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| author | Pjotr Prins | 2025-11-26 13:26:54 +0100 |
|---|---|---|
| committer | Pjotr Prins | 2025-11-26 13:26:54 +0100 |
| commit | cf4f018bd350c8202aef2ee085a2c536097895b4 (patch) | |
| tree | de59a01f23d98ab523e2ae9450b278ad0dae3fde /test | |
| parent | 806a01c27a1fd366c120820de0c38caea1d4cdcd (diff) | |
| download | pangemma-cf4f018bd350c8202aef2ee085a2c536097895b4.tar.gz | |
Fix progress bar and test larger file
Diffstat (limited to 'test')
| -rw-r--r-- | test/performance/releases.org | 7 |
1 files changed, 6 insertions, 1 deletions
diff --git a/test/performance/releases.org b/test/performance/releases.org index 792cb2e..ff18287 100644 --- a/test/performance/releases.org +++ b/test/performance/releases.org @@ -9,7 +9,7 @@ We are facing a time regression. premake5 gmake2 && make verbose=1 config=release -j 8 gemma && time LD_LIBRARY_PATH=$GUIX_ENVIRONMENT/lib ./build/bin/Release/gemma -g ./example/mouse_hs1940.geno.txt.gz -p ./example/mouse_hs1940.pheno.txt -n 1 -a ./example/mouse_hs1940.anno.txt -k ./output/result.cXX.txt -lmm -no-check -debug -With openblas 0.3.21 we go a bit faster. Still 10% behind though, there is room for tweaking. But I want to run some bigger files first. +With openblas 0.3.21 we go a bit faster. Still 10% behind though, there is room for tweaking. It may actually be a new SSD. I want to run some bigger files first. #+begin_src sh Pangemma --- GEMMA 0.98.5 compatible executable 1.0.0 (2025-11-22) with guile 3.0.9 by Xiang Zhou, Pjotr Prins and team (C) 2012-2025 @@ -82,8 +82,13 @@ to ``` time LD_LIBRARY_PATH=$GUIX_ENVIRONMENT/lib ./build/bin/Release/gemma -g tmp/pangenome-13M-genotypes.txt -p tmp/pheno.json.txt -n 1 -a tmp/snps-matched.txt -k tmp/93f6b39ec06c09fb9ba9ca628b5fb990921b6c60.3.cXX.txt.cXX.txt -lmm 9 -no-check +real 20m4.687s +user 23m42.508s +sys 9m51.929s ``` +On my AMD Ryzen 7 3700X it uses about ~10Gb of RAM. With the -debug switch it clapped out because of sqrt(NaN). There is a lot that can be gained with better IO and multi-core use. + ** GEMMA 0.98.5-pre1 Measurements taken on a recent AMD Ryzen 7 3700X 8-Core Processor @2.195GHz. |