3 files changed, 27 insertions, 3 deletions
diff --git a/guix.scm b/guix.scm
index 6dcaa29..23b7583 100644
--- a/guix.scm
+++ b/guix.scm
@@ -5,9 +5,13 @@
;;
;; To get a development container (e.g., run in emacs shell).
;;
+;; guix shell -C -D -F -v 3 -L . pangemma-shell-git # pangemma-shell-git
+;;
+;; optimized for arch:
+;;
;; guix shell --tune=native -C -D -F -v 3 -L . pangemma-shell-git # pangemma-shell-git
;;
-;; see premake5.lua header for examples.
+;; see premake5.lua header for examples.
;;
;; guix shell -C -D -F -v 3 -L . gemma-git # for specific packages
;;
@@ -75,7 +79,7 @@
#:substitutable? (not (target-ppc32?))
#:make-flags
#~(list (string-append "PREFIX=" #$output)
- (string-append "CFLAGS=-O3 -g -Wno-error -Wno-error=implicit-function-declaration")
+ (string-append "CFLAGS=-O3 -g -Wno-incompatible-pointer-types -Wno-error=implicit-function-declaration")
"SHELL=bash"
"MAKE_NB_JOBS=0" ;use jobserver for submakes
diff --git a/premake5.lua b/premake5.lua
index 3ccbdbc..bb06cbd 100644
--- a/premake5.lua
+++ b/premake5.lua
@@ -1,6 +1,6 @@
-- Build with
--
--- make clean && rm build/Release/ -rf
+-- make clean && rm build -rf
-- premake5 gmake2 && make verbose=1 gemmalib -j 8
--
-- Including bin
diff --git a/test/performance/releases.org b/test/performance/releases.org
index af0cbb7..4cc92f1 100644
--- a/test/performance/releases.org
+++ b/test/performance/releases.org
@@ -8,6 +8,26 @@ We are facing a time regression.
premake5 gmake2 && make verbose=1 config=release -j 8 gemma && time LD_LIBRARY_PATH=$GUIX_ENVIRONMENT/lib ./build/bin/Release/gemma -g ./example/mouse_hs1940.geno.txt.gz -p ./example/mouse_hs1940.pheno.txt -n 1 -a ./example/mouse_hs1940.anno.txt -k ./output/result.cXX.txt -lmm -no-check -debug
+With openblas 0.3.21 we go a bit faster. Still behind though, there is room for tweaking. But I want to run some bigger files first.
+
+#+begin_src sh
+Pangemma --- GEMMA 0.98.5 compatible executable 1.0.0 (2025-11-22) with guile 3.0.9 by Xiang Zhou, Pjotr Prins and team (C) 2012-2025
+Reading Files ...
+## number of total individuals = 1940
+## number of analyzed individuals = 1410
+## number of covariates = 1
+## number of phenotypes = 1
+## number of total SNPs/var = 12226
+## number of analyzed SNPs = 10768
+Start Eigen-Decomposition...
+pve estimate =0.608801
+se(pve) =0.032774
+================================================== 100%
+real 0m9.017s
+user 0m13.168s
+sys 0m5.919s
+#+end_src sh
+
#+begin_src sh
Pangemma --- GEMMA 0.98.5 compatible executable 1.0.0 (2025-11-22) with guile 3.0.9 by Xiang Zhou, Pjotr Prins and team (C) 2012-2025
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