Changeset ff60cfa for src

Timestamp:

Jun 27, 2012, 4:07:20 PM (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:

545446

Parents:

306f60

git-author:

Frederik Heber <heber@…> (02/15/12 14:14:19)

git-committer:

Frederik Heber <heber@…> (06/27/12 16:07:20)

Message:

Controller has new function addjobs.

• addjobs parses mpqc input file and creates MPQCCommandJob which is sent to send jobs
• old sendjobs is now createjobs which creates empty SystemCommandJob.
• added new class GlobalJobId which holds a global JobId such that FragmentJobs created by Controller each have a unique id. NOTE: This should probably be replaced by IdPool implementation when Fragmentation/Automation is integrated into rest of molecuilder.
• dummyInit() to have MPQCCommandJob instances known to FragmentScheduler.
• TESTFIX: Adapted regression tests Fragmentation/Automation adding-jobs, server-worker, and completerun due to command token change.

Location:

src/Fragmentation/Automation

Files:

• FragmentScheduler.cpp (modified) (2 diffs)
• GlobalJobId.cpp (added)
• GlobalJobId.hpp (added)
• Makefile.am (modified) (2 diffs)
• controller.cpp (modified) (7 diffs)

src/Fragmentation/Automation/FragmentScheduler.cpp

@@ -34 +34 @@
 #include "CodePatterns/Info.hpp"
 #include "CodePatterns/Log.hpp"
+#include "Jobs/MPQCCommandJob.hpp"
 #include "Jobs/SystemCommandJob.hpp"
 #include "JobId.hpp"
@@ -39 +40 @@
 #include "FragmentScheduler.hpp"
 
-FragmentJob::ptr FragmentScheduler::NoJob(new SystemCommandJob(std::string("/bin/false"), std::string("NoJob"), JobId::NoJob));
+FragmentJob::ptr FragmentScheduler::NoJob(new SystemCommandJob(std::string("/bin/true"), std::string("dosomething"), JobId::NoJob));
+
+/** Helper function to enforce binding of FragmentWorker to possible derived
+ * FragmentJob classes.
+ */
+void dummyInit() {
+  SystemCommandJob("/bin/false", "something", JobId::IllegalJob);
+  MPQCCommandJob("nofile", JobId::IllegalJob);
+}
 
 /** Constructor of class FragmentScheduler.

src/Fragmentation/Automation/Makefile.am

@@ -50 +50 @@
   Controller/Commands/ReceiveJobsOperation.cpp \
   Controller/Commands/SendResultsOperation.cpp \
-  Controller/Commands/ShutdownOperation.cpp
+  Controller/Commands/ShutdownOperation.cpp \
+  GlobalJobId.cpp
 
 FRAGMENTATIONAUTOMATIONHEADER = \
@@ -62 +63 @@
   Controller/Commands/ReceiveJobsOperation.hpp \
   Controller/Commands/SendResultsOperation.hpp \
-  Controller/Commands/ShutdownOperation.hpp
+  Controller/Commands/ShutdownOperation.hpp \
+  GlobalJobId.hpp
 
 noinst_LTLIBRARIES += libMolecuilderFragmentationAutomation.la

src/Fragmentation/Automation/controller.cpp

@@ -27 +27 @@
 #include "CodePatterns/MemDebug.hpp"
 
+#include <fstream>
 #include <iostream>
+#include <map>
+#include <sstream>
+#include <streambuf>
 #include <vector>
-#include <map>
 
 #include "atexit.hpp"
@@ -39 +42 @@
 #include "Controller/Commands/SendResultsOperation.hpp"
 #include "Controller/Commands/ShutdownOperation.hpp"
+#include "GlobalJobId.hpp"
+#include "Jobs/MPQCCommandJob.hpp"
 #include "Jobs/SystemCommandJob.hpp"
 #include "Results/FragmentResult.hpp"
@@ -44 +49 @@
 enum CommandIndices {
   UnknownCommandIndex = 0,
-  SendJobsIndex = 1,
-  CheckResultsIndex = 2,
-  ReceiveResultsIndex = 3,
-  ShutdownIndex = 4
+  AddJobsIndex = 1,
+  CreateJobsIndex = 2,
+  CheckResultsIndex = 3,
+  ReceiveResultsIndex = 4,
+  ShutdownIndex = 5
 };
 
