Benchmark for a model that can also be solved with Eigenvalues

This evaluation is taken from the example section of mkinfit. When using an mkin version equal to or greater than 0.9-36 and a C compiler (gcc) is available, you will see a message that the model is being compiled from autogenerated C code when defining a model using mkinmod. The mkinmod() function checks for presence of the gcc compiler using

Sys.which("gcc")
##            gcc 
## "/usr/bin/gcc"

First, we build a simple degradation model for a parent compound with one metabolite.

library("mkin")
SFO_SFO <- mkinmod(
  parent = mkinsub("SFO", "m1"),
  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 microbenchmark package.

library("microbenchmark")
mb.1 <- microbenchmark(
  mkinfit(SFO_SFO, FOCUS_2006_D, solution_type = "deSolve", use_compiled = FALSE, 
          quiet = TRUE),
  mkinfit(SFO_SFO, FOCUS_2006_D, solution_type = "eigen", quiet = TRUE),
  mkinfit(SFO_SFO, FOCUS_2006_D, solution_type = "deSolve", quiet = TRUE),
  times = 3, control = list(warmup = 1))
smb.1 <- summary(mb.1)[-1]
rownames(smb.1) <- c("deSolve, not compiled", "Eigenvalue based", "deSolve, compiled")
print(smb.1)
##                             min        lq      mean    median        uq
## deSolve, not compiled 9442.5119 9447.2060 9458.3420 9451.9001 9466.2571
## Eigenvalue based       868.6312  872.4552  895.3422  876.2792  908.6977
## deSolve, compiled      691.9663  697.5653  701.1004  703.1643  705.6674
##                             max neval cld
## deSolve, not compiled 9480.6141     3   c
## Eigenvalue based       941.1163     3  b 
## deSolve, compiled      708.1706     3 a

We see that using the compiled model is by a factor of 13.4 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:

smb.1["median"]/smb.1["deSolve, compiled", "median"]
##                          median
## deSolve, not compiled 13.441951
## Eigenvalue based       1.246194
## deSolve, compiled      1.000000

Benchmark for a model that can not be solved with Eigenvalues

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

FOMC_SFO <- mkinmod(
  parent = mkinsub("FOMC", "m1"),
  m1 = mkinsub( "SFO"))
## Successfully compiled differential equation model from auto-generated C code.
mb.2 <- microbenchmark(
  mkinfit(FOMC_SFO, FOCUS_2006_D, use_compiled = FALSE, quiet = TRUE),
  mkinfit(FOMC_SFO, FOCUS_2006_D, quiet = TRUE),
  times = 3, control = list(warmup = 1))
smb.2 <- summary(mb.2)[-1]
rownames(smb.2) <- c("deSolve, not compiled", "deSolve, compiled")
print(smb.2)
##                             min       lq      mean    median        uq
## deSolve, not compiled 20.444632 20.48824 20.557595 20.531857 20.614077
## deSolve, compiled      1.251733  1.25179  1.275227  1.251846  1.286973
##                           max neval cld
## deSolve, not compiled 20.6963     3   b
## deSolve, compiled      1.3221     3  a
smb.2["median"]/smb.2["deSolve, compiled", "median"]
##                         median
## deSolve, not compiled 16.40126
## deSolve, compiled      1.00000

Here we get a performance benefit of a factor of 16.4 using the version of the differential equation model compiled from C code using the inline package!

This vignette was built with mkin 0.9.41 on

## R version 3.2.2 (2015-08-14)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Debian GNU/Linux 8 (jessie)
## CPU model: Intel(R) Core(TM) i7-4710MQ CPU @ 2.50GHz