Checked the timings; Travis passes for Linux and MacOS

genetics-statistics · Nov 28, 2020 · f623b47 · f623b47
1 parent 1d60d30
commit f623b47
Showing 1 changed file with 43 additions and 4 deletions.
diff --git a/test/performance/releases.org b/test/performance/releases.org
@@ -90,6 +90,48 @@ trix const*, gsl_matrix*, gsl_matrix*)
 onst*)
 #+END_SRC
 
+* GEMMA 0.98.3 (release)
+
+#+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 0.98.3 (2020-11-28) 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%
+
+real    0m7.068s
+user    0m14.904s
+sys     0m1.454s
+
+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 0.98.3 (2020-11-28) 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%
+
+real    0m12.581s
+user    0m17.318s
+sys     0m2.079s
+#+end_src
+
+
+
 * GEMMA 0.98.2 (release)
 
 Looks like openblas is getting faster. Two metrics on the same machine:
@@ -106,13 +148,13 @@ Reading Files ...
 ## number of analyzed SNPs         =    10768
 Calculating Relatedness Matrix ...
 ================================================== 100%
-**** INFO: Done.
 
 real    0m7.635s
 user    0m14.821s
 sys     0m1.077s
 #+END_SRC
 
+The static version
 
 #+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
@@ -126,7 +168,6 @@ Reading Files ...
 ## number of analyzed SNPs         =    10768
 Calculating Relatedness Matrix ...
 ================================================== 100%
-**** INFO: Done.
 
 real    0m10.663s
 user    0m20.994s
@@ -151,7 +192,6 @@ Reading Files ...
 ## number of analyzed SNPs         =    10768
 Calculating Relatedness Matrix ...
 ================================================== 100%
-**** INFO: Done.
 
 real    0m7.590s
 user    0m30.392s
@@ -180,7 +220,6 @@ Start Eigen-Decomposition...
 pve estimate =0.608801
 se(pve) =0.032774
 ================================================== 100%
-**** INFO: Done.
 
 real    0m17.813s
 user    0m43.460s