> On 13 Jun 2017, at 22:05, luke-tier...@uiowa.edu wrote: > > Thanks. This should be resolved in R-devel(r72788) and R-patched > (r72789) >
Also thanks. It is resolved in R-patched. Berend > Best, > > luke > > On Mon, 12 Jun 2017, Berend Hasselman wrote: > >> >> >> In this email to the R-help list: >> https://stat.ethz.ch/pipermail/r-help/2017-June/447474.html >> and in this question on Stackoverflow: >> https://stackoverflow.com/questions/44486643/nleqslv-memory-use-in-r >> >> Andrew Leach has raised a question about the memory usage of my package >> nleqslv. >> In a model with a loop within a function he has experienced continuously >> increasing memory usage >> by package nleqslv leading to an out of memory condition. >> >> I have been able to reproduce the continuously increasing memory usage with >> the following small example. >> >> <code> >> library(nleqslv,lib.loc="../nleqslv.Rcheck") >> library(pryr) >> dslnex <- function(x) { >> y <- numeric(2) >> y[1] <- x[1]^2 + x[2]^2 - 2 >> y[2] <- exp(x[1]-1) + x[2]^3 - 2 >> y >> } >> xstart <- c(x1=1.5,x2=2) >> nsims <- 10 >> for(test_iter in seq_len(nsims)){ >> z <- nleqslv(xstart,dslnex,jacobian=NULL) >> print(paste("nleqslv iteration",test_iter,"and memory used is",mem_used())) >> } >> memory.profile() >> gc() >> print(paste("At end memory used is", mem_used())) >> </code> >> >> The final output is >> >> <output> >> [1] "nleqslv iteration 1 and memory used is 28921288" >> [1] "nleqslv iteration 2 and memory used is 29133256" >> [1] "nleqslv iteration 3 and memory used is 29132992" >> [1] "nleqslv iteration 4 and memory used is 29134712" >> [1] "nleqslv iteration 5 and memory used is 29136432" >> [1] "nleqslv iteration 6 and memory used is 29138152" >> [1] "nleqslv iteration 7 and memory used is 29139872" >> [1] "nleqslv iteration 8 and memory used is 29141592" >> [1] "nleqslv iteration 9 and memory used is 29143312" >> [1] "nleqslv iteration 10 and memory used is 29145032" >>> >>> memory.profile() >> NULL symbol pairlist closure environment promise >> 1 8554 194726 4230 1065 6534 >> language special builtin char logical integer >> 51374 45 671 9786 8030 37258 >> double complex character ... any list >> 2645 1 53795 0 0 18487 >> expression bytecode externalptr weakref raw S4 >> 1 14662 2233 592 593 1049 >>> gc() >> used (Mb) gc trigger (Mb) max used (Mb) >> Ncells 416340 22.3 750400 40.1 581181 31.1 >> Vcells 726127 5.6 1308461 10.0 1191521 9.1 >>> print(paste("At end memory used is", mem_used())) >> [1] "At end memory used is 29126472" >> </output> >> >> Indeed memory used increases in each pass of the for loop. >> >> I have added these two lines at the top of the code after the library(pryr) >> invocation. >> >> library(compiler) >> oldJIT <- enableJIT(0) >> >> This resolves the issue in the sense that memory used remains constant after >> the first iteration. >> Output in the for loop is now: >> <output> >> [1] "nleqslv iteration 1 and memory used is 24487784" >> [1] "nleqslv iteration 2 and memory used is 24495816" >> [1] "nleqslv iteration 3 and memory used is 24495816" >> [1] "nleqslv iteration 4 and memory used is 24495816" >> [1] "nleqslv iteration 5 and memory used is 24495816" >> [1] "nleqslv iteration 6 and memory used is 24495816" >> [1] "nleqslv iteration 7 and memory used is 24495816" >> [1] "nleqslv iteration 8 and memory used is 24495816" >> [1] "nleqslv iteration 9 and memory used is 24495816" >> [1] "nleqslv iteration 10 and memory used is 24495816" >> </output> >> >> My questions are >> >> - is this a bug(let) in the JIT compiler? >> - if it isn't what would need to be changed in nleqslv.R in the package >> source? (I haven't a clue) >> >> regards >> >> Berend Hasselman >> >> My sessionInfo: >> >> R version 3.4.0 (2017-04-21) >> Platform: x86_64-apple-darwin15.6.0 (64-bit) >> Running under: macOS Sierra 10.12.5 >> >> Matrix products: default >> BLAS: >> /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRblas.0.dylib >> LAPACK: >> /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib >> >> locale: >> [1] en_IE.UTF-8/en_IE.UTF-8/en_IE.UTF-8/C/en_IE.UTF-8/en_IE.UTF-8 >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> loaded via a namespace (and not attached): >> [1] compiler_3.4.0 >> >> ______________________________________________ >> R-devel@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/r-devel >> > > -- > Luke Tierney > Ralph E. Wareham Professor of Mathematical Sciences > University of Iowa Phone: 319-335-3386 > Department of Statistics and Fax: 319-335-3017 > Actuarial Science > 241 Schaeffer Hall email: luke-tier...@uiowa.edu > Iowa City, IA 52242 WWW: http://www.stat.uiowa.edu ______________________________________________ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
