Changeset 8a8c8c

Timestamp:

Nov 13, 2012, 11:11:59 AM (12 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:

69c733

Parents:

e9cfc4

git-author:

Frederik Heber <heber@…> (07/30/12 13:05:40)

git-committer:

Frederik Heber <heber@…> (11/13/12 11:11:59)

Message:

Using CommMPI in VMGJob now.

• this is used instead of CommSerial as CommMPI is better maintained right now.
• using lx_find_mpi from Libra project to detect mpi compiler and linker flags.

Files:

• configure.ac (modified) (1 diff)
• m4/lx_find_mpi.m4 (added)
• src/Jobs/Makefile.am (modified) (1 diff)
• src/Jobs/VMGJob.cpp (modified) (3 diffs)

configure.ac ¶

@@ -210 +210 @@
   AC_SUBST(VMG_CFLAGS)
   AC_SUBST(VMG_LIBS)
+
+  # check whether to use mpi
+  AC_ARG_WITH(
+      [vmg-mpi], 
+      [AS_HELP_STRING([--with-vmg-mpi], [whether to use MPI for communication in VMGJobs])],
+      [with_vmg_mpi=yes],
+      [with_vmg_mpi=no])
+  AS_IF(
+    [test "x$with_vmg_mpi" != xno],
+    [
+      AC_LANG_SAVE
+      AC_LANG_CPLUSPLUS
+      LX_FIND_MPI
+      AC_LANG_RESTORE
+      AS_IF([test "x$have_CXX_mpi" = xyes],[
+            AC_DEFINE([MPICH_SKIP_MPICXX], [1], [Skip C++ bindings])
+            AC_DEFINE([OMPI_SKIP_MPICXX], [1], [Skip C++ bindings])
+            AC_DEFINE([MPI_NO_CPPBIND], [1], [Skip C++ bindings])
+            AC_DEFINE([_MPICC_H], [1], [Skip C++ bindings])
+            AC_DEFINE([MPIBULL_SKIP_MPICXX], [1], [Skip C++ bindings])
+           ])
+    ],
+    [])
 ])
 AM_CONDITIONAL([CONDVMG], [test x"$enable_vmg" = x"yes"])
+AM_CONDITIONAL([CONDVMGMPI], [test x"$have_CXX_mpi" = x"yes"])
 
 

src/Jobs/Makefile.am ¶

@@ -40 +40 @@
         $(top_builddir)/LinearAlgebra/src/LinearAlgebra/libLinearAlgebra.la \
   $(CodePatterns_LIBS)
-
+if CONDVMGMPI
+libMolecuilderJobs_la_CPPFLAGS += $(MPI_CXXFLAGS)
+libMolecuilderJobs_la_LDFLAGS += $(MPI_CXXLDFLAGS)
+endif
+  

src/Jobs/VMGJob.cpp ¶

@@ -34 +34 @@
 #endif
 
+#ifdef HAVE_MPI
+#include "mpi.h"
+#endif
+
 // include headers that implement a archive in simple text format
 // otherwise BOOST_CLASS_EXPORT_IMPLEMENT has no effect
@@ -46 +50 @@
 #include "base/object.hpp"
 #include "base/defs.hpp"
+
+#ifdef HAVE_MPI
+#include "comm/comm_mpi.hpp"
+#include "comm/domain_decomposition_mpi.hpp"
+#else
 #include "comm/comm_serial.hpp"
+#endif
 #include "cycles/cycle_cs_periodic.hpp"
 #include "grid/multigrid.hpp"
@@ -115 +125 @@
    * Choose multigrid components (self-registering)
    */
+#ifdef HAVE_MPI
+  new CommMPI(boundary, new DomainDecompositionMPI());
+#else
   new CommSerial(boundary);
+#endif
   new DiscretizationPoissonFD(4);
   new VMGInterfaces::InterfaceVMGJob(