData);
 
@@ -572 +599 @@
 
   // append all keysets to homology file
-  if (Exitflag == 0) {
+  if ((Exitflag == 0) && (!params.homology_file.get().empty())) {
     const boost::filesystem::path &homology_file = params.homology_file.get();
     if (homology_file.string() != "") {