Changeset fbf005 for src/Jobs


Ignore:
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.
Location:
src/Jobs
Files:
1 added
2 edited

Legend:

Unmodified
Added
Removed

  • src/Jobs/MPQCJob_Work.cpp

    rba1152 rfbf005  
    1 /*
    2  * Project: MoleCuilder
     1/* Project: MoleCuilder
    32 * Description: creates and alters molecular systems
    43 * Copyright (C)  2017 Frederik Heber. All rights reserved.
    5  * 
     4 *
    65 *
    76 *   This file is part of MoleCuilder.
    … …  
    2120 */
    2221
    23 /*
    24  * MPQCJobi_Work.cpp
     22/** \file MPCJob_Work.cpp
    2523 *
    26  *  Created on: Feb 20, 2017
    27  *      Author: heber
     24 * Function implementations for the class vector.
     25 *
    2826 */
    29 
    3027
    3128// include config.h
    … …  
    3431#endif
    3532
     33#include <sstream>
     34
     35#include "MPQCJob.hpp"
     36
     37#include "CodePatterns/Log.hpp"
     38
     39#ifdef HAVE_JOBMARKET
    3640// include headers that implement a archive in simple text format
    3741// otherwise BOOST_CLASS_EXPORT_IMPLEMENT has no effect
    3842#include <boost/archive/text_oarchive.hpp>
    3943#include <boost/archive/text_iarchive.hpp>
     44#include <boost/tokenizer.hpp>
    4045
    41 #include "CodePatterns/MemDebug.hpp"
     46#include "JobMarket/Results/FragmentResult.hpp"
    4247
    43 #include "MPQCJob.hpp"
     48#include <fstream>
     49#include <iostream>
     50#include <stdlib.h>
    4451
    45 #include <sstream>
     52#include <util/class/scexception.h>
     53#include <util/group/message.h>
    4654
    47 #include "CodePatterns/Log.hpp"
     55#include "mpqc.h"
    4856
     57using namespace std;
     58
     59using namespace sc;
     60
     61FragmentResult::ptr MPQCJob::Work()
     62{
     63  char mpqc[] = "mpqc" ;
     64  char **argv = new char*[1];
     65  argv[0] = &mpqc[0];
     66  int argc = 1;
     67
     68  // now comes the actual work
     69  mpqc::InitValues initvalues;
     70  int nfilebase = (int) inputfile.length();
     71  initvalues.in_char_array = new char[nfilebase + 1];
     72  strncpy(initvalues.in_char_array, inputfile.c_str(), nfilebase);
     73  initvalues.in_char_array[nfilebase] = '\0';
     74  initvalues.grp = MessageGrp::get_default_messagegrp();
     75  // create unique, temporary name and check whether it exists
     76  char *tempfilename = NULL;
     77  {
     78    std::ifstream test;
     79    do {
     80      if (initvalues.output != NULL) // free buffer from last round
     81        delete initvalues.output;
     82      char filename_template[] = "mpqc_temp_XXXXXX\0";
     83      char filename_suffix[] = ".in\0";
     84      tempfilename = (char *) malloc ( (strlen(filename_template)+strlen(filename_suffix)+2)*(sizeof(char)));
     85      strncpy(tempfilename, mktemp(filename_template), strlen(filename_template));
     86      tempfilename[strlen(filename_template)] = '\0';
     87      strncat(tempfilename, filename_suffix, strlen(filename_suffix));
     88      initvalues.output = tempfilename;
     89      //free(tempfilename); // don't free! output takes over pointer!
     90      test.open(initvalues.output);
     91    } while (test.good()); // test whether file does not(!) exist
     92    test.close();
     93  }
     94  // put info how to sample the density into MPQCData
     95  MPQCData data(grid);
     96  data.DoLongrange = DoLongrange; // set whether we sample the density
     97  data.DoValenceOnly = DoValenceOnly; // set whether we sample just valence electron and nuclei densities
     98// now call work horse
     99  try {
     100    mpqc::mainFunction(initvalues, argc, argv, static_cast<void *>(&data));
     101  }
     102  catch (SCException &e) {
     103    cout << argv[0] << ": ERROR: SC EXCEPTION RAISED:" << endl
     104         << e.what()
     105         << endl;
     106    detail::clean_up();
     107  }
     108
     109  //delete[] in_char_array; // is deleted in mainFunction()
     110  if (initvalues.output != 0) {
     111    free(tempfilename);
     112  }
     113  delete[] argv;
     114  initvalues.grp = NULL;
     115
     116  // place into returnstream
     117  std::stringstream returnstream;
     118  boost::archive::text_oarchive oa(returnstream);
     119  oa << data;
     120
     121  FragmentResult::ptr s( new FragmentResult(getId(), returnstream.str()) );
     122  if (s->exitflag != 0)
     123    cerr << "Job #" << s->getId() << " failed to reach desired accuracy." << endl;
     124
     125  return s;
     126}
     127#else
    49128FragmentResult::ptr MPQCJob::Work()
    50129{
    … …  
    67146  return ptr;
    68147}
     148#endif
    69149
     150// we need to explicitly instantiate the serialization functions as
     151// its is only serialized through its base class FragmentJob
     152BOOST_CLASS_EXPORT_IMPLEMENT(MPQCJob)

