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| author | Pjotr Prins | 2025-11-25 17:28:32 +0100 |
|---|---|---|
| committer | Pjotr Prins | 2025-11-25 17:28:32 +0100 |
| commit | c9824193dd3fd6ff398942885f110b27d8b646a0 (patch) | |
| tree | 1659c78b4c57d9016f3e2ffc7a873615f1092dea /test/performance/releases.org | |
| parent | be88d7a399660f3c4ddd6bce502f5b39c61b3298 (diff) | |
| download | pangemma-c9824193dd3fd6ff398942885f110b27d8b646a0.tar.gz | |
Diffstat (limited to 'test/performance/releases.org')
| -rw-r--r-- | test/performance/releases.org | 20 |
1 files changed, 20 insertions, 0 deletions
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 |