diff options
| -rw-r--r-- | guix.scm | 8 | ||||
| -rw-r--r-- | premake5.lua | 2 | ||||
| -rw-r--r-- | test/performance/releases.org | 20 |
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 |