<commit_before>############################################################################
# CMakeLists.txt file for building ROOT tmva package
# @author <NAME>, CERN
############################################################################
#---The following is needed because client codes of TMVA (in ROOT itself) assumes to find header files under /TMVA
#execute_process(COMMAND cmake -E create_symlink ${CMAKE_CURRENT_SOURCE_DIR}/inc ${CMAKE_CURRENT_SOURCE_DIR}/inc/TMVA)

if(NOT CMAKE_PROJECT_NAME STREQUAL ROOT)
  cmake_minimum_required(VERSION 2.8 FATAL_ERROR)
  project(TMVA)
  include(${ROOTSYS}/cmake/modules/StandaloneBuild.cmake)
endif()

set(headers1 Configurable.h Factory.h  MethodBase.h MethodCompositeBase.h
	     MethodANNBase.h MethodTMlpANN.h MethodRuleFit.h MethodCuts.h MethodFisher.h
	     MethodKNN.h MethodCFMlpANN.h MethodCFMlpANN_Utils.h MethodLikelihood.h
	     MethodHMatrix.h MethodPDERS.h MethodBDT.h MethodDT.h MethodSVM.h MethodBayesClassifier.h
	     MethodFDA.h MethodMLP.h MethodBoost.h
	     MethodPDEFoam.h MethodLD.h MethodCategory.h MethodDNN.h MethodDL.h
             MethodCrossValidation.h)
set(headers2 TSpline2.h TSpline1.h PDF.h BinaryTree.h BinarySearchTreeNode.h BinarySearchTree.h 
	     Timer.h RootFinder.h CrossEntropy.h DecisionTree.h DecisionTreeNode.h MisClassificationError.h 
	     Node.h SdivSqrtSplusB.h SeparationBase.h RegressionVariance.h Tools.h Reader.h 
	     GeneticAlgorithm.h GeneticGenes.h GeneticPopulation.h GeneticRange.h GiniIndex.h 
	     GiniIndexWithLaplace.h SimulatedAnnealing.h QuickMVAProbEstimator.h)
set(headers3 Config.h KDEKernel.h Interval.h LogInterval.h FitterBase.h MCFitter.h GeneticFitter.h 
         SimulatedAnnealingFitter.h MinuitFitter.h MinuitWrapper.h IFitterTarget.h
         PDEFoam.h PDEFoamDecisionTree.h PDEFoamDensityBase.h PDEFoamDiscriminantDensity.h
         PDEFoamEventDensity.h PDEFoamTargetDensity.h PDEFoamDecisionTreeDensity.h PDEFoamMultiTarget.h
         PDEFoamVect.h PDEFoamCell.h PDEFoamDiscriminant.h PDEFoamEvent.h PDEFoamTarget.h
         PDEFoamKernelBase.h PDEFoamKernelTrivial.h PDEFoamKernelLinN.h PDEFoamKernelGauss.h
         BDTEventWrapper.h CCTreeWrapper.h
         CCPruner.h CostComplexityPruneTool.h SVEvent.h OptimizeConfigParameters.h)
set(headers4 NeuralNet.h TNeuron.h TSynapse.h TActivationChooser.h TActivation.h TActivationSigmoid.h TActivationIdentity.h
         TActivationTanh.h TActivationRadial.h TActivationReLU.h TNeuronInputChooser.h TNeuronInput.h TNeuronInputSum.h
	     TNeuronInputSqSum.h TNeuronInputAbs.h Types.h Ranking.h RuleFit.h RuleFitAPI.h IMethod.h MsgLogger.h
	     VariableTransformBase.h VarTransformHandler.h VariableIdentityTransform.h VariableDecorrTransform.h VariablePCATransform.h
	     VariableGaussTransform.h VariableNormalizeTransform.h VariableRearrangeTransform.h VariableTransform.h ROCCalc.h ROCCurve.h)

set(headers5 Envelope.h VariableImportance.h CrossValidation.h CvSplit.h HyperParameterOptimisation.h Classification.h Event.h Results.h ResultsClassification.h ResultsRegression.h ResultsMulticlass.h VariableInfo.h ClassInfo.h DataLoader.h DataSet.h DataSetInfo.h DataInputHandler.h DataSetManager.h DataSetFactory.h LossFunction.h ClassifierFactory.h ConvergenceTest.h ExpectedErrorPruneTool.h IPruneTool.h LDA.h MethodCFMlpANN_def.h ModulekNN.h Monitoring.h
NodekNN.h Option.h OptionMap.h Pattern.h RuleCut.h RuleEnsemble.h RuleFitParams.h Rule.h SVKernelFunction.h SVKernelMatrix.h SVWorkingSet.h
TransformationHandler.h Version.h Volume.h)

