[Rd] invoking R function in C++ in parallel
Hello, I'm writing an R extension in C++. In the extension, I want to invoke an R function directly and it works when I use Rcpp in the serial code. But what I really want is to invoke the R function in parallel with openmp. When I do so, I got segmentation fault. I remember someone said that R isn't thread-safe. I think it's also understandable because an R function also has environment variables. My question is: Can we make a copy of an R function (including its environment variables) for each thread? Are there any ways to invoke an R function in C/C++ in multiple threads safely? Thanks, Da __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] invoking R function in C++ in parallel
Thank you both. I think I have got the answer I need. I'll need to turn to another direction to search for my solution. Best, Da On Sat, Jan 31, 2015 at 8:32 PM, Dirk Eddelbuettel e...@debian.org wrote: On 31 January 2015 at 19:29, Gábor Csárdi wrote: | On Sat, Jan 31, 2015 at 7:05 PM, Dirk Eddelbuettel e...@debian.org wrote: | [...] | | - either work in something like OpenMP and run in multiple threads that |remain /completely/ shielded from R, ie no R calls, and not even R data |types as you cannot trigger gc() calls from different threads | | | I think you can use R objects, as long as you don't call R functions on them | (not even from R's C api, although some of them are currently fine) and | consider them as read-only. E.g. if you have a numeric vector, you can do | double *cvec = REAL(vec); | and then use cvec in your thread(s). You and I are saying the same thing here: you call it read-only access; I called ot do not use R types. We recommend the same approach in other places: instantiate std::vectordouble from RcppVector, don't use R calls. My recommendation is to make it pretty plain: do not call R functions. Use other types. There are equivalent read-only constructors for some relevant data types. Recall that OP, in the parts you chose not to quote, asked to call back to R in a multithreaded way. And we both say 'nope' here. All this has come up before on rcpp-devel and SO. Dirk -- http://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] How to maintain memory in R extension
Hello, I wrote a system to perform data analysis in C++. Now I am integrating it to R. I need to allocate memory for my own C++ data structures, which can't be represented by any R data structures. I create a global hashtable to keep a reference to the C++ data structures. Whenever I allocate one, I register it in the hashtable and return its key to the R code. So later on, the R code can access the C++ data structures with their keys. The problem is how to perform garbage collection on the C++ data structures. Once an R object that contains the key is garbage collected, the R code can no longer access the corresponding C++ data structure, so I need to deallocate it. Is there any way that the C++ code can get notification when an R object gets garbage collected? If not, what is the usual way to manage memory in R extensions? Thanks, Da __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] How to maintain memory in R extension
Thank you, Gabor and Martin. It helps a lot. Da On Wed, Nov 12, 2014 at 1:20 PM, Martin Morgan mtmor...@fredhutch.org wrote: On 11/12/2014 05:36 AM, Zheng Da wrote: Hello, I wrote a system to perform data analysis in C++. Now I am integrating it to R. I need to allocate memory for my own C++ data structures, which can't be represented by any R data structures. I create a global hashtable to keep a reference to the C++ data structures. Whenever I allocate one, I register it in the hashtable and return its key to the R code. So later on, the R code can access the C++ data structures with their keys. The problem is how to perform garbage collection on the C++ data structures. Once an R object that contains the key is garbage collected, the R code can no longer access the corresponding C++ data structure, so I need to deallocate it. Is there any way that the C++ code can get notification when an R object gets garbage collected? If not, what is the usual way to manage memory in R extensions? register a finalizer that runs when there are no longer references to the R object, see ?reg.finalizer or the interface to R and C finalizers in Rinternals.h. If you return more than one reference to a key, then of course you'll have to manage these in your own C++ code. Martin Morgan Thanks, Da __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel -- Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