+// TODO: replace this instance by a IdPool owned by controller.
+GlobalJobId globalId;
+
 void createjobs(std::vector<FragmentJob::ptr> &jobs)
 {
-  FragmentJob::ptr testJob( new SystemCommandJob( std::string("cat"), std::string("Nothing"), 1) );
-  FragmentJob::ptr othertestJob( new SystemCommandJob( std::string("cat"), std::string("Nothing"), 2) );
+  FragmentJob::ptr testJob( new SystemCommandJob( std::string("cat"), std::string("Nothing"), globalId.getNextId()) );
+  FragmentJob::ptr othertestJob( new SystemCommandJob( std::string("cat"), std::string("Nothing"), globalId.getNextId()) );
   jobs.push_back(testJob);
   jobs.push_back(othertestJob);
+}
+
+void parsejob(std::vector<FragmentJob::ptr> &jobs, const std::string &filename)
+{
+  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>());
+  FragmentJob::ptr testJob( new MPQCCommandJob(output, globalId.getNextId()) );
+  jobs.push_back(testJob);
+  file.close();
+  LOG(1, "INFO: Added MPQCCommandJob from file "+filename+".");
 }
 
@@ -136 +158 @@
 
   size_t Exitflag = 0;
-  std::map<std::string, CommandIndices> CommandsMap;
-  CommandsMap.insert( std::make_pair("sendjobs", SendJobsIndex) );
+  typedef std::map<std::string, CommandIndices> CommandsMap_t;
+  CommandsMap_t CommandsMap;
+  CommandsMap.insert( std::make_pair("addjobs", AddJobsIndex) );
+  CommandsMap.insert( std::make_pair("createjobs", CreateJobsIndex) );
   CommandsMap.insert( std::make_pair("checkresults", CheckResultsIndex) );
   CommandsMap.insert( std::make_pair("receiveresults", ReceiveResultsIndex) );
@@ -144 +168 @@
   {
     // Check command line arguments.
-    if (argc != 4)
+    if (argc < 4)
     {
-      std::cerr << "Usage: " << argv[0] << " <host> <port> <command>" << std::endl;
+      std::cerr << "Usage: " << argv[0] << " <host> <port> <command> [options to command]" << std::endl;
+      std::cerr << "List of available commands:" << std::endl;
+      for(CommandsMap_t::const_iterator iter = CommandsMap.begin();
+          iter != CommandsMap.end(); ++iter) {
+        std::cerr << "\t" << iter->first << std::endl;
+      }
       return 1;
     }
@@ -154 +183 @@
 
     switch(getCommandIndex(CommandsMap, argv[3])) {
-      case SendJobsIndex:
+      case AddJobsIndex:
+      {
+        std::vector<FragmentJob::ptr> jobs;
+        if (argc == 4) {
+          ELOG(1, "Please add a filename for the MPQCCommandJob.");
+        } else {
+          for (int argcount = 4; argcount < argc; ++argcount) {
+            LOG(1, "INFO: Parsing job for file " << argv[argcount] << ".");
+            parsejob(jobs, argv[argcount]);
+          }
+          addjobs(controller, jobs);
+          sendjobs(controller, argv[1], argv[2]);
+        }
+        break;
+      }
+      case CreateJobsIndex:
       {
         std::vector<FragmentJob::ptr> jobs;
@@ -189 +233 @@
 
     switch(getCommandIndex(CommandsMap, argv[3])) {
-      case SendJobsIndex:
+      case AddJobsIndex:
+      case CreateJobsIndex:
         break;
       case CheckResultsIndex: