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| author | Pjotr Prins | 2020-05-28 07:25:26 -0500 |
|---|---|---|
| committer | Pjotr Prins | 2020-05-28 07:25:26 -0500 |
| commit | 85b688357a83cce5e884eb439dd541772368c5b4 (patch) | |
| tree | 27ecfe9ad50da5b221d1e9d33c1b445f847cee03 /test | |
| parent | f2fb0a6c0d8e8a849d5e8acc975111e1ff6bb714 (diff) | |
| download | pangemma-85b688357a83cce5e884eb439dd541772368c5b4.tar.gz | |
Checking performance
Diffstat (limited to 'test')
| -rw-r--r-- | test/performance/releases.org | 64 |
1 files changed, 64 insertions, 0 deletions
diff --git a/test/performance/releases.org b/test/performance/releases.org index d16260d..e1cd4d1 100644 --- a/test/performance/releases.org +++ b/test/performance/releases.org @@ -90,6 +90,70 @@ trix const*, gsl_matrix*, gsl_matrix*) onst*) #+END_SRC +* GEMMA 0.99 (release) + +On a 26 core Intel(R) Xeon(R) CPU E5-2683 v3 @ 2.00GHz + +The newer OpenBLAS is a tad faster on multi-core at the expense of +user land. + +#+begin_src sh +time ./bin/gemma -g ./example/mouse_hs1940.geno.txt.gz -p ./example/mouse_hs1940.pheno.txt -a ./example/mouse_hs1940.anno.txt -gk -no-check +GEMMA 0.98.2 (2020-05-28) by Xiang Zhou and team (C) 2012-2020 +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 +Calculating Relatedness Matrix ... +================================================== 100% +**** INFO: Done. + +real 0m7.590s +user 0m30.392s +sys 0m12.072s + +while + +time ./gemma-0.98.1-linux-static -g ./example/mouse_hs1940.geno.txt.gz -p ./example/mouse_hs1940.pheno.txt -a ./example/mouse_hs1940.anno.txt -gk -no-check +GEMMA 0.98.1 (2018-12-10) by Xiang Zhou and team (C) 2012-2018 +real 0m9.272s +user 0m13.904s +sys 0m1.636s +#+end_src + +#+begin_src sh +penguin2:~/iwrk/opensource/code/genetics/gemma$ time ./bin/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 +GEMMA 0.98.2 (2020-05-28) by Xiang Zhou and team (C) 2012-2020 +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% +**** INFO: Done. + +real 0m17.813s +user 0m43.460s +sys 0m36.208s + +penguin2:~/iwrk/opensource/code/genetics/gemma$ time ./gemma-0.98.1-linux-static -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 +GEMMA 0.98.1 (2018-12-10) by Xiang Zhou and team (C) 2012-2018 +Reading Files ... + +real 0m19.481s +user 0m23.072s +sys 0m2.684s + +#+end_src + * GEMMA 0.98 (release) #+BEGIN_SRC bash |