diff options
| author | Pjotr Prins | 2020-11-28 15:22:41 +0000 |
|---|---|---|
| committer | Pjotr Prins | 2020-11-28 15:23:15 +0000 |
| commit | f623b4775d47b2c2697a4925bd044412a7db49d3 (patch) | |
| tree | f1c5cbebdec42753a175a4762653bbcf50b68b0f /test | |
| parent | 1d60d303945b4976984f379e420217a7230d79a9 (diff) | |
| download | pangemma-f623b4775d47b2c2697a4925bd044412a7db49d3.tar.gz | |
Checked the timings; Travis passes for Linux and MacOS
Diffstat (limited to 'test')
| -rw-r--r-- | test/performance/releases.org | 47 |
1 files changed, 43 insertions, 4 deletions
diff --git a/test/performance/releases.org b/test/performance/releases.org index 1be5818..79d830b 100644 --- a/test/performance/releases.org +++ b/test/performance/releases.org @@ -90,6 +90,48 @@ trix const*, gsl_matrix*, gsl_matrix*) onst*) #+END_SRC +* GEMMA 0.98.3 (release) + +#+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 0.98.3 (2020-11-28) 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% + +real 0m7.068s +user 0m14.904s +sys 0m1.454s + +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 0.98.3 (2020-11-28) 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% + +real 0m12.581s +user 0m17.318s +sys 0m2.079s +#+end_src + + + * GEMMA 0.98.2 (release) Looks like openblas is getting faster. Two metrics on the same machine: @@ -106,13 +148,13 @@ Reading Files ... ## number of analyzed SNPs = 10768 Calculating Relatedness Matrix ... ================================================== 100% -**** INFO: Done. real 0m7.635s user 0m14.821s sys 0m1.077s #+END_SRC +The static version #+BEGIN_SRC sh lario:~/iwrk/opensource/code/genetics/gemma$ time ./bin/gemma-0.98-linux-static -g ./example/mouse_hs1940.geno.txt.gz -p ./example/mouse_hs1940.pheno.txt -a ./example/mouse_hs1940.anno.txt -gk -no-check @@ -126,7 +168,6 @@ Reading Files ... ## number of analyzed SNPs = 10768 Calculating Relatedness Matrix ... ================================================== 100% -**** INFO: Done. real 0m10.663s user 0m20.994s @@ -151,7 +192,6 @@ Reading Files ... ## number of analyzed SNPs = 10768 Calculating Relatedness Matrix ... ================================================== 100% -**** INFO: Done. real 0m7.590s user 0m30.392s @@ -180,7 +220,6 @@ Start Eigen-Decomposition... pve estimate =0.608801 se(pve) =0.032774 ================================================== 100% -**** INFO: Done. real 0m17.813s user 0m43.460s |