Changeset d6a7b9

Timestamp:

Jul 13, 2014, 6:04:51 PM (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:

99692c

Parents:

18ed8c

git-author:

Frederik Heber <heber@…> (07/12/14 23:05:27)

git-committer:

Frederik Heber <heber@…> (07/13/14 18:04:51)

Message:

Specifying executable and suffix in SystemCommandJob with MPQCCommandFragmentController.

• now requiring JobMarket 1.1.5 (if given) for updated SystemCommandJob.
• SystemCommandJob allows specifying a suffix to the temporary file.
• this allows adding ".in" to MPQCCommandJob's temporary file name.

Files:

• configure.ac (modified) (1 diff)
• src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) (1 diff)
• src/Fragmentation/Automation/MPQCCommandFragmentController.cpp (modified) (2 diffs)
• src/Fragmentation/Automation/MPQCCommandFragmentController.hpp (modified) (1 diff)
• src/Jobs/JobMarket/SystemCommandJob.cpp (modified) (3 diffs)
• src/Jobs/JobMarket/SystemCommandJob.hpp (modified) (2 diffs)
• src/Jobs/MPQCCommandJob.hpp (modified) (3 diffs)

configure.ac

@@ -235 +235 @@
 AC_MSG_RESULT($enable_jobmarket)
 AS_IF([test x"$enable_jobmarket" != x"no"],[
-  # JobMarket library (needs priorizing of jobs)
-  AM_PATH_JOBMARKET([1.1.4], $have_debug,[
+  # JobMarket library (needs SystemCommandJob with suffix)
+  AM_PATH_JOBMARKET([1.1.5], $have_debug,[
     # the following is only required if we have JobMarket
     BOOST_ASIO

src/Actions/FragmentationAction/FragmentationAutomationAction.cpp

@@ -169 +169 @@
     const size_t NoJobs = mpqccontroller.addJobsFromQueue(
         params.DoLongrange.get() ? MPQCData::DoSampleDensity : MPQCData::DontSampleDensity,
-        params.DoValenceOnly.get() ? MPQCData::DoSampleValenceOnly : MPQCData::DontSampleValenceOnly
+        params.DoValenceOnly.get() ? MPQCData::DoSampleValenceOnly : MPQCData::DontSampleValenceOnly,
+        params.executable.get().string()
         );
     LOG(1, "INFO: Added " << NoJobs << " from FragmentJobsQueue.");

src/Fragmentation/Automation/MPQCCommandFragmentController.cpp

@@ -61 +61 @@
 bool MPQCCommandFragmentController::addJobsFromQueue(
     const MPQCData::DoLongrange_t _DoLongrange,
-    const MPQCData::DoValenceOnly_t _DoValenceOnly
+    const MPQCData::DoValenceOnly_t _DoValenceOnly,
+    const std::string &_executable
     )
 {
@@ -74 +75 @@
 #ifndef HAVE_JOBMARKET
     job->setId(getAvailableId());
+    if (!_executable.empty())
+      job->setCommand(_executable);
+    job->setSuffix(".in");
 #endif /* cause we don't inherit from FragmentController */
     // add the jobs

src/Fragmentation/Automation/MPQCCommandFragmentController.hpp

@@ -44 +44 @@
    * \param _DoSampleDensity whether to actually sample the resulting electronic density
    * \param _DoValenceOnly whether to sample just the valence or the total elctron and nuclei density
+   * \param _command command to pass to jobs for execution
    * \return true - jobs obtained, false - queue empty
    */
   bool addJobsFromQueue(
       const MPQCData::DoLongrange_t _DoLongrange,
-      const MPQCData::DoValenceOnly_t _DoValenceOnly
+      const MPQCData::DoValenceOnly_t _DoValenceOnly,
+      const std::string &_command
       );
 

src/Jobs/JobMarket/SystemCommandJob.cpp

@@ -77 +77 @@
  * \param _outputfile configuration file for solver
  * \param _JobId unique id of this job
- */
-SystemCommandJob::SystemCommandJob(const std::string &_command, const std::string &_outputfile, const JobId_t _JobId) :
+ * \param _suffix possible suffix for temporary filenames, may be left empty
+ */
+SystemCommandJob::SystemCommandJob(
+    const std::string &_command, 
+    const std::string &_outputfile, 
+    const JobId_t _JobId,
+    const std::string &_suffix) :
   FragmentJob(_JobId),
   command(_command),
+  suffix(_suffix),
   outputfile(_outputfile)
 {}
@@ -121 +127 @@
     "SystemCommandJob::Work() - the temporary file could not be opened.");
   output << outputfile << std::endl;
+  output.close();
 
   // fork into subprocess and launch command
@@ -163 +170 @@
 
   // close temporary file and remove it
-  output.close();
   boost::filesystem::path tmpPath(tmpTemplate);
   if (boost::filesystem::exists(boost::filesystem::status(tmpPath))) {

src/Jobs/JobMarket/SystemCommandJob.hpp

@@ -42 +42 @@
   friend class SystemCommandJobTest;
 public:
-  SystemCommandJob(const std::string &_command, const std::string &_outputfile, const JobId_t _JobId);
+  SystemCommandJob(const std::string &_command, const std::string &_outputfile, const JobId_t _JobId, const std::string &_suffix = std::string(""));
   virtual ~SystemCommandJob();
 
@@ -53 +53 @@
   }
 
-private:
+  const std::string& getOutputfile() const {
+    return outputfile;
+  }
+
+  const std::string& getCommand() const {
+    return command;
+  }
+
+protected:
   virtual FragmentResult::ptr extractResult(const std::string &resultstring);
 
   //!> string containing the command to launch the solver
   std::string command;
+
+  //!> suffix to be appended to output file name
+  std::string suffix;
 
   //!> string containing the configuration file for the solver

src/Jobs/MPQCCommandJob.hpp

@@ -29 +29 @@
 
 class MPQCCommandJobTest;
+class MPQCCommandFragmentController;
 
 /** This class calls mpqc for solving a specific Hartree Fock problem.
@@ -37 +38 @@
   //!> grant unit test access
   friend class MPQCCommandJobTest;
+  //!> grant access to controller
+  friend class MPQCCommandFragmentController;
 public:
   MPQCCommandJob(const std::string &_inputfile, const JobId_t _JobId, const std::string &_command = std::string("mpqc"));
@@ -48 +51 @@
 
 private:
+  //!> Allow controller access to changing the commands
+  void setCommand(const std::string &_command)
+  { command = _command; }
+
+  //!> Allow controller access to changing the suffix
+  void setSuffix(const std::string &_suffix)
+  { suffix = _suffix; }
+
   //!> private default cstor only for serializatio
   MPQCCommandJob();