Changeset d8821e for src/Actions/FragmentationAction

Timestamp:

Jul 14, 2014, 11:16:23 AM (11 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:

2a03b0

Parents:

c73e35 (diff), a61dbb (diff)
Note: this is a merge changeset, the changes displayed below correspond to the merge itself.
Use the (diff) links above to see all the changes relative to each parent.

Message:

Merge branch 'Fragmentation_Automation_wo_JobMarket' into stable

Conflicts:

src/Actions/ActionQueue.cpp
src/Actions/FragmentationAction/FragmentationAction.cpp
src/Actions/PotentialAction/FitParticleChargesAction.cpp

• in ActionQueue taking over both changes.
• FragmentationAction added Status message where we don't complain for not having HAVE_JOBMARKET anymore. Removed.
• FitParticleChargesAction had charge averaging and error message in case of no present fragments overlapping.

Location:

src/Actions/FragmentationAction

Files:

• AnalyseFragmentationResultsAction.cpp (modified) (9 diffs)
• FragmentationAction.cpp (modified) (2 diffs)
• FragmentationAutomationAction.cpp (modified) (7 diffs)

src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.cpp

@@ -63 +63 @@
 #include "Descriptors/AtomIdDescriptor.hpp"
 #include "Fragmentation/Summation/Containers/FragmentationChargeDensity.hpp"
-#include "Fragmentation/Summation/Containers/FragmentationLongRangeResults.hpp"
 #include "Fragmentation/Summation/Containers/FragmentationResultContainer.hpp"
 #include "Fragmentation/Summation/Containers/FragmentationShortRangeResults.hpp"
@@ -78 +77 @@
 #include "Fragmentation/Summation/writeIndexedTable.hpp"
 #include "Fragmentation/Summation/writeTable.hpp"
-#ifdef HAVE_VMG
+#if defined(HAVE_JOBMARKET) && defined(HAVE_VMG)
+#include "Fragmentation/Summation/Containers/FragmentationLongRangeResults.hpp"
 #include "Fragmentation/Summation/Containers/VMGData.hpp"
 #include "Fragmentation/Summation/Containers/VMGDataFused.hpp"
@@ -232 +232 @@
 
 
+#if defined(HAVE_JOBMARKET) && defined(HAVE_VMG)
 /** Print long range energy from received results.
  *
@@ -261 +262 @@
   }
 }
+#endif
 
 void appendToHomologies(
     const FragmentationShortRangeResults &shortrangeresults,
+#if defined(HAVE_JOBMARKET) && defined(HAVE_VMG)
     const FragmentationLongRangeResults &longrangeresults,
+#endif
     const bool storeGrids
     )
@@ -311 +315 @@
     // only store sampled grids if desired
     if (storeGrids) {
+#if defined(HAVE_JOBMARKET) && defined(HAVE_VMG)
       // obtain charge distribution
       std::map<IndexSet::ptr, std::pair< MPQCDataGridMap_t, MPQCDataGridMap_t> >::const_iterator chargeiter
@@ -338 +343 @@
 //          ++iter)
 //        *iter -= offset;
+#else
+      ELOG(1, "Long-range information in homology desired but long-range analysis capability not compiled in.");
+#endif
     }
     values.insert( std::make_pair( graph, value) );
@@ -362 +370 @@
           << ", associated energy " << iter->second.energy;
       if (iter->second.containsGrids)
+#if defined(HAVE_JOBMARKET) && defined(HAVE_VMG)
         output  << ", and sampled grid integral " << iter->second.charge_distribution.integral();
+#else
+        output << ", and there are sampled grids but capability not compiled in";
+#endif
       output << ".";
       LOG(2, output.str());
@@ -610 +622 @@
   }
 
-#ifdef HAVE_VMG
+#if defined(HAVE_JOBMARKET) && defined(HAVE_VMG)
   if (DoLongrange) {
     if ( World::getInstance().getAllAtoms().size() == 0) {
@@ -651 +663 @@
   }
 #else
-  if (DoLongrange)
+  if (DoLongrange) {
     ELOG(2, "File contains long-range information but long-range analysis capability not compiled in.");
+  }
 
   // append all keysets to homology file with short-range info only (without grids)
-  {
-    std::map<JobId_t, VMGData> longrangeData;
-    FragmentationLongRangeResults longrangeresults(
-        shortrangedata,longrangeData,keysets, forcekeysets);
-    appendToHomologies(shortrangeresults, longrangeresults, false);
-  }
+  appendToHomologies(shortrangeresults, false);
 #endif
 