  • src/Jobs/Makefile.am

    rba1152 rfbf005  
    5656
    5757lib_LTLIBRARIES += \
    58         libMolecuilderJobs.la
     58        libMolecuilderJobs.la \
     59        libmolecuilder_mpqc_extract.la
    5960noinst_LTLIBRARIES += \
    6061        libMolecuilderJobs_Work.la
     62
     63### libmolecuilder_mpqc_extract.la
     64libmolecuilder_mpqc_extract_la_SOURCES = \
     65        Jobs/mpqc_extract.cc \
     66        $(top_srcdir)/ThirdParty/mpqc_open/src/bin/mpqc/mpqc.h
     67libmolecuilder_mpqc_extract_la_LDFLAGS = \
     68        $(AM_CPPFLAGS) \
     69        -L$(abs_top_builddir)/../JobMarket/src/JobMarket/.libs -Wl,-rpath,$(abs_top_builddir)/../JobMarket/src/JobMarket/.libs \
     70        -L$(abs_top_builddir)/../../src/.libs -Wl,-rpath,$(abs_top_builddir)/../../src/.libs \
     71        $(BOOST_SYSTEM_LDFLAGS)
     72libmolecuilder_mpqc_extract_la_CPPFLAGS = \
     73        $(AM_CPPFLAGS) \
     74        ${CodePatterns_CFLAGS} ${JobMarket_CFLAGS} \
     75        $(BOOST_SYSTEM_CFLAGS) \
     76        -DHAVE_MPQCDATA \
     77        -DHAVE_JOBMARKET \
     78        -I$(top_builddir)/ThirdParty/mpqc_open/src/lib \
     79        -I$(top_srcdir)/ThirdParty/mpqc_open/src/lib \
     80        -I$(top_srcdir)/ThirdParty/mpqc_open/src/bin/mpqc
     81libmolecuilder_mpqc_extract_la_LIBADD = \
     82        libMolecuilderJobs.la \
     83        libMolecuilderFragmentationSummation.la \
     84        -lboost_serialization
     85
     86### libMolecuilderJobs_Work.la
     87libMolecuilderJobs_Work_la_CPPFLAGS = \
     88        $(AM_CPPFLAGS) ${BOOST_CPPFLAGS} ${CodePatterns_CFLAGS} ${JobMarket_CFLAGS} -Dvmg_float=double -Dvmg_int=int $(VMG_CFLAGS) \
     89        -I$(top_builddir)/ThirdParty/mpqc_open/src/lib \
     90        -I$(top_srcdir)/ThirdParty/mpqc_open/src/lib \
     91        -I$(top_srcdir)/ThirdParty/mpqc_open/src/bin/mpqc
     92libMolecuilderJobs_Work_la_LDFLAGS = $(AM_LDFLAGS)
     93if CONDJOBMARKET
     94libMolecuilderJobs_Work_la_LDFLAGS += \
     95  $(JobMarket_LDFLAGS)
     96endif
     97
     98### libMolecuilderJobs.la
    6199libMolecuilderJobs_la_includedir = $(includedir)/MoleCuilder/
    62100nobase_libMolecuilderJobs_la_include_HEADERS = $(JOBSHEADER)
    63 libMolecuilderJobs_la_CPPFLAGS = $(AM_CPPFLAGS) ${BOOST_CPPFLAGS} ${CodePatterns_CFLAGS} ${JobMarket_CFLAGS} -Dvmg_float=double -Dvmg_int=int $(VMG_CFLAGS)
    64 libMolecuilderJobs_Work_la_CPPFLAGS = $(AM_CPPFLAGS) ${BOOST_CPPFLAGS} ${CodePatterns_CFLAGS} ${JobMarket_CFLAGS} -Dvmg_float=double -Dvmg_int=int $(VMG_CFLAGS)
     101libMolecuilderJobs_la_CPPFLAGS = \
     102        $(AM_CPPFLAGS) ${BOOST_CPPFLAGS} ${CodePatterns_CFLAGS} ${JobMarket_CFLAGS} -Dvmg_float=double -Dvmg_int=int $(VMG_CFLAGS)
    65103libMolecuilderJobs_la_LDFLAGS = $(AM_LDFLAGS) \
    66104  $(BOOST_IOSTREAMS_LDFLAGS) \
    67105  $(BOOST_SERIALIZATION_LDFLAGS) \
    68106  $(BOOST_SYSTEM_LDFLAGS)
    69 libMolecuilderJobs_Work_la_LDFLAGS = $(AM_LDFLAGS)
    70 if CONDJOBMARKET
    71107libMolecuilderJobs_la_LDFLAGS += \
    72108  $(JobMarket_LDFLAGS)
    73 libMolecuilderJobs_Work_la_LDFLAGS += \
    74   $(JobMarket_LDFLAGS)
    75 endif
    76 
    77109libMolecuilderJobs_la_LDFLAGS += \
    78110  $(CodePatterns_LDFLAGS)
    … …  
    87119endif
    88120endif
    89 
    90121if CONDJOBMARKET
    91122libMolecuilderJobs_la_LIBADD += \
    92123  $(JobMarket_LIBS)
    93124libMolecuilderJobs_Work_la_LIBADD = \
     125        $(top_builddir)/ThirdParty/mpqc_open/src/bin/mpqc/libmolecuilder_mpqc.la \
     126        libmolecuilder_mpqc_extract.la \
    94127  $(JobMarket_LIBS)
    95128endif
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