diff options
| -rw-r--r-- | .travis.yml | 8 | ||||
| -rw-r--r-- | test/performance/releases.org | 64 |
2 files changed, 68 insertions, 4 deletions
diff --git a/.travis.yml b/.travis.yml index 7a48f94..6fd48bd 100644 --- a/.travis.yml +++ b/.travis.yml @@ -12,8 +12,8 @@ matrix: - ubuntu-toolchain-r-test packages: # Our dev environment is a more recent GNU C++ and GSL2 - - g++ - - libopenblas-dev + - g++-4.9 + - libopenblas-dev - zlib1g-dev - libgsl0-dev - os: osx @@ -27,8 +27,8 @@ matrix: # - g++-6 # env: # - MATRIX_EVAL="CC=gcc-6 && CXX=g++-6" -# before_install: -# - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then brew cask uninstall oclint && brew update && brew install gsl openblas zlib eigen lapack ; fi +before_install: + - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then brew update && brew install gsl openblas zlib eigen lapack ; fi script: - echo $MATRIX_EVAL - eval "${MATRIX_EVAL}" 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 |