Merge pull request #3669 from OXPHOS/linalg_temp

LinalgRefactor - remove HAVE_LINALG_LIB
shogun-toolbox · Mar 2, 2017 · e4e6def · e4e6def
2 parents 65effed + 3316f24
commit e4e6def
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Showing 22 changed files with 2 additions and 91 deletions.
diff --git a/src/interfaces/modular/Kernel.i b/src/interfaces/modular/Kernel.i
@@ -104,12 +104,10 @@ PROTOCOLS_CUSTOMKERNEL(CustomKernel, float32_t, "f\0", NPY_FLOAT32)
 %rename(MultiquadricKernel) CMultiquadricKernel;
 %rename(JensenShannonKernel) CJensenShannonKernel;
 
-#ifdef HAVE_LINALG_LIB
 %rename(ExponentialARDKernel) CExponentialARDKernel;
 %rename(GaussianARDKernel) CGaussianARDKernel;
 
 %rename(GaussianARDSparseKernel) CGaussianARDSparseKernel;
-#endif
 
 %rename(SubsequenceStringKernel) CSubsequenceStringKernel;
 %rename(PeriodicKernel) CPeriodicKernel;
@@ -227,11 +225,9 @@ namespace shogun
 %include <shogun/kernel/MultiquadricKernel.h>
 %include <shogun/kernel/RationalQuadraticKernel.h>
 %include <shogun/kernel/JensenShannonKernel.h>
-#ifdef HAVE_LINALG_LIB
 %include <shogun/kernel/ExponentialARDKernel.h>
 %include <shogun/kernel/GaussianARDKernel.h>
 %include <shogun/machine/gp/GaussianARDSparseKernel.h>
-#endif
 %include <shogun/kernel/string/SubsequenceStringKernel.h>
 %include <shogun/kernel/PeriodicKernel.h>
 

diff --git a/src/interfaces/modular/Kernel_includes.i b/src/interfaces/modular/Kernel_includes.i
@@ -76,9 +76,7 @@
 #include <shogun/kernel/string/SubsequenceStringKernel.h>
 #include <shogun/kernel/PeriodicKernel.h>
 #include <shogun/kernel/LinearKernel.h>
-#ifdef HAVE_LINALG_LIB
 #include <shogun/kernel/ExponentialARDKernel.h>
 #include <shogun/kernel/GaussianARDKernel.h>
 #include <shogun/machine/gp/GaussianARDSparseKernel.h>
-#endif
 %}
diff --git a/src/shogun/CMakeLists.txt b/src/shogun/CMakeLists.txt
@@ -231,22 +231,10 @@ SHOGUN_DEPENDENCIES(
   VERSION ${VIENNACL_VERSION_MINIMUM}
   CONFIG_FLAG HAVE_VIENNACL)
 
-# Check if supported linear algebra backend is found
-IF (HAVE_CXX0X OR HAVE_CXX11)
-  SET(HAVE_LINALG_LIB 1)
-ELSE ()
-  MESSAGE (STATUS "LINALG uses c++11 features. Please use a supported compiler")
-ENDIF ()
-
 # Linear algebra default global backend setups
 SET_LINALG_BACKEND(LINALG_DEFAULT_BACKEND GLOBAL)
 
 # Linear algebra default module specific backend setup
-# Core module
-SET_LINALG_BACKEND(LINALG_CORE_LIB CORE)
-# Reduction module
-SET_LINALG_BACKEND(LINALG_REDUX_LIB REDUX)
-
 # Linear solver module
 SET_LINALG_BACKEND(LINALG_LINEAR_SOLVER_LIB LINSLV)
 

diff --git a/src/shogun/clustering/KMeansBase.cpp b/src/shogun/clustering/KMeansBase.cpp
@@ -18,10 +18,6 @@
 #include <shogun/base/Parallel.h>
 #include <shogun/mathematics/eigen3.h>
 
-#ifdef HAVE_LINALG_LIB
-#include <shogun/mathematics/linalg/linalg.h>
-#endif
-
 using namespace shogun;
 using namespace Eigen;
 
