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-rw-r--r--INSTALL.md3
-rw-r--r--src/fastblas.cpp27
-rw-r--r--src/fastopenblas.h28
-rw-r--r--src/gemma.cpp4
-rw-r--r--src/io.cpp2
-rw-r--r--src/ldr.cpp7
-rw-r--r--src/mathfunc.cpp7
-rw-r--r--src/mathfunc.h6
-rw-r--r--src/vc.cpp4
9 files changed, 51 insertions, 37 deletions
diff --git a/INSTALL.md b/INSTALL.md
index 897b062..dc03a71 100644
--- a/INSTALL.md
+++ b/INSTALL.md
@@ -115,7 +115,8 @@ To link a new version, compile OpenBlas as per
 
     make -j 4
 
-or play with the switches
+or play with the switches (note NO_AFFINITY may be needed in a future
+version)
 
     make USE_THREAD=1 NUM_THREADS=16 NO_AFFINITY=1 -j 4
 
diff --git a/src/fastblas.cpp b/src/fastblas.cpp
index 0a4eba3..3fe712c 100644
--- a/src/fastblas.cpp
+++ b/src/fastblas.cpp
@@ -24,6 +24,7 @@
 #include "debug.h"
 #include "fastblas.h"
 #include "mathfunc.h"
+#include <string.h>
 #ifndef NDEBUG
 #include "eigenlib.h"
 #endif
@@ -61,20 +62,20 @@ gsl_matrix *fast_copy(gsl_matrix *m, const double *mem) {
 /*
     Helper function fast_cblas_dgemm runs the local dgemm
 */
-void fast_cblas_dgemm(OPENBLAS_CONST enum CBLAS_ORDER Order,
-                      OPENBLAS_CONST enum CBLAS_TRANSPOSE TransA,
-                      OPENBLAS_CONST enum CBLAS_TRANSPOSE TransB,
-                      OPENBLAS_CONST blasint M,
-                      OPENBLAS_CONST blasint N,
-                      OPENBLAS_CONST blasint K,
-                      OPENBLAS_CONST double alpha,
-                      OPENBLAS_CONST double *A,
-                      OPENBLAS_CONST blasint lda,
-                      OPENBLAS_CONST double *B,
-                      OPENBLAS_CONST blasint ldb,
-                      OPENBLAS_CONST double beta,
+void fast_cblas_dgemm(const enum CBLAS_ORDER Order,
+                      const enum CBLAS_TRANSPOSE TransA,
+                      const enum CBLAS_TRANSPOSE TransB,
+                      const blasint M,
+                      const blasint N,
+                      const blasint K,
+                      const double alpha,
+                      const double *A,
+                      const blasint lda,
+                      const double *B,
+                      const blasint ldb,
+                      const double beta,
                       double *C,
-                      OPENBLAS_CONST blasint ldc) {
+                      const blasint ldc) {
 #ifndef NDEBUG
   size_t i,j;
   if (is_debug_mode()) {
diff --git a/src/fastopenblas.h b/src/fastopenblas.h
index 824b686..a0904c3 100644
--- a/src/fastopenblas.h
+++ b/src/fastopenblas.h
@@ -6,19 +6,21 @@
 #include <cblas.h>   // For OpenBlas
 #include "gsl/gsl_matrix.h"
 
-void fast_cblas_dgemm(OPENBLAS_CONST enum CBLAS_ORDER Order,
-                      OPENBLAS_CONST enum CBLAS_TRANSPOSE TransA,
-                      OPENBLAS_CONST enum CBLAS_TRANSPOSE TransB,
-                      OPENBLAS_CONST blasint M,
-                      OPENBLAS_CONST blasint N,
-                      OPENBLAS_CONST blasint K,
-                      OPENBLAS_CONST double alpha,
-                      OPENBLAS_CONST double *A,
-                      OPENBLAS_CONST blasint lda,
-                      OPENBLAS_CONST double *B,
-                      OPENBLAS_CONST blasint ldb,
-                      OPENBLAS_CONST double beta,
+#ifndef
+
+void fast_cblas_dgemm(const enum CBLAS_ORDER Order,
+                      const enum CBLAS_TRANSPOSE TransA,
+                      const enum CBLAS_TRANSPOSE TransB,
+                      const blasint M,
+                      const blasint N,
+                      const blasint K,
+                      const double alpha,
+                      const double *A,
+                      const blasint lda,
+                      const double *B,
+                      const blasint ldb,
+                      const double beta,
                       double *C,
-                      OPENBLAS_CONST blasint ldc);
+                      const blasint ldc);
 
 #endif
diff --git a/src/gemma.cpp b/src/gemma.cpp
index e2881a4..a1aeaa3 100644
--- a/src/gemma.cpp
+++ b/src/gemma.cpp
@@ -3087,6 +3087,9 @@ void GEMMA::BatchRun(PARAM &cPar) {
   return;
 }
 
