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Diffstat (limited to 'test/performance/releases.org')
| -rw-r--r-- | test/performance/releases.org | 61 |
1 files changed, 61 insertions, 0 deletions
diff --git a/test/performance/releases.org b/test/performance/releases.org index f1772dc..4e70c14 100644 --- a/test/performance/releases.org +++ b/test/performance/releases.org @@ -125,6 +125,8 @@ user 0m13.656s sys 0m1.584s #+END_SRC +Multivariate analysis is still slow. + #+BEGIN_SRC bash 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 (2018-09-26) by Xiang Zhou and team (C) 2012-2018 @@ -146,6 +148,65 @@ user 0m15.788s sys 0m3.036s #+END_SRC +Full multivariate analysis is still slow. Mostly because of CalcQi - see above profiling. + +#+BEGIN_SRC bash +time ./bin/gemma -g ./example/mouse_hs1940.geno.txt.gz -p ./example/mouse_hs1940.pheno.txt -n 1 2 -a ./example/mouse_hs1940.anno.txt -k ./output/result.cXX.txt -lmm -no-check +GEMMA 0.98 (2018-09-26) by Xiang Zhou and team (C) 2012-2018 +Reading Files ... +## number of total individuals = 1940 +## number of analyzed individuals = 757 +## number of covariates = 1 +## number of phenotypes = 2 +## number of total SNPs/var = 12226 +## number of analyzed SNPs = 10775 +Start Eigen-Decomposition... +REMLE estimate for Vg in the null model: +1.3210 +1.3210 1.3210 +se(Vg): +0.8217 +0.7152 0.7198 +REMLE estimate for Ve in the null model: +0.3257 +0.3257 0.3257 +se(Ve): +1.9191 +2.6491 1.9101 +REMLE likelihood = 0.0000 +MLE estimate for Vg in the null model: +1.3215 +1.3215 1.3215 +se(Vg): +0.8217 +0.7152 0.7198 +MLE estimate for Ve in the null model: +0.3249 +0.3249 0.3249 +se(Ve): +1.9191 +2.6491 1.9101 +MLE likelihood = 0.0000 +================================================== 100% +**** INFO: Done. + +real 1m38.057s +user 1m39.320s +sys 0m2.116s +#+END_SRC + +using GSL inline functions improved it a bit to + +#+BEGIN_SRC +real 1m29.697s +user 1m30.896s +sys 0m2.148s +#+END_SRC + +otherwise the obvious way to improve things is to rejig these CalcXHiY, CalcQi and +CalcSigma functions. + + * GEMMA 0.98-pre #+BEGIN_SRC bash |