#---Need to suffix each header name by TMVA/  -----------------
foreach(hs headers1 headers2 headers3 headers4 headers5)
  foreach(h ${${hs}})
    set(t${hs} ${t${hs}} TMVA/${h})
  endforeach()
endforeach()

#---Assign source files to the implementations -----------------
SET(DNN_FILES      src/DNN/Architectures/Reference.cxx
                   src/DNN/Architectures/Reference/DataLoader.cxx
                   src/DNN/Architectures/Reference/TensorDataLoader.cxx)
SET(DNN_CUDA_FILES src/DNN/Architectures/Cuda.cu
                   src/DNN/Architectures/Cuda/CudaBuffers.cxx
                   src/DNN/Architectures/Cuda/CudaMatrix.cu)
SET(DNN_CPU_FILES  src/DNN/Architectures/Cpu.cxx
                   src/DNN/Architectures/Cpu/CpuBuffer.cxx
                   src/DNN/Architectures/Cpu/CpuMatrix.cxx)

#---Handle CUDA dependent code. -----------------
if(CUDA_FOUND)
  message(STATUS "Using TMVA-DNN with CUDA installation") 
  set(CUDA_NVCC_FLAGS "${CUDA_NVCC_FLAGS} --compiler-options -fPIC")
  CUDA_INCLUDE_DIRECTORIES("${CMAKE_BINARY_DIR}/include")	
  CUDA_ADD_LIBRARY(dnn_cuda ${DNN_CUDA_FILES})
  set_property(TARGET dnn_cuda PROPERTY POSITION_INDEPENDENT_CODE ON)	
  set(DNN_CUDA_LIBRARIES dnn_cuda ${CUDA_CUBLAS_LIBRARIES})
  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -DNNCUDA")
  add_dependencies(dnn_cuda move_headers)
  include_directories(SYSTEM ${CUDA_INCLUDE_DIRS} )
  message("Cuda include ${CUDA_INCLUDE_DIRS}")
else()
  set(DNN_CUDA_LIBRARIES)
  set(installoptions ${installoptions} FILTER "Cuda")
endif()

#---Handle BLAS dependent code. -----------------
if(BLAS_FOUND AND imt)
   message(STATUS "Using TMVA-DNN with BLAS installation: ${BLAS_LIBRARIES}") 
  set(DNN_CPU_LIBRARIES MathCore Matrix ${BLAS_LINKER_FLAGS} ${BLAS_LIBRARIES} ${TBB_LIBRARIES} ${CMAKE_THREAD_LIBS_INIT}) 
  include_directories(SYSTEM ${TBB_INCLUDE_DIRS})
  if (CUDA_FOUND)
     include_directories(SYSTEM ${TBB_INCLUDE_DIRS} ${CUDA_INCLUDE_DIRS})
  endif()
else()
if (tmva-cpu AND mathmore AND imt)
#use GSL cblas installation
  message(STATUS "Using TMVA-DNN with gslcblas installation") 
  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -DDNN_USE_CBLAS")
  set(DNN_CPU_LIBRARIES MathCore Matrix ${TBB_LIBRARIES} ${GSL_LIBRARIES}  ${CMAKE_THREAD_LIBS_INIT})
  include_directories(SYSTEM ${TBB_INCLUDE_DIRS} ${GSL_INCLUDE_DIR} )
  if (CUDA_FOUND)
     include_directories(SYSTEM ${TBB_INCLUDE_DIRS} ${GSL_INCLUDE_DIR} ${CUDA_INCLUDE_DIRS})
  endif()
else()
  message(STATUS "No blas or cblas found . TMVA-DNN-CPU is disabled")  
  set(DNN_CPU_LIBRARIES)
  set(DNN_CPU_FILES)
  set(installoptions ${installoptions} FILTER "Cpu")
endif()
endif()

ROOT_STANDARD_LIBRARY_PACKAGE(TMVA
                              HEADERS ${theaders1} ${theaders2} ${theaders3} ${theaders4} ${theaders5}
                              SOURCES *.cxx ${DNN_FILES} ${DNN_CPU_FILES} DICTIONARY_OPTIONS "-writeEmptyRootPCM"
                              LIBRARIES Core MathCore Matrix ${DNN_CUDA_LIBRARIES} ${DNN_CPU_LIBRARIES}
                              DEPENDENCIES Core RIO Hist Tree TreePlayer MLP Minuit XMLIO
                              INSTALL_OPTIONS ${installoptions})

