Dear Sara, Hm.. so sorry, I have no more idea... Ákos 2019.06.25. 9:55 keltezéssel, Sara Shaeri írta: > Dear Ákos, > I tried it on a small partition of my data. However, the processing > time is the same :(. Any other suggestion? > > ------------------------- > *Sara Shaeri Karimi* > PhD Candidate, Department of Environmental Sciences > Faculty of Science and Engineering > Macquarie University, NSW 2109 Australia > /Researchgate <https://www.researchgate.net/profile/Sara_Shaeri> > / > /Linkedin <https://www.linkedin.com/in/sara-shaeri-karimi-94351433>/ > > > > > > > > > On Tuesday, June 25, 2019, 4:33:34 PM GMT+10, Bede-Fazekas Ákos > <bfalevl...@gmail.com> wrote: > > > Dear Sara, > > it is faster if you first convert the integer vector to logical, and > then run rle(). > > set.seed(12345) > random_sample <- sample.int(n = 10, size = 1e5, replace = TRUE) - 1 > > original <- function(x){ > y <- rle(x) > return(max(y$lengths[y$values == 0])) > } > > faster <- function(x){ > y <- rle(x == 0) > return(max(y$lengths[y$values])) > } > > original(random_sample) == faster(random_sample) > > library(microbenchmark) > microbenchmark( > original(random_sample), > faster(random_sample) > ) > > Hence, this may be faster: > interflood <- clusterR(all_predictions, calc, args=list(function(x){y <- > rle(as.numeric(x) == 0; return(max(y$lengths[y$values]))})) > > HTH, > Ákos Bede-Fazekas > Hungarian Academy of Sciences > > 2019.06.25. 3:32 keltezéssel, Sara Shaeri via R-sig-Geo írta: > > Dear community, > > I’m trying to use the Calc function in a raster stack (8000 binary > format rasters). Each raster covers 2,421,090 cells, as such, I’m > using parallel coding to make the most of the available cores for this > computation, however, this process is extremely slow on a 36 core and > 76 Gb RAM. How could I speed up the calculations? This is the code I’m > using: > > > > beginCluster(30) > > > > interflood <- clusterR(all_predictions, calc, > args=list(function(x){y <- rle(as.numeric(x));return(max( > y$lengths[y$values == 0]))})) > > > > endCluster() > > > > > > RegardsSara > > > > > > ------------------------- > > Sara Shaeri KarimiPhD Candidate, Department of Environmental > SciencesFaculty of Science and EngineeringMacquarie University, NSW > 2109 Australia > > Researchgate > > Linkedin > > > > > > > > > > > > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > R-sig-Geo mailing list > > R-sig-Geo@r-project.org <mailto:R-sig-Geo@r-project.org> > > https://stat.ethz.ch/mailman/listinfo/r-sig-geo > > > > _______________________________________________ > R-sig-Geo mailing list > R-sig-Geo@r-project.org <mailto:R-sig-Geo@r-project.org> > https://stat.ethz.ch/mailman/listinfo/r-sig-geo >
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