@@ -160,13 +156,7 @@ void CKMeansBase::initialize_training(CFeatures* data)
 
 	/* if kmeans++ to be used */
 	if (use_kmeanspp)
-	{
-#ifdef HAVE_LINALG_LIB
 		mus_initial=kmeanspp();
-#else
-		SG_WARNING("LINALG library not available for KMeans++, resorting to random initialisation");
-#endif
-	}
 
 	R=SGVector<float64_t>(k);
 

diff --git a/src/shogun/kernel/CustomKernel.cpp b/src/shogun/kernel/CustomKernel.cpp
@@ -18,12 +18,7 @@
 #include <shogun/mathematics/linalg/LinalgNamespace.h>
 
 using namespace shogun;
-
-#ifdef HAVE_LINALG_LIB
-#include <shogun/mathematics/linalg/linalg.h>
-
 using namespace linalg;
-#endif // HAVE_LINALG_LIB
 
 void CCustomKernel::init()
 {
@@ -161,7 +156,6 @@ bool CCustomKernel::init(CFeatures* l, CFeatures* r)
 	return init_normalizer();
 }
 
-#ifdef HAVE_LINALG_LIB
 float64_t CCustomKernel::sum_symmetric_block(index_t block_begin,
 		index_t block_size, bool no_diag)
 {
@@ -366,7 +360,6 @@ SGVector<float64_t> CCustomKernel::row_col_wise_sum_block(index_t
 
 	return sum;
 }
-#endif // HAVE_LINALG_LIB
 
 void CCustomKernel::cleanup_custom()
 {

diff --git a/src/shogun/kernel/CustomKernel.h b/src/shogun/kernel/CustomKernel.h
@@ -318,8 +318,6 @@ class CCustomKernel: public CKernel
 			return true;
 		}
 
-#ifdef HAVE_LINALG_LIB
-
 		/**
 		 * Overrides the sum_symmetric_block method of CKernel to compute the
 		 * sum directly from the precomputed kernel matrix.
@@ -439,7 +437,6 @@ class CCustomKernel: public CKernel
 				index_t block_begin_row, index_t block_begin_col,
 				index_t block_size_row, index_t block_size_col,
 				bool no_diag=false);
-#endif // HAVE_LINALG_LIB
 
 		/** Adds a row subset of indices on top of the current subsets (possibly
 		 * subset of subset). Every call causes a new active index vector

diff --git a/src/shogun/kernel/ExponentialARDKernel.cpp b/src/shogun/kernel/ExponentialARDKernel.cpp
@@ -14,10 +14,7 @@
 #include <shogun/features/DenseFeatures.h>
 #include <shogun/mathematics/Math.h>
 #include <shogun/mathematics/linalg/LinalgNamespace.h>
-
-#ifdef HAVE_LINALG_LIB
 #include <shogun/mathematics/linalg/linalg.h>
-#endif
 
 using namespace shogun;
 
@@ -67,7 +64,6 @@ SGVector<float64_t> CExponentialARDKernel::get_feature_vector(int32_t idx, CFeat
 
 }
 
-#ifdef HAVE_LINALG_LIB
 
 void CExponentialARDKernel::set_weights(SGMatrix<float64_t> weights)
 {
@@ -169,7 +165,7 @@ void CExponentialARDKernel::set_matrix_weights(SGMatrix<float64_t> weights)
 	m_ARD_type=KT_FULL;
 	index_t len=(2*m_weights_rows+1-m_weights_cols)*m_weights_cols/2;
 	m_log_weights=SGVector<float64_t>(len);
-		
+
 	index_t offset=0;
 	for (int i=0; i<weights.num_cols && i<weights.num_rows; i++)
 	{
@@ -280,4 +276,3 @@ void CExponentialARDKernel::check_weight_gradient_index(index_t index)
 			index, m_log_weights.vlen);
 	}
 }
-#endif //HAVE_LINALG_LIB
diff --git a/src/shogun/kernel/ExponentialARDKernel.h b/src/shogun/kernel/ExponentialARDKernel.h
@@ -150,7 +150,6 @@ class CExponentialARDKernel: public CDotKernel
 		return CMath::exp(-distance(idx_a,idx_b));
 	}
 