src/Actions/FragmentationAction/FragmentationAction.cpp

@@ -41 +41 @@
 #include "Descriptors/AtomSelectionDescriptor.hpp"
 #include "Fragmentation/Exporters/ExportGraph_ToFiles.hpp"
-#ifdef HAVE_JOBMARKET
 #include "Fragmentation/Exporters/ExportGraph_ToJobs.hpp"
-#endif
 #include "Fragmentation/Fragmentation.hpp"
 #include "Fragmentation/Graph.hpp"
@@ -273 +271 @@
       exporter();
     } else {
-#ifdef HAVE_JOBMARKET
       // store molecule's fragment in FragmentJobQueue
       ExportGraph_ToJobs exporter(TotalGraph, treatment, saturation);
       exporter.setLevel(params.level.get());
       exporter();
-#else
-      STATUS("No output file types specified and JobMarket support is not compiled in.");
-      return Action::failure;
-#endif
     }
   }

src/Actions/FragmentationAction/FragmentationAutomationAction.cpp

@@ -53 +53 @@
 #include "CodePatterns/Info.hpp"
 #include "CodePatterns/Log.hpp"
+
+#ifdef HAVE_JOBMARKET
 #include "JobMarket/Jobs/FragmentJob.hpp"
+#else
+#include "Jobs/JobMarket/FragmentJob.hpp"
+#endif
 
 #include "Fragmentation/Automation/FragmentJobQueue.hpp"
+#ifdef HAVE_JOBMARKET
 #include "Fragmentation/Automation/MPQCFragmentController.hpp"
+#else
+#include "Fragmentation/Automation/MPQCCommandFragmentController.hpp"
+#endif
 #include "Fragmentation/Summation/Containers/FragmentationChargeDensity.hpp"
 #include "Fragmentation/Summation/Containers/FragmentationLongRangeResults.hpp"
@@ -63 +72 @@
 #include "Fragmentation/Summation/Containers/MPQCData.hpp"
 #include "Fragmentation/KeySetsContainer.hpp"
-#ifdef HAVE_VMG
+#if defined(HAVE_JOBMARKET) && defined(HAVE_VMG)
 #include "Fragmentation/Automation/VMGDebugGridFragmentController.hpp"
 #include "Fragmentation/Automation/VMGFragmentController.hpp"
@@ -99 +108 @@
 }
 
+#ifdef HAVE_JOBMARKET
 static void updateSteps(Process &p, const size_t step, const size_t total)
 {
@@ -104 +114 @@
   p.setCurrStep(step);
 }
+#endif
 
 ActionState::ptr FragmentationFragmentationAutomationAction::performCall() {
@@ -117 +128 @@
   size_t Exitflag = 0;
   std::map<JobId_t, MPQCData> shortrangedata;
+#ifdef HAVE_JOBMARKET
   {
     const size_t NumberJobs = FragmentJobQueue::getInstance().size();
@@ -126 +138 @@
 
     // Phase Two: add MPQCJobs and send
-    const size_t NoJobs = mpqccontroller.addJobsFromQueue(
+    const bool AddJobsStatus = mpqccontroller.addJobsFromQueue(
         params.DoLongrange.get() ? MPQCData::DoSampleDensity : MPQCData::DontSampleDensity,
         params.DoValenceOnly.get() ? MPQCData::DoSampleValenceOnly : MPQCData::DontSampleValenceOnly
         );
-    LOG(1, "INFO: Added " << NoJobs << " from FragmentJobsQueue.");
+    if (AddJobsStatus)
+      LOG(1, "INFO: Added jobs from FragmentJobsQueue.");
+    else {
+      ELOG(1, "Adding jobs failed.");
+      return Action::failure;
+    }
     mpqccontroller.run();
 
@@ -148 +165 @@
     Exitflag += mpqccontroller.getExitflag();
   }
-
-#ifdef HAVE_VMG
+#else
+  {
+    const size_t NumberJobs = FragmentJobQueue::getInstance().size();
+    MPQCCommandFragmentController mpqccontroller;
+    // Phase One: obtain ids: not needed, we have infinite pool
+
+    // Phase Two: add MPQCJobs and send
+    const size_t NoJobs = mpqccontroller.addJobsFromQueue(
+        params.DoLongrange.get() ? MPQCData::DoSampleDensity : MPQCData::DontSampleDensity,
+        params.DoValenceOnly.get() ? MPQCData::DoSampleValenceOnly : MPQCData::DontSampleValenceOnly,
+        params.executable.get().string()
+        );
+    LOG(1, "INFO: Added " << NoJobs << " from FragmentJobsQueue.");
+    mpqccontroller.run();
+
+    // get back the results and place them in shortrangedata
+    mpqccontroller.getResults(shortrangedata);
+    ASSERT( shortrangedata.size() == NumberJobs,
+        "FragmentationFragmentationAutomationAction::performCall() - number of converted results "
+        +toString(shortrangedata.size())+" and number of jobs "+toString(NumberJobs)+ " differ.");
+
+    Exitflag += mpqccontroller.getExitflag();
+  }
+#endif
+
+#if defined(HAVE_JOBMARKET) && defined(HAVE_VMG)
   if (params.DoLongrange.get()) {
   if ( World::getInstance().getAllAtoms().size() == 0) {