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Diffstat (limited to 'vignettes/compiled_models.html')
| -rw-r--r-- | vignettes/compiled_models.html | 47 |
1 files changed, 26 insertions, 21 deletions
diff --git a/vignettes/compiled_models.html b/vignettes/compiled_models.html index 8d4c36a4..12454559 100644 --- a/vignettes/compiled_models.html +++ b/vignettes/compiled_models.html @@ -10,7 +10,7 @@ <meta name="author" content="Johannes Ranke" /> -<meta name="date" content="2015-06-23" /> +<meta name="date" content="2015-06-26" /> <title>Performance benefit by using compiled model definitions in mkin</title> @@ -65,7 +65,7 @@ img { <div id="header"> <h1 class="title">Performance benefit by using compiled model definitions in mkin</h1> <h4 class="author"><em>Johannes Ranke</em></h4> -<h4 class="date"><em>2015-06-23</em></h4> +<h4 class="date"><em>2015-06-26</em></h4> </div> <div id="TOC"> @@ -82,8 +82,13 @@ img { <pre><code>## gcc ## "/usr/bin/gcc"</code></pre> <p>First, we build a simple degradation model for a parent compound with one metabolite.</p> -<pre class="r"><code>library("mkin") -SFO_SFO <- mkinmod( +<pre class="r"><code>library("mkin")</code></pre> +<pre><code>## Loading required package: minpack.lm +## Loading required package: rootSolve +## Loading required package: inline +## Loading required package: methods +## Loading required package: parallel</code></pre> +<pre class="r"><code>SFO_SFO <- mkinmod( parent = mkinsub("SFO", "m1"), m1 = mkinsub("SFO"))</code></pre> <pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre> @@ -99,18 +104,18 @@ smb.1 <- summary(mb.1)[-1] rownames(smb.1) <- c("deSolve, not compiled", "Eigenvalue based", "deSolve, compiled") print(smb.1)</code></pre> <pre><code>## min lq mean median uq -## deSolve, not compiled 6555.9044 6654.5464 6693.6732 6753.1885 6762.5577 -## Eigenvalue based 941.4496 949.4094 972.3045 957.3693 987.7320 -## deSolve, compiled 743.6684 756.3411 761.1512 769.0139 769.8926 +## deSolve, not compiled 5292.0165 5313.7620 5364.5733 5335.5075 5400.8517 +## Eigenvalue based 893.9459 921.1984 936.1750 948.4509 957.2895 +## deSolve, compiled 742.7723 745.4243 750.1963 748.0763 753.9083 ## max neval -## deSolve, not compiled 6771.9268 3 -## Eigenvalue based 1018.0946 3 -## deSolve, compiled 770.7713 3</code></pre> -<p>We see that using the compiled model is by a factor of 8.8 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:</p> +## deSolve, not compiled 5466.1959 3 +## Eigenvalue based 966.1282 3 +## deSolve, compiled 759.7404 3</code></pre> +<p>We see that using the compiled model is by a factor of 7.1 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:</p> <pre class="r"><code>smb.1["median"]/smb.1["deSolve, compiled", "median"]</code></pre> <pre><code>## median -## deSolve, not compiled 8.781621 -## Eigenvalue based 1.244931 +## deSolve, not compiled 7.132304 +## Eigenvalue based 1.267853 ## deSolve, compiled 1.000000</code></pre> </div> <div id="benchmark-for-a-model-that-can-not-be-solved-with-eigenvalues" class="section level2"> @@ -128,17 +133,17 @@ smb.2 <- summary(mb.2)[-1] rownames(smb.2) <- c("deSolve, not compiled", "deSolve, compiled") print(smb.2)</code></pre> <pre><code>## min lq mean median uq -## deSolve, not compiled 14.202106 14.342265 14.430352 14.482424 14.544475 -## deSolve, compiled 1.363102 1.367979 1.377016 1.372857 1.383973 +## deSolve, not compiled 11.277340 11.336373 11.392883 11.395407 11.450654 +## deSolve, compiled 1.339204 1.342662 1.350783 1.346121 1.356573 ## max neval -## deSolve, not compiled 14.606526 3 -## deSolve, compiled 1.395088 3</code></pre> +## deSolve, not compiled 11.505901 3 +## deSolve, compiled 1.367025 3</code></pre> <pre class="r"><code>smb.2["median"]/smb.2["deSolve, compiled", "median"]</code></pre> <pre><code>## median -## deSolve, not compiled 10.54912 -## deSolve, compiled 1.00000</code></pre> -<p>Here we get a performance benefit of a factor of 10.5 using the version of the differential equation model compiled from C code using the inline package!</p> -<p>This vignette was built with mkin 0.9.38 on</p> +## deSolve, not compiled 8.465368 +## deSolve, compiled 1.000000</code></pre> +<p>Here we get a performance benefit of a factor of 8.5 using the version of the differential equation model compiled from C code using the inline package!</p> +<p>This vignette was built with mkin 0.9.39 on</p> <pre><code>## R version 3.2.1 (2015-06-18) ## Platform: x86_64-pc-linux-gnu (64-bit) ## Running under: Debian GNU/Linux 8 (jessie)</code></pre> |