Changeset 142ff5 for src/Fragmentation

Timestamp:

Jun 22, 2012, 8:19:31 AM (13 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:

78ad7d

Parents:

246d97

git-author:

Frederik Heber <heber@…> (01/17/12 19:10:35)

git-committer:

Frederik Heber <heber@…> (06/22/12 08:19:31)

Message:

FragmentJob now executes a specific string as command along with an outputfile to work on.

• stdout is parsed in as FragmentResult::result, return from std::system is placed into FragmentResult::exitflag.
• createjobs() in controller.cpp uses cat and "Nothing" to mimick the same behavior as before.
• removed intermediate deadline_timer usage in ::Work().

Location:

src/Fragmentation/Automation

Files:

• FragmentJob.cpp (modified) (4 diffs)
• FragmentJob.hpp (modified) (3 diffs)
• FragmentScheduler.cpp (modified) (1 diff)
• controller.cpp (modified) (1 diff)
• unittests/FragmentJobUnitTest.cpp (modified) (4 diffs)
• unittests/FragmentJobUnitTest.hpp (modified) (1 diff)

src/Fragmentation/Automation/FragmentJob.cpp

@@ -18 +18 @@
 #endif
 
-// boost asio needs specific operator new
-#include <boost/asio.hpp>
-#include <boost/date_time/posix_time/posix_time.hpp>
+#include "CodePatterns/MemDebug.hpp"
 
-#include "CodePatterns/MemDebug.hpp"
+#include <cstdlib>
+#include <fstream>
+#include <string>
 
 #include "CodePatterns/Info.hpp"
@@ -40 +40 @@
 /** Constructor for class FragmentJob.
  *
+ * \param _command command to execute
  * \param _outputfile configuration file for solver
  * \param _JobId unique id of this job
  */
-FragmentJob::FragmentJob(const std::string &_outputfile, const JobId_t _JobId) :
+FragmentJob::FragmentJob(const std::string &_command, const std::string &_outputfile, const JobId_t _JobId) :
   JobId(_JobId),
+  command(_command),
   outputfile(_outputfile)
 {}
@@ -67 +69 @@
   FragmentResult s(getId());
 
-  boost::asio::io_service io;
-  boost::asio::deadline_timer t(io, boost::posix_time::seconds(1));
-  LOG(1, "INFO: Deadline timer will now wait for 1 seconds.");
-  t.wait();
-  LOG(1, "INFO: Deadline timer is done.");
+  // write outputfile to file
+  std::string inputfilename =
+      std::string("/tmp/dummy_")
+      +toString(getId());
+  std::string outputfilename = inputfilename+std::string(".out");
+  inputfilename += std::string(".dat");
+  std::ofstream output(outputfilename.c_str());
+  output << outputfile << std::endl;
+  output.close();
+
+  // fork into subprocess and launch command
+  s.exitflag = std::system((command+std::string(" ")+inputfilename
+                        +std::string(" >")+outputfilename).c_str());
+  std::ifstream resultfile;
+  resultfile.open(outputfilename.c_str(), ifstream::in);
+  char line[1024];
+  while (resultfile.good()) {
+    resultfile.getline(line, 1023);
+    s.result += line;
+  }
+  resultfile.close();
 
   return s;
@@ -82 +100 @@
 bool FragmentJob::operator==(const FragmentJob &other) const
 {
-  return (outputfile == other.outputfile) && (getId() == other.getId());
+  return (command == other.command)
+      && (outputfile == other.outputfile)
+      && (getId() == other.getId());
 }

src/Fragmentation/Automation/FragmentJob.hpp

@@ -40 +40 @@
 public:
   FragmentJob();
-  FragmentJob(const std::string &_outputfile, const JobId_t _JobId);
+  FragmentJob(const std::string &_command, const std::string &_outputfile, const JobId_t _JobId);
   ~FragmentJob();
 
@@ -50 +50 @@
     return !(*this == other);
   }
+
+  //!> string containing the command to launch the solver
+  std::string command;
 
   //!> string containing the configuration file for the solver
@@ -61 +64 @@
   {
     ar & boost::serialization::base_object<JobId>(*this);
+    ar & command;
     ar & outputfile;
   }

src/Fragmentation/Automation/FragmentScheduler.cpp

@@ -39 +39 @@
 #include "FragmentScheduler.hpp"
 
-FragmentJob FragmentScheduler::NoJob(std::string("NoJob"), JobId::NoJob);
+FragmentJob FragmentScheduler::NoJob(std::string("/bin/false"), std::string("NoJob"), JobId::NoJob);
 
 /** Constructor of class FragmentScheduler.

src/Fragmentation/Automation/controller.cpp

@@ -52 +52 @@
 void createjobs(std::vector<FragmentJob> &jobs)
 {
-  FragmentJob testJob(std::string("do something"), 1);
-  FragmentJob othertestJob(std::string("do something else"), 2);
+  FragmentJob testJob(std::string("cat"), std::string("Nothing"), 1);
+  FragmentJob othertestJob(std::string("cat"), std::string("Nothing"), 2);
   jobs.push_back(testJob);
   jobs.push_back(othertestJob);

src/Fragmentation/Automation/unittests/FragmentJobUnitTest.cpp

@@ -49 +49 @@
   ASSERT_DO(Assert::Throw);
 
-  command = std::string("do something");
+  command = std::string("/bin/true");
+  outputfile = std::string("do something");
 }
 
@@ -61 +62 @@
 void FragmentJobTest::equalityTest()
 {
-  FragmentJob testJob(command, 1);
-  FragmentJob sameIdJob(command, 1);
-  FragmentJob otherIdJob(command, 2);
+  FragmentJob testJob(command, outputfile, 1);
+  FragmentJob sameIdJob(command, outputfile, 1);
+  FragmentJob otherIdJob(command, outputfile, 2);
   FragmentJob copiedJob(testJob);
   FragmentJob copiedchangedJob(testJob);
@@ -78 +79 @@
 void FragmentJobTest::WorkTest()
 {
-  FragmentJob testJob(command, 1);
-  FragmentJob othertestJob(command, 2);
+  FragmentJob testJob(command, outputfile, 1);
+  FragmentJob othertestJob(command, outputfile, 2);
 
   FragmentResult testResult(testJob.Work());
@@ -92 +93 @@
 void FragmentJobTest::serializationTest()
 {
-  FragmentJob testJob(command, 1);
+  FragmentJob testJob(command, outputfile, 1);
   // write element to stream
   std::stringstream stream;

src/Fragmentation/Automation/unittests/FragmentJobUnitTest.hpp

@@ -37 +37 @@
 private:
       std::string command;
+      std::string outputfile;
 
 };