if(NOT gnuinstall)
  install(DIRECTORY test DESTINATION tmva 
  FILES_MATCHING PATTERN "*.C" <commit_msg>Add Imt as TMVA dependency<commit_after>############################################################################
# CMakeLists.txt file for building ROOT tmva package
# @author <NAME>, CERN
############################################################################
#---The following is needed because client codes of TMVA (in ROOT itself) assumes to find header files under /TMVA
#execute_process(COMMAND cmake -E create_symlink ${CMAKE_CURRENT_SOURCE_DIR}/inc ${CMAKE_CURRENT_SOURCE_DIR}/inc/TMVA)

if(NOT CMAKE_PROJECT_NAME STREQUAL ROOT)
  cmake_minimum_required(VERSION 2.8 FATAL_ERROR)
  project(TMVA)
  include(${ROOTSYS}/cmake/modules/StandaloneBuild.cmake)
endif()

set(headers1 Configurable.h Factory.h  MethodBase.h MethodCompositeBase.h
	     MethodANNBase.h MethodTMlpANN.h MethodRuleFit.h MethodCuts.h MethodFisher.h
	     MethodKNN.h MethodCFMlpANN.h MethodCFMlpANN_Utils.h MethodLikelihood.h
	     MethodHMatrix.h MethodPDERS.h MethodBDT.h MethodDT.h MethodSVM.h MethodBayesClassifier.h
	     MethodFDA.h MethodMLP.h MethodBoost.h
	     MethodPDEFoam.h MethodLD.h MethodCategory.h MethodDNN.h MethodDL.h
             MethodCrossValidation.h)
set(headers2 TSpline2.h TSpline1.h PDF.h BinaryTree.h BinarySearchTreeNode.h BinarySearchTree.h 
	     Timer.h RootFinder.h CrossEntropy.h DecisionTree.h DecisionTreeNode.h MisClassificationError.h 
	     Node.h SdivSqrtSplusB.h SeparationBase.h RegressionVariance.h Tools.h Reader.h 
	     GeneticAlgorithm.h GeneticGenes.h GeneticPopulation.h GeneticRange.h GiniIndex.h 
	     GiniIndexWithLaplace.h SimulatedAnnealing.h QuickMVAProbEstimator.h)
set(headers3 Config.h KDEKernel.h Interval.h LogInterval.h FitterBase.h MCFitter.h GeneticFitter.h 
         SimulatedAnnealingFitter.h MinuitFitter.h MinuitWrapper.h IFitterTarget.h
         PDEFoam.h PDEFoamDecisionTree.h PDEFoamDensityBase.h PDEFoamDiscriminantDensity.h
         PDEFoamEventDensity.h PDEFoamTargetDensity.h PDEFoamDecisionTreeDensity.h PDEFoamMultiTarget.h
         PDEFoamVect.h PDEFoamCell.h PDEFoamDiscriminant.h PDEFoamEvent.h PDEFoamTarget.h
         PDEFoamKernelBase.h PDEFoamKernelTrivial.h PDEFoamKernelLinN.h PDEFoamKernelGauss.h
         BDTEventWrapper.h CCTreeWrapper.h
         CCPruner.h CostComplexityPruneTool.h SVEvent.h OptimizeConfigParameters.h)
set(headers4 NeuralNet.h TNeuron.h TSynapse.h TActivationChooser.h TActivation.h TActivationSigmoid.h TActivationIdentity.h
         TActivationTanh.h TActivationRadial.h TActivationReLU.h TNeuronInputChooser.h TNeuronInput.h TNeuronInputSum.h
	     TNeuronInputSqSum.h TNeuronInputAbs.h Types.h Ranking.h RuleFit.h RuleFitAPI.h IMethod.h MsgLogger.h
	     VariableTransformBase.h VarTransformHandler.h VariableIdentityTransform.h VariableDecorrTransform.h VariablePCATransform.h
	     VariableGaussTransform.h VariableNormalizeTransform.h VariableRearrangeTransform.h VariableTransform.h ROCCalc.h ROCCurve.h)

set(headers5 Envelope.h VariableImportance.h CrossValidation.h CvSplit.h HyperParameterOptimisation.h Classification.h Event.h Results.h ResultsClassification.h ResultsRegression.h ResultsMulticlass.h VariableInfo.h ClassInfo.h DataLoader.h DataSet.h DataSetInfo.h DataInputHandler.h DataSetManager.h DataSetFactory.h LossFunction.h ClassifierFactory.h ConvergenceTest.h ExpectedErrorPruneTool.h IPruneTool.h LDA.h MethodCFMlpANN_def.h ModulekNN.h Monitoring.h
NodekNN.h Option.h OptionMap.h Pattern.h RuleCut.h RuleEnsemble.h RuleFitParams.h Rule.h SVKernelFunction.h SVKernelMatrix.h SVWorkingSet.h
TransformationHandler.h Version.h Volume.h)