+#include "Eigen/Dense"
+// using namespace Eigen;
+
 void GEMMA::WriteLog(int argc, char **argv, PARAM &cPar) {
   string file_str;
   file_str = cPar.path_out + "/" + cPar.file_out;
@@ -3103,6 +3106,7 @@ void GEMMA::WriteLog(int argc, char **argv, PARAM &cPar) {
   outfile << "## GSL Version      = " << GSL_VERSION << endl;
   outfile << "## Eigen Version    = " << EIGEN_WORLD_VERSION << "." << EIGEN_MAJOR_VERSION << "." << EIGEN_MINOR_VERSION << endl;
   #ifdef OPENBLAS
+
   outfile << "## OpenBlas         = " << openblas_get_config() << " - " << openblas_get_corename() << endl;
 
   outfile << "##   threads        = " << openblas_get_num_threads() << endl;
diff --git a/src/io.cpp b/src/io.cpp
index cc0f064..d1c4bc2 100644
--- a/src/io.cpp
+++ b/src/io.cpp
@@ -3017,7 +3017,7 @@ bool PlinkKin(const string &file_bed, const int display_pace,
           gsl_matrix_submatrix(Xlarge, 0, msize * i_vc, ni_test, msize);
       gsl_matrix_view kin_sub =
           gsl_matrix_submatrix(matrix_kin, 0, ni_test * i_vc, ni_test, ni_test);
-      eigenlib_dgemm("N", "T", 1.0, &X_sub.matrix, &X_sub.matrix, 1.0,
+      fast_dgemm("N", "T", 1.0, &X_sub.matrix, &X_sub.matrix, 1.0,
                      &kin_sub.matrix);
     }
   }
diff --git a/src/ldr.cpp b/src/ldr.cpp
index 3554efa..f70eb85 100644
--- a/src/ldr.cpp
+++ b/src/ldr.cpp
@@ -29,7 +29,7 @@
 #include <stdio.h>
 #include <stdlib.h>
 
-#include "Eigen/Dense"
+// #include "Eigen/Dense"
 #include "gsl/gsl_blas.h"
 #include "gsl/gsl_cdf.h"
 #include "gsl/gsl_eigen.h"
@@ -46,7 +46,7 @@
 #include "param.h"
 
 using namespace std;
-using namespace Eigen;
+// using namespace Eigen;
 
 void LDR::CopyFromParam(PARAM &cPar) {
   a_mode = cPar.a_mode;
@@ -70,8 +70,10 @@ void LDR::CopyFromParam(PARAM &cPar) {
   return;
 }
 
+
 void LDR::CopyToParam(PARAM &cPar) { return; }
 
+/*
 // X is a p by n matrix.
 void LDR::VB(const vector<vector<unsigned char>> &Xt, const gsl_matrix *W_gsl,
              const gsl_vector *y_gsl) {
@@ -107,3 +109,4 @@ void LDR::VB(const vector<vector<unsigned char>> &Xt, const gsl_matrix *W_gsl,
 
   return;
 }
+*/
diff --git a/src/mathfunc.cpp b/src/mathfunc.cpp
index d0a9d65..f55f3c6 100644
--- a/src/mathfunc.cpp
+++ b/src/mathfunc.cpp
@@ -32,7 +32,7 @@
 #include <tuple>
 #include <vector>
 
-#include "Eigen/Dense"
+// #include "Eigen/Dense"
 
 #include "gsl/gsl_version.h"
 
@@ -54,7 +54,7 @@
 #include "mathfunc.h"
 
 using namespace std;
-using namespace Eigen;
+// using namespace Eigen;
 
 bool has_nan(const vector<double> v) {
   for (const auto& e: v) {
@@ -524,6 +524,7 @@ unsigned char Double02ToUchar(const double dosage) {
   return (int)(dosage * 100);
 }
 
+/*
 void uchar_matrix_get_row(const vector<vector<unsigned char>> &X,
                           const size_t i_row, VectorXd &x_row) {
   if (i_row < X.size()) {
@@ -535,3 +536,5 @@ void uchar_matrix_get_row(const vector<vector<unsigned char>> &X,
     exit(1);
   }
 }
+
+*/
diff --git a/src/mathfunc.h b/src/mathfunc.h
index 804bc20..1319a64 100644
--- a/src/mathfunc.h
+++ b/src/mathfunc.h
@@ -19,7 +19,7 @@
 #ifndef __MATHFUNC_H__
 #define __MATHFUNC_H__
 
-#include "Eigen/Dense"
+// #include "Eigen/Dense"
 #include "gsl/gsl_matrix.h"
 #include "gsl/gsl_vector.h"
 
@@ -57,7 +57,7 @@ void KroneckerSym(const gsl_matrix *K, const gsl_matrix *V, gsl_matrix *H);
 
 double UcharToDouble02(const unsigned char c);
 unsigned char Double02ToUchar(const double dosage);
-void uchar_matrix_get_row(const vector<vector<unsigned char>> &X,
-                          const size_t i_row, Eigen::VectorXd &x_row);
+// void uchar_matrix_get_row(const vector<vector<unsigned char>> &X,
+//                          const size_t i_row, Eigen::VectorXd &x_row);
 
 #endif
diff --git a/src/vc.cpp b/src/vc.cpp
index 1465f16..f8cc2b5 100644
--- a/src/vc.cpp
+++ b/src/vc.cpp
@@ -41,7 +41,7 @@
 #include "gsl/gsl_min.h"
 #include "gsl/gsl_multiroots.h"
 
-#include "Eigen/Dense"
+// #include "Eigen/Dense"
 
 #include "eigenlib.h"
 #include "gzstream.h"
@@ -53,7 +53,7 @@
 #include "vc.h"
 
 using namespace std;
-using namespace Eigen;
+// using namespace Eigen;
 
 // In this file, X, Y are already transformed (i.e. UtX and UtY).
 void VC::CopyFromParam(PARAM &cPar) {
generated by cgit-pink 1.4.1 (git 2.36.1) at 2025-10-18 22:36:46 +0000