diff options
| author | Pjotr Prins | 2020-08-26 12:26:18 +0100 |
|---|---|---|
| committer | Pjotr Prins | 2020-08-26 12:26:18 +0100 |
| commit | 7286000660c54c9989f49164ca4800d687b7a315 (patch) | |
| tree | 898fc3110c23a905e0183f895601242677f39d02 /test | |
| parent | 97547ee82e0bd1cc2210612415b0ceb135dbba6d (diff) | |
| download | pangemma-7286000660c54c9989f49164ca4800d687b7a315.tar.gz | |
Performance
Diffstat (limited to 'test')
| -rw-r--r-- | test/performance/releases.org | 45 |
1 files changed, 44 insertions, 1 deletions
diff --git a/test/performance/releases.org b/test/performance/releases.org index e1cd4d1..1be5818 100644 --- a/test/performance/releases.org +++ b/test/performance/releases.org @@ -90,7 +90,49 @@ trix const*, gsl_matrix*, gsl_matrix*) onst*) #+END_SRC -* GEMMA 0.99 (release) +* GEMMA 0.98.2 (release) + +Looks like openblas is getting faster. Two metrics on the same machine: + +#+BEGIN_SRC sh +lario:~/iwrk/opensource/code/genetics/gemma$ time ~/opt/gemma-gn2/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 0m7.635s +user 0m14.821s +sys 0m1.077s +#+END_SRC + + +#+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 +GEMMA 0.98 (2018-09-28) by Xiang Zhou and team (C) 2012-2018 +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 0m10.663s +user 0m20.994s +sys 0m4.268s +#+END_SRC + On a 26 core Intel(R) Xeon(R) CPU E5-2683 v3 @ 2.00GHz @@ -156,6 +198,7 @@ sys 0m2.684s * GEMMA 0.98 (release) + #+BEGIN_SRC bash libgsl.so.23 => /gnu/store/79fw0qqlgpk7n8vll6lnlc4ahahn4gbw-profile/lib/libgsl.so.23 (0x00007fcb53b1f000) libz.so.1 => /gnu/store/79fw0qqlgpk7n8vll6lnlc4ahahn4gbw-profile/lib/libz.so.1 (0x00007fcb53903000) |