Changeset d3a46d

Timestamp:

Apr 24, 2008, 1:52:02 PM (17 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:

2cab01c

Parents:

943d02

Message:

added --enable-optimization, thrown -g -O specifics out of Makefile.am's

--enable-optimization is added to each configure.ac and is linked with --enable-debug (no debug and optimization at the same time, debug is normally off and -O2 on), implemented via C(XX)FLAGS
Henceforth, -g, -O and -cc=... specifics are thrown out of the Makefile.am's, so that the optimiziation and debugging is streamlined throughout the whole package

Files:

• configure.ac (modified) (3 diffs)
• src/Makefile.am (modified) (1 diff)
• src/helpers.cpp (modified) (1 diff)
• src/helpers.hpp (modified) (1 diff)
• src/molecules.cpp (modified) (1 diff)

configure.ac

@@ -16 +16 @@
 
 
-AC_FUNC_MALLOC
-AC_FUNC_REALLOC
-AC_CHECK_FUNCS([floor pow sqrt strchr])
-
 # Checks for libraries.
 AC_CHECK_LIB(m, sqrt, ,AC_MSG_ERROR([compatible libc math library not found]))
@@ -27 +23 @@
 AC_CHECK_HEADERS([sys/time.h])
 AC_HEADER_STDBOOL
+
+AC_FUNC_MALLOC
+AC_FUNC_REALLOC
+AC_CHECK_FUNCS([floor pow sqrt strchr])
 
 # Checks for typedefs, structures, and compiler characteristics.
@@ -41 +41 @@
 
 # debugging info
-AC_ARG_ENABLE([debug],AS_HELP_STRING([--enable-debug],[Output debugging information (default is no)]),
-              [enable_debug=$enableval], [enable_debug=maybe])
-if test x"$enable_debug" = xyes; then
+AC_ARG_ENABLE([debug],AS_HELP_STRING([--enable-debug],[Output debugging information, argument is yes or debugging level (default is no).]),
+              [enable_debug=$enableval], [enable_debug=no])
+if ! test x"$enable_debug" = xno; then
+        if test x"${enable_debug}" = xyes; then
+                CFLAGS="-g3"
+                CXXFLAGS="-g3"
+        else
+                CFLAGS="-g${enable_debug}"
+                CXXFLAGS="-g${enable_debug}"
+        fi
   AC_DEFINE(HAVE_DEBUG,1, ["Output debugging info"])
   AC_SUBST(HAVE_DEBUG)
+fi
+
+# optimization level
+AC_ARG_ENABLE([optimization],AS_HELP_STRING([--enable-optimization],[Optimization level of compiler. Argument is yes or debugging level. (default is 2)]),
+              [enable_optimization=$enableval], [enable_optimization=yes])
+if test ! x"$enable_optimization" = xno; then
+        if test x"$enable_debug" = xno; then
+                if test x"${enable_optimization}" = xyes; then
+                        CFLAGS="-O2"
+                        CXXFLAGS="-O2"
+                else
+                        CFLAGS="-O${enable_optimization}"
+                        CXXFLAGS="-O${enable_optimization}"
+                fi
+        else
+                AC_MSG_WARN(["Already specified --enable-debug!"])
+        fi
 fi
 

src/Makefile.am

@@ -8 +8 @@
 joiner_SOURCES = joiner.cpp parser.cpp helpers.cpp verbose.cpp helpers.hpp parser.hpp
 analyzer_SOURCES = analyzer.cpp parser.cpp datacreator.cpp helpers.cpp verbose.cpp helpers.hpp parser.hpp datacreator.hpp 
-#molecuilder_CXXFLAGS = -cc=/opt/packages/gcc-4.0.2/bin/gcc  -g -O -march=nocona -Wall -DBIGENDIAN=0
-molecuilder_CXXFLAGS = -g3 -march=nocona -Wall -DBIGENDIAN=0
-joiner_CXXFLAGS = -g3 -march=nocona -Wall -DBIGENDIAN=0
-analyzer_CXXFLAGS = -g3 -march=nocona -Wall -DBIGENDIAN=0
+molecuilder_CXXFLAGS = -march=nocona -Wall -DBIGENDIAN=0
+joiner_CXXFLAGS = -march=nocona -Wall -DBIGENDIAN=0
+analyzer_CXXFLAGS = -march=nocona -Wall -DBIGENDIAN=0
 
 #EXTRA_DIST = ${molecuilder_DATA}

src/helpers.cpp

@@ -23 +23 @@
 };
 
+/** Output of a debug message to stderr.
+ * \param *P Problem at hand, points to ParallelSimulationData#me
+ * \param output output string
+ */
+#ifdef HAVE_DEBUG
+void debug_in(const char *output, const char *file, const int line) {
+  if (output) fprintf(stderr,"DEBUG: in %s at line %i: %s\n", file, line, output);
+}
+#else
+void debug_in(const char *output, const char *file, const int line) {}  // print nothing
+#endif
 
 /** Wrapper for allocating'ing a memory range with *output if it fails.

src/helpers.hpp

@@ -22 +22 @@
 
 /********************************************** helpful functions *********************************/
+
+// taken out of TREMOLO
+/*@-namechecks@*/
+#ifndef __GNUC__
+# undef __attribute__
+# define __attribute__(x)
+#endif
+/*@=namechecks@*/
+
+/* Behandelt aufgetretene Fehler. error ist der Fehlertyp(enum Errors)
+   void *SpecialData ist ein untypisierter Zeiger auf Spezielle Daten zur Fehlerbehandlung.
+   Man koennte auch noch einen Zeiger auf eine Funktion uebergeben */
+extern void /*@exits@*/ debug(const char *output);
+  //__attribute__ ((__return__));
+#define debug(data) debug_in((data), __FILE__, __LINE__)
+
+extern void /*@exits@*/ debug_in(const char *output,
+    const char *file, const int line);
+  //__attribute__ ((__return__));
 
 double ask_value(const char *text);

src/molecules.cpp

@@ -1871 +1871 @@
   MoleculeLeafClass *Subgraphs = NULL;      // list of subgraphs from DFS analysis
 
+#ifdef ADDHYDROGEN
+  debug("Test");
+  cout << Verbose(0) << "I will treat hydrogen special and saturate dangling bonds with it." << endl;
+#else
+  debug("Test2");
+  cout << Verbose(0) << "Hydrogen is treated just like the rest of the lot." << endl;
+#endif
+  
   CreateListOfBondsPerAtom(out);