diff options
Diffstat (limited to 'src')
| -rw-r--r-- | src/fastblas.cpp | 43 | ||||
| -rw-r--r-- | src/fastblas.h | 3 | ||||
| -rw-r--r-- | src/lmm.cpp | 8 | ||||
| -rw-r--r-- | src/mathfunc.cpp | 2 | ||||
| -rw-r--r-- | src/version.h | 8 |
5 files changed, 32 insertions, 32 deletions
diff --git a/src/fastblas.cpp b/src/fastblas.cpp index 41ee741..efa8412 100644 --- a/src/fastblas.cpp +++ b/src/fastblas.cpp @@ -2,7 +2,7 @@ Genome-wide Efficient Mixed Model Association (GEMMA) Copyright © 2011-2017, Xiang Zhou Copyright © 2017, Peter Carbonetto - Copyright © 2017, Pjotr Prins + Copyright © 2017-2020, Pjotr Prins 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 @@ -25,6 +25,7 @@ #include "debug.h" #include "mathfunc.h" #include <string.h> +#include "fastblas.h" const char *FastblasTrans = "T"; const char *FastblasNoTrans = "N"; @@ -246,29 +247,27 @@ extern "C" { int gsl_linalg_LU_decomp(gsl_matrix * A, gsl_permutation * p, int * signum); } -void gsl_matrix_inv(gsl_matrix *m) -{ - size_t n=m->size1; - - gsl_matrix *temp1=gsl_matrix_calloc(n,n); - gsl_matrix_memcpy(temp1,m); - - gsl_permutation *p=gsl_permutation_calloc(n); - int sign=0; - gsl_linalg_LU_decomp(temp1,p,&sign); - gsl_matrix *inverse=gsl_matrix_calloc(n,n); - - gsl_linalg_LU_invert(temp1,p,inverse); - gsl_matrix_memcpy(m,inverse); - - gsl_permutation_free(p); - gsl_matrix_free(temp1); - gsl_matrix_free(inverse); - +void gsl_matrix_inv(gsl_matrix *m) +{ + size_t n=m->size1; + + gsl_matrix *temp1=gsl_matrix_calloc(n,n); + gsl_matrix_memcpy(temp1,m); + + gsl_permutation *p=gsl_permutation_calloc(n); + int sign=0; + gsl_linalg_LU_decomp(temp1,p,&sign); + gsl_matrix *inverse=gsl_matrix_calloc(n,n); + + gsl_linalg_LU_invert(temp1,p,inverse); + gsl_matrix_memcpy(m,inverse); + + gsl_permutation_free(p); + gsl_matrix_free(temp1); + gsl_matrix_free(inverse); + } void fast_inverse(gsl_matrix *m) { gsl_matrix_inv(m); } - - diff --git a/src/fastblas.h b/src/fastblas.h index 32253b3..b36506d 100644 --- a/src/fastblas.h +++ b/src/fastblas.h @@ -23,7 +23,8 @@ #include <assert.h> #include <iostream> -// #include "gsl/gsl_matrix.h" +#include "gsl/gsl_cblas.h" +#include "gsl/gsl_matrix.h" gsl_matrix *fast_copy(gsl_matrix *m, const double *mem); diff --git a/src/lmm.cpp b/src/lmm.cpp index b811594..6337116 100644 --- a/src/lmm.cpp +++ b/src/lmm.cpp @@ -278,8 +278,8 @@ void CalcPab(const size_t n_cvt, const size_t e_mode, const gsl_vector *Hi_eval, const gsl_matrix *Uab, const gsl_vector *unused, gsl_matrix *Pab) { - size_t n_index = (n_cvt + 2 + 1) * (n_cvt + 2) / 2; // result size - auto ni_test = Uab->size1; // inds + // size_t n_index = (n_cvt + 2 + 1) * (n_cvt + 2) / 2; // result size + // auto ni_test = Uab->size1; // inds assert(Uab->size1 == Hi_eval->size); assert(Uab->size2 == n_index); @@ -593,8 +593,8 @@ $7 = 3 $8 = 6 */ - auto Uab = p->Uab; - auto ab = p->ab; + // auto Uab = p->Uab; + // auto ab = p->ab; assert(n_index == (n_cvt + 2 + 1) * (n_cvt + 2) / 2); assert(Uab->size1 == ni_test); assert(Uab->size2 == n_index); // n_cvt == 1 -> n_index == 6? diff --git a/src/mathfunc.cpp b/src/mathfunc.cpp index cd74e09..aaa9431 100644 --- a/src/mathfunc.cpp +++ b/src/mathfunc.cpp @@ -400,7 +400,7 @@ uint count_abs_small_values(const gsl_vector *v, double min) { // and the ratio of max and min but one (min is expected to be zero). bool isMatrixIllConditioned(const gsl_vector *eigenvalues, double max_ratio) { auto t = abs_minmax(eigenvalues); - auto absmin = get<0>(t); + // auto absmin = get<0>(t); auto absmin1 = get<1>(t); auto absmax = get<2>(t); if (absmax/absmin1 > max_ratio) { diff --git a/src/version.h b/src/version.h index f97c9f1..6c22a1b 100644 --- a/src/version.h +++ b/src/version.h @@ -1,5 +1,5 @@ -// version.h generated by GEMMA ./scripts/gen_version_info.sh -#define GEMMA_VERSION "0.98.2" -#define GEMMA_DATE "2020-05-28" +// version.h generated by GEMMA scripts/gen_version_info.sh +#define GEMMA_VERSION "0.98.3" +#define GEMMA_DATE "2020-09-29" #define GEMMA_YEAR "2020" -#define GEMMA_PROFILE "" +#define GEMMA_PROFILE "/gnu/store/a7a35vv75zk9k23k8ws4v2wrs123dln1-profile" |