From 8c82a8294483ffac4d8e9635376723f26a8ae27b Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Fri, 22 May 2020 07:15:37 -0500
Subject: Fixes for gcc (GCC) 10.1.0 Started to remove eigenlib (again)
---
src/eigenlib.cpp | 107 -------------------------------------------------------
1 file changed, 107 deletions(-)
delete mode 100644 src/eigenlib.cpp
(limited to 'src/eigenlib.cpp')
diff --git a/src/eigenlib.cpp b/src/eigenlib.cpp
deleted file mode 100644
index 470aa08..0000000
--- a/src/eigenlib.cpp
+++ /dev/null
@@ -1,107 +0,0 @@
-/*
- Genome-wide Efficient Mixed Model Association (GEMMA)
- Copyright (C) 2011-2017, Xiang Zhou
-
- This program is free software: you can redistribute it and/or modify
- it under the terms of the GNU General Public License as published by
- the Free Software Foundation, either version 3 of the License, or
- (at your option) any later version.
-
- This program is distributed in the hope that it will be useful,
- but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- GNU General Public License for more details.
-
- You should have received a copy of the GNU General Public License
- along with this program. If not, see .
-*/
-
-#include "Eigen/Dense"
-// #include "gsl/gsl_linalg.h"
-#include "gsl/gsl_matrix.h"
-// #include "gsl/gsl_vector.h"
-#include
-#include
-#include
-// #include
-
-using namespace std;
-using namespace Eigen;
-
-
-// On two different clusters, compare eigen vs lapack/gsl:
-//
-// dgemm, 5x or 0.5x faster or slower than lapack, 5x or 4x faster than gsl
-// dgemv, 20x or 4x faster than gsl,
-// eigen, 1x or 0.3x slower than lapack
-// invert, 20x or 10x faster than lapack
-//
-void eigenlib_dgemm(const char *TransA, const char *TransB, const double alpha,
- const gsl_matrix *A, const gsl_matrix *B, const double beta,
- gsl_matrix *C) {
- Map, 0, OuterStride>
- A_mat(A->data, A->size1, A->size2, OuterStride(A->tda));
- Map, 0, OuterStride>
- B_mat(B->data, B->size1, B->size2, OuterStride(B->tda));
- Map, 0, OuterStride>
- C_mat(C->data, C->size1, C->size2, OuterStride(C->tda));
-
- if (*TransA == 'N' || *TransA == 'n') {
- if (*TransB == 'N' || *TransB == 'n') {
- C_mat = alpha * A_mat * B_mat + beta * C_mat;
- } else {
- C_mat = alpha * A_mat * B_mat.transpose() + beta * C_mat;
- }
- } else {
- if (*TransB == 'N' || *TransB == 'n') {
- C_mat = alpha * A_mat.transpose() * B_mat + beta * C_mat;
- } else {
- C_mat = alpha * A_mat.transpose() * B_mat.transpose() + beta * C_mat;
- }
- }
-}
-
-void eigenlib_dgemv(const char *TransA, const double alpha, const gsl_matrix *A,
- const gsl_vector *x, const double beta, gsl_vector *y) {
- Map, 0, OuterStride>
- A_mat(A->data, A->size1, A->size2, OuterStride(A->tda));
- Map, 0, InnerStride> x_vec(
- x->data, x->size, InnerStride(x->stride));
- Map, 0, InnerStride> y_vec(
- y->data, y->size, InnerStride(y->stride));
-
- if (*TransA == 'N' || *TransA == 'n') {
- y_vec = alpha * A_mat * x_vec + beta * y_vec;
- } else {
- y_vec = alpha * A_mat.transpose() * x_vec + beta * y_vec;
- }
-}
-
-void eigenlib_invert(gsl_matrix *A) {
- Map> A_mat(A->data, A->size1,
- A->size2);
- A_mat = A_mat.inverse();
-}
-
-void eigenlib_dsyr(const double alpha, const gsl_vector *b, gsl_matrix *A) {
- Map> A_mat(A->data, A->size1,
- A->size2);
- Map, 0, OuterStride> b_vec(
- b->data, b->size, OuterStride(b->stride));
- A_mat = alpha * b_vec * b_vec.transpose() + A_mat;
-}
-
-void eigenlib_eigensymm(const gsl_matrix *G, gsl_matrix *U, gsl_vector *eval) {
- Map, 0, OuterStride>
- G_mat(G->data, G->size1, G->size2, OuterStride(G->tda));
- Map, 0, OuterStride>
- U_mat(U->data, U->size1, U->size2, OuterStride(U->tda));
- Map, 0, OuterStride> eval_vec(
- eval->data, eval->size, OuterStride(eval->stride));
-
- SelfAdjointEigenSolver es(G_mat);
- if (es.info() != Success)
- abort();
- eval_vec = es.eigenvalues();
- U_mat = es.eigenvectors();
-}
--
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