-#ifdef HAVE_LINALG_LIB
 public:
 	/** constructor
 	 *
@@ -250,7 +249,6 @@ class CExponentialARDKernel: public CDotKernel
 	 *
 	 */
 	virtual void check_weight_gradient_index(index_t index);
-#endif /* HAVE_LINALG_LIB */
 };
 }
 #endif /* EXPONENTIALARDKERNEL_H */
diff --git a/src/shogun/kernel/GaussianARDKernel.h b/src/shogun/kernel/GaussianARDKernel.h
@@ -93,7 +93,6 @@ class CGaussianARDKernel: public CExponentialARDKernel
 	 */
 	virtual float64_t distance(int32_t idx_a, int32_t idx_b);
 
-#ifdef HAVE_LINALG_LIB
 public:
 	/** constructor
 	 *
@@ -205,8 +204,6 @@ class CGaussianARDKernel: public CExponentialARDKernel
 	virtual float64_t get_parameter_gradient_helper(const TParameter* param,
 		index_t index, int32_t idx_a, int32_t idx_b,
 		SGVector<float64_t> avec, SGVector<float64_t> bvec);
-
-#endif /* HAVE_LINALG_LIB */
 };
 }
 #endif /* _GAUSSIANARDKERNEL_H_ */
diff --git a/src/shogun/lib/config.h.in b/src/shogun/lib/config.h.in
@@ -43,17 +43,9 @@
 #cmakedefine VIENNACL_WITH_OPENCL 1
 
 /* for linear algebra global backend setups */
-#cmakedefine HAVE_LINALG_LIB 1
-
 #cmakedefine USE_EIGEN3_GLOBAL 1
 #cmakedefine USE_VIENNACL_GLOBAL 1
 
-#cmakedefine USE_EIGEN3_CORE 1
-#cmakedefine USE_VIENNACL_CORE 1
-
-#cmakedefine USE_EIGEN3_REDUX 1
-#cmakedefine USE_VIENNACL_REDUX 1
-
 #cmakedefine USE_EIGEN3_LINSLV 1
 #cmakedefine USE_VIENNACL_LINSLV 1
 

diff --git a/src/shogun/machine/gp/GaussianARDSparseKernel.cpp b/src/shogun/machine/gp/GaussianARDSparseKernel.cpp
@@ -46,7 +46,6 @@ CGaussianARDSparseKernel::~CGaussianARDSparseKernel()
 {
 }
 
-#ifdef HAVE_LINALG_LIB
 using namespace Eigen;
 
 CGaussianARDSparseKernel::CGaussianARDSparseKernel(int32_t size)
@@ -146,5 +145,3 @@ SGMatrix<float64_t> CGaussianARDSparseKernel::get_parameter_gradient(
 		return CGaussianARDKernel::get_parameter_gradient(param, index);
 	}
 }
-#endif /* HAVE_LINALG_LIB */
-
diff --git a/src/shogun/machine/gp/GaussianARDSparseKernel.h b/src/shogun/machine/gp/GaussianARDSparseKernel.h
@@ -71,7 +71,6 @@ class CGaussianARDSparseKernel: public CGaussianARDKernel
 private:
 	void initialize_sparse_kernel();
 
-#ifdef HAVE_LINALG_LIB
 public:
 	/** constructor
 	 *
@@ -115,7 +114,6 @@ class CGaussianARDSparseKernel: public CGaussianARDKernel
 	 */
 	virtual SGVector<float64_t> get_parameter_gradient_diagonal(
 		const TParameter* param, index_t index=-1);
-#endif /* HAVE_LINALG_LIB */
 };
 }
 

diff --git a/src/shogun/mathematics/linalg/internal/modules/SpecialPurpose.h b/src/shogun/mathematics/linalg/internal/modules/SpecialPurpose.h
@@ -32,8 +32,6 @@
 #ifndef SPECIAL_PURPOSE_H_
 #define SPECIAL_PURPOSE_H_
 
