Saving the dso from expose_stan_functions


#1

I have a workflow where I write unit test for my Stan functions in R, but run my test scripts through Makefiles. Often the test code changes faster than the Stan code and if there was a convenient way to save the functions that expose_stan_functions() exposes (like you can save the stanmodel object it would avoid needless recompilations and speed up testing.

Does anyone have any experiences or ideas with this?

Just saving the object returned by Rcpp::sourceCpp() using saveRDS() does not keep dso around, so that didn’t work. For the stanmodel object the magic seems to happen in cxxfunplus.R, but I can’t quite figure out how that would be adapted for expose_stan_functions().


Standalone use of ode integrator in R
#2

My impression is that it does not work, and it is a Rcpp limitation. You can look at args(Rcpp::sourceCpp) and see that it has a cacheDir argument that defaults to tempdir. If you set that option to something permanent, that may be a start.


#3

That led me to the solution! I’d been thinking too complicated. No need to fiddle with the source of expose_stan_functions().

By setting rcpp.cache.dir with options() I get access to the .so and .cpp.R files, which I can rename and use as Makefile targets. After substituting the new filename of the .so in the .cpp.R, the latter can be sourced from my test scripts.

Thank you!


#4

Thank you guys for pointing me in this direction. This rcpp.cache.dir is a life-saver. A few notes for anyone who finds this: If you want to avoid recompilation every time you load the exposed stan functions, you have to follow these steps:

  1. set the rcpp.cache.dir option as described avove
  2. Use the stanc_builder function with the (default) obfuscate_model_name=FALSE setting in order to ensure that the same c++ code is generated each time
  3. pass the result from stanc_builder into expose_stan_functions

So like this:

options(rccp.cpp.dir="cache")
model_src <- stanc_builder("foo.stan")
expose_stan_functions(model_src)

Also make sure that a recent enough Rcpp is installed which supports dso caching.

@bgoodri: Should we make expose_stan_functions by default such that the model name is not obfuscated? This would lead to easier caching of this. Maybe we could even switch on the caching stuff if rstan_auto_write is set to true?

User who use exposed stan functions will love this caching.


#5

Yes


#6

I did this lines, and I obtain those files (1 directory and 7 files):

sourceCpp-x86_64-pc-linux-gnu-0.12.12/
β”œβ”€β”€ cache.rds
β”œβ”€β”€ file4d514aa30c17.cpp
β”œβ”€β”€ sourcecpp_4d513d5901ee
β”‚   β”œβ”€β”€ file4d514aa30c17.cpp
β”‚   β”œβ”€β”€ file4d514aa30c17.cpp.R
β”‚   β”œβ”€β”€ file4d514aa30c17.o
β”‚   └── sourceCpp_2.so
└── token.rds

Which files should I use to include in the /src file to produce the RcppExports.cpp for a package?
I hope the question is not totally unclear…


#7

It will involve file4d514aa30c17.cpp, but you are going to have to copy and manually edit it a bit to make it compatible with a Rcpp-based package.