From 98d684becd9495d370e1bcc8f9c7ca758caa4dd8 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 17 Nov 2016 22:58:28 +0100 Subject: Static documentation rebuilt by pkgdown::build_site() --- docs/articles/compiled_models.html | 42 +++++++++++++++++++------------------- 1 file changed, 21 insertions(+), 21 deletions(-) (limited to 'docs/articles/compiled_models.html') diff --git a/docs/articles/compiled_models.html b/docs/articles/compiled_models.html index 153841ae..1446a357 100644 --- a/docs/articles/compiled_models.html +++ b/docs/articles/compiled_models.html @@ -41,7 +41,7 @@

Performance benefit by using compiled model definitions in mkin

Johannes Ranke

-

2016-11-04

+

2016-11-17

@@ -63,12 +63,12 @@ SFO_SFO <- 
library("microbenchmark")
 library("ggplot2")
 mb.1 <- microbenchmark(
-  "deSolve, not compiled" = mkinfit(SFO_SFO, FOCUS_2006_D, 
-                                    solution_type = "deSolve", 
+  "deSolve, not compiled" = mkinfit(SFO_SFO, FOCUS_2006_D,
+                                    solution_type = "deSolve",
                                     use_compiled = FALSE, quiet = TRUE),
-  "Eigenvalue based" = mkinfit(SFO_SFO, FOCUS_2006_D, 
+  "Eigenvalue based" = mkinfit(SFO_SFO, FOCUS_2006_D,
                                solution_type = "eigen", quiet = TRUE),
-  "deSolve, compiled" = mkinfit(SFO_SFO, FOCUS_2006_D, 
+  "deSolve, compiled" = mkinfit(SFO_SFO, FOCUS_2006_D,
                                 solution_type = "deSolve", quiet = TRUE),
   times = 3, control = list(warmup = 0))
## Warning in microbenchmark(`deSolve, not compiled` = mkinfit(SFO_SFO,
@@ -78,21 +78,21 @@ mb.1 <- micr
 print(mb.1)
## Unit: milliseconds
 ##                   expr       min        lq      mean    median        uq
-##  deSolve, not compiled 6282.2220 6293.7637 6323.0479 6305.3053 6343.4608
-##       Eigenvalue based  873.2553  886.5949  903.6178  899.9345  918.7990
-##      deSolve, compiled  737.7899  738.8794  752.3343  739.9689  759.6065
+##  deSolve, not compiled 6251.2433 6291.2435 6315.5160 6331.2438 6347.6524
+##       Eigenvalue based  858.2035  903.1770  926.2132  948.1505  960.2181
+##      deSolve, compiled  721.0067  739.1361  745.9964  757.2656  758.4913
 ##        max neval cld
-##  6381.6162     3   c
-##   937.6634     3  b 
-##   779.2441     3 a
+## 6364.0611 3 c +## 972.2856 3 b +## 759.7171 3 a 
autoplot(mb.1)

-

We see that using the compiled model is by a factor of 8.5 faster than using the R version with the default ode solver, and it is even faster than the Eigenvalue based solution implemented in R which does not need iterative solution of the ODEs:

+

We see that using the compiled model is by a factor of 8.4 faster than using the R version with the default ode solver, and it is even faster than the Eigenvalue based solution implemented in R which does not need iterative solution of the ODEs:

rownames(smb.1) <- smb.1$expr
 smb.1["median"]/smb.1["deSolve, compiled", "median"]
##                         median
-## deSolve, not compiled 8.521041
-## Eigenvalue based      1.216179
+## deSolve, not compiled 8.360665
+## Eigenvalue based      1.252071
 ## deSolve, compiled     1.000000
@@ -103,7 +103,7 @@ smb.1["median"]/smbm1 = mkinsub( "SFO"))
## Successfully compiled differential equation model from auto-generated C code.
mb.2 <- microbenchmark(
-  "deSolve, not compiled" = mkinfit(FOMC_SFO, FOCUS_2006_D, 
+  "deSolve, not compiled" = mkinfit(FOMC_SFO, FOCUS_2006_D,
                                     use_compiled = FALSE, quiet = TRUE),
   "deSolve, compiled" = mkinfit(FOMC_SFO, FOCUS_2006_D, quiet = TRUE),
   times = 3, control = list(warmup = 0))
@@ -114,18 +114,18 @@ smb.1["median"]/smbprint(mb.2) 
## Unit: seconds
 ##                   expr       min        lq      mean    median        uq
-##  deSolve, not compiled 13.644880 13.648332 13.835874 13.651784 13.931372
-##      deSolve, compiled  1.422381  1.448574  1.495091  1.474767  1.531446
-##        max neval cld
-##  14.210959     3   b
-##   1.588125     3  a
+## deSolve, not compiled 13.601046 13.602861 13.619563 13.604676 13.628821 +## deSolve, compiled 1.341581 1.346263 1.348298 1.350944 1.351657 +## max neval cld +## 13.65297 3 b +## 1.35237 3 a 
smb.2["median"]/smb.2["deSolve, compiled", "median"]
##   median
 ## 1     NA
 ## 2     NA
autoplot(mb.2)

-

Here we get a performance benefit of a factor of 9.3 using the version of the differential equation model compiled from C code!

+

Here we get a performance benefit of a factor of 10.1 using the version of the differential equation model compiled from C code!

This vignette was built with mkin 0.9.44.9000 on

## R version 3.3.2 (2016-10-31)
 ## Platform: x86_64-pc-linux-gnu (64-bit)
-- 
cgit v1.2.1