-#ifdef HAVE_LINALG_LIB
-
 #include <shogun/mathematics/linalg/internal/implementation/SpecialPurpose.h>
 
 namespace shogun
@@ -108,5 +106,4 @@ typename Matrix::Scalar squared_error(Matrix P, Matrix Q)
 }
 
 }
-#endif // HAVE_LINALG_LIB
 #endif // SPECIAL_PURPOSE_H_
diff --git a/tests/unit/classifier/GaussianProcessClassification_unittest.cc b/tests/unit/classifier/GaussianProcessClassification_unittest.cc
@@ -33,10 +33,7 @@
  */
 
 #include <shogun/lib/config.h>
-#ifdef HAVE_LINALG_LIB
 #include <shogun/machine/gp/GaussianARDSparseKernel.h>
-#endif
-
 
 #include <shogun/labels/BinaryLabels.h>
 #include <shogun/features/DenseFeatures.h>
@@ -3703,7 +3700,6 @@ TEST(GaussianProcessClassificationUsingSingleLaplaceWithNLOPT,get_variance_vecto
 
 
 
-#ifdef HAVE_LINALG_LIB
 TEST(GaussianProcessClassificationUsingSingleFITCLaplace,get_mean_vector)
 {
 	index_t n=6;
@@ -4046,5 +4042,3 @@ TEST(GaussianProcessClassificationUsingSingleFITCLaplace,get_probabilities)
 	SG_UNREF(gpc);
 	SG_UNREF(latent_features_train);
 }
-
-#endif /* HAVE_LINALG_LIB */
diff --git a/tests/unit/kernel/GaussianARDKernel_unittest.cc b/tests/unit/kernel/GaussianARDKernel_unittest.cc
@@ -30,7 +30,6 @@
 
 #include <shogun/lib/config.h>
 
-#ifdef HAVE_LINALG_LIB
 #include <shogun/lib/common.h>
 #include <shogun/lib/SGVector.h>
 #include <shogun/lib/SGMatrix.h>
@@ -730,4 +729,3 @@ TEST(GaussianARDKernel,get_parameter_gradient_diagonal)
 	SG_UNREF(features_train)
 	SG_UNREF(latent_features_train)
 }
-#endif /* HAVE_LINALG_LIB */
diff --git a/tests/unit/machine/gp/FITCInferenceMethod_unittest.cc b/tests/unit/machine/gp/FITCInferenceMethod_unittest.cc
@@ -661,7 +661,7 @@ TEST(FITCInferenceMethod,get_marginal_likelihood_derivatives_sparse)
 	SG_UNREF(inf);
 	SG_UNREF(inducing_features_train);
 }
-#ifdef HAVE_LINALG_LIB
+
 TEST(FITCInferenceMethod,get_marginal_likelihood_derivatives_for_ARD_kernel1)
 {
 	index_t n=6;
@@ -1070,5 +1070,3 @@ TEST(FITCInferenceMethod,get_marginal_likelihood_derivatives_for_inducing_featur
 	SG_UNREF(inf);
 	SG_UNREF(latent_features_train);
 }
-
-#endif /* HAVE_LINALG_LIB */
diff --git a/tests/unit/machine/gp/SingleFITCInference_unittest.cc b/tests/unit/machine/gp/SingleFITCInference_unittest.cc
@@ -30,7 +30,6 @@
  */
 
 #include <shogun/lib/config.h>
-#if defined(HAVE_LINALG_LIB)
 
 #include <shogun/labels/RegressionLabels.h>
 #include <shogun/features/DenseFeatures.h>
@@ -209,4 +208,3 @@ TEST(SingleFITCInference,set_kernel)
 
