search for: rcppparallel

I made the mistake of updating to Ubuntu 20.10 from 20.04 before before debian repo supports 20.10.? This broke RcppParallel and plotly.? Any idea with 20.10 will be available for r-cran-* debian packages? Thanks Frank http://fharrell.com http://biostat.mc.vanderbilt.edu/FrankHarrell Twitter: @f2harrell

Hi Dirk, I didn't capture the output but using Focal I got an error with RcppParallel trying to open a file that wasn't found, and plotly::ggplot() would not render a ggplot graph. 20.10 is working well for me otherwise. Frank http://fharrell.com http://biostat.mc.vanderbilt.edu/FrankHarrell Twitter: @f2harrell ---- On Sun, 25 Oct 2020 11:52:4...

...ld someone help explain what it means that R is single threaded? I am trying to understand what is actually going on inside R when users want to parallelize code. For example, using mclapply or foreach (with some backend) somehow allows users to benefit from multiple CPUs. Similarly there is the RcppParallel package for RMatrix/RVector objects. But none of these address the general XPtr objects in Rcpp. Some readers here may recognize my question on SO ( http://stackoverflow.com/questions/37167479/rcpp-parallelize-functions-that-return-xptr) where I was curious about parallel calls to C++/Rcpp functio...

...ed" that a couple of years ago but keep forgetting how to get the latest and greatest r-debian repo. I just had to edit /etc/apt/sources.list.d/c2d4u_team*.list to change groovy to focal. I now see 4448 r-cran-* packages. I'll contact the debian package maintainer about the problem with RcppParallel. I'm still now clear why there is no bug when I do a manual install from .tar.gz. Frank ---- On Mon, 26 Oct 2020 09:32:11 -0500 Dirk Eddelbuettel <edd at debian.org> wrote ---- > > Frank > > It is STILL unreadable (to me) html. > > Your entry is simply o...

Dirk, thank you a thousand times. Indeed, src/Makevars was wrong. I modified Makevars so that now looks like the below and the package now compiled and linked properly. CXX_STD = CXX11 PKG_LIBS += $(SHLIB_OPENMP_CXXFLAGS) $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS) $(shell ${R_HOME}/bin/Rscript -e "RcppParallel::RcppParallelLibs()") PKG_CXXFLAGS = $(SHLIB_OPENMP_CXXFLAGS) -I../inst/include Best, Sam On Thu, Oct 8, 2020 at 3:39 PM Dirk Eddelbuettel <edd at debian.org> wrote: > > Sam, > > PS It could of course also be something else: Is you src/Makevars for your > test package c...

...what it means that R is single threaded? I am > trying to understand what is actually going on inside R when users want to > parallelize code. For example, using mclapply or foreach (with some > backend) somehow allows users to benefit from multiple CPUs. > > Similarly there is the RcppParallel package for RMatrix/RVector objects. > But none of these address the general XPtr objects in Rcpp. Some readers > here may recognize my question on SO ( > > http://stackoverflow.com/questions/37167479/rcpp-parallelize-functions-that-return-xptr > ) > where I was curious about par...

...ans that R is single threaded? I am | > trying to understand what is actually going on inside R when users want to | > parallelize code. For example, using mclapply or foreach (with some | > backend) somehow allows users to benefit from multiple CPUs. | > | > Similarly there is the RcppParallel package for RMatrix/RVector objects. | > But none of these address the general XPtr objects in Rcpp. Some readers | > here may recognize my question on SO ( | > | > http://stackoverflow.com/questions/37167479/rcpp-parallelize-functions-that-return-xptr | > ) | > where I was curio...

Hi Dirk, One side observation: r-cran debian now seems to be in Ubuntu 20.10 Universe so I don't need to add the repo any more. Here is a reproducible example that fails with the latest r-cran-rcppparallel but works when I manually install the source package: require(rstan) stancode <- 'data {real y_mean;} parameters {real y;} model {y ~ normal(y_mean,1);}' mod <- stan_model(model_code = stancode, verbose = TRUE) TRANSLATING MODEL '16a540c6086086816528e4524def24d9' FROM...

The new staged package installation shells out to the 'file' utility on Unix systems: https://github.com/wch/r-source/blob/31ee14c620eb1b939acd322f3b5617f998aab8e8/src/library/tools/R/install.R#L578 Although 'file' is usually present on most Unix systems, it might be missing from small Docker containers, where the aim is to make the container as small possible. The magic file of

...o far. :) Kind regards, Willem Dirk Eddelbuettel <edd at debian.org> schreef op 25 oktober 2020 17:52:43 CET: > >On 25 October 2020 at 11:37, Frank Harrell wrote: >| I made the mistake of updating to Ubuntu 20.10 from 20.04 before >before debian repo supports 20.10.? This broke RcppParallel and >plotly.? Any idea with 20.10 will be available for r-cran-* debian >packages? > >Just continue to point to the focal ("20.04") repos. They _will_ run >because >this is the standard "forward compatible" mode. Binaries built on >older >systems almost...