#---Need to suffix each header name by TMVA/  -----------------
foreach(hs headers1 headers2 headers3 headers4 headers5)
  foreach(h ${${hs}})
    set(t${hs} ${t${hs}} TMVA/${h})
  endforeach()
endforeach()

#---Assign source files to the implementations -----------------
SET(DNN_FILES      src/DNN/Architectures/Reference.cxx
                   src/DNN/Architectures/Reference/DataLoader.cxx
                   src/DNN/Architectures/Reference/TensorDataLoader.cxx)
SET(DNN_CUDA_FILES src/DNN/Architectures/Cuda.cu
                   src/DNN/Architectures/Cuda/CudaBuffers.cxx
                   src/DNN/Architectures/Cuda/CudaMatrix.cu)
SET(DNN_CPU_FILES  src/DNN/Architectures/Cpu.cxx
                   src/DNN/Architectures/Cpu/CpuBuffer.cxx
                   src/DNN/Architectures/Cpu/CpuMatrix.cxx)

#---Handle CUDA dependent code. -----------------
if(CUDA_FOUND)
  message(STATUS "Using TMVA-DNN with CUDA installation") 
  set(CUDA_NVCC_FLAGS "${CUDA_NVCC_FLAGS} --compiler-options -fPIC")
  CUDA_INCLUDE_DIRECTORIES("${CMAKE_BINARY_DIR}/include")	
  CUDA_ADD_LIBRARY(dnn_cuda ${DNN_CUDA_FILES})
  set_property(TARGET dnn_cuda PROPERTY POSITION_INDEPENDENT_CODE ON)	
  set(DNN_CUDA_LIBRARIES dnn_cuda ${CUDA_CUBLAS_LIBRARIES})
  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -DNNCUDA")
  add_dependencies(dnn_cuda move_headers)
  include_directories(SYSTEM ${CUDA_INCLUDE_DIRS} )
  message("Cuda include ${CUDA_INCLUDE_DIRS}")
else()
  set(DNN_CUDA_LIBRARIES)
  set(installoptions ${installoptions} FILTER "Cuda")
endif()

#---Handle BLAS dependent code. -----------------
if(BLAS_FOUND AND imt)
   message(STATUS "Using TMVA-DNN with BLAS installation: ${BLAS_LIBRARIES}") 
  set(DNN_CPU_LIBRARIES MathCore Matrix ${BLAS_LINKER_FLAGS} ${BLAS_LIBRARIES} ${TBB_LIBRARIES} ${CMAKE_THREAD_LIBS_INIT}) 
  include_directories(SYSTEM ${TBB_INCLUDE_DIRS})
  if (CUDA_FOUND)
     include_directories(SYSTEM ${TBB_INCLUDE_DIRS} ${CUDA_INCLUDE_DIRS})
  endif()
else()
if (tmva-cpu AND mathmore AND imt)
#use GSL cblas installation
  message(STATUS "Using TMVA-DNN with gslcblas installation") 
  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -DDNN_USE_CBLAS")
  set(DNN_CPU_LIBRARIES MathCore Matrix ${TBB_LIBRARIES} ${GSL_LIBRARIES} ${CMAKE_THREAD_LIBS_INIT})
  include_directories(SYSTEM ${TBB_INCLUDE_DIRS} ${GSL_INCLUDE_DIR} )
  if (CUDA_FOUND)
     include_directories(SYSTEM ${TBB_INCLUDE_DIRS} ${GSL_INCLUDE_DIR} ${CUDA_INCLUDE_DIRS})
  endif()
else()
  message(STATUS "No blas or cblas found . TMVA-DNN-CPU is disabled")  
  set(DNN_CPU_LIBRARIES)
  set(DNN_CPU_FILES)
  set(installoptions ${installoptions} FILTER "Cpu")
endif()
endif()

if(imt)
  set(TMVA_DEPENDENCIES Imt)
endif()

ROOT_STANDARD_LIBRARY_PACKAGE(TMVA
                              HEADERS ${theaders1} ${theaders2} ${theaders3} ${theaders4} ${theaders5}
                              SOURCES *.cxx ${DNN_FILES} ${DNN_CPU_FILES} DICTIONARY_OPTIONS "-writeEmptyRootPCM"
                              LIBRARIES Core MathCore Matrix ${DNN_CUDA_LIBRARIES} ${DNN_CPU_LIBRARIES}
                              DEPENDENCIES Core RIO Hist Tree TreePlayer MLP Minuit XMLIO ${TMVA_DEPENDENCIES}
                              INSTALL_OPTIONS ${installoptions})

if(NOT gnuinstall)
  install(DIRECTORY test DESTINATION tmva 
  FILES_MATCHING PATTERN "*.C" 
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