 	SG_UNREF(inf);
 }
-#endif /* HAVE_LINALG_LIB */
diff --git a/tests/unit/machine/gp/SingleFITCLaplaceInferenceMethodWithLBFGS_unittest.cc b/tests/unit/machine/gp/SingleFITCLaplaceInferenceMethodWithLBFGS_unittest.cc
@@ -31,7 +31,6 @@
 
 
 #include <shogun/lib/config.h>
-#if defined(HAVE_LINALG_LIB)
 #include <shogun/labels/BinaryLabels.h>
 #include <shogun/features/DenseFeatures.h>
 #include <shogun/kernel/GaussianKernel.h>
@@ -466,5 +465,3 @@ TEST(SingleFITCLaplaceInferenceMethodWithLBFGS,get_marginal_likelihood_derivativ
 	SG_UNREF(inf);
 	SG_UNREF(latent_features_train);
 }
-
-#endif /* HAVE_LINALG_LIB */
diff --git a/tests/unit/machine/gp/SingleFITCLaplaceInferenceMethod_unittest.cc b/tests/unit/machine/gp/SingleFITCLaplaceInferenceMethod_unittest.cc
@@ -31,7 +31,6 @@
 
 
 #include <shogun/lib/config.h>
-#if defined(HAVE_LINALG_LIB)
 #include <shogun/labels/BinaryLabels.h>
 #include <shogun/features/DenseFeatures.h>
 #include <shogun/kernel/GaussianKernel.h>
@@ -472,5 +471,3 @@ TEST(SingleFITCLaplaceInferenceMethod,get_marginal_likelihood_derivatives)
 	SG_UNREF(latent_features_train);
 	SG_UNREF(inf);
 }
-
-#endif /* HAVE_LINALG_LIB */
diff --git a/tests/unit/machine/gp/VarDTCInferenceMethod_unittest.cc b/tests/unit/machine/gp/VarDTCInferenceMethod_unittest.cc
@@ -225,7 +225,6 @@ TEST(VarDTCInferenceMethod,get_marginal_likelihood_derivatives)
 	SG_UNREF(inducing_features_train);
 }
 
-#ifdef HAVE_LINALG_LIB
 TEST(VarDTCInferenceMethod,get_marginal_likelihood_derivative_wrt_inducing_features)
 {
 	float64_t rel_tolerance=1e-5;
@@ -333,4 +332,3 @@ TEST(VarDTCInferenceMethod,get_marginal_likelihood_derivative_wrt_inducing_featu
 	SG_UNREF(inf);
 	SG_UNREF(inducing_features_train);
 }
-#endif /* HAVE_LINALG_LIB */
diff --git a/tests/unit/mathematics/linalg/SpecialPurpose_unittest.cc b/tests/unit/mathematics/linalg/SpecialPurpose_unittest.cc
@@ -30,7 +30,6 @@
 
 #include <shogun/lib/config.h>
 
-#ifdef HAVE_LINALG_LIB
 #include <shogun/mathematics/linalg/linalg.h>
 #include <shogun/mathematics/Math.h>
 #include <shogun/lib/SGMatrix.h>
@@ -317,5 +316,3 @@ TEST(SpecialPurpose, squared_error_viennacl_backend)
 	EXPECT_NEAR(se, linalg::special_purpose::squared_error<linalg::Backend::VIENNACL>(A, B), 1e-15);
 }
 #endif // HAVE_VIENNACL
-
-#endif // HAVE_LINALG_LIB
diff --git a/tests/unit/regression/GaussianProcessRegression_unittest.cc b/tests/unit/regression/GaussianProcessRegression_unittest.cc
@@ -613,7 +613,6 @@ TEST(GaussianProcessRegression,var_dtc_regression)
 	SG_UNREF(inducing_features_train);
 }
 
-#ifdef HAVE_LINALG_LIB
 TEST(GaussianProcessRegression,fitc_regression)
 {
 	index_t n=6;
@@ -738,4 +737,3 @@ TEST(GaussianProcessRegression,fitc_regression)
 	SG_UNREF(latent_features_train);
 	SG_UNREF(gpr);
 }
-#endif /* HAVE_LINALG_LIB */