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| author | Pjotr Prins | 2021-08-11 08:00:57 +0200 |
|---|---|---|
| committer | Pjotr Prins | 2021-08-11 08:00:57 +0200 |
| commit | f1529c7ea9b212c5024b083a380deb0b4f64126b (patch) | |
| tree | 2a9c5ec888b4099ec83a7edd102ea5a42a61f120 /test/performance/releases.org | |
| parent | e1a7aaddf987667d3e7ca3caa856e634750408b2 (diff) | |
| download | pangemma-f1529c7ea9b212c5024b083a380deb0b4f64126b.tar.gz | |
Update performance notes
Diffstat (limited to 'test/performance/releases.org')
| -rw-r--r-- | test/performance/releases.org | 65 |
1 files changed, 65 insertions, 0 deletions
diff --git a/test/performance/releases.org b/test/performance/releases.org index 79d830b..2e6bf6a 100644 --- a/test/performance/releases.org +++ b/test/performance/releases.org @@ -1,5 +1,70 @@ * GEMMA performance stats +** GEMMA 0.99.0-pre1 + +Measurements taken on a recent AMD Ryzen 7 3700X 8-Core Processor @2.195GHz. + +#+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 0.99.0-pre1 (2021-08-11) by Xiang Zhou, Pjotr Prins and team (C) 2012-2021 +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 0m5.288s +user 0m11.829s +sys 0m1.992s + +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 0.99.0-pre1 (2021-08-11) by Xiang Zhou, Pjotr Prins and team (C) 2012-2021 +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 0m8.383s +user 0m12.863s +sys 0m4.943s + +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 0.99.0-pre1 (2021-08-11) by Xiang Zhou, Pjotr Prins and team (C) 2012-2021 +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 + +real 0m47.586s +user 0m49.588s +sys 0m3.521s +#+end_src + +Built with: + + libopenblas.so.0 => /gnu/store/bs9pl1f805ins80xaf4s3n35a0x2lyq3-openblas-0.3.9/lib/libopenblas.so.0 + libstdc++.so.6 => /gnu/store/01b4w3m6mp55y531kyi1g8shh722kwqm-gcc-7.5.0-lib/lib/libstdc++.so.6 (0x00007f2d61ba9000) + libm.so.6 => /gnu/store/fa6wj5bxkj5ll1d7292a70knmyl7a0cr-glibc-2.31/lib/libm.so.6 (0x00007f2d61a68000) + libc.so.6 => /gnu/store/fa6wj5bxkj5ll1d7292a70knmyl7a0cr-glibc-2.31/lib/libc.so.6 (0x00007f2d6186f000) + libgfortran.so.4 => /gnu/store/741057r2x06zwg6zcmqmdyv51spm6n9i-gfortran-7.5.0-lib/lib/libgfortran.so.4 (0x00007f2d61699000) + + +** GEMMA 0.98.4 + Below measurements are taken on 4x Intel(R) Core(TM) i7-6770HQ CPU @ 2.60GHz with hyperthreading and 16 GB RAM with warmed up memory buffers. |