diff options
Diffstat (limited to 'test')
| -rw-r--r-- | test/performance/releases.org | 58 |
1 files changed, 58 insertions, 0 deletions
diff --git a/test/performance/releases.org b/test/performance/releases.org index ca77ad3..30c96f8 100644 --- a/test/performance/releases.org +++ b/test/performance/releases.org @@ -13,6 +13,63 @@ slowed things down. In 0.98 openblas is mostly used and is faster. Note also that the recent static versions are slower than the dynamically linked ones. Not sure why that is. +The test commands are + +#+BEGIN_SRC +# kinship +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 +# univariate LMM +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 +# multivariate LMM +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 +#+END_SRC + +Currently on my laptop there is no difference in running these tests +using gcc or clang. + +#+BEGIN_SRC +Clang: + +real 0m25.758s +user 0m46.380s +sys 0m0.852s + +real 0m22.173s +user 0m29.420s +sys 0m1.540s + +GNU C + +real 0m24.540s +user 0m43.948s +sys 0m1.276s + +real 0m22.504s +user 0m29.768s +sys 0m1.544s +#+END_SRC + +Running the GNU profiler on the MVLMM one rendered + +#+BEGIN_SRC + % cumulative self self total + time seconds seconds calls s/call s/call name + 22.73 0.90 0.90 41121 0.00 0.00 CalcQi(gsl_vector const*, gsl_vector const*, gsl_matrix const*, gsl_matrix*) + 13.64 1.44 0.54 30313 0.00 0.00 CalcXHiY(gsl_vector const*, gsl_vector const*, gsl_matrix const*, gsl_matrix const*, gsl_v +ector*) + 11.87 1.91 0.47 19536 0.00 0.00 CalcSigma(char, gsl_vector const*, gsl_vector const*, gsl_matrix const*, gsl_matrix const* +, gsl_matrix const*, gsl_matrix const*, gsl_matrix const*, gsl_matrix*, gsl_matrix*) + 10.86 2.34 0.43 38621 0.00 0.00 safeGetline(std::istream&, std::__cxx11::basic_string<char, std::char_traits<char>, std::a +llocator<char> >&) + 8.33 2.67 0.33 10805 0.00 0.00 MphCalcP(gsl_vector const*, gsl_vector const*, gsl_matrix const*, gsl_matrix const*, gsl_m +atrix const*, gsl_matrix const*, gsl_matrix*, gsl_vector*, gsl_matrix*) + 6.06 2.91 0.24 1 0.24 0.43 ReadFile_geno + 5.30 3.12 0.21 19536 0.00 0.00 UpdateV(gsl_vector const*, gsl_matrix const*, gsl_matrix const*, gsl_matrix const*, gsl_ma +trix const*, gsl_matrix*, gsl_matrix*) + 5.30 3.33 0.21 1 0.21 3.27 MVLMM::AnalyzeBimbam(gsl_matrix const*, gsl_vector const*, gsl_matrix const*, gsl_matrix c +onst*) +#+END_SRC + * GEMMA 0.98-beta1 #+BEGIN_SRC bash @@ -30,6 +87,7 @@ dynamically linked ones. Not sure why that is. #+END_SRC #+BEGIN_SRC bash + time ./bin/gemma -g ~/tmp/mouse_hs1940/mouse_hs1940.geno.txt.gz -p ~/tmp/mouse_hs1940/mouse_hs1940.pheno.txt -a ~/tmp/mouse_hs1940/mouse_hs1940.anno.txt -gk -no-check GEMMA 0.98-beta1 (2018-09-06) by Xiang Zhou and team (C) 2012-2018 Reading Files ... |