Changeset fbf005 for src/Jobs/MPQCJob_Work.cpp

Timestamp:

Mar 9, 2017, 9:43:23 AM (8 years ago)

Author:

Frederik Heber <heber@…>

Branches:

Action_Thermostats, Add_AtomRandomPerturbation, Add_RotateAroundBondAction, Add_SelectAtomByNameAction, Adding_Graph_to_ChangeBondActions, Adding_MD_integration_tests, Adding_StructOpt_integration_tests, AutomationFragmentation_failures, Candidate_v1.6.0, Candidate_v1.6.1, ChangeBugEmailaddress, ChangingTestPorts, ChemicalSpaceEvaluator, Combining_Subpackages, Debian_Package_split, Debian_package_split_molecuildergui_only, Disabling_MemDebug, Docu_Python_wait, EmpiricalPotential_contain_HomologyGraph_documentation, Enable_parallel_make_install, Enhance_userguide, Enhanced_StructuralOptimization, Enhanced_StructuralOptimization_continued, Example_ManyWaysToTranslateAtom, Exclude_Hydrogens_annealWithBondGraph, FitPartialCharges_GlobalError, Fix_ChronosMutex, Fix_StatusMsg, Fix_StepWorldTime_single_argument, Fix_Verbose_Codepatterns, ForceAnnealing_goodresults, ForceAnnealing_oldresults, ForceAnnealing_tocheck, ForceAnnealing_with_BondGraph, ForceAnnealing_with_BondGraph_continued, ForceAnnealing_with_BondGraph_continued_betteresults, ForceAnnealing_with_BondGraph_contraction-expansion, GeometryObjects, Gui_displays_atomic_force_velocity, IndependentFragmentGrids_IntegrationTest, JobMarket_RobustOnKillsSegFaults, JobMarket_StableWorkerPool, JobMarket_unresolvable_hostname_fix, PartialCharges_OrthogonalSummation, PythonUI_with_named_parameters, QtGui_reactivate_TimeChanged_changes, Recreated_GuiChecks, RotateToPrincipalAxisSystem_UndoRedo, StoppableMakroAction, TremoloParser_IncreasedPrecision, TremoloParser_MultipleTimesteps, Ubuntu_1604_changes, stable

Children:

7672284

Parents:

ba1152

git-author:

Frederik Heber <heber@…> (03/08/17 08:11:59)

git-committer:

Frederik Heber <heber@…> (03/09/17 09:43:23)

Message:

HUGE: Extracted libmolecuilder_mpqc that is now linked to poolworker.

• This stops the problems with MemDebug and mpqc when linking against libLinearAlgebra in debug mode: static global variables in libLinAlg are allocated using MemDebug (prefixed with a checksum) but are deallocated using normal libc's free() on exit. This causes an invalid free() as the ptr given to free points inside the block and not at its start. The problem comes from mpqc's use of own new and delete implementation. I'm guessing its reference counting is the culprit. Hence, we need to separate these two compilations from another in different units/libraries. Therefore, we have split off libmolecuilder_mpqc, .._mpqc_extract and additionally place the MPQCJob::Work() implementation inside libMolecuilderJobs_Work.
• libmolecuilder_mpqc contains all MPQC's code in mpqc.cc (and linked libraries) that is not the main() function.
• libmolecuilder_mpqc_extract contains functions that extract results such as energies, forces, charge grids from the obtained mpqc solution. These were added by myself to the mpqc code before.
• molecuilder_mpqc is then linked against a NoOp .._extract library version. Thereby, it does not use any of the Molecuilder or related libraries and does not come in contact with MemDebug.
• molecuilder_poolworker however is linked with the full .._extract library and hence performs these extractions.
• poolworker now executes MPQCJob, MPQCCommandJob, and VMGJob and therefore needs to enforce binding to all of them.
• TESTS: renamed molecuilder_mpqc.in to molecuilder_poolworker.in.