...that a couple of years ago but keep forgetting how to get the latest and greatest r-debian repo. | | I just had to edit /etc/apt/sources.list.d/c2d4u_team*.list to change groovy to focal. I now see 4448 r-cran-* packages. | | I'll contact the debian package maintainer about the problem with RcppParallel. I'm still now clear why there is no bug when I do a manual install from .tar.gz. Sounds good. They are a bunch of very-well-meaning Debian folks looking after a number of those 900+ packages in the distro, but they sometimes prioritise Debian views / experience over R and CRAN so issues like...

...alls from different threads - or work via, say, the parallel or Rmpi packages in multiple _processes_ each of which could call its corresponding R interpreter (but that is still slower). There are some examples for OpenMP at the Rcpp Gallery: http://gallery.rcpp.org. You may also enjoy the RcppParallel package. But none of this overcomes your main hurdle: no, you cannot call R from different threads. | Are there any ways to invoke an R function in C/C++ in multiple threads safely? No. It is a design constraint. Dirk -- http://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org

...the overall speed benefits far outweighed the costs. MRO helped to overcome this problem with an interface to change the number of threads to use. In MRO, it is on the user to switch this before using any explicit parallel functionality. Another question, does using multithreaded OpenBLAS mess with RcppParallel? > | My sense is there're a lot of wasted resources on laptops and personal > | desktops around the world that could be utilised by such a switch. I > | believe most unix-like users don't know about OpenBLAS and are blissfully > | ignorant of the available speed gains. It seem...

...f Brian Ripley <ripley at stats.ox.ac.uk> wrote: > > This concerns CRAN packages > > Amelia C50 Cubist Cyclops DetSel GENLIB IRISSeismic KSgeneral > MigClim MonetDBLite Numero OpenMx PBSmapping PSPManalysis > PropClust RArcInfo RandomFields RandomFieldsUtils RcppMsgPack > RcppParallel RcppRedis RecordLinkage Rmalschains RnavGraph Rvcg > RxODE SiMRiv antiword bigrquery bsamGP catnet coxme dbarts > dggridR divest dpglasso earth epanet2toolkit fs gap geojsonsf > gglasso graphql hashmap haven hier.part imager iptools jiebaR > kernlab lpridge lvec mlvocab mongolite nandb...

...quot; only when it is available. When it isn't and some file with extension sl, so, dylib or dll in the package installation is not in fact a shared object, one will get a number of error messages from the respective tools, but the installation passes. Currently on Linux this is the case of RcppParallel and FastRWeb. Tomas On 3/7/19 11:57 PM, G?bor Cs?rdi wrote: > The new staged package installation shells out to the 'file' utility > on Unix systems: > https://github.com/wch/r-source/blob/31ee14c620eb1b939acd322f3b5617f998aab8e8/src/library/tools/R/install.R#L578 > > Alth...

...kage provides the R user with access to the functionality of the underlying TRNG C++ library. It embeds TRNG sources and headers and makes them available to other projects combining R with C++. Beyond this, rTRNG exposes the creation, manipulation and use of pseudo-random streams to R, via Rcpp and RcppParallel. rTRNG on CRAN <https://cran.r-project.org/package=rTRNG> Public repository <https://github.com/miraisolutions/rTRNG#readme> More on the history behind rTRNG and its way to CRAN at <https://mirai-solutions.ch/news/2019/05/04/rTRNG-on-CRAN/> -- Riccardo Porreca Senior Solution...

...kage provides the R user with access to the functionality of the underlying TRNG C++ library. It embeds TRNG sources and headers and makes them available to other projects combining R with C++. Beyond this, rTRNG exposes the creation, manipulation and use of pseudo-random streams to R, via Rcpp and RcppParallel. rTRNG on CRAN <https://cran.r-project.org/package=rTRNG> Public repository <https://github.com/miraisolutions/rTRNG#readme> More on the history behind rTRNG and its way to CRAN at <https://mirai-solutions.ch/news/2019/05/04/rTRNG-on-CRAN/> -- Riccardo Porreca Senior Solution...

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

...is single threaded? I am >> trying to understand what is actually going on inside R when users want to >> parallelize code. For example, using mclapply or foreach (with some >> backend) somehow allows users to benefit from multiple CPUs. >> >> Similarly there is the RcppParallel package for RMatrix/RVector objects. >> But none of these address the general XPtr objects in Rcpp. Some readers >> here may recognize my question on SO ( >> >> http://stackoverflow.com/questions/37167479/rcpp-parallelize-functions-that-return-xptr >> ) >> where...

Hi Dirk, Apologies for the html. I think I'm missing something simple.?? Ubuntu 20.10 uses /etc/apt/sources.list.d to hold repo information and I have this file there: marutter-ubuntu-rrutter4_0-focal.list with contents: deb http://ppa.launchpad.net/marutter/rrutter4.0/ubuntu/ focal main # deb-src http://ppa.launchpad.net/marutter/rrutter4.0/ubuntu/ groovy main I ran sudo apt