Changeset ac9ca4 for src/Fragmentation/Automation

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().

Location:

src/Fragmentation/Automation

Files:

• FragmentJobQueue.cpp (added)
• FragmentJobQueue.hpp (added)
• MPQCFragmentController.cpp (modified) (1 diff)
• MPQCFragmentController.hpp (modified) (1 diff)
• Makefile.am (modified) (2 diffs)

src/Fragmentation/Automation/MPQCFragmentController.cpp

@@ -45 +45 @@
 #include "Box.hpp"
 #include "Helpers/defs.hpp"
+#include "Fragmentation/Automation/FragmentJobQueue.hpp"
 #include "Jobs/MPQCJob.hpp"
 #include "LinearAlgebra/RealSpaceMatrix.hpp"
 #include "World.hpp"
 
-bool MPQCFragmentController::addJobsFromFiles(
-    const std::string &executable,
-    const std::vector< boost::filesystem::path > &jobfiles)
+bool MPQCFragmentController::addJobsFromQueue()
 {
-  std::vector<FragmentJob::ptr> jobs;
-  for (std::vector< boost::filesystem::path >::const_iterator iter = jobfiles.begin();
-      iter != jobfiles .end(); ++iter) {
-    const std::string &filename = (*iter).string();
-    if (boost::filesystem::exists(filename)) {
-      const JobId_t next_id = getAvailableId();
-      LOG(1, "INFO: Creating MPQCCommandJob with filename'"
-          +filename+"', and id "+toString(next_id)+".");
-      parsejob(jobs, executable, filename, next_id);
-    } else {
-      ELOG(1, "Fragment job "+filename+" does not exist.");
-      return false;
-    }
+  // give them all valid ids
+  std::vector<FragmentJob::ptr> newjobs = FragmentJobQueue::getInstance().getJobs();
+  for (std::vector<FragmentJob::ptr>::iterator jobiter = newjobs.begin();
+      jobiter != newjobs.end();
+      ++jobiter) {
+    changeJobId((*jobiter), getAvailableId());
   }
-  addJobs(jobs);
+  // add the jobs
+  addJobs(newjobs);
+
+  return (newjobs.size() != 0);
+}
+
+void MPQCFragmentController::run()
+{
+  // take jobs from queue and add them
   sendJobs(host, port);
   RunService("Adding MPQCJobs");
-
-  return true;
 }
-
-/** Creates a MPQCCommandJob with argument \a filename.
- *
- * @param jobs created job is added to this vector
- * @param command mpqc command to execute
- * @param filename filename being argument to job
- * @param nextid id for this job
- */
-void MPQCFragmentController::parsejob(
-    std::vector<FragmentJob::ptr> &jobs,
-    const std::string &command,
-    const std::string &filename,
-    const JobId_t nextid)
-{
-  std::ifstream file;
-  file.open(filename.c_str());
-  ASSERT( file.good(), "parsejob() - file "+filename+" does not exist.");
-  std::string output((std::istreambuf_iterator<char>(file)),
-      std::istreambuf_iterator<char>());
-  double begin[NDIM] = { 0., 0., 0. };
-  RealSpaceMatrix M = World::getInstance().getDomain().getM();
-  M *= 1./AtomicLengthToAngstroem;  // scale to atomic length units
-  const double size = M.at(0,0);
-  double end[NDIM] = { size, size, size };
-  ASSERT( M.determinant() == size*size*size,
-      "parsejob() - current domain matrix "+toString(M)+" is not cubic.");
-  FragmentJob::ptr testJob( new MPQCJob(nextid, output, begin, end, level) );
-  jobs.push_back(testJob);
-  file.close();
-  LOG(1, "INFO: Added MPQCCommandJob from file "+filename+".");
-}

src/Fragmentation/Automation/MPQCFragmentController.hpp

@@ -34 +34 @@
 public:
   MPQCFragmentController(boost::asio::io_service &io_service) :
-    SpecificFragmentController(io_service),
-    level(5)
+    SpecificFragmentController(io_service)
   {}
   virtual ~MPQCFragmentController()
   {}
 
-  bool addJobsFromFiles(
-      const std::string &executable,
-      const std::vector< boost::filesystem::path > &jobfiles);
+  /** Command Controller to fill its hold of jobs from FragmentJobQueue.
+   *
+   * \return true - jobs obtained, false - queue empty
+   */
+  bool addJobsFromQueue();
+
+  /** Get results map of calculated jobs.
+   *
+   * \param fragmentData contains map of results on output
+   */
   void getResults(std::map<JobId_t, MPQCData> &fragmentData) {
     SpecificFragmentController::getResults<MPQCData>(fragmentData);
   }
 
-  void setLevel(const size_t _level) { level = _level; }
-
-private:
-  void parsejob(
-      std::vector<FragmentJob::ptr> &jobs,
-      const std::string &command,
-      const std::string &filename,
-      const JobId_t nextid);
-
-private:
-  //!> resolution of sampled electron density as \f$2^{\mathrm{level}}\f$
-  size_t level;
+  /** Runs the service.
+   *
+   * Here, we finalize each job's id and push them to the server.
+   */
+  void run();
 };
 

src/Fragmentation/Automation/Makefile.am

@@ -6 +6 @@
         Fragmentation/Automation/FragmentationChargeDensity.cpp \
         Fragmentation/Automation/FragmentationResults.cpp \
+        Fragmentation/Automation/FragmentJobQueue.cpp \
         Fragmentation/Automation/MPQCFragmentController.cpp \
         Fragmentation/Automation/parseKeySetFile.cpp \
@@ -21 +22 @@
         Fragmentation/Automation/FragmentationChargeDensity.hpp \
         Fragmentation/Automation/FragmentationResults.hpp \
+        Fragmentation/Automation/FragmentJobQueue.hpp \
         Fragmentation/Automation/MPQCFragmentController.hpp \
         Fragmentation/Automation/parseKeySetFile.hpp \