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-rw-r--r--.guix-dev-gcc-older2
-rw-r--r--.travis.yml34
-rw-r--r--INSTALL.md2
-rw-r--r--RELEASE-NOTES.md5
-rw-r--r--VERSION2
-rw-r--r--src/fastblas.cpp43
-rw-r--r--src/fastblas.h3
-rw-r--r--src/lmm.cpp8
-rw-r--r--src/mathfunc.cpp2
-rw-r--r--src/version.h8
10 files changed, 43 insertions, 66 deletions
diff --git a/.guix-dev-gcc-older b/.guix-dev-gcc-older
new file mode 100644
index 0000000..7d37f7d
--- /dev/null
+++ b/.guix-dev-gcc-older
@@ -0,0 +1,2 @@
+# Typical Guix container invocation
+~/opt/guix/bin/guix environment -C guix --ad-hoc gcc-toolchain@6.5.0 gdb gsl openblas zlib bash ld-wrapper perl vim which
diff --git a/.travis.yml b/.travis.yml
index 6fd48bd..5bc64eb 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -1,8 +1,5 @@
language: C++
matrix:
- # OSX testing is under development
- # allow_failures:
- # - os: osx
include:
- os: linux
compiler: gcc
@@ -11,36 +8,11 @@ matrix:
sources:
- ubuntu-toolchain-r-test
packages:
- # Our dev environment is a more recent GNU C++ and GSL2
- - g++-4.9
+ - libgsl-dev
- libopenblas-dev
- - zlib1g-dev
- - libgsl0-dev
- - os: osx
- compiler: clang
-# - os: linux
-# addons:
-# apt:
-# sources:
-# - ubuntu-toolchain-r-test
-# packages:
-# - g++-6
-# env:
-# - MATRIX_EVAL="CC=gcc-6 && CXX=g++-6"
-before_install:
- - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then brew update && brew install gsl openblas zlib eigen lapack ; fi
script:
- echo $MATRIX_EVAL
- eval "${MATRIX_EVAL}"
- $CXX --version
- # build and test debug version
- - make CXX=$CXX OPENBLAS_LEGACY=1 WITH_GSLCBLAS=1 -j 4 -k
- - time make CXX=$CXX OPENBLAS_LEGACY=1 WITH_GSLCBLAS=1 check
- # - make clean
- # build and test release version (integration test mostly)
- # - make CXX=$CXX EIGEN_INCLUDE_PATH=$EIGEN_INCLUDE_PATH DEBUG= FORCE_DYNAMIC=1 WITH_OPENBLAS=1 OPENBLAS_LEGACY=1 -j 4
- # - time make CXX=$CXX DEBUG= WITH_OPENBLAS=1 fast-check
- # build static release (fast-check only)
- # - make clean
- # - make CXX=$CXX TRAVIS_CI=1 -j 4 fast-check
- # - ldd ./bin/gemma
+ - make -j 4 OPENBLAS_LEGACY=1
+ - make OPENBLAS_LEGACY=1 fast-check
diff --git a/INSTALL.md b/INSTALL.md
index 29b50d6..f807a7b 100644
--- a/INSTALL.md
+++ b/INSTALL.md
@@ -13,7 +13,7 @@ and it should give you the version.
GEMMA runs on Linux and MAC OSX and the runtime has the following
dependencies:
-* C++ tool chain >= 4.9
+* C++ tool chain >= 6.5.0 (we test with file .guix-dev-gcc-older)
* GNU Science library (GSL) 1.x (GEMMA does not currently work with GSL >= 2).
* blas/openblas
* lapack
diff --git a/RELEASE-NOTES.md b/RELEASE-NOTES.md
index 53674d8..4345c27 100644
--- a/RELEASE-NOTES.md
+++ b/RELEASE-NOTES.md
@@ -4,7 +4,10 @@ see
and
[commits](https://github.com/genetics-statistics/GEMMA/commits/master).
-## ChangeLog v0.98.2 (2018/05/28)
+## ChangeLog v0.98.3 (2020/?)
+
+
+## ChangeLog v0.98.2 (2019/05/28)
GCC 10.1 fix release
diff --git a/VERSION b/VERSION
index 85b51db..cb48b48 100644
--- a/VERSION
+++ b/VERSION
@@ -1 +1 @@
-0.98.2
+0.98.3
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"
generated by cgit v1.2.3 (git 2.44.0) at 2025-01-18 13:13:36 +0000