From 0b677308e3ffbf742880f05cc54da469f3ecc854 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Fri, 9 Mar 2018 23:14:39 +0100 Subject: Another rebuild of the static docs Now with rbenchmark installed, to get results for the compiled_models vignette --- vignettes/compiled_models.html | 38 +++++++++++++++++++------------------- 1 file changed, 19 insertions(+), 19 deletions(-) (limited to 'vignettes/compiled_models.html') diff --git a/vignettes/compiled_models.html b/vignettes/compiled_models.html index 8aaa70d6..d8c5b19b 100644 --- a/vignettes/compiled_models.html +++ b/vignettes/compiled_models.html @@ -12,7 +12,7 @@ - + Performance benefit by using compiled model definitions in mkin @@ -70,7 +70,7 @@ code > span.in { color: #60a0b0; font-weight: bold; font-style: italic; } /* Inf

Performance benefit by using compiled model definitions in mkin

Johannes Ranke

-

2018-01-14

+

2018-03-09

@@ -87,27 +87,27 @@ SFO_SFO <- mkinmod( m1 = mkinsub("SFO")) 
## Successfully compiled differential equation model from auto-generated C code.

We can compare the performance of the Eigenvalue based solution against the compiled version and the R implementation of the differential equations using the benchmark package.

-
if (require(rbenchmark)) {
+
if (require(rbenchmark)) {
   b.1 <- benchmark(
-    "deSolve, not compiled" = mkinfit(SFO_SFO, FOCUS_2006_D,
+    "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),
     replications = 3)
   print(b.1)
   factor_SFO_SFO <- round(b.1["1", "relative"])
-} else {
+} else {
   factor_SFO_SFO <- NA
   print("R package benchmark is not available")
 }

 
## Loading required package: rbenchmark

 
##                    test replications elapsed relative user.self sys.self
-## 3     deSolve, compiled            3   2.005    1.000     2.000    0.004
-## 1 deSolve, not compiled            3  14.202    7.083    14.196    0.000
-## 2      Eigenvalue based            3   2.427    1.210     2.428    0.000
+## 3     deSolve, compiled            3   1.980    1.000     1.979        0
+## 1 deSolve, not compiled            3  13.926    7.033    13.914        0
+## 2      Eigenvalue based            3   2.362    1.193     2.360        0
 ##   user.child sys.child
 ## 3          0         0
 ## 1          0         0
@@ -117,35 +117,35 @@ SFO_SFO <- mkinmod(
 

 
Model that can not be solved with Eigenvalues

 
This evaluation is also taken from the example section of mkinfit.

-
if (require(rbenchmark)) {
+
if (require(rbenchmark)) {
   FOMC_SFO <- mkinmod(
     parent = mkinsub("FOMC", "m1"),
     m1 = mkinsub( "SFO"))
 
   b.2 <- benchmark(
-    "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),
+    "deSolve, compiled" = mkinfit(FOMC_SFO, FOCUS_2006_D, quiet = TRUE),
     replications = 3)
   print(b.2)
   factor_FOMC_SFO <- round(b.2["1", "relative"])
-} else {
+} else {
   factor_FOMC_SFO <- NA
   print("R package benchmark is not available")
 }

 
## Successfully compiled differential equation model from auto-generated C code.

 
##                    test replications elapsed relative user.self sys.self
-## 2     deSolve, compiled            3   3.489    1.000     3.488        0
-## 1 deSolve, not compiled            3  28.906    8.285    28.904        0
+## 2     deSolve, compiled            3   3.437    1.000     3.433        0
+## 1 deSolve, not compiled            3  30.406    8.847    30.380        0
 ##   user.child sys.child
 ## 2          0         0
 ## 1          0         0

-
Here we get a performance benefit of a factor of 8 using the version of the differential equation model compiled from C code!

-
This vignette was built with mkin 0.9.47.1 on

+
Here we get a performance benefit of a factor of 9 using the version of the differential equation model compiled from C code!

+
This vignette was built with mkin 0.9.46.3 on

 
## R version 3.4.3 (2017-11-30)
 ## Platform: x86_64-pc-linux-gnu (64-bit)
 ## Running under: Debian GNU/Linux 9 (stretch)

-
## CPU model: Intel(R) Core(TM) i7-4710MQ CPU @ 2.50GHz

+
## CPU model: AMD Ryzen 7 1700 Eight-Core Processor

 

 
 
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