File:

• src/Jobs/MPQCJob_Work.cpp (modified) (4 diffs)

src/Jobs/MPQCJob_Work.cpp

@@ -1 @@
-/*
- * Project: MoleCuilder
+/* Project: MoleCuilder
  * Description: creates and alters molecular systems
  * Copyright (C)  2017 Frederik Heber. All rights reserved.
- * 
+ *
  *
  *   This file is part of MoleCuilder.
@@ -21 +20 @@
  */
 
-/*
- * MPQCJobi_Work.cpp
+/** \file MPCJob_Work.cpp
  *
- *  Created on: Feb 20, 2017
- *      Author: heber
+ * Function implementations for the class vector.
+ *
  */
-
 
 // include config.h
@@ -34 +31 @@
 #endif
 
+#include <sstream>
+
+#include "MPQCJob.hpp"
+
+#include "CodePatterns/Log.hpp"
+
+#ifdef HAVE_JOBMARKET
 // include headers that implement a archive in simple text format
 // otherwise BOOST_CLASS_EXPORT_IMPLEMENT has no effect
 #include <boost/archive/text_oarchive.hpp>
 #include <boost/archive/text_iarchive.hpp>
+#include <boost/tokenizer.hpp>
 
-#include "CodePatterns/MemDebug.hpp"
+#include "JobMarket/Results/FragmentResult.hpp"
 
-#include "MPQCJob.hpp"
+#include <fstream>
+#include <iostream>
+#include <stdlib.h>
 
-#include <sstream>
+#include <util/class/scexception.h>
+#include <util/group/message.h>
 
-#include "CodePatterns/Log.hpp"
+#include "mpqc.h"
 
+using namespace std;
+
+using namespace sc;
+
+FragmentResult::ptr MPQCJob::Work()
+{
+  char mpqc[] = "mpqc" ;
+  char **argv = new char*[1];
+  argv[0] = &mpqc[0];
+  int argc = 1;
+
+  // now comes the actual work
+  mpqc::InitValues initvalues;
+  int nfilebase = (int) inputfile.length();
+  initvalues.in_char_array = new char[nfilebase + 1];
+  strncpy(initvalues.in_char_array, inputfile.c_str(), nfilebase);
+  initvalues.in_char_array[nfilebase] = '\0';
+  initvalues.grp = MessageGrp::get_default_messagegrp();
+  // create unique, temporary name and check whether it exists
+  char *tempfilename = NULL;
+  {
+    std::ifstream test;
+    do {
+      if (initvalues.output != NULL) // free buffer from last round
+        delete initvalues.output;
+      char filename_template[] = "mpqc_temp_XXXXXX\0";
+      char filename_suffix[] = ".in\0";
+      tempfilename = (char *) malloc ( (strlen(filename_template)+strlen(filename_suffix)+2)*(sizeof(char)));
+      strncpy(tempfilename, mktemp(filename_template), strlen(filename_template));
+      tempfilename[strlen(filename_template)] = '\0';
+      strncat(tempfilename, filename_suffix, strlen(filename_suffix));
+      initvalues.output = tempfilename;
+      //free(tempfilename); // don't free! output takes over pointer!
+      test.open(initvalues.output);
+    } while (test.good()); // test whether file does not(!) exist
+    test.close();
+  }
+  // put info how to sample the density into MPQCData
+  MPQCData data(grid);
+  data.DoLongrange = DoLongrange; // set whether we sample the density
+  data.DoValenceOnly = DoValenceOnly; // set whether we sample just valence electron and nuclei densities
+// now call work horse
+  try {
+    mpqc::mainFunction(initvalues, argc, argv, static_cast<void *>(&data));
+  }
+  catch (SCException &e) {
+    cout << argv[0] << ": ERROR: SC EXCEPTION RAISED:" << endl
+         << e.what()
+         << endl;
+    detail::clean_up();
+  }
+
+  //delete[] in_char_array; // is deleted in mainFunction()
+  if (initvalues.output != 0) {
+    free(tempfilename);
+  }
+  delete[] argv;
+  initvalues.grp = NULL;
+
+  // place into returnstream
+  std::stringstream returnstream;
+  boost::archive::text_oarchive oa(returnstream);
+  oa << data;
+
+  FragmentResult::ptr s( new FragmentResult(getId(), returnstream.str()) );
+  if (s->exitflag != 0)
+    cerr << "Job #" << s->getId() << " failed to reach desired accuracy." << endl;
+
+  return s;
+}
+#else
 FragmentResult::ptr MPQCJob::Work()
 {
@@ -67 +146 @@
   return ptr;
 }
+#endif
 
+// we need to explicitly instantiate the serialization functions as
+// its is only serialized through its base class FragmentJob
+BOOST_CLASS_EXPORT_IMPLEMENT(MPQCJob)